In the past months I’ve set up LDAP at home, to avoid having different user accounts for the services that I run on my home hardware. Rather than the venerable OpenLDAP I settled for 389 Directory Server, commercially known as Red Hat Directory Server, mainly because I was more familiar with it. Rather than describing how to set that up (Red Hat’s own documentation is excellent on that regard), this post will focus on the steps required to enable encryption using Let’s Encrypt certificates.

Recently I’ve been setting up LDAP authentication on CentOS servers to give a shared authentication method to all the compute nodes I use for my day job. I use 389-DS as it’s in my opinion much better to administer and configure than openLDAP (plus, it has very good documentation). As I have a self built NAS at home (with openSUSE Tumbleweed), I thought it’d be nice to use LDAP for all the web applications I run there.

The 4.10 release for the KDE Development Platform, Workspaces and Applications is drawing nigh… as you may have read, there is now an additional release candidate in order to test some last-minute changes. Of course, the KDE developers can only do so much: it’s impossible to test all possible combinations. That is, unless the community at large helps by finding and reporting issues the developers can fix. But doing so requires a 4.

As you all know, KDE 4.3.0 has been releeased today! Now it’s the time to tell the developers “thanks” for their hard work. Join us in the KDE Community Forums and spread the word!

As others, bigger members in the KDE community say, “nobody will do it for you, and therefore they will”. The patch from the title comes from such a story. Let’s give some background first: I’m really a heavy activity user, especially when working. My home PC has about five activities, my work one 3, and I managed to compartimentalize the various “topics” that each activity does pretty well. After an update a couple of weeks ago from the latest code from KDE git, I started noticing weird behavior.

Today I was looking for an easy way to do some calculations of raw expression data on Affymetrix arrays, but I didn’t want to use R: I have already mentioned how I don’t like its design and implementation. While looking for some documentation, I stumbled upon this nifty little program called RMAExpress.

You might have heard it in the past few months: some areas of the Internet are buzzing with discussions on “generative art”, that is, artwork generated from “AI” models that were fed with an absurdly large amount of images as training as a base. There are supporters, there are critics, and techology advances: among all this, this post offers my humble experience with computer-generated imagery. In this post, you’ll be guided by Yumiko, Satsuki, and Maya: the first two are characters created by someone else I know (who wants to remain anonymous) which I then expanded, cooperating with their creator in a certain project from a few years ago; the latter is… well, a character with an interesting history, which will be explained later.

 My Akademy talk proposal was not accepted, but the organizers were kind enough to offer me the chance to hold a BoF on the same subject. Now I bet you wonder on what I’m going to discuss, and I think the title already gives you an idea: KDE and bioinformatics: the missing link Although in the KDE community we have our fair share of scientists (hey there, Stuart!

By browsing through sites, I noticed that the Spanish site Akihabara Denno Gumi Universe has posted a translation of an interview the webmaster had with me through email. Here it is (Spanish language). It feels nice to recall some memories of the past once in a while, especially since I couldn’t still believe that dennogumi.org had been such a resource back in the days…

[]({{ site.url }}/images/2007/11/patapi.png)

After a long time I’ve finally got hold (thanks, Melissa) of Akihabara Denno Gumi PataPi!, that is the manga version of Akihabara Denno Gumi (or Cyber Team in Akihabara, if you prefer): some of you may even remember a rather sparse description on this very page when it was still devoted to ADG (almost eight years ago, time flies…).

Recently, a question came up on the KDE Community Forums regarding the use of multiple Google Calendars with KOrganizer. The preferred access up to now has been with googledata Akonadi resource, however that doesn’t support more than one calendar, and (at least from my unscientific observation) seems to be rather unmaintained these days.

Luckily, not all’s lost. Akonadi recently gained the opportunity of accessing CalDAV resources, and Google Calendar also offers a CalDAV interface, hence this is possible.

This post will briefly describe how (thanks go to PIMster krop, which casually mentioned the possibility on IRC and prompted me to investigate).

Currently, the openSUSE Build Service contains Amarok 2.1 beta packages only for the KDE:KDE4:UNSTABLE repository (i.e. current trunk, soon-to-be 4.3). However, a quick search identified a repository that contains a RPM of current 2.0.90 compiled for the KDE:KDE4:Factory Desktop (which will change to 4.3 with Beta 1) andanother one for the KDE:42 repository. So you can add them using YaST or zypper and download the relevant package. I had to force a repository using zypper, otherwise zypper would complain and try to install amarok 1.

You might have heard it in the past few months: some areas of the Internet are buzzing with discussions on “generative art”, that is, artwork generated from “AI” models that were fed with an absurdly large amount of images as training as a base. There are supporters, there are critics, and techology advances: among all this, this post offers my humble experience with computer-generated imagery. In this post, you’ll be guided by Yumiko, Satsuki, and Maya: the first two are characters created by someone else I know (who wants to remain anonymous) which I then expanded, cooperating with their creator in a certain project from a few years ago; the latter is… well, a character with an interesting history, which will be explained later.

After quite a long time, I was finally able to take a look at this series: a rather atypical mecha show that despite some bad production, still manages to be interesting.

Header image credit: 1840151sudarshan (Wikimedia Commons, CC BY-SA) A while ago I posted a way to download 実況動画 from Nicovideo. One of my acquaintances publishes videos there, and he wanted to collect the various comments to reply in a follow up video (what the Nico users call the コメント返し). When the comments are more than just a few, it’s hard to find where they refer to without watching them on Nicovideo itself, and its UI is suboptimal.

実況? Is it something edible? In recent times, I’ve been watching a lot of VOICEROID実況 (じっきょう, jikkyou, literally “commentary”) videos from the rather famous (in Japan) video service ニコニコ動画, better known as “Nicovideo”. In this case, the commentary actually refers to games: they’re basically a Japanese version of the Let’s Play videos that are all around other places like YouTube. The difference from “regular” videos lies in the “VOICEROID” term: this is a name of a TTS software developed by AH Software using an engine devised by a company called AI Inc.

[]({{ site.url }}/images/2013/01/mmBvi.jpg)

A few days ago I finally completed (after about 3 months) 神次元ゲームネプテューヌV, or “Kami Jigen Game Neptune V”, the latest instalment from Compile Heart in the Neptune franchise of PS3 games. It took quite a while (approximately 3 months), and I think it’s about time to wrap things up.

Sometimes Christmas presents are really unexpected, and today I found out I was given one such gift: the limited edition of _THE IDOLM@STER 2, _PS3 version. It was quite a bulky box, showing all the main characters from the game (and from the recently-ended anime) (click to enlarge):  Of course, having such a box means that there’s a lot of stuff inside. In fact, once opened, there are two game BDs (one being the actual game, the second being the first volume of Gravure for you!

By browsing through sites, I noticed that the Spanish site Akihabara Denno Gumi Universe has posted a translation of an interview the webmaster had with me through email. Here it is (Spanish language). It feels nice to recall some memories of the past once in a while, especially since I couldn’t still believe that dennogumi.org had been such a resource back in the days…

Recently I had the opportunity of viewing a DVD that I had bought in 2006 but never had the chance of seeing: it was the third season of Galaxy Angel, of which I had already viewed the first two years before. After viewing it, I realized I could have viewed it sooner, as I liked it quite a bit. Not only that, but I brought myself up to speed by getting what was left in the series, that is the second half of the third season (marketed by Bandai Visual as Galaxy Angel AA) and the fourth and final season (known in the English speaking market as Galaxy Angel X).

Well, I found the whole franchise quite good: and after having explored also other bits of it, including the manga and the games related to it, I thought it’d be nice to have a retrospective with my own views. Which is the point of this post.

Some of the oldest readers of this blog are well aware of [a certain hobby of mine]({{ site.url }}/category/anime). Over the years I’ve always wanted to write more about that, including the stuff I’m viewing nowadays, but I found a hassle to collect snapshots from videos / DVDs, selecting them, and so on. Recently I learnt that VLC has some rather complete Python bindings, and I thought, why not make the process automated?

 It’s been a while since I blogged about anything non-FOSS. This time I’ll be sharing some impressions on one of the games I’m playing at the moment, that is,** Ar Tonelico III** (which arrived at my doorstep two days ago). I admit I haven’t been a fan of Gust games (aside from Ar Tonelico, they’re known mostly for the Atelier series), mostly because technically wise they didn’t really perform that well.

If you dabble with [anime]({{ site.url }}/category/Anime) and related things like I do, you may have heard about imageboards. A known variant, which powers sites such as moe.imouto (some links may be NSFW) or Konachan, is Danbooru, a Ruby on Rails application. One of the characteristics of this software is that images stored there can be tagged to be identified as precisely as possible: common tags are for example the magazine where the image was taken from, the characters depicted, and so on.

Today, after some customs delay and courier problems, I finally received the first volume of Tears to Tiara. Having got a PS3, I chose the Blu-Ray version (priced 8,192 yen, quite steep if you hear me): as I preordered it soon enough, I got the first presse edition, which, according to CDJapan, was comprised of a “deluxe outer case”, a “stick poster” and a booklet, in addition to the Blu-ray itself.


So I’ve heard that _Tears to Tiara _is coming in animated form. Being in the middle of playing its PS3 incarnation, Tears to Tiara - Kaikan no Daichi, I decided to take a look at some images that have been recently published on news.dengeki.com. It was already known that the anime would be an adaptation of the PS3 game, which is a good thing (I didn’t like the original character design). Animation is done by _Oriental Light and _Magic (OLM), and the same staff who adapted another Aquaplus game, Utawarerumono (or should I say Underwater Ray Romano ? snicker).

[]({{ site.url }}/images/kurokamititle.jpg)

New season, new anime to see. Since a certain guy kept me telling wonders about Kurokami (黒神), a manga serialized in Young Gangan by Dall-Young Lim and Sung-woo Park, two Korean artists, I decided to give a go to the animated version, produced by Bandai Visual, which has just been out.

[]({{ site.url }}/images/2008/07/slayers3.jpg)

It’s been a long time since Slayers had aired on TV, basically since Slayers TRY was released, which means more than 10 years ago. Then, this year news told that two new series were planned, and this post is about the first episode (out of 13, aired on July 2nd; the second series will start sometime around January).

Yesterday I got a few novels that I’ve been waiting for a while: _Slayers _(the last two volumes published by Tokyopop, as ) and Shakugan no Shana 2. I bought the latter as a “final warning” because I’m not very sure I’ll ever continue: the first Shana was written poorly and with a plot that didn’t make much sense (but again, I don’t think the animated version was shining in that respect).

[]({{ site.url }}/images/2008/04/ookami_cover.png)

A rather large number of days ago I got the first DVD of Ookami to koshinryo, better known as Spice and Wolf, which I when the first episode was released. I got the limited edition, which came in with a number of extra features (which still don’t justify its ~ ¥6800 price tag, though). The main one is the inclusion of a 300 piece puzzle, illustrated by the artist who works on the original novels.

Interested by some promotional art and by a resemblance of the main female character to my brother’s own Yumiko, I took a look at the first episode of Ookami to Koshinryo, better known as Spice and Wolf. I’m being told it is inspired by a series of novels and that there is also a manga version.

For a change, my brother has found a place (DLsite.com) that sells dojinshi even to non-Japanese people, and also found three non-hentai Final Fantasy XI dojins, which I’m going to cover in this post. For reference, they are available with these prices:

• FFXI-URUSHI-Chaos: 01 - ¥ 735;

• FFXI-URUSHI-Chaos: 02 - ¥ 735;

• FFXI-URUSHI-Chaos:03 - ¥ 945.

When Tokyopop announced _Slayers, Kino no Tabi _and _Scrapped Princess _my interest was piqued: even more when I read about Seikai no Monsho. After getting what was available (three volumes of Scrapped Princess, the whole Seikai no Monsho trilogy and the single volume of Kino no Tabi) I waited for the rest.

[]({{ site.url }}/images/2007/11/patapi.png)

After a long time I’ve finally got hold (thanks, Melissa) of Akihabara Denno Gumi PataPi!, that is the manga version of Akihabara Denno Gumi (or Cyber Team in Akihabara, if you prefer): some of you may even remember a rather sparse description on this very page when it was still devoted to ADG (almost eight years ago, time flies…).

Straight out of my anime backlog, I watched the first episode of Clannad. I don’t know much about the original name (save for the time it took to be released), but I knew that the animation studio who did this series was Kyoto Animation (The Melancholy of Haruhi Suzumiya, Air, Kanon and Lucky Star).

From the already large backlog of new series, I recently watched the first episode of Prism Ark, an anime adaptation of the H-Game _PRISM ARK ~ PRISM HEART II ~ _by Pajamas Soft (I wonder how some Japanese companies get to choose their names…). It is being directed by Masami Obari, who did Dancougar Nova the last season.

I’m back from holidays, and when I got back I found the Saber Revoltech figure I had preordered in May (!) in the mail. This is the package when I pulled it out from the box it came in (apologies for the image quality, I only had my mobile phone to take it):

[]({{ site.url }}/images/2007/07/strikers_dvd_1_cover.png)

Today I got the first Maho Shojo Lyrical Nanoha StrikerS R2 DVD in the mail. Even though I haven’t watched it properly yet (I plan on doing so tomorrow) I can say I’m already impressed. Usually Japanese DVDs are little more than improved video tapes: they provide just the bare minimum (and not for a cheap price). However, this is not the case with Nanoha StrikerS.

According to the Anime News Network, Geneon Entertainment has bought the license for distributing Maho Shojo Lyrical Nanoha and Nanoha A’s in the United States. Fans rejoice? I think not. Being outside of the USA market, I view things with a different approach. The companies here in Italy have all their problems, but to a certain degree they care about delivering to the user something more than just the episodes. Extras that can also be an incentive over downloading (illegally) over the Internet.

When Tokyopop announced _Slayers, Kino no Tabi _and _Scrapped Princess _my interest was piqued: even more when I read about Seikai no Monsho. After getting what was available (three volumes of Scrapped Princess, the whole Seikai no Monsho trilogy and the single volume of Kino no Tabi) I waited for the rest.

According to the Anime News Network, Geneon Entertainment has bought the license for distributing Maho Shojo Lyrical Nanoha and Nanoha A’s in the United States. Fans rejoice? I think not. Being outside of the USA market, I view things with a different approach. The companies here in Italy have all their problems, but to a certain degree they care about delivering to the user something more than just the episodes. Extras that can also be an incentive over downloading (illegally) over the Internet.

Recently I had to annotate a large (10,000+) number of genes identified by Entrez Gene IDs. My goal was to avoid “annotation files” (basically CSV files) that a part of wet lab group likes, because I wanted to stay up-to-date without having to remember to update them. So the obvious solution was to use a service available on the web, and in an automated way. For reference, I just tried to attach gene symbol, gene name, chromosome and cytoband.

While working today on an annotation class in Python I stumbled on a problem. Normally I work with lists of genes that are consistent, i.e. all Entrez Gene IDs (or RefSeq IDs, or Genome Browser IDs…), but today I had a list of mixed identifiers. The subsequent idea was “let’s implement auto-detection of common identifiers in the class”. The problem is… is there any actual documentation on how identifiers are made?

During the discussions for the release of openSUSE 12.3, the topic of update notifications and applets was brought up again. Originally openSUSE shipped with a custom update applet, but since it was basically unmaintained, the decision was made to switch to Apper for openSUSE 12.2 The original Apper used in that version had a number of issues, which the upstream developer (Daniel Nicoletti) fixed in a newer version, which also had a lot of other improvments.

 It’s been a while since I blogged about anything non-FOSS. This time I’ll be sharing some impressions on one of the games I’m playing at the moment, that is,** Ar Tonelico III** (which arrived at my doorstep two days ago). I admit I haven’t been a fan of Gust games (aside from Ar Tonelico, they’re known mostly for the Atelier series), mostly because technically wise they didn’t really perform that well.

I was thinking about writing something on the line of what I announced in the past entry, but what has happened recently surrounding the artist who does the work for The S.T.E.A.L. Saga, that is Too, made me change my mind.

The other day I was thinking about how to make screencaps for the anime I watch. Windows users often use Media Player Classic, which can create a video contact sheet (i.e., a series of captures) out of a movie file. I had two problems with this: The biggest is that it runs on Windows, and I don’t use Windows; The frames needed to be manually cropped every time, which was slow.

Yesterday KDE released their first beta of the upcoming 4.13 version of Workspaces, Applications and Development platform. As usual with the major releases from KDE, it’s packed with a lot of “good stuff”. Giving a list of all the improvements is daunting, however there are some key points that stand out: Searching: KDE’s next generation semantic search is a prominent feature of this release. It’s several orders of magnitude faster, much leaner on memory and generally is a great improvement from the previous situation (this writer has been testing it for the past months and he’s absolutely delighted about it).

KDE released the second beta of the KDE Platform, Workspaces and Applications 4.11, and after the necessary time for the OBS to build packages from the released tarballs, packages are available for openSUSE 12.3 and openSUSE Factory. Like the previous beta, they are available through the KDE:Distro:Factory repository. 4.11.x is is targeted for inclusion in the upcoming openSUSE 13.1. So far 4.11 has been pretty stable for me, but you should never forget these packages are for testing and bug reporting purposes: don’t use them on production systems.

Since KDE has released the first beta of Platform, Workspaces, and Applications 4.11, there will be some changes in the packages offered in the openSUSE repositories. In short: KDE:Distro:Factory will now start tracking 4.11 betas and RCs: packages are being worked on. Use this version to test packages and to report bugs upstream. KDE:Release:410 has been decoupled from KDE:Distro:Factory. If you were using 4.10 packages from KDF, you’re highly encouraged to move to this repository.

The KDE community has just released Beta 2 of the upcoming 4.10 release of the Development Platform, Workspaces, and Applications. Of course, distributions are providing binary packages for the adventurous… and how could the green distro be left out? In fact, it is not. Beta 2 packages were uploaded and built in the KDE:Distro:Factory repository. Updated packages have also been submitted to the development version of openSUSE (Factory) as the ultimate goal is having 4.

In the past months I’ve always wanted to write a small Plasma applet to aid me in some boring tasks as a bioinformatician. One example (for the non-scientific crowd out there) is when I find a specific gene out of my analysis work which I want to take a look at. I am often lazy, so instead of firing up the browser to look at the online resources, I wanted to write something which could access said resources programmatically.

I’ve been wondering about why FOSS is often compared to the academic world, but at least in my limited experience, I see little people that grasp its concept in the world of research. On a quick look, developing FOSS in a research environment would be very good: not only you’d get publicly available results when you publish, but at the same time you can make sure that in an extreme case your application will be carried on by someone else should you not be able to continue development.

I’m often wondering why people only resort to R when working with microarrays. I can understand that Bioconductor offers a plethora of different packages and that R’s statistical functions come in handy for many applications, but still, I think people underestimate the impact of performance. R is not a performing language at all, it doesn’t parallelize well when using HPC (at least from the talks I’ve had with people studying the matter), and in general is a memory and resource hog.

While working today on an annotation class in Python I stumbled on a problem. Normally I work with lists of genes that are consistent, i.e. all Entrez Gene IDs (or RefSeq IDs, or Genome Browser IDs…), but today I had a list of mixed identifiers. The subsequent idea was “let’s implement auto-detection of common identifiers in the class”. The problem is… is there any actual documentation on how identifiers are made?

**Notice:**Just now I realized this has been linked to to a Stack Overflow question. I recently wrote a new post that uses a different technique and a combination of R and Python. [Check it out!]({{ site.url }}/2011/05/multiscale-bootstrap-clustering-with-python-and-r)

Following up my recent post, I’ve been looking for alternatives to TMeV. So far I’ve found the R package pvclust and the Pycluster library, part of BioPython. The first one also performs bootstrapping (I’m not sure if it’s similar to what support trees do, but it’s still better than no resampling at all). I’ve found another Python project but it is still too basic to perform what I need.

As people who read my science-related posts know already, I’m not a big fan of {{post id=“software-and-biological-research” text=“software made just to support a publication”}}. Recently I’ve stumbled again into similar software. Namely, I’m talking about the TIGR Multiexperiment Viewer (TMeV), a Java-based program which is often used for microarray analysis. It’s not exactly “fit for publication”, because it has reached version 4 last year, but shows some of the problems ({{post id=“genbugg” text=“mentioned already”}}) with releasing bioinformatics software.

I use TMeV mostly because I didn’t find any other implementation of the hierarchical clustering algorithm with support trees. However, I’ve stumbled upon a very annoying bug in the most recent version. Normally I use average linkage clustering and as the distance metric I employ the Pearson’s correlation, and with gene and sample bootstrapping: with certain files this makes TMeV report errors at random during the iterations.

Today I started working on a data set published on GEO. As the sample data were somehow inconsistent (they mentioned 23 controls when I found 28), I decided to parse the SOFT file from GEO in order to get the exact sample information. I did a grave mistake. First of all, Biopython’s SOFT parser is horribly broken (doesn’t work at all) and quite undocumented: I could work around the lack of documentation (API docs) but not with the fact that it wouldn’t work.

Today I was looking for an easy way to do some calculations of raw expression data on Affymetrix arrays, but I didn’t want to use R: I have already mentioned how I don’t like its design and implementation. While looking for some documentation, I stumbled upon this nifty little program called RMAExpress.

(Inspired by http://viccuad.me/blog/GPG-transition-statement/) This exact same text can be found at this location. -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Sun Jun 7 14:12:39 CEST 2015 For a number of reasons, i've recently set up a new OpenPGP key, and will be transitioning away from my old one. The old key will continue to be valid for some time, but i prefer all future correspondence to come to the new one. I would also like this new key to be re-integrated into the web of trust.

As I said in my latest post, I wasn’t very happy with using Disqus to store my comments, mainly because I do not want my data to be hosted by someone else. Thanks to some commenters, I was made aware of an alternative, called isso. After reading the online documentation, I decided to set it up with dennogumi.org. It was all a matter of creating a new user called isso, setting a virtualenv to its home dir, and then installing isso itself and uWSGI:

Since [26th December 2005]({{ site.url }}/2005/12/up-and-running/), I’ve been runnning this blog with Wordpress. At the time there were little alternatives and finally I had got hold of a host (Dreamhost, at the time) that supported PHP and MySQL without being overly restrictive. 10 years later, things have somehow changed. The issue The main reason lies in how Wordpress has evolved over time: no, I’m not speaking about the subjective “bloat”, but the fact that it’s been moving towards a full-blown CMS, which is not what I have in mind to run my blog.

After many years of (good) service, I’m in the process of moving from Dreamhost web hosting to a Virtual Private Server (VPS) service hosted by the folks at Linode. It’s definitely more pricey but I like the control and freedom that I have at my disposal. Thanks to a number of guides and some help, I was able to set up lighttpd and php-fpm to serve web pages, and Postfix+dovecot+amavisd-new for email.

I just read from Weblog Tools Collection that CollegeScholarships.org is hosting a vote for a round of $10,000 blogging scholarships. Now, I may be a little out of the “Web 2.0” trend (actually for me “2.0” does not relate to Tim O’Reilly’s buzzword, but to real and interesting technologies like the Semantic Web), but I find this absurd. I mean, I have no doubts that the people listed there have made interesting blogs.

Mtux, of choqok fame, along with another person, has written Bilbo Blogger, a blogging utility for Blogger or any blog that supports Blogger1.0, MetaWeblog, and MovableType APIs (EDIT: also GData). It is based on the KDE4 libraries and it includes a WYSIWYG editor, an HTML editor, and a Post Preview function that can even fetch your blog’s CSS to render the entry and see how it looks. It’s not released yet, but for the daring, you can actually try and compile it.

Many of you know that KDE Brainstorm ideas aren’t posted straight away: they are always pre-screened to avoid repetitions, features that cannot be implemented technically, violations of the Code of Conduct, and so on. This is possible thanks to the work of the Idea Moderators, that patrol Brainstorm and evaluate the new ideas being posted. Recently, a few of them got too busy and thus we’re experiencing a backlog of ideas staying in the Vault (the staging area for evaluation) for longer times than usual.

The recent post by Dario on the KDE Workspace Vision raised some concerns on why Brainstorm was not used.One commenter even said _Right now it feels like “Throw an idea over a wall for no-one but end users to discuss until it bitrot’s”. _ _ _ The Brainstorm section is indeed in need of help. To make it more useful, a couple of things are needed: Statistics to evaluate which ideas are best representative: it can’t be just the number of votes per se as there are things like confirmation bias or controversies that may inflate the numbers Integration with Bugzilla: a way to automatically (using XML-RPC) send the ideas flagged as representative to a bug report filed under “wishlist”.

The KDE Brainstorm, where users can post and vote for feature requests for KDE, is the most visited area of the KDE Community Forums. In an effort to improve the experience of both users and developers, the KDE Community Forums staff is proud to present a brand new version of the KDE Brainstorm.  The new interface resembles the IdeaTorrent sites, but it is still powered by the forum software (phpBB), a clear example of the flexibility of the platform.

Hello, and welcome to the first “issue” of the KDE Brainstorm monthly digest. First of all, a few words of introduction. There are quite a number of ideas being posted on the KDE Brainstorm, and it would be nice to know how the initiative is faring, and important highlights, like what ideas are more popular, which are more controversial, etc. That is why the idea of a monthly digest was born (in a similar fashion as the fabolous Commit Digest).

Via Harald Hvaal’s blog I learnt that the first non-forum suggestion has been implemented! I think this shows without doubt that initiatives like the KDE Brainstorm are undoubtedly useful to the community at large, both users and developers. Keep on rocking!

Now that the KDE Brainstorm has been launched, it’s time to take a look at the results so far. Currently, the forum hosts 160 threads, approximately one for each idea, and 441 posts. Not bad for the first two days of operation. At the same time, the staff has been working hard to make sure only appropriate ideas (not bug reports, not duplicates…) are on the forum. People have also begun voting, although slowly: it’s understandable, given the fact that there are so many threads in so little time.

It’s finally there: KDE Brainstorm has been launched today! Like this, it will be possible to propose features and have them voted by the community, and then submit the most voted requests to the developers. Every feature request is screened prior to posting, so duplicates, spam and flames are unlikely to occur. There is no guarantee that the voted upon features will be implemented, but as opposed to individual postings, this approach reduces the noise a lot, and allows a better communication between the “two worlds” (users and developers).

Hello, and welcome to the second issue of the KDE Brainstorm Digest! This issue comes in slightly late, due to some real time commitments, but I couldn’t leave you without it, could I?

And so, with yesterday’s update, FFXI has gained a windowed mode. This has been a much-requested feature from the playerbase, especially from people who didn’t want to use the “unofficial” windower.

However, being the first major touch to the rendering engine, I think something got broken along the way. Mainly, I’m talking about a 20% performance drop of the engine (which didn’t shine before, but that’s another matter).

Like everything, openSUSE is not perfect. Bugs crop here and there, or there is missing / quirky functionality that users may run into. Being a distribution of heterogeneous software, this means that bugs fall into these categories: Upstream bugs in the software shipped by openSUSE Bugs in the packaging Bugs in distribution-specific setups or that derive from interactions with these setups (e.g. kernel, low level software stack, etc.

The title clearly shows what I think about the aforementioned company. The reason surfaced a few days ago, when I tried to see if they would ship Wings of the Goddess to Italy. I had ordered from them a few times before, and although their customer service left a lot to be desired, I couldn’t complain much. Two days ago I found that they will no longer ship anything to Italy.

Some of you may remember a semi-complex application I wrote back in the days, namely [Danbooru Client]({{ site.url }}/projects/danbooru-client/). Written in PyKDE4, it provided a semi-decent interface to Danbooru-style boards. It mostly worked and received little maintenance (also because I didn’t have that much time for maintenance). In the mean time, I started learning some C++. No, it’s not that I don’t like Python (in fact I do, I use it a lot in my day job), but I wanted to gain at least some basic skills to be able to contribute directly to KDE software.

(Note: I should really start posting more often nowadays) Last monday, for one of my group, I re-did one of the hardest missions of the whole Chains of Promathia expansion: PM6-4, better known as “One to be Feared”. I was looking forward to redoing it, mainly because I wanted to see if the adjustments that came after I finished the expansion (Sentinel modification, shield blocks modification, etc.) made the job easier.

Straight out of my anime backlog, I watched the first episode of Clannad. I don’t know much about the original name (save for the time it took to be released), but I knew that the animation studio who did this series was Kyoto Animation (The Melancholy of Haruhi Suzumiya, Air, Kanon and Lucky Star).

**Notice:**Just now I realized this has been linked to to a Stack Overflow question. I recently wrote a new post that uses a different technique and a combination of R and Python. [Check it out!]({{ site.url }}/2011/05/multiscale-bootstrap-clustering-with-python-and-r)

Following up my recent post, I’ve been looking for alternatives to TMeV. So far I’ve found the R package pvclust and the Pycluster library, part of BioPython. The first one also performs bootstrapping (I’m not sure if it’s similar to what support trees do, but it’s still better than no resampling at all). I’ve found another Python project but it is still too basic to perform what I need.

While reading the statistics for my blog, I noticed that a number of searches looked for hierarchical clustering with Python, which [I covered quite a while ago]({{ site.url }}/2007/11/data-clustering-with-python). Today I’d like to present an updated version which uses more robust techniques.

As I said in my latest post, I wasn’t very happy with using Disqus to store my comments, mainly because I do not want my data to be hosted by someone else. Thanks to some commenters, I was made aware of an alternative, called isso. After reading the online documentation, I decided to set it up with dennogumi.org. It was all a matter of creating a new user called isso, setting a virtualenv to its home dir, and then installing isso itself and uWSGI:

In line with the project’s committment to openness, the KDE developers and contributors are not a secretive bunch. In fact, the “People Behind KDE” initiative has provided the community with interviews of quite a number of the developers. And by reading those interviews, haven’t you ever felt the need of asking a specific question, outside from those prepared by the interviewer? For example, more details about what the specific developer is doing, or what his/her plans are for the next version of KDE.

One thing I always wanted to do when going on holiday is to track where I go, the places I’ve been, and see how much I’ve travelled around. This is true in particular when going to places where I walk around a lot (Japan stays at the top of the list, also for other reasons that are not related to this post). Something like viewing a map showing where you were, and where did you go, with optional export to KML or GPX to import into other programs like Marble.

Recently we’ve seen several blog posts on Planet KDE related to Nepomuk. Reading those I thought that I could add some (little) semantic features to [Danbooru Client]({{ site.url }}/projects/danbooru-client). Danbooru Client already makes use of Nepomuk: if enabled, tags extracted from Danbooru items are added as Nepomuk tags. But since at least some Danbooru boards are specialized in certain types of images (e.g., wallpapers only, for examples) I found it would be nice to have Nepomuk show me only the images that come from a specific Danbooru board.

A while ago I presented [“danbooru2nepomuk”]({{ site.url }}/2009/10/danbooru2nepomuk-a-nepomuk-tagger-for-danbooru-images), a small program to tag images coming from Danbooru-based image boards. Today I want to present the evolution of that program, that is a PyKDE4 client for those boards.

If you dabble with [anime]({{ site.url }}/category/Anime) and related things like I do, you may have heard about imageboards. A known variant, which powers sites such as moe.imouto (some links may be NSFW) or Konachan, is Danbooru, a Ruby on Rails application. One of the characteristics of this software is that images stored there can be tagged to be identified as precisely as possible: common tags are for example the magazine where the image was taken from, the characters depicted, and so on.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highlights of the new version Unbreak konachan.com support (change in URL format) Coming up next HTTPS support!

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version Support for width / height based filtering: now you can exclude posts that are below a specific width or height (or both) New dependency: KTextWidgets Coming up next Sooner or later I’ll get to finish the multiple API support, but given that there’s close to no interest for these programs (people are happy to use a browser) and that I work on this very irregularly (every 6-7 months at best), there’s no ETA at all.

Following up on yesterday’s release, I’ve released Danbooru Client 0.3.0. This early new release is mostly due to the fact that the QML view file wasn’t installed (sorry!) so part of the UI would not even load (or even crash). That said, I’ve managed to get some extra features in: Fade-in/out animation when posts are being downloaded Support for tagging is back (EXPERIMENTAL): it is optional, and requires KFileMetaData (not yet a framework, but should be distributed with Plasma 5).

After my previous post, development went quicker than expected, so I’ve actually managed to get a real version out. ;) So without much ado… here’s Danbooru Client 0.2.0! This redesigned C++ version brings a few more features compared to the PyKDE4 version, notably: Infinite scrolling (experimental) - Just scroll down to load the next set of posts QML-based thumbnail view Click on the image below to have a demonstration of what’s in this release (warning: 2M GIF file): [!

Some of you may remember a semi-complex application I wrote back in the days, namely [Danbooru Client]({{ site.url }}/projects/danbooru-client/). Written in PyKDE4, it provided a semi-decent interface to Danbooru-style boards. It mostly worked and received little maintenance (also because I didn’t have that much time for maintenance). In the mean time, I started learning some C++. No, it’s not that I don’t like Python (in fact I do, I use it a lot in my day job), but I wanted to gain at least some basic skills to be able to contribute directly to KDE software.

Sometimes answering apparently harmless questions on instant messaging can have unexpected results. In particular, I was telling about Danbooru Client to someone and a question popped up “Why don’t you support pages?”. It seemed a nice idea, so I branched off the code (yay for git!) and started working on it. Well, it took me more than a month to get this thing done… I didn’t spend every day coding, but it was a challenge.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version The image window is shown again with recent Qt and KF5 versions; Remember the last directory saved when saving images; Remove (hopefully) hang when saving images.

Recently I had to annotate a large (10,000+) number of genes identified by Entrez Gene IDs. My goal was to avoid “annotation files” (basically CSV files) that a part of wet lab group likes, because I wanted to stay up-to-date without having to remember to update them. So the obvious solution was to use a service available on the web, and in an automated way. For reference, I just tried to attach gene symbol, gene name, chromosome and cytoband.

At last, after months of inactivity, I pushed out a new release of [DataMatrix]({{ site.url }}/projects/datamatrix). Although the version bump is small (0.8) there are a lot of changes since last releases. The most notable include: Ability to apply functions to elements of the matrix Ability to filter rows by column contents Ability to transpose rows with columns An option to load text files produced by R (which are, by design, broken) Removed the getter for columns, using dictionary-like syntax directly A lot of bug fixes The download links on [the project page]({{ site.

Finally a new entry! I’ve been extremely busy with other things, that is why I did not have time to write more. One of the main reason is related to an important landmark in my professional career, but I’ll write more about it after January 1st (hint: those who follow my Twitter updates may have already understood). As a nice way to break the hiatus, I’m releasing a new version of DataMatrix, my implementation of R’s data.

Ok, ok… my definition of “tomorrow” is not like what most people use, apparently. Although I took quite a while, now [there is a static page on DataMatrix]({{ site.url }}/projects-2/datamatrix). There you will find a summary of wht I wrote in my other blog posts regarding this module. Of course, it will be kept up-to-date should I release a new version. Aside that, I put a contact form on this blog.

At last, since it’s been like ages, I decided to put out a new version of DataMatrix. For those who haven’t seen my previous post, DataMatrix is a Pythonic implementation of R’s data.frame. It enables you to manipulate a text file by columns or rows, to your liking, using a dictionary-like syntax. In this new version there have been a few improvements and correction to a couple bugs (for example saveMatrix did not really save) and the start (only a stub at the moment) of an append function to add more columns (I’ll also think about a function to add rows).

Hello, and welcome to the first “issue” of the KDE Brainstorm monthly digest. First of all, a few words of introduction. There are quite a number of ideas being posted on the KDE Brainstorm, and it would be nice to know how the initiative is faring, and important highlights, like what ideas are more popular, which are more controversial, etc. That is why the idea of a monthly digest was born (in a similar fashion as the fabolous Commit Digest).

Currently I have Kubuntu 8.04 (Hardy) installed on my Eee PC. Version 8.10, the Intrepid Ibex, is due on October 30th. However, I will not install it. The reason is that Kubuntu developers intentionally disabled the zoom function, and I have three activities on this machine. How come I’m supposed to use them? Also, space is pretty tight so install a build environment just to remove one patch seems overkill. So, I’m moving away from it.

(Note: this post also appears in Planet KDE and Planet openSUSE because I thought this might be interesting to others) As I mentioned in some other posts, I have a small “server” which I use as a NAS to provide archiving for photos and other files of interest. As it runs in a remarkably small (and quiet) enclosure, I’ve managed to put it in an incospicuous part of the room it is in.

For a change, my brother has found a place (DLsite.com) that sells dojinshi even to non-Japanese people, and also found three non-hentai Final Fantasy XI dojins, which I’m going to cover in this post. For reference, they are available with these prices:

• FFXI-URUSHI-Chaos: 01 - ¥ 735;

• FFXI-URUSHI-Chaos: 02 - ¥ 735;

• FFXI-URUSHI-Chaos:03 - ¥ 945.

[]({{ site.url }}/images/2008/04/ookami_cover.png)

A rather large number of days ago I got the first DVD of Ookami to koshinryo, better known as Spice and Wolf, which I when the first episode was released. I got the limited edition, which came in with a number of extra features (which still don’t justify its ~ ¥6800 price tag, though). The main one is the inclusion of a 300 piece puzzle, illustrated by the artist who works on the original novels.

[]({{ site.url }}/images/2007/07/strikers_dvd_1_cover.png)

Today I got the first Maho Shojo Lyrical Nanoha StrikerS R2 DVD in the mail. Even though I haven’t watched it properly yet (I plan on doing so tomorrow) I can say I’m already impressed. Usually Japanese DVDs are little more than improved video tapes: they provide just the bare minimum (and not for a cheap price). However, this is not the case with Nanoha StrikerS.

I’ve found myself in a situation where my ISP, notorious for having problems with certain online services (not to mention putting everyone under a permanent NAT) started misbehaving with Sony’s Playstation Network: I was getting timeouts of all sorts with no reason (and reading online you see all sorts of attempts from people to work around the issue). When using my phone as hotspot, everything worked, as I went through my mobile operator’s network.

After almost a month of wait (Dynamism.com doesn’t like simple order procedures), I finally got hold of an Asus Eee PC 900 (obviously - for the readers of this blog - the 20 Gb Linux version). Read more for some quick impressions and pictures.

Since my work schedule is bordering on the hectic, I was thinking on buying something to get me more organized. Rather than a PDA, I’ve been rather interested in the Asus Eee PC: small form factor, SSDs and Linux preinstalled are definitely pluses. It’s too bad that at least in Italy Asus sells only the 512M RAM version (when there are more powerful options available elsewhere). I’d like to get impressions on the Asus Eee, before considering a purchase (€ 300 are still a lot): did you try it?

I’m a (happy!) owner of a Casio EX-WORD Dataplus 5 XD-A4700, a Japanese electronic dictionary. Recently I looked into updating the Japanese-English dictionary (currently the Shogakukan PROGRESSIVE dictionary) installed, because it’s not good enough: too often when looking up odd sentences (like the ones in Fate/Extra CCC) I do not find any matches. EDICT is adequate, and while I can use it on my phone and tablet, I like the fact that the EX-WORD has a physical keyboard along with the stylus, and a very nice kanji handwriting recognition.

Following up on my previous post, a different type of image has been made by the openSUSE KDE community members. In particular, alin has created images sporting the same software from KDE (4.10 RC2) but using the upcoming openSUSE 12.3 as base. Download links: 32 bit version 64 bit version Release directory (in case the above links go 404; the files are named KDE4-.4.10.RC2-Live) These images are provided not only to test 4.

I’m back from holidays, and when I got back I found the Saber Revoltech figure I had preordered in May (!) in the mail. This is the package when I pulled it out from the box it came in (apologies for the image quality, I only had my mobile phone to take it):

The ever-amazing Plasma team from KDEjust put out a new release of Plasma. I won’t spend much describing how big of an improvement it is - the release announcement at KDE has all the details needed to whet your appetite. And of course, now it’s the turn of distributions to get out packages for the users at large. This is also the case for openSUSE. The KDE:Frameworks5 repository hosts the new 5.

This is a guest post by Raymond “tittiatcoke” Wooninck, with contributions from myself and Hrvoje “shumski” Senjan In the next hours the [KDE:Current]({{ site.url }}/2014/03/being-current/) repository will publish the latest release from KDE (4.13). As that this release comes with a big change (the new semantic search), we would like some simple steps in order to perform the right upgrade. Before the upgrade In order to migrate data automatically from the Nepomuk store to the new format, you will need Nepomuk up and running, and just for the time needed for the migration.

I’m a (happy!) owner of a Casio EX-WORD Dataplus 5 XD-A4700, a Japanese electronic dictionary. Recently I looked into updating the Japanese-English dictionary (currently the Shogakukan PROGRESSIVE dictionary) installed, because it’s not good enough: too often when looking up odd sentences (like the ones in Fate/Extra CCC) I do not find any matches. EDICT is adequate, and while I can use it on my phone and tablet, I like the fact that the EX-WORD has a physical keyboard along with the stylus, and a very nice kanji handwriting recognition.

Recently Fedora’s Lukas Tinkl pushed to kdelibs (for the 4.10 release) a patch that enabled Solid to talk to udisks2, which is a replacement for udisks. Fedora already moved to udisks2 (and killed HAL) and future GNOME releases will only use udisks2, so the need for a working backend was a necessity, and at the same time they acted like good open source citizens, and pushed the code both to 4.

 On Septemer 1st the open beta of Square Enix’s new MMORPG, FINAL FANTASY XIV Online was launched. I’ve been playing its predecessor since December 2003, although nowadays my presence is limited to doing the “missions” (quests that advance the main storyline). Of course I was interested in the “new MMO” in the works at Square since it was mentioned in 2006. When the official release was announced, I preordered the so-called Limited Collector’s Edition (it comes with nice items inside, along with an in-game item).

All right, it didn’t quite turn out as I had expected. This post wasn’t “soon"as I predicted originally. The reason? The fact that the video card I bought died after three days of usage, and getting a replacement took a while. Finally though, I have a functional system. It’s a Core 2 Duo CPU (7200) with 2 Gb of RAM and an ATI Radeon 3870 HD video card. I installed Linux on it, of course, but instead of Kubuntu I gave openSUSE a try.

Sadly (for me) I’m back from the holidays. For those of you who wondered why the updates on Japan stopped: when I got back to Tokyo I didn’t have an Internet connection, so I had no means to update. The whole holiday was a blast, though, and we’re considering getting back in two years. Aside from that, work has picked up a really fast pace immediately (why on Earth journals don’t accept LaTeX-produced PDFs?

(Note: I should really start posting more often nowadays) Last monday, for one of my group, I re-did one of the hardest missions of the whole Chains of Promathia expansion: PM6-4, better known as “One to be Feared”. I was looking forward to redoing it, mainly because I wanted to see if the adjustments that came after I finished the expansion (Sentinel modification, shield blocks modification, etc.) made the job easier.

I haven’t posted anything in a month or so. Quite a long time, considering I used to write at least once per week. The reasons are mainly two: first of all, my work schedule has taken a turn for the worse, which means I have to do my job a lot harder than before; secondly, there wasn’t much interesting stuff to report. Let’s resume from the hiatus by writing about my latest Final Fantasy XI session.

For a change, my brother has found a place (DLsite.com) that sells dojinshi even to non-Japanese people, and also found three non-hentai Final Fantasy XI dojins, which I’m going to cover in this post. For reference, they are available with these prices:

• FFXI-URUSHI-Chaos: 01 - ¥ 735;

• FFXI-URUSHI-Chaos: 02 - ¥ 735;

• FFXI-URUSHI-Chaos:03 - ¥ 945.

Despite the utter lack of content in Wings of the Goddess my brother has managed to create a movie clip (inspired by the opening of Wild ARMs The Vth Vanguard). You can view it below (streaming) or obtain a higher quality version. [googlevideo]http://video.google.com/videoplay?docid=8316261647217076877[/googlevideo] (apologies for the lack of updates. I’ve been quite busy. I will probably post more in during the Christmas holidays)

While I’m waiting for KDE 4.0 to compile, I just wanted to share a small clip of my brother’s character doing the Drain Samba animation. A bit of background: he has leveled Dancer up to level 7, and now he stopped because there is no artifact armor available yet (probably out in February) and because he’s also leveling another job, monk. Given how people rushed to get Dancer to 75 in less than a week (comments are left to the reader) it is a nice change.

[]({{ site.url }}/images/2007/11/pol-2007-11-30-14-56-28-86.png)

Finally my copy of Wings of the Goddess has arrived. It was just a matter of putting the DVD in the drive and let install the measly 350+ Mb of update (rather low for a DVD). As usual, Square Enix’s installation program is greedy with regards to information. Once it was installed, I enabled the expansion in PlayOnline and was good to go (save a 20,000+ file check).

With the new version update, these strange portals have been appearing throughout Vana’diel. They’re supposedly the gateways to the past, but since I don’t have Wings of the Goddess yet I can’t really see what will they do. Nevertheless, I was curious and went to take a look at them. They’re **huge. **I estimate at least twice the height of my character. For those curious, here are two photos (one is of my brother’s character, the other is mine):

And so, with yesterday’s update, FFXI has gained a windowed mode. This has been a much-requested feature from the playerbase, especially from people who didn’t want to use the “unofficial” windower.

However, being the first major touch to the rendering engine, I think something got broken along the way. Mainly, I’m talking about a 20% performance drop of the engine (which didn’t shine before, but that’s another matter).

And so I’m reading that the FFXI Fan Festival has kicked off yesterday (I wish I could have been there). Naturally, reports have been flowing. The FFXI Encyclopedia has a good report of what has been said so far. 1up, the online branch of EGM, has also covered the event, but the article is only focusing on the new jobs (talk about explaining something no one else will ask… not to mention the attitude of that “journalist”).

I was thinking about writing something on the line of what I announced in the past entry, but what has happened recently surrounding the artist who does the work for The S.T.E.A.L. Saga, that is Too, made me change my mind.

Every day, a sizable number of people posts problems on the KDE Community Forums and the ever-helpful staff does their best to solve whatever issues they’re facing. But what exactly does one do when this happens? This post provides more insights on the process. NOTE: The following applies to my workflow for the Kontact & PIM subforum. Step 1: Someone posts a problem The questions posted are various, and range from simple tasks (“how I do XXX”) to very specific workflows.

The recent post by Dario on the KDE Workspace Vision raised some concerns on why Brainstorm was not used.One commenter even said _Right now it feels like “Throw an idea over a wall for no-one but end users to discuss until it bitrot’s”. _ _ _ The Brainstorm section is indeed in need of help. To make it more useful, a couple of things are needed: Statistics to evaluate which ideas are best representative: it can’t be just the number of votes per se as there are things like confirmation bias or controversies that may inflate the numbers Integration with Bugzilla: a way to automatically (using XML-RPC) send the ideas flagged as representative to a bug report filed under “wishlist”.

For KDE developers, web-based forums are often uncommon workflows. Indeed, for communication among developers mailing lists are much better tools, especially since you can handle everything inside a client (most of the time), compared to forums where you have to use a web browser. The ways of reading, replying and interacting with posters are dramatically different. And that is why some developers find themselves uncomfortable with the KDE Community Forums.

In the past weeks and days, the KDE Community Forums staff has been working to bring new features to improve even more the user experience. A few months ago, the staff was discussing the idea of finding a way to guide users to the most appropriate forum to post their questions or discussions. Now, thanks also to the return in service of one of our admins (welcome back, sayakb!) the feature is now being implemented, as the screenshots below will show.

Today, a major upgrade of the KDE Community Forums took place. The change brings quite a number of changes to the forums themselves, and it’s a further step towards providing a better experience for KDE users (and developers too!).

Recently Fedora’s Lukas Tinkl pushed to kdelibs (for the 4.10 release) a patch that enabled Solid to talk to udisks2, which is a replacement for udisks. Fedora already moved to udisks2 (and killed HAL) and future GNOME releases will only use udisks2, so the need for a working backend was a necessity, and at the same time they acted like good open source citizens, and pushed the code both to 4.

I’ve been wondering about why FOSS is often compared to the academic world, but at least in my limited experience, I see little people that grasp its concept in the world of research. On a quick look, developing FOSS in a research environment would be very good: not only you’d get publicly available results when you publish, but at the same time you can make sure that in an extreme case your application will be carried on by someone else should you not be able to continue development.

Recently I had the opportunity of viewing a DVD that I had bought in 2006 but never had the chance of seeing: it was the third season of Galaxy Angel, of which I had already viewed the first two years before. After viewing it, I realized I could have viewed it sooner, as I liked it quite a bit. Not only that, but I brought myself up to speed by getting what was left in the series, that is the second half of the third season (marketed by Bandai Visual as Galaxy Angel AA) and the fourth and final season (known in the English speaking market as Galaxy Angel X).

Well, I found the whole franchise quite good: and after having explored also other bits of it, including the manga and the games related to it, I thought it’d be nice to have a retrospective with my own views. Which is the point of this post.

[]({{ site.url }}/images/2013/01/mmBvi.jpg)

A few days ago I finally completed (after about 3 months) 神次元ゲームネプテューヌV, or “Kami Jigen Game Neptune V”, the latest instalment from Compile Heart in the Neptune franchise of PS3 games. It took quite a while (approximately 3 months), and I think it’s about time to wrap things up.

Sometimes Christmas presents are really unexpected, and today I found out I was given one such gift: the limited edition of _THE IDOLM@STER 2, _PS3 version. It was quite a bulky box, showing all the main characters from the game (and from the recently-ended anime) (click to enlarge):  Of course, having such a box means that there’s a lot of stuff inside. In fact, once opened, there are two game BDs (one being the actual game, the second being the first volume of Gravure for you!

 It’s been a while since I blogged about anything non-FOSS. This time I’ll be sharing some impressions on one of the games I’m playing at the moment, that is,** Ar Tonelico III** (which arrived at my doorstep two days ago). I admit I haven’t been a fan of Gust games (aside from Ar Tonelico, they’re known mostly for the Atelier series), mostly because technically wise they didn’t really perform that well.

The title clearly shows what I think about the aforementioned company. The reason surfaced a few days ago, when I tried to see if they would ship Wings of the Goddess to Italy. I had ordered from them a few times before, and although their customer service left a lot to be desired, I couldn’t complain much. Two days ago I found that they will no longer ship anything to Italy.

After quite a long time, I was finally able to take a look at this series: a rather atypical mecha show that despite some bad production, still manages to be interesting.

Because changes occur when one least expects them. This post is about one such change.

(Note: this post also appears in Planet KDE and Planet openSUSE because I thought this might be interesting to others) As I mentioned in some other posts, I have a small “server” which I use as a NAS to provide archiving for photos and other files of interest. As it runs in a remarkably small (and quiet) enclosure, I’ve managed to put it in an incospicuous part of the room it is in.

Omnia? The Turris Omnia is quite a nice (although a little pricey) OpenWRT-based router from CZ.NIC. It provides a fairly powerful CPU, relatively unconstrained eMMC space, and quite a lot of hackability (some revisions even have GPIO ports to play with). It runs a modified version of OpenWRT, named TurrisOS. The problem A few years ago, I built a custom NAS for my storage needs, using a cheap Intel SoC (J1900 chipset) and a (much pricier) mini-ITX small form factor server tower.

The migration happened and well… it turns out that it was not as smooth as I expected. In particular, comments weren’t working at all due to a filesystem permission on the database (which meant nothing would get written at all). That is now fixed. Sorry for the problems. To add problems over problems, I had a hardware failure (RAID card) last June, which wrecked the root filesystem and I had to reinstall everything from scratch.

You might have noticed that the blog has a markedly different look than before. It has not only changed visually, but also under the hood. This (brief) post summarizes the reasons behind the change. Why? Simply put, the previous solution was unmaintainable. “But,” you might say, “it was a static site generator! How could it become unmaintainable?”. It can. You might recall I moved from Wordpress to Jekyll about six years ago.

Sadly (for me) I’m back from the holidays. For those of you who wondered why the updates on Japan stopped: when I got back to Tokyo I didn’t have an Internet connection, so I had no means to update. The whole holiday was a blast, though, and we’re considering getting back in two years. Aside from that, work has picked up a really fast pace immediately (why on Earth journals don’t accept LaTeX-produced PDFs?

As you may already know, recently the KDE sysadmins completely overhauled the commit hooks used with the Git infrastructure. Written in Python, they have already brought significant improvements to the current workflows. These hooks include keywords that when specified trigger particular actions: the most used are to CC specific email addresses (CCMAIL), to CC bug reports (CCBUG) or to close bug reports (BUG). With the adoption of Review Board to facilitate code reviews, there were also requests for a REVIEW keyword that could close the review requests without asking the submitters to do so manually (which is slow and not always effective).

(Inspired by http://viccuad.me/blog/GPG-transition-statement/) This exact same text can be found at this location. -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Sun Jun 7 14:12:39 CEST 2015 For a number of reasons, i've recently set up a new OpenPGP key, and will be transitioning away from my old one. The old key will continue to be valid for some time, but i prefer all future correspondence to come to the new one. I would also like this new key to be re-integrated into the web of trust.

My supervisor has given me an OK for my thesis (save for a couple of cosmetic changes), therefore now I have just to wait for the verdict of the Ph.D. council then fill in some paperwork: the next step is the defense, sometime in January. After that I’ll probably put my thesis online and post a few articles on the concept of group testing for microarray data.

If you look through this blog’s archives, you may notice that although Free and Open Source Software is what I write most about, it is not the exclusive topic. I’ve written on science (my day job) as well as other interests. And today I’d like to lift the wraps on another project which I take part on, unrelated to the above. Notice for those who read my blog coming from FOSS aggregators like Planet KDE: this is fairly different than most recent topics from me, so be warned before you continue reading.

Yesterday I finally flipped the switch on the MX record and moved to a new server (still aptly named after another character from アキハバラ電脳組). The machine was found through Hetzner’s server auctions and has quite a good configuration for the price paid: Intel Xeon CPU E31245 @ 3.30GHz 16G ECC RAM (ECC was the deciding factor) LSI Hardware RAID 1 with two 3x2T disks Now, since the old server has been chugging along since 2011, the 5 eurocent question is why did you move at all?

Header image credit: 1840151sudarshan (Wikimedia Commons, CC BY-SA) A while ago I posted a way to download 実況動画 from Nicovideo. One of my acquaintances publishes videos there, and he wanted to collect the various comments to reply in a follow up video (what the Nico users call the コメント返し). When the comments are more than just a few, it’s hard to find where they refer to without watching them on Nicovideo itself, and its UI is suboptimal.

実況? Is it something edible? In recent times, I’ve been watching a lot of VOICEROID実況 (じっきょう, jikkyou, literally “commentary”) videos from the rather famous (in Japan) video service ニコニコ動画, better known as “Nicovideo”. In this case, the commentary actually refers to games: they’re basically a Japanese version of the Let’s Play videos that are all around other places like YouTube. The difference from “regular” videos lies in the “VOICEROID” term: this is a name of a TTS software developed by AH Software using an engine devised by a company called AI Inc.

Recently I was looking for a laptop: the previous one I had (an Asus EeePC 900) was almost dead (the fan broke, and the idea of dismantling everything to get to it wasn’t appealing). When looking around, I had the following requirements: It needed to run on Linux well. No exceptions. _Portable: _ at home and at my workplace I have rather powerful machines, so a desktop replacement was not needed.

All right, it didn’t quite turn out as I had expected. This post wasn’t “soon"as I predicted originally. The reason? The fact that the video card I bought died after three days of usage, and getting a replacement took a while. Finally though, I have a functional system. It’s a Core 2 Duo CPU (7200) with 2 Gb of RAM and an ATI Radeon 3870 HD video card. I installed Linux on it, of course, but instead of Kubuntu I gave openSUSE a try.

Many of you know that KDE Brainstorm ideas aren’t posted straight away: they are always pre-screened to avoid repetitions, features that cannot be implemented technically, violations of the Code of Conduct, and so on. This is possible thanks to the work of the Idea Moderators, that patrol Brainstorm and evaluate the new ideas being posted. Recently, a few of them got too busy and thus we’re experiencing a backlog of ideas staying in the Vault (the staging area for evaluation) for longer times than usual.

Yesterday I’ve been in Camogli and Portofino, two small towns in the eastern part of Liguria. The weather was nice and warm, and I took the opportunity of taking a few photos: [singlepic id=328 w=320 h=240 float=] [singlepic id=331 w=320 h=240 float=] Those are samples, the rest are available [in the gallery.]({{ site.url }}/nggallery/page-494/album-1/gallery-9)

Like every year, it’s finally time for me to go away and enjoy some hard-earned holidays. I’ll be spending next week traveling around France, then going to the sea. As such, my online presence will be reduced to the minimum: reports from the trip and some photos when I’m in France. See you on August 30th!

Sadly (for me) I’m back from the holidays. For those of you who wondered why the updates on Japan stopped: when I got back to Tokyo I didn’t have an Internet connection, so I had no means to update. The whole holiday was a blast, though, and we’re considering getting back in two years. Aside from that, work has picked up a really fast pace immediately (why on Earth journals don’t accept LaTeX-produced PDFs?

After many years of (good) service, I’m in the process of moving from Dreamhost web hosting to a Virtual Private Server (VPS) service hosted by the folks at Linode. It’s definitely more pricey but I like the control and freedom that I have at my disposal. Thanks to a number of guides and some help, I was able to set up lighttpd and php-fpm to serve web pages, and Postfix+dovecot+amavisd-new for email.

Sometimes Christmas presents are really unexpected, and today I found out I was given one such gift: the limited edition of _THE IDOLM@STER 2, _PS3 version. It was quite a bulky box, showing all the main characters from the game (and from the recently-ended anime) (click to enlarge):  Of course, having such a box means that there’s a lot of stuff inside. In fact, once opened, there are two game BDs (one being the actual game, the second being the first volume of Gravure for you!

As I said in my latest post, I wasn’t very happy with using Disqus to store my comments, mainly because I do not want my data to be hosted by someone else. Thanks to some commenters, I was made aware of an alternative, called isso. After reading the online documentation, I decided to set it up with dennogumi.org. It was all a matter of creating a new user called isso, setting a virtualenv to its home dir, and then installing isso itself and uWSGI:

Today we went to Nar, site of the first capital of Japan, especially to see the Todaiji Temple, designated as a World Heritage site by UNESCO. We used an express train to get to Nara and then a bus to get to the Todaiji itself (actually it’s a quick walk, I just didn’t know the distance was so short). The temple lies inside the Nara-koen, or Nara park, which is famous for its 1200 tame sacred deers.

It’s been a hot day here in Kyoto. And I don’t mean lame second meanings, just that the temperature was really over the top. As a consequence, we changed our plans: we were supposed to visit the so-called “path of the philosophy” but instead we set for Nijo Castle. Nijo Castle was the Kyoto residence of Ieyasu Tokugawa (I suspect to tell the emperor who was the real person in power) and it can be visited.

I was too tired to write an entry yesterday, so I’ll just sum things up here. Yesterday we went to Nikko, home of the Rinnoji Temple, the Toshogu Shrine and the Futarasan Shrine. We decided to visit it to see the tomb of Ieyasu Tokugawa. We took the Tobu Railways SPACIA train to Nikko then used a special pass I had bought beforehand online (the World Heritage Pass) to see the places.

I’m aching all over but I managed to write this entry. Today I went to the Ueno area first, hoping to go to the National Museum: however I forgot it was closed on Mondays, so I had to go to the National Science Museum instead. It turned out that it wasn’t a bad choice after all, as the museum is rich with exhibits and has a very good presentation. After that we moved to the Toshogu Shrine in Ueno Park, a shrine that was dedicated to the shogun Ieyasu Tokugawa.

I didn’t get time to write before about it, but I and my brother went to Japan for a 10-day holiday there, starting on yesterday. After a 12 hour trip, we arrived in Narita Airport and I took the chance of getting an IC card (prepaid subway/bus card) plus a shinkansen reservation I could only make in Japan (and that cost me “just” 27,000 yen). Once that was settled, we boarded the Japan Rail (JR) Narita Express and arrived in Tokyo.

I’m a (happy!) owner of a Casio EX-WORD Dataplus 5 XD-A4700, a Japanese electronic dictionary. Recently I looked into updating the Japanese-English dictionary (currently the Shogakukan PROGRESSIVE dictionary) installed, because it’s not good enough: too often when looking up odd sentences (like the ones in Fate/Extra CCC) I do not find any matches. EDICT is adequate, and while I can use it on my phone and tablet, I like the fact that the EX-WORD has a physical keyboard along with the stylus, and a very nice kanji handwriting recognition.

As people who read my science-related posts know already, I’m not a big fan of {{post id=“software-and-biological-research” text=“software made just to support a publication”}}. Recently I’ve stumbled again into similar software. Namely, I’m talking about the TIGR Multiexperiment Viewer (TMeV), a Java-based program which is often used for microarray analysis. It’s not exactly “fit for publication”, because it has reached version 4 last year, but shows some of the problems ({{post id=“genbugg” text=“mentioned already”}}) with releasing bioinformatics software.

I use TMeV mostly because I didn’t find any other implementation of the hierarchical clustering algorithm with support trees. However, I’ve stumbled upon a very annoying bug in the most recent version. Normally I use average linkage clustering and as the distance metric I employ the Pearson’s correlation, and with gene and sample bootstrapping: with certain files this makes TMeV report errors at random during the iterations.

As I said in my latest post, I wasn’t very happy with using Disqus to store my comments, mainly because I do not want my data to be hosted by someone else. Thanks to some commenters, I was made aware of an alternative, called isso. After reading the online documentation, I decided to set it up with dennogumi.org. It was all a matter of creating a new user called isso, setting a virtualenv to its home dir, and then installing isso itself and uWSGI:

Since [26th December 2005]({{ site.url }}/2005/12/up-and-running/), I’ve been runnning this blog with Wordpress. At the time there were little alternatives and finally I had got hold of a host (Dreamhost, at the time) that supported PHP and MySQL without being overly restrictive. 10 years later, things have somehow changed. The issue The main reason lies in how Wordpress has evolved over time: no, I’m not speaking about the subjective “bloat”, but the fact that it’s been moving towards a full-blown CMS, which is not what I have in mind to run my blog.

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A few days ago I finally completed (after about 3 months) 神次元ゲームネプテューヌV, or “Kami Jigen Game Neptune V”, the latest instalment from Compile Heart in the Neptune franchise of PS3 games. It took quite a while (approximately 3 months), and I think it’s about time to wrap things up.

The migration happened and well… it turns out that it was not as smooth as I expected. In particular, comments weren’t working at all due to a filesystem permission on the database (which meant nothing would get written at all). That is now fixed. Sorry for the problems. To add problems over problems, I had a hardware failure (RAID card) last June, which wrecked the root filesystem and I had to reinstall everything from scratch.

If I look back at the last post I made on ths blog… let’s say quite a lot of time has passed. The reason? Well, first of all, one would call it a lack of motivation1, and afterwards, the emergence of a small yet quite annoying pathogen which caused a bit of a stir worldwide. But today I’m not going to talk about viruses: perhaps some other time when you can avoid hear about it for breakfast, lunch, and dinner.

Part of this post is about openQA, openSUSE’s automated tool which tests a number of different scenarios, from installation to the behavior of the different desktop environments, plus testing the freshest code from KDE git. Recently, thanks to KDE team member Fabian Vogt, there has been important progress when testing KDE software. Testing the Dolphin file manager Those who use KDE software, either in Plasma or in other desktop environments have at least heard of Dolphin, the powerful file manager part of KDE Applications (by the way, have you checked out the recent beta yet?

As you may already know (if you don’t, please check these older posts) openQA, the automated testing system used by openSUSE runs daily tests on the latest KDE software from git. It works well and uncovered a number of bugs. However, it only tested X11. With Wayland starting to become usable, and some developers even switching to Wayland full time, it was a notable shortcoming. Until now. Why would openQA not run on Wayland?

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highlights of the new version Unbreak konachan.com support (change in URL format) Coming up next HTTPS support!

In the past three weeks, the openSUSE community KDE team has been pretty busy to package the latest release of Applications from KDE, 16.12. It was a pretty large task, due to the number of programs involved, and the fact that several monolithic projects were split (in particular KDE PIM). This post goes through what we did, and how we improved our packaging workflow. Some prerequisites In openSUSE speak, packages are developed in “projects”, which are separate repositories maintained on the OBS.

Admit it: how many times you have seen “software from this branch is completely untested, use it at your own risk” when you checked the latest code from any FOSS project? I bet you have, many times. For any reasonably modern project, this is not entirely true: Continuous Integration and automated testing are a huge help in ensuring that the code builds and at least does what it is supposed to do.

You may be aware that openSUSE Leap 42.2 is now in the release candidate stage, and there’s a lot of activity aimed at squashing those pesky bugs before they hit the final release. One particular bug proved to be quite tough to fix, and it was only solved thanks to the “heroes” mentioned in the title. This is the history of the bug. The report October 6th, 2016 - A bug iss reported against Plasma reporting a hard freeze of Plasma when using the Noveau driver, but not with the closed NVIDIA blob.

As you may know (unless you’ve been living in Alpha Centauri for the past century) the openSUSE community KDE team publishes LiveCD images for those willing to test the latest state of KDE software from the git master branches without having to break machines, causing a zombie apocalypse and so on. This post highlights the most recent developments in the area. Up to now, we had 3 different media, depending on the base distribution (stable Leap, ever-rolling Tumbleweed) and whether you wanted to go with the safe road (X11 session) or the dangerous path (Wayland):

Every day, a sizable number of people posts problems on the KDE Community Forums and the ever-helpful staff does their best to solve whatever issues they’re facing. But what exactly does one do when this happens? This post provides more insights on the process. NOTE: The following applies to my workflow for the Kontact & PIM subforum. Step 1: Someone posts a problem The questions posted are various, and range from simple tasks (“how I do XXX”) to very specific workflows.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version Support for width / height based filtering: now you can exclude posts that are below a specific width or height (or both) New dependency: KTextWidgets Coming up next Sooner or later I’ll get to finish the multiple API support, but given that there’s close to no interest for these programs (people are happy to use a browser) and that I work on this very irregularly (every 6-7 months at best), there’s no ETA at all.

Ever since the launch of Argon and Krypton, the openSUSE community KDE team didn’t really stand still: a number of changes (and potentially nice additions) have been brewing this week. This post recapitulates the most important one. I’d like the most recent Qt, please As pre-announced by a G+ post, the openSUSE repositories bringing KDE software directly from KDE git (KDE:Unstable:Frameworks and KDE:Unstable:Applications) have switched their Qt libraries from Qt 5.

As KDE software (be it the Frameworks libraries, the Plasma 5 workspace, or the Applications) develops during a normal release cycle, a lot of things happen. New and exciting features emerge, bugs get fixed, and the software becomes better and more useful than it was before. Thanks to code review and continuous integration, the code quality of KDE software has also tremendously improved. Given how things are improving, it is tempting to follow development as it happens.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version The image window is shown again with recent Qt and KF5 versions; Remember the last directory saved when saving images; Remove (hopefully) hang when saving images.

In the past week, the KDE Community Forums administrators had been discussing how to improve the current forum layout. There are a few reasons in favor of a reorganization. First of all, to reflect better what KDE is (a community that produces software). Secondly, to provide a better organinzation for all kinds of people: those that require support, those that offer support, and those who want to contribute. All of this within a (hopefully) logical structure.

KDE has recently released the newest Release Candidate of the Applications 15.08 release. Among the new features and changes of this release, there is a technology preview of the new KF5-based KDE PIM suite (including reworked, faster Akonadi internals), new applications ported to KF5 (the most notable ones being Dolphin and Ark). After some consideration and thinking on how to allow users to test this release without affecting their setups too much, the openSUSE community KDE team is happy to bring this latest RC to openSUSE Tumbleweed and openSUSE 13.

Since [26th December 2005]({{ site.url }}/2005/12/up-and-running/), I’ve been runnning this blog with Wordpress. At the time there were little alternatives and finally I had got hold of a host (Dreamhost, at the time) that supported PHP and MySQL without being overly restrictive. 10 years later, things have somehow changed. The issue The main reason lies in how Wordpress has evolved over time: no, I’m not speaking about the subjective “bloat”, but the fact that it’s been moving towards a full-blown CMS, which is not what I have in mind to run my blog.

A lot has been happening on the KDE side of openSUSE… this post summarizes what’s been going on so far. Live media for Plasma 5 One of the most-often requested ways to test Plasma 5, given it can’t be coinstalled with the 4.x Workspace, is the availability of live images to test either in VM or bare metal without touching existing systems. Given that other distributions started doing so since a while, naturally openSUSE couldn’t stay still.

Following up on yesterday’s release, I’ve released Danbooru Client 0.3.0. This early new release is mostly due to the fact that the QML view file wasn’t installed (sorry!) so part of the UI would not even load (or even crash). That said, I’ve managed to get some extra features in: Fade-in/out animation when posts are being downloaded Support for tagging is back (EXPERIMENTAL): it is optional, and requires KFileMetaData (not yet a framework, but should be distributed with Plasma 5).

After my previous post, development went quicker than expected, so I’ve actually managed to get a real version out. ;) So without much ado… here’s Danbooru Client 0.2.0! This redesigned C++ version brings a few more features compared to the PyKDE4 version, notably: Infinite scrolling (experimental) - Just scroll down to load the next set of posts QML-based thumbnail view Click on the image below to have a demonstration of what’s in this release (warning: 2M GIF file): [!

Some of you may remember a semi-complex application I wrote back in the days, namely [Danbooru Client]({{ site.url }}/projects/danbooru-client/). Written in PyKDE4, it provided a semi-decent interface to Danbooru-style boards. It mostly worked and received little maintenance (also because I didn’t have that much time for maintenance). In the mean time, I started learning some C++. No, it’s not that I don’t like Python (in fact I do, I use it a lot in my day job), but I wanted to gain at least some basic skills to be able to contribute directly to KDE software.

The ever-amazing Plasma team from KDEjust put out a new release of Plasma. I won’t spend much describing how big of an improvement it is - the release announcement at KDE has all the details needed to whet your appetite. And of course, now it’s the turn of distributions to get out packages for the users at large. This is also the case for openSUSE. The KDE:Frameworks5 repository hosts the new 5.

Short version: the KDE PIM in openSUSE Tumbleweed is moving from 4.14.x to the KF5 based version. More details below. Some history As you may know, up to now the default PIM suite for Plasma 5 in openSUSE Tumbleweed was the KDE PIM 4.14, based on kdelibs 4.x. While upstream KDE has offered a KF5-based version since Applications 15.08, it has been originally marked as a technology preview, so we (the openSUSE community KDE team) thought it would be more prudent to stick with the 4.

Following up onKDE’s announcement of the latest stable release, we have now packages available for 12.3 and 13.1 (a 13.2 repository will be made available after it is out). You will find them in the KDE:Current repository. Current users of this repository will get the new release automatically once they update. Why you should upgrade? You can take a look at the list of changes to get an idea. These fixes touch many important KDE applications, including KMail, Okular and Dolphin.

Congratulations to KDE (of which I’m proud of being a part of) for the newest release of the Plasma workspace! At the same time, the 4.x series has seen a new beta release, and the stable branch got updated, too. I’m betting a few people will ask “Are these available for openSUSE?” and of course the answer is yes, thanks to the efforts of the openSUSE community KDE team and the Open Build Service.

Since a couple of weeks the packages offered by openSUSE in the KDE:Unstable:Frameworks repository have undergone a series of changes. In particular, the packages now install to /usr. For the libraries (KDE Frameworks 5) this will mean a transparent change for the userbase as they are expected to be co-installable, but the workspace components (Plasma 5) will confict with the existing Plasma 4.11.x installation. What does this mean in practice? If you want to use Plasma 5 you will not be able to use a 4.

Recently I was looking for a laptop: the previous one I had (an Asus EeePC 900) was almost dead (the fan broke, and the idea of dismantling everything to get to it wasn’t appealing). When looking around, I had the following requirements: It needed to run on Linux well. No exceptions. _Portable: _ at home and at my workplace I have rather powerful machines, so a desktop replacement was not needed.

Requests to unlock KWallet automatically on login (assuming the wallet password and user password are the same), like gnome-keyring can do, have been going on for years: in fact, bug reports requesting this feature are quite old. Recently, thanks to the efforts of Alex Fiestas, a PAM module, which interfaces KWallet to the system authentication methods, has been developed. In parallel, the necessary glue code has been also added to the various parts of the KDE workspace so that it could make use of it.

This is a guest post by Raymond “tittiatcoke” Wooninck, with contributions from myself and Hrvoje “shumski” Senjan In the next hours the [KDE:Current]({{ site.url }}/2014/03/being-current/) repository will publish the latest release from KDE (4.13). As that this release comes with a big change (the new semantic search), we would like some simple steps in order to perform the right upgrade. Before the upgrade In order to migrate data automatically from the Nepomuk store to the new format, you will need Nepomuk up and running, and just for the time needed for the migration.

It is not news that openSUSE, through to the effort of the openSUSE community KDE team, offers several third-party repositories for those who want the latest software from KDE. Since a while, stable releases were offered in the KDE:Release:4x repositories, created with every major release of KDE software. These were meant to offer the latest and greatest to the users without having them to track KDE:Distro:Factory, which is instead used to track packaging for the next openSUSE release and is more in a state of flux.

Yesterday KDE released their first beta of the upcoming 4.13 version of Workspaces, Applications and Development platform. As usual with the major releases from KDE, it’s packed with a lot of “good stuff”. Giving a list of all the improvements is daunting, however there are some key points that stand out: Searching: KDE’s next generation semantic search is a prominent feature of this release. It’s several orders of magnitude faster, much leaner on memory and generally is a great improvement from the previous situation (this writer has been testing it for the past months and he’s absolutely delighted about it).

Among the different widgets I use on my desktop, there is a small one which tells me my current public IP address. The reason I’m having it is due to the fact that my own ISP uses a NAT for almost all its customers (don’t ask - long story) and so I need to keep tabs on my current IP, because it may have been blacklisted, and so on. Up to now I was using this plasmoid written in Python, but the code had several issues and used its own way of getting the public IP.

And so, finally openSUSE 13.1 is out of the door (I couldn’t celebrate like I wanted, as I’ve been very busy). This release has lots of improvements, and of course, the latest stable software from KDE. It is time (perhaps?) to look back and see what the team has done during this development cycle. With regards to the KDE software packaging, the past 8 months have seen quite an increase in the involvement of poeple from the community.

As you may know, there is an ongoing effort to rearrange and adjust the openSUSE KDE repositories. In line with the previously announced deletions, and more recent adjustments, a number of changes went into the organization and layout of the KDE repositories: KDE:Distro:Factory and KDE:Release:4xy will now hold the “core” KDE packages: this means the base Development Platform, Workspaces and Applications, and additional applications for a basic desktop experience.

Summer is ending soon (at least for those living in the northern hemisphere) and while usually cleaning is done during spring, the KDE team decided to do what I’d call… autumn cleaning of repositories. You may know that the KDE presence in openSUSE, aside being the default desktop, is quite a long one. In the past years different repositories were created by the members of the openSUSE KDE team (at the time mostly made up by KDE people hired by Novell) in order to review and test packages, like newer Qt versions, KDE software, and so on.

In the past few days, the openSUSE KDE team has been working hard, following the footsteps of the nice work done by the Kubuntu and Arch Linux communities, to provide Qt5 packages for the distribution. In fact, work was already done in the past, but the packages were not coinstallable with the existing Qt4 installation. Thanks to a renewed effort, the OBS holds now Qt5 packages that won’t overwrite the existing Qt4 install: they currently live in the KDE:Qt51 repository (Factory and openSUSE 12.

The latest release of the KDE Platform, Workspaces, and Applications (4.11) is around the corner: in fact, the last RC was recently made available. We’re almost there, but it doesn’t mean that testing and reporting should stop: on the contrary, it is needed even more to ensure that no bad bugs crawl up in the final release. As part of this effort, openSUSE packages for RC2 have been released through the OBS, and are available in the KDE:Distro:Factory repository.

The latest release from KDE moved from beta to RC stage, thus finding and reporting bugs is more important that ever. At the same time, the distribution packaging teams are also working in polishing their packages. As far as openSUSE is concerned (not dissing other distros, just mentioning the one I’m involved in ;), you can kill two birds with one stone by installing the packages provided in the KDE:Distro:Factory repository.

KDE released the second beta of the KDE Platform, Workspaces and Applications 4.11, and after the necessary time for the OBS to build packages from the released tarballs, packages are available for openSUSE 12.3 and openSUSE Factory. Like the previous beta, they are available through the KDE:Distro:Factory repository. 4.11.x is is targeted for inclusion in the upcoming openSUSE 13.1. So far 4.11 has been pretty stable for me, but you should never forget these packages are for testing and bug reporting purposes: don’t use them on production systems.

As a consequence of [the recent changes in the repositories]({{ site.url }}/2013/06/upcoming-changes-to-opensuse-kde-repositories), the openSUSE KDE team is happy to announce the availability of packages containing the first beta of the KDE Platform, Workspaces and Applications 4.11. Packages are available in the KDE:Distro:Factory repository. As it is beta software, it may have not-yet-discovered bugs, and its use is recommended only if you are willing to test packaging (reporting bugs to Novell’s bugzilla) or the software (reporting bugs directly to KDE).

Since KDE has released the first beta of Platform, Workspaces, and Applications 4.11, there will be some changes in the packages offered in the openSUSE repositories. In short: KDE:Distro:Factory will now start tracking 4.11 betas and RCs: packages are being worked on. Use this version to test packages and to report bugs upstream. KDE:Release:410 has been decoupled from KDE:Distro:Factory. If you were using 4.10 packages from KDF, you’re highly encouraged to move to this repository.

These posts kind of sound like a broken record, right? ;) Anyway, since KDE has released new versions of Platform, Workspaces and Applications as part of the stable release cycle, thanks to the OBS we have packages available for openSUSE 12.2 and 12.3. The 4.10.4 update will also be released as an official update for 12.3 in due time. Where you can get the packages? Two places, as usual: KDE:Distro:Factory in case you are interested in contributing to packaging for the next openSUSE release; KDE:Release:410 (openSUSE 12.

KDE released 4.10.3 versions of the Platform, Workspaces and Applications yesterday, with more than 70 bugs being fixed. Notably: Several fixes in handling encrypted mails in KMail Fixes for KDEPIM syncing and ownCloud A number of improvements in Dolphin, including crash fixes Optimizations in the Plasma Workspaces [The full list](https://bugs.kde.org/buglist.cgi?query_format=advanced&bug_status=RESOLVED&bug_status=VERIFIED&bug_status=CLOSED&bugidtype=include&chfieldfrom=2013-01-01&chfieldto=Now&chfield=cf_versionfixedin&chfieldvalue=4.10.3&order=Bug Number&list_id=638034) has other important changes. As usual, there are two different repositories from which you can get them:

KDE has released its monthly update for the 4.10 release, and after a brief wait while the Open Build Service worked over the released tarballs, the openSUSE KDE team is pleased to announce the availability of the 4.10.2 release packages for openSUSE 12.2 and 12.3. []({{ site.url }}/images/2013/04/757111961.png) Despite being a minor release, more than 100 bugs were fixed, in particular there were many KDEPIM fixes touching both the low level stack and KMail/KAddressbook/Kontact.

Hot on the heels of the announcement from KDE, the openSUSE KDE team is happy to announce the availability of packages for the latest stable release of the KDE Platform, Workspaces, and Applications. Packages are available in the KDE:Distro:Factory repository (which is where the packages to land in 12.3 are tested) for openSUSE Factory (soon to be 12.3) and openSUSE 12.2 and soon (when the Open Build Systen finishes rebuilding a number of packages) in the KDE:Release:410  repository for openSUSE 12.

Following up on the announcement from KDE, the openSUSE KDE team is happy to announce the availability of 4.10 RC3 packages. Remember that they are packages meant for testing and reporting bugs, so that the next release will be as polished as possible. You will find the packages in the KDE:Distro:Factory repository. An updated live media based on the upcoming openSUSE 12.3 ([see previous post]({{ site.url }}/2013/01/test-the-upcoming-opensuse-12-3-and-kde-workspace-applications-and-platform-4-10-rc2)) is also available (files named KDE4-4.

Following up on my previous post, a different type of image has been made by the openSUSE KDE community members. In particular, alin has created images sporting the same software from KDE (4.10 RC2) but using the upcoming openSUSE 12.3 as base. Download links: 32 bit version 64 bit version Release directory (in case the above links go 404; the files are named KDE4-.4.10.RC2-Live) These images are provided not only to test 4.

The 4.10 release for the KDE Development Platform, Workspaces and Applications is drawing nigh… as you may have read, there is now an additional release candidate in order to test some last-minute changes. Of course, the KDE developers can only do so much: it’s impossible to test all possible combinations. That is, unless the community at large helps by finding and reporting issues the developers can fix. But doing so requires a 4.

Yesterday Alex Fiestas showed on his blog a video of a recent development version of the KScreen library, created to handle easily multiple monitor setups in KDE, almost in an “automagic” way. As this is a project where configurations and setups are highly heterogeneous, a lot of testing is required to ensure things work reliably. Of course, you cannot ask a developer to have all sorts of screen combinations, but remember one of the strengths of FOSS: “many eyes make bugs shallow”.

openSUSE is migrating to the use of systemd for the upcoming 12.3 version, given the difficulties that emerged in trying to co-maintain two different init systems (SysV + systemd). While I am not going into the details of this choice (I leave this to more informed people), this has some consequences for software higher in the stack. As ConsoleKit is deprecated, systemd offers its own daemon to keep track of sessions and assigned seats in a system.

The KDE community has just released Beta 2 of the upcoming 4.10 release of the Development Platform, Workspaces, and Applications. Of course, distributions are providing binary packages for the adventurous… and how could the green distro be left out? In fact, it is not. Beta 2 packages were uploaded and built in the KDE:Distro:Factory repository. Updated packages have also been submitted to the development version of openSUSE (Factory) as the ultimate goal is having 4.

When I’m not on forum duty or handling openSUSE-related contributions, I try to improve my code contributions to KDE, even though I’m by no means an experienced programmer (I program all day long in Python, but I’m still a biologist after all). For the upcoming 4.10 release I’ve been polishing up Python 3 support. As you may know, Python 3 isn’t the standard in many distributions (Arch Linux excluded), but despite the slow start, it is slowly gaining steam.

Following up my [earlier post]({{ site.url }}/2012/10/whats-cooking-for-kde-in-opensuse-12-3-theming), the new openSUSE 12.3 theme has finally landed into the official openSUSE repositories  and will be part of the upcoming 12.3. A lot of work has gone into the new theme since I last posted about it, so this post will show how things look at the moment.

A few caveats:

• The theme targets the 4.10 release of the KDE Workspaces, so it may be not be perfect under 4.9;

• The default wallpaper has not been chosen yet.

Without further ado, let’s get down to seeing what’s improved.

Like everything, openSUSE is not perfect. Bugs crop here and there, or there is missing / quirky functionality that users may run into. Being a distribution of heterogeneous software, this means that bugs fall into these categories: Upstream bugs in the software shipped by openSUSE Bugs in the packaging Bugs in distribution-specific setups or that derive from interactions with these setups (e.g. kernel, low level software stack, etc.

Although the release of openSUSE 12.3 is yet to come, the people of the openSUSE community contributing to KDE are already at work to bring the best possible KDE experience for the new release.

As others, bigger members in the KDE community say, “nobody will do it for you, and therefore they will”. The patch from the title comes from such a story. Let’s give some background first: I’m really a heavy activity user, especially when working. My home PC has about five activities, my work one 3, and I managed to compartimentalize the various “topics” that each activity does pretty well. After an update a couple of weeks ago from the latest code from KDE git, I started noticing weird behavior.

Recently Fedora’s Lukas Tinkl pushed to kdelibs (for the 4.10 release) a patch that enabled Solid to talk to udisks2, which is a replacement for udisks. Fedora already moved to udisks2 (and killed HAL) and future GNOME releases will only use udisks2, so the need for a working backend was a necessity, and at the same time they acted like good open source citizens, and pushed the code both to 4.

Many of you know that KDE Brainstorm ideas aren’t posted straight away: they are always pre-screened to avoid repetitions, features that cannot be implemented technically, violations of the Code of Conduct, and so on. This is possible thanks to the work of the Idea Moderators, that patrol Brainstorm and evaluate the new ideas being posted. Recently, a few of them got too busy and thus we’re experiencing a backlog of ideas staying in the Vault (the staging area for evaluation) for longer times than usual.

The recent post by Dario on the KDE Workspace Vision raised some concerns on why Brainstorm was not used.One commenter even said _Right now it feels like “Throw an idea over a wall for no-one but end users to discuss until it bitrot’s”. _ _ _ The Brainstorm section is indeed in need of help. To make it more useful, a couple of things are needed: Statistics to evaluate which ideas are best representative: it can’t be just the number of votes per se as there are things like confirmation bias or controversies that may inflate the numbers Integration with Bugzilla: a way to automatically (using XML-RPC) send the ideas flagged as representative to a bug report filed under “wishlist”.

Recently we’ve seen several blog posts on Planet KDE related to Nepomuk. Reading those I thought that I could add some (little) semantic features to [Danbooru Client]({{ site.url }}/projects/danbooru-client). Danbooru Client already makes use of Nepomuk: if enabled, tags extracted from Danbooru items are added as Nepomuk tags. But since at least some Danbooru boards are specialized in certain types of images (e.g., wallpapers only, for examples) I found it would be nice to have Nepomuk show me only the images that come from a specific Danbooru board.

Recently in the Plasma mailing list, KDE developers have discussed a new screen-locking implementation that could be added to the upcoming 4.8 release of the KDE Workspaces. The first reason to do so was to solve some security constraints of the existing implementation. As an added bonus, screen locking should be also more aestetically pleasing. There is however a trade-off: such implementation would mean that screensavers that rely on X (also called X screensavers) would not be compatible.

In one of my previous blog posts I dealt with [tagging files and resources with Nepomuk]({{ site.url }}/2010/10/pykde4-tag-and-annotate-files-using-nepomuk). But Nepomuk is not only about storing metadata, it is also about retrieving and _interrogating _data. Normally, this would mean querying the metadata database directly, using queries written in SPARQL. But this is not intuitive, can be inefficient (if you do things the wrong way) and error prone (oops, I messed up a parameter!

Recently, a question came up on the KDE Community Forums regarding the use of multiple Google Calendars with KOrganizer. The preferred access up to now has been with googledata Akonadi resource, however that doesn’t support more than one calendar, and (at least from my unscientific observation) seems to be rather unmaintained these days.

Luckily, not all’s lost. Akonadi recently gained the opportunity of accessing CalDAV resources, and Google Calendar also offers a CalDAV interface, hence this is possible.

This post will briefly describe how (thanks go to PIMster krop, which casually mentioned the possibility on IRC and prompted me to investigate).

Some of the oldest readers of this blog are well aware of [a certain hobby of mine]({{ site.url }}/category/anime). Over the years I’ve always wanted to write more about that, including the stuff I’m viewing nowadays, but I found a hassle to collect snapshots from videos / DVDs, selecting them, and so on. Recently I learnt that VLC has some rather complete Python bindings, and I thought, why not make the process automated?

As you may already know, recently the KDE sysadmins completely overhauled the commit hooks used with the Git infrastructure. Written in Python, they have already brought significant improvements to the current workflows. These hooks include keywords that when specified trigger particular actions: the most used are to CC specific email addresses (CCMAIL), to CC bug reports (CCBUG) or to close bug reports (BUG). With the adoption of Review Board to facilitate code reviews, there were also requests for a REVIEW keyword that could close the review requests without asking the submitters to do so manually (which is slow and not always effective).

One of the greatest strengths of KDE is undoubtedly the asynchronous and network-transparent I/O access, employed by the so-called “I/O” slaves, part of the KIO class. If you are developing an application that requires file or network access, those classes make things incredibly simple to do, and they don’t freeze your GUI when you are in the middle of a process. In this post I’ll show how to use KIO to retrieve files from network resources using PyKDE4.

Some time has passed since I last blogged… this was not only due to lack of time but also due to motivation (writing long texts can be discouraging at times). In any case, I’d like to rectify for that. In this post, I’ll talk about Nepomuk, and in particular how to use it to tag and annotate arbitrary files using its API in PyKDE4. Before starting, let me say that creating this tutorial was only possible thanks to the help of Sebastian Trueg, who helped me by pointing out some mistakes I was doing.

The rest is up to you to figure out.

With my last entry, I announced the start of the work for an OCS library for the KDE Community Forums. Today I’d like to blog again about the recent developments. First of all, now there isn’t one, but two Python modules: _ocslib, _ a pure Python module that can be used to interface with OCS-based forum systems; ocslibkde, a PyKDE4 based module that can be used to interface with OCS-based forum system in KDE applications.

For KDE developers, web-based forums are often uncommon workflows. Indeed, for communication among developers mailing lists are much better tools, especially since you can handle everything inside a client (most of the time), compared to forums where you have to use a web browser. The ways of reading, replying and interacting with posters are dramatically different. And that is why some developers find themselves uncomfortable with the KDE Community Forums.

In the past weeks and days, the KDE Community Forums staff has been working to bring new features to improve even more the user experience. A few months ago, the staff was discussing the idea of finding a way to guide users to the most appropriate forum to post their questions or discussions. Now, thanks also to the return in service of one of our admins (welcome back, sayakb!) the feature is now being implemented, as the screenshots below will show.

 My Akademy talk proposal was not accepted, but the organizers were kind enough to offer me the chance to hold a BoF on the same subject. Now I bet you wonder on what I’m going to discuss, and I think the title already gives you an idea: KDE and bioinformatics: the missing link Although in the KDE community we have our fair share of scientists (hey there, Stuart!

Those who use PyQt and PyKDE4 are certainly familiar with the syntax used to connect signals and slots: [python] from PyQt4 import QtCore from PyQt4 import QtGui from PyKDE4 import kdeui class MyGUI(QtGui.QWidget): def __init__(self, parent=None): super(MyGUI, self).__init__(parent) self.pushbutton = kdeui.KPushButton() self.pushbutton.setText("Push me!") QObject.connect(self.pushbutton, QtCore.SIGNAL("clicked()"), self.button_pushed) def button_pushed(self): print "Button clicked" [/python] The main advantage of this syntax is that it’s very close to the C++ equivalent, and so you can translate easily from C++ to Python.

Recently, I investigated how to perform some checks on web addresses using KIO for Danbooru Client. My old code was synchronous, so it blocked the application while checking, thus causing all sort of troubles (UI freezing, etc.). Therefore, making the switch to KIO was the best solution. However, I had one problem: how could I check the HTTP response? I knew already that the various ioslaves can store metadata, consisting of key-value pairs which are specific on the slave used.

With my brand-new SVN account, I just committed some code to kdeexamples, KDE’s example code module. In particular, I committed a simple example which shows how to use KConfigXT via PyKDE4, a simplified version of [what I wrote about here]({{ site.url }}/2009/10/howto-kconfigxt-with-pykde4). As most of KDE is C++, and the Python API docs are translated directly from the C++ API docs, it is essential to have good examples to help newcomers learn faster.

Sometimes answering apparently harmless questions on instant messaging can have unexpected results. In particular, I was telling about Danbooru Client to someone and a question popped up “Why don’t you support pages?”. It seemed a nice idea, so I branched off the code (yay for git!) and started working on it. Well, it took me more than a month to get this thing done… I didn’t spend every day coding, but it was a challenge.

KDE SC 4.4 Beta 1 has been released, and of course I couldn’t stay still. Thanks to the friendly openSUSE Build Service, there were packages available, so I just pointed my zypper sources to KDE:KDE4:UNSTABLE:Desktop repository, adjusted a few other things (mainly other third-party repositories) and updated.

Do you like KDE? Did you ever find yourself in a position of wanting to help, but you didn’t know what to do, or who to talk to? Do you feel you could use help to get started? Today, the KDE Community Forums would like to provide the opportunity to answer those questions by annoucing the continuation of the tutorial courses known as Klassrooms. What are Klassrooms? Klassrooms are tutorial “lessons” held in a specific area of the forum.

Well, there wasn’t a Day 1 for me (I got to the hotel too late to follow the first day of the meeting), so that is why I’m starting on day 2. To start, I need to say that I had never been to a sprint before: I am already accustomed to meeting for real someone from online, but for all the attendants, they had been just names or nicks on IRC.

A while ago I presented [“danbooru2nepomuk”]({{ site.url }}/2009/10/danbooru2nepomuk-a-nepomuk-tagger-for-danbooru-images), a small program to tag images coming from Danbooru-based image boards. Today I want to present the evolution of that program, that is a PyKDE4 client for those boards.

If you read around the KDE Techbase, or if you develop KDE applications, you may have heard about KDE’s KConfigXT. This is an extension of KDE’s KConfig, and can be used to generate nice configure dialogs with multiple pages with minimal effort, also taking care of saving and applying settings. In short, something really neat! But there are problems when using it with interpreted language bindings (such as PyKDE, which is the one I use):

• KConfigXT requires an XML file and an INI-like file to be compiled by kconfig_compiler in order to produce C++ files
• There is no such a tool (at least to my knowledge) that does the same job for bindings

So what to do? Either give up on the niceness of KConfigXT, or work around the issue. I chose the latter.

If you dabble with [anime]({{ site.url }}/category/Anime) and related things like I do, you may have heard about imageboards. A known variant, which powers sites such as moe.imouto (some links may be NSFW) or Konachan, is Danbooru, a Ruby on Rails application. One of the characteristics of this software is that images stored there can be tagged to be identified as precisely as possible: common tags are for example the magazine where the image was taken from, the characters depicted, and so on.

In line with the project’s committment to openness, the KDE developers and contributors are not a secretive bunch. In fact, the “People Behind KDE” initiative has provided the community with interviews of quite a number of the developers. And by reading those interviews, haven’t you ever felt the need of asking a specific question, outside from those prepared by the interviewer? For example, more details about what the specific developer is doing, or what his/her plans are for the next version of KDE.

While browsing around kde-look.org, I’ve stumbled upon a nice little Plasma scripted widget, and I’m publishing this to have it get more exposure. A good part of the KDE community knows at least little about Nepomuk, and its ability to attach semantic tags to your files - basically words that describe the file, be it an image, a text document, or anything you’d like. For example, you could tag all the photos from your vacation with the name of the place you’ve been.

As you all know, KDE 4.3.0 has been releeased today! Now it’s the time to tell the developers “thanks” for their hard work. Join us in the KDE Community Forums and spread the word!

Up to now, the main language in which KDE applications are developed is C++. This is a perfectly valid choice: however, at least for users that don’t have a computing background (I include myself in the list: I do science) C++ can be a rather steep requirement (although Hans, fellow staff member at the KDE Community forums, is doing a nice job in explaining his learning experience). Scripted language bindings (that have a lower barrier of entry) for KDE exist: on top of my memory I can list Python, Ruby, and C# (and I’ve probably missed a few).

The KDE Brainstorm, where users can post and vote for feature requests for KDE, is the most visited area of the KDE Community Forums. In an effort to improve the experience of both users and developers, the KDE Community Forums staff is proud to present a brand new version of the KDE Brainstorm.  The new interface resembles the IdeaTorrent sites, but it is still powered by the forum software (phpBB), a clear example of the flexibility of the platform.

A few may know that I more or less maintain the Plasma FAQ page on KDE’s UserBase. Given the rapid advance of Plasma between KDE versions, each time a new version is out a new FAQ needs to be made, as the content rapidly becomes obsolete. For 4.3, unfortunately, I’m not sure I’ll be able to put a new version up in time for the 4.3 release. The reason is mostly practical: it takes a bit of work to collect and add information, and currently my free time is limited due to a rather heavy workload and some other commitments.

Today, a major upgrade of the KDE Community Forums took place. The change brings quite a number of changes to the forums themselves, and it’s a further step towards providing a better experience for KDE users (and developers too!).

Hello, and welcome to the second issue of the KDE Brainstorm Digest! This issue comes in slightly late, due to some real time commitments, but I couldn’t leave you without it, could I?

A rather big change has gone into KDE’s SVN recently: Ben Cooksley (bcooksley) and Mathias Soeken (msoeken) have committed a complete rework of System Settings.

Compared to the previous implementation, System Settings now has two operational modes, one being the current icon-based view since KDE 4 (and also seen in Kubuntu prior to KDE 4), and a second view, named “Classic”, which reimplements the old KControl look and feel. The latter change is probably very welcome to anyone who found System Settings less useful than the old KControl. The current view used can be changed in the configuration options. In addition, upon hovering an icon or module that show if there are any sub-modules associated.

Currently, the openSUSE Build Service contains Amarok 2.1 beta packages only for the KDE:KDE4:UNSTABLE repository (i.e. current trunk, soon-to-be 4.3). However, a quick search identified a repository that contains a RPM of current 2.0.90 compiled for the KDE:KDE4:Factory Desktop (which will change to 4.3 with Beta 1) andanother one for the KDE:42 repository. So you can add them using YaST or zypper and download the relevant package. I had to force a repository using zypper, otherwise zypper would complain and try to install amarok 1.

Hello, and welcome to the first “issue” of the KDE Brainstorm monthly digest. First of all, a few words of introduction. There are quite a number of ideas being posted on the KDE Brainstorm, and it would be nice to know how the initiative is faring, and important highlights, like what ideas are more popular, which are more controversial, etc. That is why the idea of a monthly digest was born (in a similar fashion as the fabolous Commit Digest).

Via Harald Hvaal’s blog I learnt that the first non-forum suggestion has been implemented! I think this shows without doubt that initiatives like the KDE Brainstorm are undoubtedly useful to the community at large, both users and developers. Keep on rocking!

In the past months I’ve always wanted to write a small Plasma applet to aid me in some boring tasks as a bioinformatician. One example (for the non-scientific crowd out there) is when I find a specific gene out of my analysis work which I want to take a look at. I am often lazy, so instead of firing up the browser to look at the online resources, I wanted to write something which could access said resources programmatically.

Now that the KDE Brainstorm has been launched, it’s time to take a look at the results so far. Currently, the forum hosts 160 threads, approximately one for each idea, and 441 posts. Not bad for the first two days of operation. At the same time, the staff has been working hard to make sure only appropriate ideas (not bug reports, not duplicates…) are on the forum. People have also begun voting, although slowly: it’s understandable, given the fact that there are so many threads in so little time.

It’s finally there: KDE Brainstorm has been launched today! Like this, it will be possible to propose features and have them voted by the community, and then submit the most voted requests to the developers. Every feature request is screened prior to posting, so duplicates, spam and flames are unlikely to occur. There is no guarantee that the voted upon features will be implemented, but as opposed to individual postings, this approach reduces the noise a lot, and allows a better communication between the “two worlds” (users and developers).

No, it’s not_ _a teen-like “I hate my life, I’m going to die tomorrow” post. I’m actually referring to the comments of a person nicknamed “I Love” that are popping up in almost all blogs that are linked to PlanetKDE which deal with Plasma or KDE4 adoption. The name “I Love” contrasts with an attitude that is unconstructive and rather trollish. This wouldn’t be such a big problem, if not for the fact that posts from said individual have had a rather negative effect: for example Aaron was forced to turn comment moderation on on his blog, Jos’ entry on the new Plasma in the upcoming KDE 4.

Mtux, of choqok fame, along with another person, has written Bilbo Blogger, a blogging utility for Blogger or any blog that supports Blogger1.0, MetaWeblog, and MovableType APIs (EDIT: also GData). It is based on the KDE4 libraries and it includes a WYSIWYG editor, an HTML editor, and a Post Preview function that can even fetch your blog’s CSS to render the entry and see how it looks. It’s not released yet, but for the daring, you can actually try and compile it.

During the course of my research work, I may obtain results that are worthy of publication in scientific journals. Since my master’s thesis I’ve been using LaTeX as my writing platform, mainly because I can concentrate on content rather than presentation (I find it useful also for writing non-scientific stuff as well). Also, I can handle bibliography (essential for a scientific publication) very well without using expensive proprietary applications (such as Endnote).

In my early days I used kLyX first, then LyX, but I found the platform to be too limited for my tastes, and also LaTeX errors were difficult to diagnose. I needed a proper editor, and that’s when I heard of kile, a KDE front-end for LaTeX. Kile is currently at version 2.0.2 and is a KDE 3 application. However, in KDE SVN work is ongoing to produce a KDE4 version (2.1) and that’s what I’ll look at in this entry.

I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.

I have been thinking of doing another Kourse at the KDE Forums, similar to the one that has produced three nice screencasts. My idea would be to show very brief and focused screencasts, a sort of “how do I…”. I have a few ideas, but I’d like to ask the KDE community at large. I’m mostly interested in showing single features (short videos), preferably of the “eye-opener” kind. If you have any suggestions, leave a comment.

Yes, I know I’m a bit late to the party (unfortunately today was one of the busiest days ever where I work), but I thought I’d join the other members of the KDE community, because KDE 4.2 has been released today. Take a look at the visual guide, or see if your distribution has already packages for you. For your enquiries, the KDE Forums are at your disposal.

If everything has gone correctly, my blog should be on PlanetKDE now. That means it’s time for an introduction for those readers. My name is Luca Beltrame, I’m a biotechnologist doing bioinformatics in the life sciences areas, and I’m a Free Software user/enthusiast since many years. I’ve been using KDE since 1.0 or so (if memory serves me well), but only recently, with the 4.x line of development, I’ve been trying to actually contribute a bit back to the project.

I just finished writing a new Python tutorial on KDE’s Techbase. This one deals with writing DataEngines in Python (a complement to Simon Edwards’s own Using DataEngines). Let me know what you think. As it’s a wiki, comments and suggestions are welcome.

As Simon Edwards already noted, thanks to me and him (mostly him, I have to say) starting to work on Plasma tutorials at the same time, now KDE’s Techbase has a nice set of Python Plasma tutorials. They cover creation of applets and connection to DataEngines (see the Plasma page on Techbase for more information). I plan on starting a tutorial on writing Plasma DataEngines on Thursday, if time permits.

It turned out I forgot to add the last screencast produced by the students of Kourse 2, so I’ll fix my mistake right now. Here’s Panel settings, by Kourse student TeaAge: [blip.tv ?posts_id=1653914&dest=-1]

Students from Kourse 2 fengshaun and Primoz have prepared two nice screencasts, dealing with the Zooming User Interface (ZUI) and desktop settings respectively. Without further ado, here they are: Zooming User Interface by fengshaun [blip.tv ?posts_id=1648944&dest=-1] Desktop settings by Primoz [blip.tv ?posts_id=1646835&dest=-1] As usual, both Free and non-Free versions are available. The students are also at work on subtitled versions, without the Notes plasmoid. I’ll be sure to post them once they’re done.

As some people already know,I’m mentoring a group of students on KDE Forum to create Plasma screencasts (from the upcoming KDE 4.2 version). After several adjustments back and forth, the first one (made by kourse student Primoz), showing off the various desktop settings, is complete. This version uses the Notes plasmoid to keep track of annotation, but we’re also evaluating subtitle-based versions. In the mean time, enjoy! (and spread the word).

Today I was adjusting a bit the layouts of the Activities (as defined in Plasma) to better suit my workflows. To do so I was using the brand new Activity Bar which is present in KDE 4.2. It’s very neat, but takes up space on the desktop, and while it’s not a big deal on my main PC (1280x1024 resolution), it is an issue on my recently-resuscitated EeePC (1024x600). It was then that it occured to me that such applets are, in Plasma-speak, PopupApplets, which means they adjust their behavior depending if they are in a panel or “free”.

Today I’m in a posting spree…This clip shows how to resize and move Plasma panels around. [youtube]http://www.youtube.com/watch?v=Rmpv-S5JJI4[/youtube]

Following up on my previous post, here is another screencast showing off how to create a sidebar panel and add a few plasmoids to it. As usual, the version on Youtube has annotations. [youtube]http://www.youtube.com/watch?v=WPeFSDdt2PY[/youtube]

I’ve put together a small video that shows what you can do with zooming in and out with Plasma’s Zooming User Interface (ZUI). Enjoy. (note: the version on Youtube has also annotations that explain better what is going on) [youtube]http://www.youtube.com/watch?v=EhODrJkoidA[/youtube] If you can, please spread the link to the video. We need more correct information out there.

Those of you that follow my Linux-related posts know that I work (along with others) on a FAQ trying to explain some magic behind KDE 4.x’s Plasma. Now, especially since on the Internet, there is the need to spread correct information (most of the naysayers are not quite informed). So, if you want to help KDE, please spread the word on the Plasma FAQ! If people have questions on Plasma, just direct them to

Now even the (once respected) Steven J. Vaughan-Nichols is jumping on the bandwagon of Plasma haters. With a rather uninformed and rant-ish entry that just advocates a fork, like some other people said on the kde-devel mailinglist a week or two ago. The entry is rather dismissive of everything in KDE 4 save Plasma (and a mention on Dolphin’s single click icon), and also gets some facts and links wrong (yes, the Plasma web site is outdated, but since the developers are busy coding, someone else should step up and help).

The word is official: KDE 4.0.0 has been released. Make sure to check out the Dot story, or the nicely done visual guide. And if you’re new to Plasma, have a look at the FAQ as well. Congratulations to all the KDE developers, translators, and coordinators for pushing forward our favorite desktop environment. Rock on!

Today is the tagging day for KDE 4.0.0. I think it speaks for itself. I have checked out the 4.0 branch and I’m going to use it in a full session real soon (so far I used nested X sessions with Xephyr). Aaron Seigo has a nice writeup on the release, some of the memes floating around and the future of KDE 4.

I’ve started working on a FAQ related to Plasma, in order to ease the transition for the early adopters of Plasma when KDE 4.0 is released. That, coupled with another idea I had (offering video tutorials of operations) should make the gap smaller. Currently the FAQ is a work in progress (still a lot of TODOs, I hope to have a look after Friday as I’m really busy now) and resides in KDE’s TechBase until a more suitable solution is found.

Yesterday I spent some of my free time to help with the KDE 4.0 Krush Day. Unfortunately, I did a lot less than what I was supposed to do, mainly because at some point the home directory ran out of space (I forgot to remove qt-copy object files), then I inadvertently removed some of the directories and I had to re-sync with SVN. Nevertheless, it was interesting and nice to be able to contribute even if you don’t speak C++.

Aseigo announced it a few days ago: on Saturday, on the Freenode IRC network, #kde4-krush channel, there will be a day-long session to triage and squash bugs in order to improve the overall quality of KDE 4.0. I will try to be there, so that I can give out my (little) contribution as non-coder. I’ll be sure to report later.

First of all let me make some disclaimers : This is **not **a Plasma bashing post (so that aseigo won’t commit suicide, should he ever read this); I’m not a KDE developer, just someone who tries out SVN and reads mailing lists; UPDATE: These statements aren’t meant to bash the collective group of the KDE developers, just to outline a bad “mood” in my opinion.

I obviously did not want to stop with a single compile of KDE4, therefore I’m updating more or less randomly my build off the SVN to check what has been changing. The first and most important change since my last post was the addition of the K-menu in the taskbar: Kickoff was moved from playground (where it resided) to kdebase. Also, kate now works perfectly, and is already usable as a full-blown text editor.

Since Beta 3 was announced a short time ago, I thought I would try testing KDE4 on my computer. Here I’m reporting on my first impressions and I’ll try to provide constructive feedback as much as possible: the developers are being already (and unjustly, in my opinion) bashed enough.

I have been thinking of doing another Kourse at the KDE Forums, similar to the one that has produced three nice screencasts. My idea would be to show very brief and focused screencasts, a sort of “how do I…”. I have a few ideas, but I’d like to ask the KDE community at large. I’m mostly interested in showing single features (short videos), preferably of the “eye-opener” kind. If you have any suggestions, leave a comment.

Yes, I know I’m a bit late to the party (unfortunately today was one of the busiest days ever where I work), but I thought I’d join the other members of the KDE community, because KDE 4.2 has been released today. Take a look at the visual guide, or see if your distribution has already packages for you. For your enquiries, the KDE Forums are at your disposal.

Taking advantage of the holidays, I’ve managed to land a number of fixes in Danbooru Client, and therefore I think it’s time for a new version, 0.4.0! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.

Do you like KDE? Did you ever find yourself in a position of wanting to help, but you didn’t know what to do, or who to talk to? Do you feel you could use help to get started? Today, the KDE Community Forums would like to provide the opportunity to answer those questions by annoucing the continuation of the tutorial courses known as Klassrooms. What are Klassrooms? Klassrooms are tutorial “lessons” held in a specific area of the forum.

In line with the project’s committment to openness, the KDE developers and contributors are not a secretive bunch. In fact, the “People Behind KDE” initiative has provided the community with interviews of quite a number of the developers. And by reading those interviews, haven’t you ever felt the need of asking a specific question, outside from those prepared by the interviewer? For example, more details about what the specific developer is doing, or what his/her plans are for the next version of KDE.

(Inspired by http://viccuad.me/blog/GPG-transition-statement/) This exact same text can be found at this location. -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Sun Jun 7 14:12:39 CEST 2015 For a number of reasons, i've recently set up a new OpenPGP key, and will be transitioning away from my old one. The old key will continue to be valid for some time, but i prefer all future correspondence to come to the new one. I would also like this new key to be re-integrated into the web of trust.

After my previous post, development went quicker than expected, so I’ve actually managed to get a real version out. ;) So without much ado… here’s Danbooru Client 0.2.0! This redesigned C++ version brings a few more features compared to the PyKDE4 version, notably: Infinite scrolling (experimental) - Just scroll down to load the next set of posts QML-based thumbnail view Click on the image below to have a demonstration of what’s in this release (warning: 2M GIF file): [!

Some of you may remember a semi-complex application I wrote back in the days, namely [Danbooru Client]({{ site.url }}/projects/danbooru-client/). Written in PyKDE4, it provided a semi-decent interface to Danbooru-style boards. It mostly worked and received little maintenance (also because I didn’t have that much time for maintenance). In the mean time, I started learning some C++. No, it’s not that I don’t like Python (in fact I do, I use it a lot in my day job), but I wanted to gain at least some basic skills to be able to contribute directly to KDE software.

Congratulations to KDE (of which I’m proud of being a part of) for the newest release of the Plasma workspace! At the same time, the 4.x series has seen a new beta release, and the stable branch got updated, too. I’m betting a few people will ask “Are these available for openSUSE?” and of course the answer is yes, thanks to the efforts of the openSUSE community KDE team and the Open Build Service.

Since a couple of weeks the packages offered by openSUSE in the KDE:Unstable:Frameworks repository have undergone a series of changes. In particular, the packages now install to /usr. For the libraries (KDE Frameworks 5) this will mean a transparent change for the userbase as they are expected to be co-installable, but the workspace components (Plasma 5) will confict with the existing Plasma 4.11.x installation. What does this mean in practice? If you want to use Plasma 5 you will not be able to use a 4.

Do you like KDE? Did you ever find yourself in a position of wanting to help, but you didn’t know what to do, or who to talk to? Do you feel you could use help to get started? Today, the KDE Community Forums would like to provide the opportunity to answer those questions by annoucing the continuation of the tutorial courses known as Klassrooms. What are Klassrooms? Klassrooms are tutorial “lessons” held in a specific area of the forum.

Recently, a question came up on the KDE Community Forums regarding the use of multiple Google Calendars with KOrganizer. The preferred access up to now has been with googledata Akonadi resource, however that doesn’t support more than one calendar, and (at least from my unscientific observation) seems to be rather unmaintained these days.

Luckily, not all’s lost. Akonadi recently gained the opportunity of accessing CalDAV resources, and Google Calendar also offers a CalDAV interface, hence this is possible.

This post will briefly describe how (thanks go to PIMster krop, which casually mentioned the possibility on IRC and prompted me to investigate).

Yesterday Alex Fiestas showed on his blog a video of a recent development version of the KScreen library, created to handle easily multiple monitor setups in KDE, almost in an “automagic” way. As this is a project where configurations and setups are highly heterogeneous, a lot of testing is required to ensure things work reliably. Of course, you cannot ask a developer to have all sorts of screen combinations, but remember one of the strengths of FOSS: “many eyes make bugs shallow”.

Currently I have Kubuntu 8.04 (Hardy) installed on my Eee PC. Version 8.10, the Intrepid Ibex, is due on October 30th. However, I will not install it. The reason is that Kubuntu developers intentionally disabled the zoom function, and I have three activities on this machine. How come I’m supposed to use them? Also, space is pretty tight so install a build environment just to remove one patch seems overkill. So, I’m moving away from it.

After some thought, I’ve joined the fray and installed the beta version of Kubuntu 7.10 (Gutsy Gibbon) on one of my computers. It hasn’t too recent hardware (AMD Thunderbird 2100+, 512 Mb RAM and a motherboard with a Nforce 2 chipset), and it is my test system for distributions. It ran Feisty Fawn, so I tried to use the upgrader tool, which crashed when removing unsupported packages. Oh well, it was a beta, so nothing to worry about (the only worry was that it didn’t output anything at all).

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New season, new anime to see. Since a certain guy kept me telling wonders about Kurokami (黒神), a manga serialized in Young Gangan by Dall-Young Lim and Sung-woo Park, two Korean artists, I decided to give a go to the animated version, produced by Bandai Visual, which has just been out.

Requests to unlock KWallet automatically on login (assuming the wallet password and user password are the same), like gnome-keyring can do, have been going on for years: in fact, bug reports requesting this feature are quite old. Recently, thanks to the efforts of Alex Fiestas, a PAM module, which interfaces KWallet to the system authentication methods, has been developed. In parallel, the necessary glue code has been also added to the various parts of the KDE workspace so that it could make use of it.

Recently I was looking for a laptop: the previous one I had (an Asus EeePC 900) was almost dead (the fan broke, and the idea of dismantling everything to get to it wasn’t appealing). When looking around, I had the following requirements: It needed to run on Linux well. No exceptions. _Portable: _ at home and at my workplace I have rather powerful machines, so a desktop replacement was not needed.

During the course of my research work, I may obtain results that are worthy of publication in scientific journals. Since my master’s thesis I’ve been using LaTeX as my writing platform, mainly because I can concentrate on content rather than presentation (I find it useful also for writing non-scientific stuff as well). Also, I can handle bibliography (essential for a scientific publication) very well without using expensive proprietary applications (such as Endnote).

In my early days I used kLyX first, then LyX, but I found the platform to be too limited for my tastes, and also LaTeX errors were difficult to diagnose. I needed a proper editor, and that’s when I heard of kile, a KDE front-end for LaTeX. Kile is currently at version 2.0.2 and is a KDE 3 application. However, in KDE SVN work is ongoing to produce a KDE4 version (2.1) and that’s what I’ll look at in this entry.

In the past months I’ve set up LDAP at home, to avoid having different user accounts for the services that I run on my home hardware. Rather than the venerable OpenLDAP I settled for 389 Directory Server, commercially known as Red Hat Directory Server, mainly because I was more familiar with it. Rather than describing how to set that up (Red Hat’s own documentation is excellent on that regard), this post will focus on the steps required to enable encryption using Let’s Encrypt certificates.

Recently I’ve been setting up LDAP authentication on CentOS servers to give a shared authentication method to all the compute nodes I use for my day job. I use 389-DS as it’s in my opinion much better to administer and configure than openLDAP (plus, it has very good documentation). As I have a self built NAS at home (with openSUSE Tumbleweed), I thought it’d be nice to use LDAP for all the web applications I run there.

As KDE software (be it the Frameworks libraries, the Plasma 5 workspace, or the Applications) develops during a normal release cycle, a lot of things happen. New and exciting features emerge, bugs get fixed, and the software becomes better and more useful than it was before. Thanks to code review and continuous integration, the code quality of KDE software has also tremendously improved. Given how things are improving, it is tempting to follow development as it happens.

As many readers of this blog are aware, openSUSE has been offering packages of git snapshots from KDE since quite a while. They are quite useful for those wiling to test, report bugs, and / or hack on the code, but also for those who want to see what’s brewing in KDE land (without touching their existing systems). However, a major drawback for non English speakers was the lack of translations.

One thing I always wanted to do when going on holiday is to track where I go, the places I’ve been, and see how much I’ve travelled around. This is true in particular when going to places where I walk around a lot (Japan stays at the top of the list, also for other reasons that are not related to this post). Something like viewing a map showing where you were, and where did you go, with optional export to KML or GPX to import into other programs like Marble.

Yesterday I finally flipped the switch on the MX record and moved to a new server (still aptly named after another character from アキハバラ電脳組). The machine was found through Hetzner’s server auctions and has quite a good configuration for the price paid: Intel Xeon CPU E31245 @ 3.30GHz 16G ECC RAM (ECC was the deciding factor) LSI Hardware RAID 1 with two 3x2T disks Now, since the old server has been chugging along since 2011, the 5 eurocent question is why did you move at all?

Header image credit: 1840151sudarshan (Wikimedia Commons, CC BY-SA) A while ago I posted a way to download 実況動画 from Nicovideo. One of my acquaintances publishes videos there, and he wanted to collect the various comments to reply in a follow up video (what the Nico users call the コメント返し). When the comments are more than just a few, it’s hard to find where they refer to without watching them on Nicovideo itself, and its UI is suboptimal.

実況? Is it something edible? In recent times, I’ve been watching a lot of VOICEROID実況 (じっきょう, jikkyou, literally “commentary”) videos from the rather famous (in Japan) video service ニコニコ動画, better known as “Nicovideo”. In this case, the commentary actually refers to games: they’re basically a Japanese version of the Let’s Play videos that are all around other places like YouTube. The difference from “regular” videos lies in the “VOICEROID” term: this is a name of a TTS software developed by AH Software using an engine devised by a company called AI Inc.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highlights of the new version Unbreak konachan.com support (change in URL format) Coming up next HTTPS support!

In the past three weeks, the openSUSE community KDE team has been pretty busy to package the latest release of Applications from KDE, 16.12. It was a pretty large task, due to the number of programs involved, and the fact that several monolithic projects were split (in particular KDE PIM). This post goes through what we did, and how we improved our packaging workflow. Some prerequisites In openSUSE speak, packages are developed in “projects”, which are separate repositories maintained on the OBS.

Admit it: how many times you have seen “software from this branch is completely untested, use it at your own risk” when you checked the latest code from any FOSS project? I bet you have, many times. For any reasonably modern project, this is not entirely true: Continuous Integration and automated testing are a huge help in ensuring that the code builds and at least does what it is supposed to do.

You may be aware that openSUSE Leap 42.2 is now in the release candidate stage, and there’s a lot of activity aimed at squashing those pesky bugs before they hit the final release. One particular bug proved to be quite tough to fix, and it was only solved thanks to the “heroes” mentioned in the title. This is the history of the bug. The report October 6th, 2016 - A bug iss reported against Plasma reporting a hard freeze of Plasma when using the Noveau driver, but not with the closed NVIDIA blob.

As you may know (unless you’ve been living in Alpha Centauri for the past century) the openSUSE community KDE team publishes LiveCD images for those willing to test the latest state of KDE software from the git master branches without having to break machines, causing a zombie apocalypse and so on. This post highlights the most recent developments in the area. Up to now, we had 3 different media, depending on the base distribution (stable Leap, ever-rolling Tumbleweed) and whether you wanted to go with the safe road (X11 session) or the dangerous path (Wayland):

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version Support for width / height based filtering: now you can exclude posts that are below a specific width or height (or both) New dependency: KTextWidgets Coming up next Sooner or later I’ll get to finish the multiple API support, but given that there’s close to no interest for these programs (people are happy to use a browser) and that I work on this very irregularly (every 6-7 months at best), there’s no ETA at all.

Ever since the launch of Argon and Krypton, the openSUSE community KDE team didn’t really stand still: a number of changes (and potentially nice additions) have been brewing this week. This post recapitulates the most important one. I’d like the most recent Qt, please As pre-announced by a G+ post, the openSUSE repositories bringing KDE software directly from KDE git (KDE:Unstable:Frameworks and KDE:Unstable:Applications) have switched their Qt libraries from Qt 5.

As KDE software (be it the Frameworks libraries, the Plasma 5 workspace, or the Applications) develops during a normal release cycle, a lot of things happen. New and exciting features emerge, bugs get fixed, and the software becomes better and more useful than it was before. Thanks to code review and continuous integration, the code quality of KDE software has also tremendously improved. Given how things are improving, it is tempting to follow development as it happens.

Recently I’ve been setting up LDAP authentication on CentOS servers to give a shared authentication method to all the compute nodes I use for my day job. I use 389-DS as it’s in my opinion much better to administer and configure than openLDAP (plus, it has very good documentation). As I have a self built NAS at home (with openSUSE Tumbleweed), I thought it’d be nice to use LDAP for all the web applications I run there.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version The image window is shown again with recent Qt and KF5 versions; Remember the last directory saved when saving images; Remove (hopefully) hang when saving images.

Recently I’ve been testing out murmur, http://wiki.mumble.info/wiki/Main_Page server component, on my CentOS 7 server. Murmur requires specific ports being open to operate, and when using it I would open them manually, and close them after the session had been completed. I found it pretty tedious: I wanted to wrap it into a single call to the service, so I could enable my user (via sudoers) to be able to start and stop the service without worrying about elevating permissions to start and stop the firewall.

Short version: the KDE PIM in openSUSE Tumbleweed is moving from 4.14.x to the KF5 based version. More details below. Some history As you may know, up to now the default PIM suite for Plasma 5 in openSUSE Tumbleweed was the KDE PIM 4.14, based on kdelibs 4.x. While upstream KDE has offered a KF5-based version since Applications 15.08, it has been originally marked as a technology preview, so we (the openSUSE community KDE team) thought it would be more prudent to stick with the 4.

I’ve found myself in a situation where my ISP, notorious for having problems with certain online services (not to mention putting everyone under a permanent NAT) started misbehaving with Sony’s Playstation Network: I was getting timeouts of all sorts with no reason (and reading online you see all sorts of attempts from people to work around the issue). When using my phone as hotspot, everything worked, as I went through my mobile operator’s network.

Requests to unlock KWallet automatically on login (assuming the wallet password and user password are the same), like gnome-keyring can do, have been going on for years: in fact, bug reports requesting this feature are quite old. Recently, thanks to the efforts of Alex Fiestas, a PAM module, which interfaces KWallet to the system authentication methods, has been developed. In parallel, the necessary glue code has been also added to the various parts of the KDE workspace so that it could make use of it.

Among the different widgets I use on my desktop, there is a small one which tells me my current public IP address. The reason I’m having it is due to the fact that my own ISP uses a NAT for almost all its customers (don’t ask - long story) and so I need to keep tabs on my current IP, because it may have been blacklisted, and so on. Up to now I was using this plasmoid written in Python, but the code had several issues and used its own way of getting the public IP.

I’m a (happy!) owner of a Casio EX-WORD Dataplus 5 XD-A4700, a Japanese electronic dictionary. Recently I looked into updating the Japanese-English dictionary (currently the Shogakukan PROGRESSIVE dictionary) installed, because it’s not good enough: too often when looking up odd sentences (like the ones in Fate/Extra CCC) I do not find any matches. EDICT is adequate, and while I can use it on my phone and tablet, I like the fact that the EX-WORD has a physical keyboard along with the stylus, and a very nice kanji handwriting recognition.

As others, bigger members in the KDE community say, “nobody will do it for you, and therefore they will”. The patch from the title comes from such a story. Let’s give some background first: I’m really a heavy activity user, especially when working. My home PC has about five activities, my work one 3, and I managed to compartimentalize the various “topics” that each activity does pretty well. After an update a couple of weeks ago from the latest code from KDE git, I started noticing weird behavior.

In one of my previous blog posts I dealt with [tagging files and resources with Nepomuk]({{ site.url }}/2010/10/pykde4-tag-and-annotate-files-using-nepomuk). But Nepomuk is not only about storing metadata, it is also about retrieving and _interrogating _data. Normally, this would mean querying the metadata database directly, using queries written in SPARQL. But this is not intuitive, can be inefficient (if you do things the wrong way) and error prone (oops, I messed up a parameter!

Recently, a question came up on the KDE Community Forums regarding the use of multiple Google Calendars with KOrganizer. The preferred access up to now has been with googledata Akonadi resource, however that doesn’t support more than one calendar, and (at least from my unscientific observation) seems to be rather unmaintained these days.

Luckily, not all’s lost. Akonadi recently gained the opportunity of accessing CalDAV resources, and Google Calendar also offers a CalDAV interface, hence this is possible.

This post will briefly describe how (thanks go to PIMster krop, which casually mentioned the possibility on IRC and prompted me to investigate).

Some of the oldest readers of this blog are well aware of [a certain hobby of mine]({{ site.url }}/category/anime). Over the years I’ve always wanted to write more about that, including the stuff I’m viewing nowadays, but I found a hassle to collect snapshots from videos / DVDs, selecting them, and so on. Recently I learnt that VLC has some rather complete Python bindings, and I thought, why not make the process automated?

As you may already know, recently the KDE sysadmins completely overhauled the commit hooks used with the Git infrastructure. Written in Python, they have already brought significant improvements to the current workflows. These hooks include keywords that when specified trigger particular actions: the most used are to CC specific email addresses (CCMAIL), to CC bug reports (CCBUG) or to close bug reports (BUG). With the adoption of Review Board to facilitate code reviews, there were also requests for a REVIEW keyword that could close the review requests without asking the submitters to do so manually (which is slow and not always effective).

In the past weeks and days, the KDE Community Forums staff has been working to bring new features to improve even more the user experience. A few months ago, the staff was discussing the idea of finding a way to guide users to the most appropriate forum to post their questions or discussions. Now, thanks also to the return in service of one of our admins (welcome back, sayakb!) the feature is now being implemented, as the screenshots below will show.

Recently, I investigated how to perform some checks on web addresses using KIO for Danbooru Client. My old code was synchronous, so it blocked the application while checking, thus causing all sort of troubles (UI freezing, etc.). Therefore, making the switch to KIO was the best solution. However, I had one problem: how could I check the HTTP response? I knew already that the various ioslaves can store metadata, consisting of key-value pairs which are specific on the slave used.

Sometimes answering apparently harmless questions on instant messaging can have unexpected results. In particular, I was telling about Danbooru Client to someone and a question popped up “Why don’t you support pages?”. It seemed a nice idea, so I branched off the code (yay for git!) and started working on it. Well, it took me more than a month to get this thing done… I didn’t spend every day coding, but it was a challenge.

Do you like KDE? Did you ever find yourself in a position of wanting to help, but you didn’t know what to do, or who to talk to? Do you feel you could use help to get started? Today, the KDE Community Forums would like to provide the opportunity to answer those questions by annoucing the continuation of the tutorial courses known as Klassrooms. What are Klassrooms? Klassrooms are tutorial “lessons” held in a specific area of the forum.

Well, there wasn’t a Day 1 for me (I got to the hotel too late to follow the first day of the meeting), so that is why I’m starting on day 2. To start, I need to say that I had never been to a sprint before: I am already accustomed to meeting for real someone from online, but for all the attendants, they had been just names or nicks on IRC.

If you dabble with [anime]({{ site.url }}/category/Anime) and related things like I do, you may have heard about imageboards. A known variant, which powers sites such as moe.imouto (some links may be NSFW) or Konachan, is Danbooru, a Ruby on Rails application. One of the characteristics of this software is that images stored there can be tagged to be identified as precisely as possible: common tags are for example the magazine where the image was taken from, the characters depicted, and so on.

While browsing around kde-look.org, I’ve stumbled upon a nice little Plasma scripted widget, and I’m publishing this to have it get more exposure. A good part of the KDE community knows at least little about Nepomuk, and its ability to attach semantic tags to your files - basically words that describe the file, be it an image, a text document, or anything you’d like. For example, you could tag all the photos from your vacation with the name of the place you’ve been.

Up to now, the main language in which KDE applications are developed is C++. This is a perfectly valid choice: however, at least for users that don’t have a computing background (I include myself in the list: I do science) C++ can be a rather steep requirement (although Hans, fellow staff member at the KDE Community forums, is doing a nice job in explaining his learning experience). Scripted language bindings (that have a lower barrier of entry) for KDE exist: on top of my memory I can list Python, Ruby, and C# (and I’ve probably missed a few).

The KDE Brainstorm, where users can post and vote for feature requests for KDE, is the most visited area of the KDE Community Forums. In an effort to improve the experience of both users and developers, the KDE Community Forums staff is proud to present a brand new version of the KDE Brainstorm.  The new interface resembles the IdeaTorrent sites, but it is still powered by the forum software (phpBB), a clear example of the flexibility of the platform.

A few may know that I more or less maintain the Plasma FAQ page on KDE’s UserBase. Given the rapid advance of Plasma between KDE versions, each time a new version is out a new FAQ needs to be made, as the content rapidly becomes obsolete. For 4.3, unfortunately, I’m not sure I’ll be able to put a new version up in time for the 4.3 release. The reason is mostly practical: it takes a bit of work to collect and add information, and currently my free time is limited due to a rather heavy workload and some other commitments.

A rather big change has gone into KDE’s SVN recently: Ben Cooksley (bcooksley) and Mathias Soeken (msoeken) have committed a complete rework of System Settings.

Compared to the previous implementation, System Settings now has two operational modes, one being the current icon-based view since KDE 4 (and also seen in Kubuntu prior to KDE 4), and a second view, named “Classic”, which reimplements the old KControl look and feel. The latter change is probably very welcome to anyone who found System Settings less useful than the old KControl. The current view used can be changed in the configuration options. In addition, upon hovering an icon or module that show if there are any sub-modules associated.

In the past months I’ve always wanted to write a small Plasma applet to aid me in some boring tasks as a bioinformatician. One example (for the non-scientific crowd out there) is when I find a specific gene out of my analysis work which I want to take a look at. I am often lazy, so instead of firing up the browser to look at the online resources, I wanted to write something which could access said resources programmatically.

Now that the KDE Brainstorm has been launched, it’s time to take a look at the results so far. Currently, the forum hosts 160 threads, approximately one for each idea, and 441 posts. Not bad for the first two days of operation. At the same time, the staff has been working hard to make sure only appropriate ideas (not bug reports, not duplicates…) are on the forum. People have also begun voting, although slowly: it’s understandable, given the fact that there are so many threads in so little time.

It’s finally there: KDE Brainstorm has been launched today! Like this, it will be possible to propose features and have them voted by the community, and then submit the most voted requests to the developers. Every feature request is screened prior to posting, so duplicates, spam and flames are unlikely to occur. There is no guarantee that the voted upon features will be implemented, but as opposed to individual postings, this approach reduces the noise a lot, and allows a better communication between the “two worlds” (users and developers).

No, it’s not_ _a teen-like “I hate my life, I’m going to die tomorrow” post. I’m actually referring to the comments of a person nicknamed “I Love” that are popping up in almost all blogs that are linked to PlanetKDE which deal with Plasma or KDE4 adoption. The name “I Love” contrasts with an attitude that is unconstructive and rather trollish. This wouldn’t be such a big problem, if not for the fact that posts from said individual have had a rather negative effect: for example Aaron was forced to turn comment moderation on on his blog, Jos’ entry on the new Plasma in the upcoming KDE 4.

Mtux, of choqok fame, along with another person, has written Bilbo Blogger, a blogging utility for Blogger or any blog that supports Blogger1.0, MetaWeblog, and MovableType APIs (EDIT: also GData). It is based on the KDE4 libraries and it includes a WYSIWYG editor, an HTML editor, and a Post Preview function that can even fetch your blog’s CSS to render the entry and see how it looks. It’s not released yet, but for the daring, you can actually try and compile it.

During the course of my research work, I may obtain results that are worthy of publication in scientific journals. Since my master’s thesis I’ve been using LaTeX as my writing platform, mainly because I can concentrate on content rather than presentation (I find it useful also for writing non-scientific stuff as well). Also, I can handle bibliography (essential for a scientific publication) very well without using expensive proprietary applications (such as Endnote).

In my early days I used kLyX first, then LyX, but I found the platform to be too limited for my tastes, and also LaTeX errors were difficult to diagnose. I needed a proper editor, and that’s when I heard of kile, a KDE front-end for LaTeX. Kile is currently at version 2.0.2 and is a KDE 3 application. However, in KDE SVN work is ongoing to produce a KDE4 version (2.1) and that’s what I’ll look at in this entry.

I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.

I have been thinking of doing another Kourse at the KDE Forums, similar to the one that has produced three nice screencasts. My idea would be to show very brief and focused screencasts, a sort of “how do I…”. I have a few ideas, but I’d like to ask the KDE community at large. I’m mostly interested in showing single features (short videos), preferably of the “eye-opener” kind. If you have any suggestions, leave a comment.

Yes, I know I’m a bit late to the party (unfortunately today was one of the busiest days ever where I work), but I thought I’d join the other members of the KDE community, because KDE 4.2 has been released today. Take a look at the visual guide, or see if your distribution has already packages for you. For your enquiries, the KDE Forums are at your disposal.

If everything has gone correctly, my blog should be on PlanetKDE now. That means it’s time for an introduction for those readers. My name is Luca Beltrame, I’m a biotechnologist doing bioinformatics in the life sciences areas, and I’m a Free Software user/enthusiast since many years. I’ve been using KDE since 1.0 or so (if memory serves me well), but only recently, with the 4.x line of development, I’ve been trying to actually contribute a bit back to the project.

I just finished writing a new Python tutorial on KDE’s Techbase. This one deals with writing DataEngines in Python (a complement to Simon Edwards’s own Using DataEngines). Let me know what you think. As it’s a wiki, comments and suggestions are welcome.

As Simon Edwards already noted, thanks to me and him (mostly him, I have to say) starting to work on Plasma tutorials at the same time, now KDE’s Techbase has a nice set of Python Plasma tutorials. They cover creation of applets and connection to DataEngines (see the Plasma page on Techbase for more information). I plan on starting a tutorial on writing Plasma DataEngines on Thursday, if time permits.

Students from Kourse 2 fengshaun and Primoz have prepared two nice screencasts, dealing with the Zooming User Interface (ZUI) and desktop settings respectively. Without further ado, here they are: Zooming User Interface by fengshaun [blip.tv ?posts_id=1648944&dest=-1] Desktop settings by Primoz [blip.tv ?posts_id=1646835&dest=-1] As usual, both Free and non-Free versions are available. The students are also at work on subtitled versions, without the Notes plasmoid. I’ll be sure to post them once they’re done.

As some people already know,I’m mentoring a group of students on KDE Forum to create Plasma screencasts (from the upcoming KDE 4.2 version). After several adjustments back and forth, the first one (made by kourse student Primoz), showing off the various desktop settings, is complete. This version uses the Notes plasmoid to keep track of annotation, but we’re also evaluating subtitle-based versions. In the mean time, enjoy! (and spread the word).

Today I was adjusting a bit the layouts of the Activities (as defined in Plasma) to better suit my workflows. To do so I was using the brand new Activity Bar which is present in KDE 4.2. It’s very neat, but takes up space on the desktop, and while it’s not a big deal on my main PC (1280x1024 resolution), it is an issue on my recently-resuscitated EeePC (1024x600). It was then that it occured to me that such applets are, in Plasma-speak, PopupApplets, which means they adjust their behavior depending if they are in a panel or “free”.

Currently I have Kubuntu 8.04 (Hardy) installed on my Eee PC. Version 8.10, the Intrepid Ibex, is due on October 30th. However, I will not install it. The reason is that Kubuntu developers intentionally disabled the zoom function, and I have three activities on this machine. How come I’m supposed to use them? Also, space is pretty tight so install a build environment just to remove one patch seems overkill. So, I’m moving away from it.

All right, it didn’t quite turn out as I had expected. This post wasn’t “soon"as I predicted originally. The reason? The fact that the video card I bought died after three days of usage, and getting a replacement took a while. Finally though, I have a functional system. It’s a Core 2 Duo CPU (7200) with 2 Gb of RAM and an ATI Radeon 3870 HD video card. I installed Linux on it, of course, but instead of Kubuntu I gave openSUSE a try.

I’ve put together a small video that shows what you can do with zooming in and out with Plasma’s Zooming User Interface (ZUI). Enjoy. (note: the version on Youtube has also annotations that explain better what is going on) [youtube]http://www.youtube.com/watch?v=EhODrJkoidA[/youtube] If you can, please spread the link to the video. We need more correct information out there.

Those of you that follow my Linux-related posts know that I work (along with others) on a FAQ trying to explain some magic behind KDE 4.x’s Plasma. Now, especially since on the Internet, there is the need to spread correct information (most of the naysayers are not quite informed). So, if you want to help KDE, please spread the word on the Plasma FAQ! If people have questions on Plasma, just direct them to

Now even the (once respected) Steven J. Vaughan-Nichols is jumping on the bandwagon of Plasma haters. With a rather uninformed and rant-ish entry that just advocates a fork, like some other people said on the kde-devel mailinglist a week or two ago. The entry is rather dismissive of everything in KDE 4 save Plasma (and a mention on Dolphin’s single click icon), and also gets some facts and links wrong (yes, the Plasma web site is outdated, but since the developers are busy coding, someone else should step up and help).

Since my work schedule is bordering on the hectic, I was thinking on buying something to get me more organized. Rather than a PDA, I’ve been rather interested in the Asus Eee PC: small form factor, SSDs and Linux preinstalled are definitely pluses. It’s too bad that at least in Italy Asus sells only the 512M RAM version (when there are more powerful options available elsewhere). I’d like to get impressions on the Asus Eee, before considering a purchase (€ 300 are still a lot): did you try it?

The word is official: KDE 4.0.0 has been released. Make sure to check out the Dot story, or the nicely done visual guide. And if you’re new to Plasma, have a look at the FAQ as well. Congratulations to all the KDE developers, translators, and coordinators for pushing forward our favorite desktop environment. Rock on!

Today is the tagging day for KDE 4.0.0. I think it speaks for itself. I have checked out the 4.0 branch and I’m going to use it in a full session real soon (so far I used nested X sessions with Xephyr). Aaron Seigo has a nice writeup on the release, some of the memes floating around and the future of KDE 4.

I’ve recently begun trying to create GUIs for my Python applications with PyQt, and I can say I’m absolutely loving the toolkit, relatively easy to use and featureful. As I’m trying to create a GUI for some module I wrote that deals with databases (using MySQLdb), I also learnt that Qt has a series of classes for dealing with databases, mainly QSql. My question, directed to whoever has experience with QSql and the Python DB-API, is: what are the advantages of one approach to the other?

I’ve started working on a FAQ related to Plasma, in order to ease the transition for the early adopters of Plasma when KDE 4.0 is released. That, coupled with another idea I had (offering video tutorials of operations) should make the gap smaller. Currently the FAQ is a work in progress (still a lot of TODOs, I hope to have a look after Friday as I’m really busy now) and resides in KDE’s TechBase until a more suitable solution is found.

Yesterday I spent some of my free time to help with the KDE 4.0 Krush Day. Unfortunately, I did a lot less than what I was supposed to do, mainly because at some point the home directory ran out of space (I forgot to remove qt-copy object files), then I inadvertently removed some of the directories and I had to re-sync with SVN. Nevertheless, it was interesting and nice to be able to contribute even if you don’t speak C++.

Aseigo announced it a few days ago: on Saturday, on the Freenode IRC network, #kde4-krush channel, there will be a day-long session to triage and squash bugs in order to improve the overall quality of KDE 4.0. I will try to be there, so that I can give out my (little) contribution as non-coder. I’ll be sure to report later.

First of all let me make some disclaimers : This is **not **a Plasma bashing post (so that aseigo won’t commit suicide, should he ever read this); I’m not a KDE developer, just someone who tries out SVN and reads mailing lists; UPDATE: These statements aren’t meant to bash the collective group of the KDE developers, just to outline a bad “mood” in my opinion.

I obviously did not want to stop with a single compile of KDE4, therefore I’m updating more or less randomly my build off the SVN to check what has been changing. The first and most important change since my last post was the addition of the K-menu in the taskbar: Kickoff was moved from playground (where it resided) to kdebase. Also, kate now works perfectly, and is already usable as a full-blown text editor.

Since Beta 3 was announced a short time ago, I thought I would try testing KDE4 on my computer. Here I’m reporting on my first impressions and I’ll try to provide constructive feedback as much as possible: the developers are being already (and unjustly, in my opinion) bashed enough.

The other day I was thinking about how to make screencaps for the anime I watch. Windows users often use Media Player Classic, which can create a video contact sheet (i.e., a series of captures) out of a movie file. I had two problems with this: The biggest is that it runs on Windows, and I don’t use Windows; The frames needed to be manually cropped every time, which was slow.

After some thought, I’ve joined the fray and installed the beta version of Kubuntu 7.10 (Gutsy Gibbon) on one of my computers. It hasn’t too recent hardware (AMD Thunderbird 2100+, 512 Mb RAM and a motherboard with a Nforce 2 chipset), and it is my test system for distributions. It ran Feisty Fawn, so I tried to use the upgrader tool, which crashed when removing unsupported packages. Oh well, it was a beta, so nothing to worry about (the only worry was that it didn’t output anything at all).

Following up on the announcement from KDE, the openSUSE KDE team is happy to announce the availability of 4.10 RC3 packages. Remember that they are packages meant for testing and reporting bugs, so that the next release will be as polished as possible. You will find the packages in the KDE:Distro:Factory repository. An updated live media based on the upcoming openSUSE 12.3 ([see previous post]({{ site.url }}/2013/01/test-the-upcoming-opensuse-12-3-and-kde-workspace-applications-and-platform-4-10-rc2)) is also available (files named KDE4-4.

The 4.10 release for the KDE Development Platform, Workspaces and Applications is drawing nigh… as you may have read, there is now an additional release candidate in order to test some last-minute changes. Of course, the KDE developers can only do so much: it’s impossible to test all possible combinations. That is, unless the community at large helps by finding and reporting issues the developers can fix. But doing so requires a 4.

As KDE software (be it the Frameworks libraries, the Plasma 5 workspace, or the Applications) develops during a normal release cycle, a lot of things happen. New and exciting features emerge, bugs get fixed, and the software becomes better and more useful than it was before. Thanks to code review and continuous integration, the code quality of KDE software has also tremendously improved. Given how things are improving, it is tempting to follow development as it happens.

Fourteen days since my last post. Quite a while, indeed. Mostly I’ve been stumbled with work and some health related issues. Anyway, I thought I’d follow up on the meta analysis matter I discussed in my last post. It turns out that it’s a fault of both limma and the data sets, because apparently the raw data found in the Stanford Microarray Database have different length, gene-wise (a result of not all spots on the array being good?

Again in the past days I’ve been banging my head thanks to the fact that doing meta-analysis with microarray data is more difficult than what it seems. The problem sometimes lies in the data, sometimes lies in the analysis software and sometimes in a combination of factors. When doing work on a public data set (Zhao et al., 2005), I had to start analysis from raw data. Now, I tried using both the limma and marray Bioconductor packages, but both of them bail out with cryptic error messages.

Recently I had to annotate a large (10,000+) number of genes identified by Entrez Gene IDs. My goal was to avoid “annotation files” (basically CSV files) that a part of wet lab group likes, because I wanted to stay up-to-date without having to remember to update them. So the obvious solution was to use a service available on the web, and in an automated way. For reference, I just tried to attach gene symbol, gene name, chromosome and cytoband.

I’m often wondering why people only resort to R when working with microarrays. I can understand that Bioconductor offers a plethora of different packages and that R’s statistical functions come in handy for many applications, but still, I think people underestimate the impact of performance. R is not a performing language at all, it doesn’t parallelize well when using HPC (at least from the talks I’ve had with people studying the matter), and in general is a memory and resource hog.

Fourteen days since my last post. Quite a while, indeed. Mostly I’ve been stumbled with work and some health related issues. Anyway, I thought I’d follow up on the meta analysis matter I discussed in my last post. It turns out that it’s a fault of both limma and the data sets, because apparently the raw data found in the Stanford Microarray Database have different length, gene-wise (a result of not all spots on the array being good?

Again in the past days I’ve been banging my head thanks to the fact that doing meta-analysis with microarray data is more difficult than what it seems. The problem sometimes lies in the data, sometimes lies in the analysis software and sometimes in a combination of factors. When doing work on a public data set (Zhao et al., 2005), I had to start analysis from raw data. Now, I tried using both the limma and marray Bioconductor packages, but both of them bail out with cryptic error messages.

While working today on an annotation class in Python I stumbled on a problem. Normally I work with lists of genes that are consistent, i.e. all Entrez Gene IDs (or RefSeq IDs, or Genome Browser IDs…), but today I had a list of mixed identifiers. The subsequent idea was “let’s implement auto-detection of common identifiers in the class”. The problem is… is there any actual documentation on how identifiers are made?

Today I was looking for an easy way to do some calculations of raw expression data on Affymetrix arrays, but I didn’t want to use R: I have already mentioned how I don’t like its design and implementation. While looking for some documentation, I stumbled upon this nifty little program called RMAExpress.

I haven’t posted anything in a month or so. Quite a long time, considering I used to write at least once per week. The reasons are mainly two: first of all, my work schedule has taken a turn for the worse, which means I have to do my job a lot harder than before; secondly, there wasn’t much interesting stuff to report. Let’s resume from the hiatus by writing about my latest Final Fantasy XI session.

Despite the utter lack of content in Wings of the Goddess my brother has managed to create a movie clip (inspired by the opening of Wild ARMs The Vth Vanguard). You can view it below (streaming) or obtain a higher quality version. [googlevideo]http://video.google.com/videoplay?docid=8316261647217076877[/googlevideo] (apologies for the lack of updates. I’ve been quite busy. I will probably post more in during the Christmas holidays)

While I’m waiting for KDE 4.0 to compile, I just wanted to share a small clip of my brother’s character doing the Drain Samba animation. A bit of background: he has leveled Dancer up to level 7, and now he stopped because there is no artifact armor available yet (probably out in February) and because he’s also leveling another job, monk. Given how people rushed to get Dancer to 75 in less than a week (comments are left to the reader) it is a nice change.

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Finally my copy of Wings of the Goddess has arrived. It was just a matter of putting the DVD in the drive and let install the measly 350+ Mb of update (rather low for a DVD). As usual, Square Enix’s installation program is greedy with regards to information. Once it was installed, I enabled the expansion in PlayOnline and was good to go (save a 20,000+ file check).

With the new version update, these strange portals have been appearing throughout Vana’diel. They’re supposedly the gateways to the past, but since I don’t have Wings of the Goddess yet I can’t really see what will they do. Nevertheless, I was curious and went to take a look at them. They’re **huge. **I estimate at least twice the height of my character. For those curious, here are two photos (one is of my brother’s character, the other is mine):

And so I’m reading that the FFXI Fan Festival has kicked off yesterday (I wish I could have been there). Naturally, reports have been flowing. The FFXI Encyclopedia has a good report of what has been said so far. 1up, the online branch of EGM, has also covered the event, but the article is only focusing on the new jobs (talk about explaining something no one else will ask… not to mention the attitude of that “journalist”).

Yesterday Alex Fiestas showed on his blog a video of a recent development version of the KScreen library, created to handle easily multiple monitor setups in KDE, almost in an “automagic” way. As this is a project where configurations and setups are highly heterogeneous, a lot of testing is required to ensure things work reliably. Of course, you cannot ask a developer to have all sorts of screen combinations, but remember one of the strengths of FOSS: “many eyes make bugs shallow”.

I was thinking about writing something on the line of what I announced in the past entry, but what has happened recently surrounding the artist who does the work for The S.T.E.A.L. Saga, that is Too, made me change my mind.

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Today I got the first Maho Shojo Lyrical Nanoha StrikerS R2 DVD in the mail. Even though I haven’t watched it properly yet (I plan on doing so tomorrow) I can say I’m already impressed. Usually Japanese DVDs are little more than improved video tapes: they provide just the bare minimum (and not for a cheap price). However, this is not the case with Nanoha StrikerS.

According to the Anime News Network, Geneon Entertainment has bought the license for distributing Maho Shojo Lyrical Nanoha and Nanoha A’s in the United States. Fans rejoice? I think not. Being outside of the USA market, I view things with a different approach. The companies here in Italy have all their problems, but to a certain degree they care about delivering to the user something more than just the episodes. Extras that can also be an incentive over downloading (illegally) over the Internet.

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A few days ago I finally completed (after about 3 months) 神次元ゲームネプテューヌV, or “Kami Jigen Game Neptune V”, the latest instalment from Compile Heart in the Neptune franchise of PS3 games. It took quite a while (approximately 3 months), and I think it’s about time to wrap things up.

This was inspired by this forum thread on the Piwigo forums. Set up rewrite rules in nginx where “piwigo” is the path the gallery lies in: location @rewrite { rewrite ^/piwigo/picture((/|$).*)$ /piwigo/picture.php$1 last; rewrite ^/piwigo/index((/|$).*)$ /piwigo/index.php$1 last; # The following is needed for batch operations which use i.php rewrite ^/piwigo/i((/|$).*)$ /piwigo/i.php$1 last; } location /piwigo { index index.php; try_files $uri $uri/ @rewrite; } location ~ ^(?

Yesterday I got a few novels that I’ve been waiting for a while: _Slayers _(the last two volumes published by Tokyopop, as ) and Shakugan no Shana 2. I bought the latter as a “final warning” because I’m not very sure I’ll ever continue: the first Shana was written poorly and with a plot that didn’t make much sense (but again, I don’t think the animated version was shining in that respect).

When Tokyopop announced _Slayers, Kino no Tabi _and _Scrapped Princess _my interest was piqued: even more when I read about Seikai no Monsho. After getting what was available (three volumes of Scrapped Princess, the whole Seikai no Monsho trilogy and the single volume of Kino no Tabi) I waited for the rest.

If I look back at the last post I made on ths blog… let’s say quite a lot of time has passed. The reason? Well, first of all, one would call it a lack of motivation1, and afterwards, the emergence of a small yet quite annoying pathogen which caused a bit of a stir worldwide. But today I’m not going to talk about viruses: perhaps some other time when you can avoid hear about it for breakfast, lunch, and dinner.

With my last entry, I announced the start of the work for an OCS library for the KDE Community Forums. Today I’d like to blog again about the recent developments. First of all, now there isn’t one, but two Python modules: _ocslib, _ a pure Python module that can be used to interface with OCS-based forum systems; ocslibkde, a PyKDE4 based module that can be used to interface with OCS-based forum system in KDE applications.

For KDE developers, web-based forums are often uncommon workflows. Indeed, for communication among developers mailing lists are much better tools, especially since you can handle everything inside a client (most of the time), compared to forums where you have to use a web browser. The ways of reading, replying and interacting with posters are dramatically different. And that is why some developers find themselves uncomfortable with the KDE Community Forums.

 On Septemer 1st the open beta of Square Enix’s new MMORPG, FINAL FANTASY XIV Online was launched. I’ve been playing its predecessor since December 2003, although nowadays my presence is limited to doing the “missions” (quests that advance the main storyline). Of course I was interested in the “new MMO” in the works at Square since it was mentioned in 2006. When the official release was announced, I preordered the so-called Limited Collector’s Edition (it comes with nice items inside, along with an in-game item).

I wanted to write this earier, but I couldn’t: I’m now in a hotel in Maastricht, Netherlands, and waiting to get back tomorrow. I’ve been attending the 4th NuGO hands-on advanced microarray data analysis course and I even wanted to blog about it… but the hotel’s connection did not resolve any non-European web page until late today.

Part of this post is about openQA, openSUSE’s automated tool which tests a number of different scenarios, from installation to the behavior of the different desktop environments, plus testing the freshest code from KDE git. Recently, thanks to KDE team member Fabian Vogt, there has been important progress when testing KDE software. Testing the Dolphin file manager Those who use KDE software, either in Plasma or in other desktop environments have at least heard of Dolphin, the powerful file manager part of KDE Applications (by the way, have you checked out the recent beta yet?

As many readers of this blog are aware, openSUSE has been offering packages of git snapshots from KDE since quite a while. They are quite useful for those wiling to test, report bugs, and / or hack on the code, but also for those who want to see what’s brewing in KDE land (without touching their existing systems). However, a major drawback for non English speakers was the lack of translations.

In the past months I’ve set up LDAP at home, to avoid having different user accounts for the services that I run on my home hardware. Rather than the venerable OpenLDAP I settled for 389 Directory Server, commercially known as Red Hat Directory Server, mainly because I was more familiar with it. Rather than describing how to set that up (Red Hat’s own documentation is excellent on that regard), this post will focus on the steps required to enable encryption using Let’s Encrypt certificates.

One thing I always wanted to do when going on holiday is to track where I go, the places I’ve been, and see how much I’ve travelled around. This is true in particular when going to places where I walk around a lot (Japan stays at the top of the list, also for other reasons that are not related to this post). Something like viewing a map showing where you were, and where did you go, with optional export to KML or GPX to import into other programs like Marble.

If I look back at the last post I made on ths blog… let’s say quite a lot of time has passed. The reason? Well, first of all, one would call it a lack of motivation1, and afterwards, the emergence of a small yet quite annoying pathogen which caused a bit of a stir worldwide. But today I’m not going to talk about viruses: perhaps some other time when you can avoid hear about it for breakfast, lunch, and dinner.

Part of this post is about openQA, openSUSE’s automated tool which tests a number of different scenarios, from installation to the behavior of the different desktop environments, plus testing the freshest code from KDE git. Recently, thanks to KDE team member Fabian Vogt, there has been important progress when testing KDE software. Testing the Dolphin file manager Those who use KDE software, either in Plasma or in other desktop environments have at least heard of Dolphin, the powerful file manager part of KDE Applications (by the way, have you checked out the recent beta yet?

As you may already know (if you don’t, please check these older posts) openQA, the automated testing system used by openSUSE runs daily tests on the latest KDE software from git. It works well and uncovered a number of bugs. However, it only tested X11. With Wayland starting to become usable, and some developers even switching to Wayland full time, it was a notable shortcoming. Until now. Why would openQA not run on Wayland?

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highlights of the new version Unbreak konachan.com support (change in URL format) Coming up next HTTPS support!

In the past three weeks, the openSUSE community KDE team has been pretty busy to package the latest release of Applications from KDE, 16.12. It was a pretty large task, due to the number of programs involved, and the fact that several monolithic projects were split (in particular KDE PIM). This post goes through what we did, and how we improved our packaging workflow. Some prerequisites In openSUSE speak, packages are developed in “projects”, which are separate repositories maintained on the OBS.

Admit it: how many times you have seen “software from this branch is completely untested, use it at your own risk” when you checked the latest code from any FOSS project? I bet you have, many times. For any reasonably modern project, this is not entirely true: Continuous Integration and automated testing are a huge help in ensuring that the code builds and at least does what it is supposed to do.

You may be aware that openSUSE Leap 42.2 is now in the release candidate stage, and there’s a lot of activity aimed at squashing those pesky bugs before they hit the final release. One particular bug proved to be quite tough to fix, and it was only solved thanks to the “heroes” mentioned in the title. This is the history of the bug. The report October 6th, 2016 - A bug iss reported against Plasma reporting a hard freeze of Plasma when using the Noveau driver, but not with the closed NVIDIA blob.

As you may know (unless you’ve been living in Alpha Centauri for the past century) the openSUSE community KDE team publishes LiveCD images for those willing to test the latest state of KDE software from the git master branches without having to break machines, causing a zombie apocalypse and so on. This post highlights the most recent developments in the area. Up to now, we had 3 different media, depending on the base distribution (stable Leap, ever-rolling Tumbleweed) and whether you wanted to go with the safe road (X11 session) or the dangerous path (Wayland):

Every day, a sizable number of people posts problems on the KDE Community Forums and the ever-helpful staff does their best to solve whatever issues they’re facing. But what exactly does one do when this happens? This post provides more insights on the process. NOTE: The following applies to my workflow for the Kontact & PIM subforum. Step 1: Someone posts a problem The questions posted are various, and range from simple tasks (“how I do XXX”) to very specific workflows.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version Support for width / height based filtering: now you can exclude posts that are below a specific width or height (or both) New dependency: KTextWidgets Coming up next Sooner or later I’ll get to finish the multiple API support, but given that there’s close to no interest for these programs (people are happy to use a browser) and that I work on this very irregularly (every 6-7 months at best), there’s no ETA at all.

Ever since the launch of Argon and Krypton, the openSUSE community KDE team didn’t really stand still: a number of changes (and potentially nice additions) have been brewing this week. This post recapitulates the most important one. I’d like the most recent Qt, please As pre-announced by a G+ post, the openSUSE repositories bringing KDE software directly from KDE git (KDE:Unstable:Frameworks and KDE:Unstable:Applications) have switched their Qt libraries from Qt 5.

As KDE software (be it the Frameworks libraries, the Plasma 5 workspace, or the Applications) develops during a normal release cycle, a lot of things happen. New and exciting features emerge, bugs get fixed, and the software becomes better and more useful than it was before. Thanks to code review and continuous integration, the code quality of KDE software has also tremendously improved. Given how things are improving, it is tempting to follow development as it happens.

Recently I’ve been setting up LDAP authentication on CentOS servers to give a shared authentication method to all the compute nodes I use for my day job. I use 389-DS as it’s in my opinion much better to administer and configure than openLDAP (plus, it has very good documentation). As I have a self built NAS at home (with openSUSE Tumbleweed), I thought it’d be nice to use LDAP for all the web applications I run there.

KDE has recently released the newest Release Candidate of the Applications 15.08 release. Among the new features and changes of this release, there is a technology preview of the new KF5-based KDE PIM suite (including reworked, faster Akonadi internals), new applications ported to KF5 (the most notable ones being Dolphin and Ark). After some consideration and thinking on how to allow users to test this release without affecting their setups too much, the openSUSE community KDE team is happy to bring this latest RC to openSUSE Tumbleweed and openSUSE 13.

A lot has been happening on the KDE side of openSUSE… this post summarizes what’s been going on so far. Live media for Plasma 5 One of the most-often requested ways to test Plasma 5, given it can’t be coinstalled with the 4.x Workspace, is the availability of live images to test either in VM or bare metal without touching existing systems. Given that other distributions started doing so since a while, naturally openSUSE couldn’t stay still.

The ever-amazing Plasma team from KDEjust put out a new release of Plasma. I won’t spend much describing how big of an improvement it is - the release announcement at KDE has all the details needed to whet your appetite. And of course, now it’s the turn of distributions to get out packages for the users at large. This is also the case for openSUSE. The KDE:Frameworks5 repository hosts the new 5.

Short version: the KDE PIM in openSUSE Tumbleweed is moving from 4.14.x to the KF5 based version. More details below. Some history As you may know, up to now the default PIM suite for Plasma 5 in openSUSE Tumbleweed was the KDE PIM 4.14, based on kdelibs 4.x. While upstream KDE has offered a KF5-based version since Applications 15.08, it has been originally marked as a technology preview, so we (the openSUSE community KDE team) thought it would be more prudent to stick with the 4.

Following up onKDE’s announcement of the latest stable release, we have now packages available for 12.3 and 13.1 (a 13.2 repository will be made available after it is out). You will find them in the KDE:Current repository. Current users of this repository will get the new release automatically once they update. Why you should upgrade? You can take a look at the list of changes to get an idea. These fixes touch many important KDE applications, including KMail, Okular and Dolphin.

Congratulations to KDE (of which I’m proud of being a part of) for the newest release of the Plasma workspace! At the same time, the 4.x series has seen a new beta release, and the stable branch got updated, too. I’m betting a few people will ask “Are these available for openSUSE?” and of course the answer is yes, thanks to the efforts of the openSUSE community KDE team and the Open Build Service.

Since a couple of weeks the packages offered by openSUSE in the KDE:Unstable:Frameworks repository have undergone a series of changes. In particular, the packages now install to /usr. For the libraries (KDE Frameworks 5) this will mean a transparent change for the userbase as they are expected to be co-installable, but the workspace components (Plasma 5) will confict with the existing Plasma 4.11.x installation. What does this mean in practice? If you want to use Plasma 5 you will not be able to use a 4.

Recently I was looking for a laptop: the previous one I had (an Asus EeePC 900) was almost dead (the fan broke, and the idea of dismantling everything to get to it wasn’t appealing). When looking around, I had the following requirements: It needed to run on Linux well. No exceptions. _Portable: _ at home and at my workplace I have rather powerful machines, so a desktop replacement was not needed.

This is a guest post by Raymond “tittiatcoke” Wooninck, with contributions from myself and Hrvoje “shumski” Senjan In the next hours the [KDE:Current]({{ site.url }}/2014/03/being-current/) repository will publish the latest release from KDE (4.13). As that this release comes with a big change (the new semantic search), we would like some simple steps in order to perform the right upgrade. Before the upgrade In order to migrate data automatically from the Nepomuk store to the new format, you will need Nepomuk up and running, and just for the time needed for the migration.

It is not news that openSUSE, through to the effort of the openSUSE community KDE team, offers several third-party repositories for those who want the latest software from KDE. Since a while, stable releases were offered in the KDE:Release:4x repositories, created with every major release of KDE software. These were meant to offer the latest and greatest to the users without having them to track KDE:Distro:Factory, which is instead used to track packaging for the next openSUSE release and is more in a state of flux.

Yesterday KDE released their first beta of the upcoming 4.13 version of Workspaces, Applications and Development platform. As usual with the major releases from KDE, it’s packed with a lot of “good stuff”. Giving a list of all the improvements is daunting, however there are some key points that stand out: Searching: KDE’s next generation semantic search is a prominent feature of this release. It’s several orders of magnitude faster, much leaner on memory and generally is a great improvement from the previous situation (this writer has been testing it for the past months and he’s absolutely delighted about it).

And so, finally openSUSE 13.1 is out of the door (I couldn’t celebrate like I wanted, as I’ve been very busy). This release has lots of improvements, and of course, the latest stable software from KDE. It is time (perhaps?) to look back and see what the team has done during this development cycle. With regards to the KDE software packaging, the past 8 months have seen quite an increase in the involvement of poeple from the community.

As you may know, there is an ongoing effort to rearrange and adjust the openSUSE KDE repositories. In line with the previously announced deletions, and more recent adjustments, a number of changes went into the organization and layout of the KDE repositories: KDE:Distro:Factory and KDE:Release:4xy will now hold the “core” KDE packages: this means the base Development Platform, Workspaces and Applications, and additional applications for a basic desktop experience.

Summer is ending soon (at least for those living in the northern hemisphere) and while usually cleaning is done during spring, the KDE team decided to do what I’d call… autumn cleaning of repositories. You may know that the KDE presence in openSUSE, aside being the default desktop, is quite a long one. In the past years different repositories were created by the members of the openSUSE KDE team (at the time mostly made up by KDE people hired by Novell) in order to review and test packages, like newer Qt versions, KDE software, and so on.

In the past few days, the openSUSE KDE team has been working hard, following the footsteps of the nice work done by the Kubuntu and Arch Linux communities, to provide Qt5 packages for the distribution. In fact, work was already done in the past, but the packages were not coinstallable with the existing Qt4 installation. Thanks to a renewed effort, the OBS holds now Qt5 packages that won’t overwrite the existing Qt4 install: they currently live in the KDE:Qt51 repository (Factory and openSUSE 12.

The latest release of the KDE Platform, Workspaces, and Applications (4.11) is around the corner: in fact, the last RC was recently made available. We’re almost there, but it doesn’t mean that testing and reporting should stop: on the contrary, it is needed even more to ensure that no bad bugs crawl up in the final release. As part of this effort, openSUSE packages for RC2 have been released through the OBS, and are available in the KDE:Distro:Factory repository.

The latest release from KDE moved from beta to RC stage, thus finding and reporting bugs is more important that ever. At the same time, the distribution packaging teams are also working in polishing their packages. As far as openSUSE is concerned (not dissing other distros, just mentioning the one I’m involved in ;), you can kill two birds with one stone by installing the packages provided in the KDE:Distro:Factory repository.

KDE released the second beta of the KDE Platform, Workspaces and Applications 4.11, and after the necessary time for the OBS to build packages from the released tarballs, packages are available for openSUSE 12.3 and openSUSE Factory. Like the previous beta, they are available through the KDE:Distro:Factory repository. 4.11.x is is targeted for inclusion in the upcoming openSUSE 13.1. So far 4.11 has been pretty stable for me, but you should never forget these packages are for testing and bug reporting purposes: don’t use them on production systems.

As a consequence of [the recent changes in the repositories]({{ site.url }}/2013/06/upcoming-changes-to-opensuse-kde-repositories), the openSUSE KDE team is happy to announce the availability of packages containing the first beta of the KDE Platform, Workspaces and Applications 4.11. Packages are available in the KDE:Distro:Factory repository. As it is beta software, it may have not-yet-discovered bugs, and its use is recommended only if you are willing to test packaging (reporting bugs to Novell’s bugzilla) or the software (reporting bugs directly to KDE).

Since KDE has released the first beta of Platform, Workspaces, and Applications 4.11, there will be some changes in the packages offered in the openSUSE repositories. In short: KDE:Distro:Factory will now start tracking 4.11 betas and RCs: packages are being worked on. Use this version to test packages and to report bugs upstream. KDE:Release:410 has been decoupled from KDE:Distro:Factory. If you were using 4.10 packages from KDF, you’re highly encouraged to move to this repository.

These posts kind of sound like a broken record, right? ;) Anyway, since KDE has released new versions of Platform, Workspaces and Applications as part of the stable release cycle, thanks to the OBS we have packages available for openSUSE 12.2 and 12.3. The 4.10.4 update will also be released as an official update for 12.3 in due time. Where you can get the packages? Two places, as usual: KDE:Distro:Factory in case you are interested in contributing to packaging for the next openSUSE release; KDE:Release:410 (openSUSE 12.

KDE released 4.10.3 versions of the Platform, Workspaces and Applications yesterday, with more than 70 bugs being fixed. Notably: Several fixes in handling encrypted mails in KMail Fixes for KDEPIM syncing and ownCloud A number of improvements in Dolphin, including crash fixes Optimizations in the Plasma Workspaces [The full list](https://bugs.kde.org/buglist.cgi?query_format=advanced&bug_status=RESOLVED&bug_status=VERIFIED&bug_status=CLOSED&bugidtype=include&chfieldfrom=2013-01-01&chfieldto=Now&chfield=cf_versionfixedin&chfieldvalue=4.10.3&order=Bug Number&list_id=638034) has other important changes. As usual, there are two different repositories from which you can get them:

KDE has released its monthly update for the 4.10 release, and after a brief wait while the Open Build Service worked over the released tarballs, the openSUSE KDE team is pleased to announce the availability of the 4.10.2 release packages for openSUSE 12.2 and 12.3. []({{ site.url }}/images/2013/04/757111961.png) Despite being a minor release, more than 100 bugs were fixed, in particular there were many KDEPIM fixes touching both the low level stack and KMail/KAddressbook/Kontact.

Hot on the heels of the announcement from KDE, the openSUSE KDE team is happy to announce the availability of packages for the latest stable release of the KDE Platform, Workspaces, and Applications. Packages are available in the KDE:Distro:Factory repository (which is where the packages to land in 12.3 are tested) for openSUSE Factory (soon to be 12.3) and openSUSE 12.2 and soon (when the Open Build Systen finishes rebuilding a number of packages) in the KDE:Release:410  repository for openSUSE 12.

During the discussions for the release of openSUSE 12.3, the topic of update notifications and applets was brought up again. Originally openSUSE shipped with a custom update applet, but since it was basically unmaintained, the decision was made to switch to Apper for openSUSE 12.2 The original Apper used in that version had a number of issues, which the upstream developer (Daniel Nicoletti) fixed in a newer version, which also had a lot of other improvments.

Following up on the announcement from KDE, the openSUSE KDE team is happy to announce the availability of 4.10 RC3 packages. Remember that they are packages meant for testing and reporting bugs, so that the next release will be as polished as possible. You will find the packages in the KDE:Distro:Factory repository. An updated live media based on the upcoming openSUSE 12.3 ([see previous post]({{ site.url }}/2013/01/test-the-upcoming-opensuse-12-3-and-kde-workspace-applications-and-platform-4-10-rc2)) is also available (files named KDE4-4.

Following up on my previous post, a different type of image has been made by the openSUSE KDE community members. In particular, alin has created images sporting the same software from KDE (4.10 RC2) but using the upcoming openSUSE 12.3 as base. Download links: 32 bit version 64 bit version Release directory (in case the above links go 404; the files are named KDE4-.4.10.RC2-Live) These images are provided not only to test 4.

The 4.10 release for the KDE Development Platform, Workspaces and Applications is drawing nigh… as you may have read, there is now an additional release candidate in order to test some last-minute changes. Of course, the KDE developers can only do so much: it’s impossible to test all possible combinations. That is, unless the community at large helps by finding and reporting issues the developers can fix. But doing so requires a 4.

Yesterday Alex Fiestas showed on his blog a video of a recent development version of the KScreen library, created to handle easily multiple monitor setups in KDE, almost in an “automagic” way. As this is a project where configurations and setups are highly heterogeneous, a lot of testing is required to ensure things work reliably. Of course, you cannot ask a developer to have all sorts of screen combinations, but remember one of the strengths of FOSS: “many eyes make bugs shallow”.

openSUSE is migrating to the use of systemd for the upcoming 12.3 version, given the difficulties that emerged in trying to co-maintain two different init systems (SysV + systemd). While I am not going into the details of this choice (I leave this to more informed people), this has some consequences for software higher in the stack. As ConsoleKit is deprecated, systemd offers its own daemon to keep track of sessions and assigned seats in a system.

The KDE community has just released Beta 2 of the upcoming 4.10 release of the Development Platform, Workspaces, and Applications. Of course, distributions are providing binary packages for the adventurous… and how could the green distro be left out? In fact, it is not. Beta 2 packages were uploaded and built in the KDE:Distro:Factory repository. Updated packages have also been submitted to the development version of openSUSE (Factory) as the ultimate goal is having 4.

Following up my [earlier post]({{ site.url }}/2012/10/whats-cooking-for-kde-in-opensuse-12-3-theming), the new openSUSE 12.3 theme has finally landed into the official openSUSE repositories  and will be part of the upcoming 12.3. A lot of work has gone into the new theme since I last posted about it, so this post will show how things look at the moment.

A few caveats:

• The theme targets the 4.10 release of the KDE Workspaces, so it may be not be perfect under 4.9;

• The default wallpaper has not been chosen yet.

Without further ado, let’s get down to seeing what’s improved.

Like everything, openSUSE is not perfect. Bugs crop here and there, or there is missing / quirky functionality that users may run into. Being a distribution of heterogeneous software, this means that bugs fall into these categories: Upstream bugs in the software shipped by openSUSE Bugs in the packaging Bugs in distribution-specific setups or that derive from interactions with these setups (e.g. kernel, low level software stack, etc.

Although the release of openSUSE 12.3 is yet to come, the people of the openSUSE community contributing to KDE are already at work to bring the best possible KDE experience for the new release.

Recently Fedora’s Lukas Tinkl pushed to kdelibs (for the 4.10 release) a patch that enabled Solid to talk to udisks2, which is a replacement for udisks. Fedora already moved to udisks2 (and killed HAL) and future GNOME releases will only use udisks2, so the need for a working backend was a necessity, and at the same time they acted like good open source citizens, and pushed the code both to 4.

Omnia? The Turris Omnia is quite a nice (although a little pricey) OpenWRT-based router from CZ.NIC. It provides a fairly powerful CPU, relatively unconstrained eMMC space, and quite a lot of hackability (some revisions even have GPIO ports to play with). It runs a modified version of OpenWRT, named TurrisOS. The problem A few years ago, I built a custom NAS for my storage needs, using a cheap Intel SoC (J1900 chipset) and a (much pricier) mini-ITX small form factor server tower.

One thing I always wanted to do when going on holiday is to track where I go, the places I’ve been, and see how much I’ve travelled around. This is true in particular when going to places where I walk around a lot (Japan stays at the top of the list, also for other reasons that are not related to this post). Something like viewing a map showing where you were, and where did you go, with optional export to KML or GPX to import into other programs like Marble.

It is not news that openSUSE, through to the effort of the openSUSE community KDE team, offers several third-party repositories for those who want the latest software from KDE. Since a while, stable releases were offered in the KDE:Release:4x repositories, created with every major release of KDE software. These were meant to offer the latest and greatest to the users without having them to track KDE:Distro:Factory, which is instead used to track packaging for the next openSUSE release and is more in a state of flux.

Yesterday KDE released their first beta of the upcoming 4.13 version of Workspaces, Applications and Development platform. As usual with the major releases from KDE, it’s packed with a lot of “good stuff”. Giving a list of all the improvements is daunting, however there are some key points that stand out: Searching: KDE’s next generation semantic search is a prominent feature of this release. It’s several orders of magnitude faster, much leaner on memory and generally is a great improvement from the previous situation (this writer has been testing it for the past months and he’s absolutely delighted about it).

In the past few days, the openSUSE KDE team has been working hard, following the footsteps of the nice work done by the Kubuntu and Arch Linux communities, to provide Qt5 packages for the distribution. In fact, work was already done in the past, but the packages were not coinstallable with the existing Qt4 installation. Thanks to a renewed effort, the OBS holds now Qt5 packages that won’t overwrite the existing Qt4 install: they currently live in the KDE:Qt51 repository (Factory and openSUSE 12.

The latest release of the KDE Platform, Workspaces, and Applications (4.11) is around the corner: in fact, the last RC was recently made available. We’re almost there, but it doesn’t mean that testing and reporting should stop: on the contrary, it is needed even more to ensure that no bad bugs crawl up in the final release. As part of this effort, openSUSE packages for RC2 have been released through the OBS, and are available in the KDE:Distro:Factory repository.

The latest release from KDE moved from beta to RC stage, thus finding and reporting bugs is more important that ever. At the same time, the distribution packaging teams are also working in polishing their packages. As far as openSUSE is concerned (not dissing other distros, just mentioning the one I’m involved in ;), you can kill two birds with one stone by installing the packages provided in the KDE:Distro:Factory repository.

As a consequence of [the recent changes in the repositories]({{ site.url }}/2013/06/upcoming-changes-to-opensuse-kde-repositories), the openSUSE KDE team is happy to announce the availability of packages containing the first beta of the KDE Platform, Workspaces and Applications 4.11. Packages are available in the KDE:Distro:Factory repository. As it is beta software, it may have not-yet-discovered bugs, and its use is recommended only if you are willing to test packaging (reporting bugs to Novell’s bugzilla) or the software (reporting bugs directly to KDE).

These posts kind of sound like a broken record, right? ;) Anyway, since KDE has released new versions of Platform, Workspaces and Applications as part of the stable release cycle, thanks to the OBS we have packages available for openSUSE 12.2 and 12.3. The 4.10.4 update will also be released as an official update for 12.3 in due time. Where you can get the packages? Two places, as usual: KDE:Distro:Factory in case you are interested in contributing to packaging for the next openSUSE release; KDE:Release:410 (openSUSE 12.

KDE has released its monthly update for the 4.10 release, and after a brief wait while the Open Build Service worked over the released tarballs, the openSUSE KDE team is pleased to announce the availability of the 4.10.2 release packages for openSUSE 12.2 and 12.3. []({{ site.url }}/images/2013/04/757111961.png) Despite being a minor release, more than 100 bugs were fixed, in particular there were many KDEPIM fixes touching both the low level stack and KMail/KAddressbook/Kontact.

A lot has been happening on the KDE side of openSUSE… this post summarizes what’s been going on so far. Live media for Plasma 5 One of the most-often requested ways to test Plasma 5, given it can’t be coinstalled with the 4.x Workspace, is the availability of live images to test either in VM or bare metal without touching existing systems. Given that other distributions started doing so since a while, naturally openSUSE couldn’t stay still.

KDE released the second beta of the KDE Platform, Workspaces and Applications 4.11, and after the necessary time for the OBS to build packages from the released tarballs, packages are available for openSUSE 12.3 and openSUSE Factory. Like the previous beta, they are available through the KDE:Distro:Factory repository. 4.11.x is is targeted for inclusion in the upcoming openSUSE 13.1. So far 4.11 has been pretty stable for me, but you should never forget these packages are for testing and bug reporting purposes: don’t use them on production systems.

Since KDE has released the first beta of Platform, Workspaces, and Applications 4.11, there will be some changes in the packages offered in the openSUSE repositories. In short: KDE:Distro:Factory will now start tracking 4.11 betas and RCs: packages are being worked on. Use this version to test packages and to report bugs upstream. KDE:Release:410 has been decoupled from KDE:Distro:Factory. If you were using 4.10 packages from KDF, you’re highly encouraged to move to this repository.

Requests to unlock KWallet automatically on login (assuming the wallet password and user password are the same), like gnome-keyring can do, have been going on for years: in fact, bug reports requesting this feature are quite old. Recently, thanks to the efforts of Alex Fiestas, a PAM module, which interfaces KWallet to the system authentication methods, has been developed. In parallel, the necessary glue code has been also added to the various parts of the KDE workspace so that it could make use of it.

Finally I can lift the curtain of silence and tell the reason why I’ve been very busy before Christmas: it all lies in the publication of a paper, “Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments”, which is finally out on this week’s issue of PLoS ONE. It’s different from [the previous paper I mentioned]({{ site.url }}/2008/01/phd) (which was not my first publication, either), for two main reasons:

The title says it all. After all these years, I was finally able to get my Ph.D. in Molecular Medicine this morning, with my thesis “Identification of disregulated metabolic pathways by transcriptomic analysis in renal carcinoma samples” (yes, that’s a long title). The defense was a success and I admit I was surprised when the commitee actually expressed a significant interest in my work. In any case, I’m happy that it’s over, as the past period has been rather hectic.

My supervisor has given me an OK for my thesis (save for a couple of cosmetic changes), therefore now I have just to wait for the verdict of the Ph.D. council then fill in some paperwork: the next step is the defense, sometime in January. After that I’ll probably put my thesis online and post a few articles on the concept of group testing for microarray data.

Yesterday I’ve been in Camogli and Portofino, two small towns in the eastern part of Liguria. The weather was nice and warm, and I took the opportunity of taking a few photos: [singlepic id=328 w=320 h=240 float=] [singlepic id=331 w=320 h=240 float=] Those are samples, the rest are available [in the gallery.]({{ site.url }}/nggallery/page-494/album-1/gallery-9)

(Note: this post also appears in Planet KDE and Planet openSUSE because I thought this might be interesting to others) As I mentioned in some other posts, I have a small “server” which I use as a NAS to provide archiving for photos and other files of interest. As it runs in a remarkably small (and quiet) enclosure, I’ve managed to put it in an incospicuous part of the room it is in.

This was inspired by this forum thread on the Piwigo forums. Set up rewrite rules in nginx where “piwigo” is the path the gallery lies in: location @rewrite { rewrite ^/piwigo/picture((/|$).*)$ /piwigo/picture.php$1 last; rewrite ^/piwigo/index((/|$).*)$ /piwigo/index.php$1 last; # The following is needed for batch operations which use i.php rewrite ^/piwigo/i((/|$).*)$ /piwigo/i.php$1 last; } location /piwigo { index index.php; try_files $uri $uri/ @rewrite; } location ~ ^(?

Among the different widgets I use on my desktop, there is a small one which tells me my current public IP address. The reason I’m having it is due to the fact that my own ISP uses a NAT for almost all its customers (don’t ask - long story) and so I need to keep tabs on my current IP, because it may have been blacklisted, and so on. Up to now I was using this plasmoid written in Python, but the code had several issues and used its own way of getting the public IP.

As others, bigger members in the KDE community say, “nobody will do it for you, and therefore they will”. The patch from the title comes from such a story. Let’s give some background first: I’m really a heavy activity user, especially when working. My home PC has about five activities, my work one 3, and I managed to compartimentalize the various “topics” that each activity does pretty well. After an update a couple of weeks ago from the latest code from KDE git, I started noticing weird behavior.

Recently in the Plasma mailing list, KDE developers have discussed a new screen-locking implementation that could be added to the upcoming 4.8 release of the KDE Workspaces. The first reason to do so was to solve some security constraints of the existing implementation. As an added bonus, screen locking should be also more aestetically pleasing. There is however a trade-off: such implementation would mean that screensavers that rely on X (also called X screensavers) would not be compatible.

While browsing around kde-look.org, I’ve stumbled upon a nice little Plasma scripted widget, and I’m publishing this to have it get more exposure. A good part of the KDE community knows at least little about Nepomuk, and its ability to attach semantic tags to your files - basically words that describe the file, be it an image, a text document, or anything you’d like. For example, you could tag all the photos from your vacation with the name of the place you’ve been.

A few may know that I more or less maintain the Plasma FAQ page on KDE’s UserBase. Given the rapid advance of Plasma between KDE versions, each time a new version is out a new FAQ needs to be made, as the content rapidly becomes obsolete. For 4.3, unfortunately, I’m not sure I’ll be able to put a new version up in time for the 4.3 release. The reason is mostly practical: it takes a bit of work to collect and add information, and currently my free time is limited due to a rather heavy workload and some other commitments.

I just finished writing a new Python tutorial on KDE’s Techbase. This one deals with writing DataEngines in Python (a complement to Simon Edwards’s own Using DataEngines). Let me know what you think. As it’s a wiki, comments and suggestions are welcome.

As Simon Edwards already noted, thanks to me and him (mostly him, I have to say) starting to work on Plasma tutorials at the same time, now KDE’s Techbase has a nice set of Python Plasma tutorials. They cover creation of applets and connection to DataEngines (see the Plasma page on Techbase for more information). I plan on starting a tutorial on writing Plasma DataEngines on Thursday, if time permits.

It turned out I forgot to add the last screencast produced by the students of Kourse 2, so I’ll fix my mistake right now. Here’s Panel settings, by Kourse student TeaAge: [blip.tv ?posts_id=1653914&dest=-1]

Students from Kourse 2 fengshaun and Primoz have prepared two nice screencasts, dealing with the Zooming User Interface (ZUI) and desktop settings respectively. Without further ado, here they are: Zooming User Interface by fengshaun [blip.tv ?posts_id=1648944&dest=-1] Desktop settings by Primoz [blip.tv ?posts_id=1646835&dest=-1] As usual, both Free and non-Free versions are available. The students are also at work on subtitled versions, without the Notes plasmoid. I’ll be sure to post them once they’re done.

As some people already know,I’m mentoring a group of students on KDE Forum to create Plasma screencasts (from the upcoming KDE 4.2 version). After several adjustments back and forth, the first one (made by kourse student Primoz), showing off the various desktop settings, is complete. This version uses the Notes plasmoid to keep track of annotation, but we’re also evaluating subtitle-based versions. In the mean time, enjoy! (and spread the word).

Today I was adjusting a bit the layouts of the Activities (as defined in Plasma) to better suit my workflows. To do so I was using the brand new Activity Bar which is present in KDE 4.2. It’s very neat, but takes up space on the desktop, and while it’s not a big deal on my main PC (1280x1024 resolution), it is an issue on my recently-resuscitated EeePC (1024x600). It was then that it occured to me that such applets are, in Plasma-speak, PopupApplets, which means they adjust their behavior depending if they are in a panel or “free”.

Today I’m in a posting spree…This clip shows how to resize and move Plasma panels around. [youtube]http://www.youtube.com/watch?v=Rmpv-S5JJI4[/youtube]

Following up on my previous post, here is another screencast showing off how to create a sidebar panel and add a few plasmoids to it. As usual, the version on Youtube has annotations. [youtube]http://www.youtube.com/watch?v=WPeFSDdt2PY[/youtube]

I’ve put together a small video that shows what you can do with zooming in and out with Plasma’s Zooming User Interface (ZUI). Enjoy. (note: the version on Youtube has also annotations that explain better what is going on) [youtube]http://www.youtube.com/watch?v=EhODrJkoidA[/youtube] If you can, please spread the link to the video. We need more correct information out there.

Those of you that follow my Linux-related posts know that I work (along with others) on a FAQ trying to explain some magic behind KDE 4.x’s Plasma. Now, especially since on the Internet, there is the need to spread correct information (most of the naysayers are not quite informed). So, if you want to help KDE, please spread the word on the Plasma FAQ! If people have questions on Plasma, just direct them to

Since a couple of weeks the packages offered by openSUSE in the KDE:Unstable:Frameworks repository have undergone a series of changes. In particular, the packages now install to /usr. For the libraries (KDE Frameworks 5) this will mean a transparent change for the userbase as they are expected to be co-installable, but the workspace components (Plasma 5) will confict with the existing Plasma 4.11.x installation. What does this mean in practice? If you want to use Plasma 5 you will not be able to use a 4.

Congratulations to KDE (of which I’m proud of being a part of) for the newest release of the Plasma workspace! At the same time, the 4.x series has seen a new beta release, and the stable branch got updated, too. I’m betting a few people will ask “Are these available for openSUSE?” and of course the answer is yes, thanks to the efforts of the openSUSE community KDE team and the Open Build Service.

While browsing around kde-look.org, I’ve stumbled upon a nice little Plasma scripted widget, and I’m publishing this to have it get more exposure. A good part of the KDE community knows at least little about Nepomuk, and its ability to attach semantic tags to your files - basically words that describe the file, be it an image, a text document, or anything you’d like. For example, you could tag all the photos from your vacation with the name of the place you’ve been.

One thing I always wanted to do when going on holiday is to track where I go, the places I’ve been, and see how much I’ve travelled around. This is true in particular when going to places where I walk around a lot (Japan stays at the top of the list, also for other reasons that are not related to this post). Something like viewing a map showing where you were, and where did you go, with optional export to KML or GPX to import into other programs like Marble.

From the already large backlog of new series, I recently watched the first episode of Prism Ark, an anime adaptation of the H-Game _PRISM ARK ~ PRISM HEART II ~ _by Pajamas Soft (I wonder how some Japanese companies get to choose their names…). It is being directed by Masami Obari, who did Dancougar Nova the last season.

Those who use PyQt and PyKDE4 are certainly familiar with the syntax used to connect signals and slots: [python] from PyQt4 import QtCore from PyQt4 import QtGui from PyKDE4 import kdeui class MyGUI(QtGui.QWidget): def __init__(self, parent=None): super(MyGUI, self).__init__(parent) self.pushbutton = kdeui.KPushButton() self.pushbutton.setText("Push me!") QObject.connect(self.pushbutton, QtCore.SIGNAL("clicked()"), self.button_pushed) def button_pushed(self): print "Button clicked" [/python] The main advantage of this syntax is that it’s very close to the C++ equivalent, and so you can translate easily from C++ to Python.

Ok, ok… my definition of “tomorrow” is not like what most people use, apparently. Although I took quite a while, now [there is a static page on DataMatrix]({{ site.url }}/projects-2/datamatrix). There you will find a summary of wht I wrote in my other blog posts regarding this module. Of course, it will be kept up-to-date should I release a new version. Aside that, I put a contact form on this blog.

At last, since it’s been like ages, I decided to put out a new version of DataMatrix. For those who haven’t seen my previous post, DataMatrix is a Pythonic implementation of R’s data.frame. It enables you to manipulate a text file by columns or rows, to your liking, using a dictionary-like syntax. In this new version there have been a few improvements and correction to a couple bugs (for example saveMatrix did not really save) and the start (only a stub at the moment) of an append function to add more columns (I’ll also think about a function to add rows).

For a long time I have tried to handle text files in Python in the same way that R’s data.frame does - that is, direct access to columns and rows of a loaded text file. As I don’t like R at all, I struggled to find a Pythonic equivalent, and since I found none, I decided to eat my own food and write an implementation, which is what you’ll find below.

I’ve recently begun trying to create GUIs for my Python applications with PyQt, and I can say I’m absolutely loving the toolkit, relatively easy to use and featureful. As I’m trying to create a GUI for some module I wrote that deals with databases (using MySQLdb), I also learnt that Qt has a series of classes for dealing with databases, mainly QSql. My question, directed to whoever has experience with QSql and the Python DB-API, is: what are the advantages of one approach to the other?

If you look through this blog’s archives, you may notice that although Free and Open Source Software is what I write most about, it is not the exclusive topic. I’ve written on science (my day job) as well as other interests. And today I’d like to lift the wraps on another project which I take part on, unrelated to the above. Notice for those who read my blog coming from FOSS aggregators like Planet KDE: this is fairly different than most recent topics from me, so be warned before you continue reading.

Sometimes Christmas presents are really unexpected, and today I found out I was given one such gift: the limited edition of _THE IDOLM@STER 2, _PS3 version. It was quite a bulky box, showing all the main characters from the game (and from the recently-ended anime) (click to enlarge):  Of course, having such a box means that there’s a lot of stuff inside. In fact, once opened, there are two game BDs (one being the actual game, the second being the first volume of Gravure for you!

The title says it all. After all these years, I was finally able to get my Ph.D. in Molecular Medicine this morning, with my thesis “Identification of disregulated metabolic pathways by transcriptomic analysis in renal carcinoma samples” (yes, that’s a long title). The defense was a success and I admit I was surprised when the commitee actually expressed a significant interest in my work. In any case, I’m happy that it’s over, as the past period has been rather hectic.

I’ve been wondering about why FOSS is often compared to the academic world, but at least in my limited experience, I see little people that grasp its concept in the world of research. On a quick look, developing FOSS in a research environment would be very good: not only you’d get publicly available results when you publish, but at the same time you can make sure that in an extreme case your application will be carried on by someone else should you not be able to continue development.

There is always a lot of talk about “brain drain” (fuga di cervelli in Italian) from my country. I keep on reading disgruntled comments of low pays and poor research, and that going abroad is the only solution for an Italian scientist to be successful.

While I believe that research done outside of my country can be handled better (but it’s impossible to know for sure: never tar everyone with the same brush), I think that, also thanks to the way the media and the scientists themselves handle it, in everyone’s view it has almost become like the El Dorado. And that, in my opinion, is incorrect.

As people who read my science-related posts know already, I’m not a big fan of {{post id=“software-and-biological-research” text=“software made just to support a publication”}}. Recently I’ve stumbled again into similar software. Namely, I’m talking about the TIGR Multiexperiment Viewer (TMeV), a Java-based program which is often used for microarray analysis. It’s not exactly “fit for publication”, because it has reached version 4 last year, but shows some of the problems ({{post id=“genbugg” text=“mentioned already”}}) with releasing bioinformatics software.

I use TMeV mostly because I didn’t find any other implementation of the hierarchical clustering algorithm with support trees. However, I’ve stumbled upon a very annoying bug in the most recent version. Normally I use average linkage clustering and as the distance metric I employ the Pearson’s correlation, and with gene and sample bootstrapping: with certain files this makes TMeV report errors at random during the iterations.

When I’m not on forum duty or handling openSUSE-related contributions, I try to improve my code contributions to KDE, even though I’m by no means an experienced programmer (I program all day long in Python, but I’m still a biologist after all). For the upcoming 4.10 release I’ve been polishing up Python 3 support. As you may know, Python 3 isn’t the standard in many distributions (Arch Linux excluded), but despite the slow start, it is slowly gaining steam.

In one of my previous blog posts I dealt with [tagging files and resources with Nepomuk]({{ site.url }}/2010/10/pykde4-tag-and-annotate-files-using-nepomuk). But Nepomuk is not only about storing metadata, it is also about retrieving and _interrogating _data. Normally, this would mean querying the metadata database directly, using queries written in SPARQL. But this is not intuitive, can be inefficient (if you do things the wrong way) and error prone (oops, I messed up a parameter!

One of the greatest strengths of KDE is undoubtedly the asynchronous and network-transparent I/O access, employed by the so-called “I/O” slaves, part of the KIO class. If you are developing an application that requires file or network access, those classes make things incredibly simple to do, and they don’t freeze your GUI when you are in the middle of a process. In this post I’ll show how to use KIO to retrieve files from network resources using PyKDE4.

With my brand-new SVN account, I just committed some code to kdeexamples, KDE’s example code module. In particular, I committed a simple example which shows how to use KConfigXT via PyKDE4, a simplified version of [what I wrote about here]({{ site.url }}/2009/10/howto-kconfigxt-with-pykde4). As most of KDE is C++, and the Python API docs are translated directly from the C++ API docs, it is essential to have good examples to help newcomers learn faster.

A while ago I presented [“danbooru2nepomuk”]({{ site.url }}/2009/10/danbooru2nepomuk-a-nepomuk-tagger-for-danbooru-images), a small program to tag images coming from Danbooru-based image boards. Today I want to present the evolution of that program, that is a PyKDE4 client for those boards.

If you read around the KDE Techbase, or if you develop KDE applications, you may have heard about KDE’s KConfigXT. This is an extension of KDE’s KConfig, and can be used to generate nice configure dialogs with multiple pages with minimal effort, also taking care of saving and applying settings. In short, something really neat! But there are problems when using it with interpreted language bindings (such as PyKDE, which is the one I use):

• KConfigXT requires an XML file and an INI-like file to be compiled by kconfig_compiler in order to produce C++ files
• There is no such a tool (at least to my knowledge) that does the same job for bindings

So what to do? Either give up on the niceness of KConfigXT, or work around the issue. I chose the latter.

When I’m not on forum duty or handling openSUSE-related contributions, I try to improve my code contributions to KDE, even though I’m by no means an experienced programmer (I program all day long in Python, but I’m still a biologist after all). For the upcoming 4.10 release I’ve been polishing up Python 3 support. As you may know, Python 3 isn’t the standard in many distributions (Arch Linux excluded), but despite the slow start, it is slowly gaining steam.

Recently we’ve seen several blog posts on Planet KDE related to Nepomuk. Reading those I thought that I could add some (little) semantic features to [Danbooru Client]({{ site.url }}/projects/danbooru-client). Danbooru Client already makes use of Nepomuk: if enabled, tags extracted from Danbooru items are added as Nepomuk tags. But since at least some Danbooru boards are specialized in certain types of images (e.g., wallpapers only, for examples) I found it would be nice to have Nepomuk show me only the images that come from a specific Danbooru board.

In one of my previous blog posts I dealt with [tagging files and resources with Nepomuk]({{ site.url }}/2010/10/pykde4-tag-and-annotate-files-using-nepomuk). But Nepomuk is not only about storing metadata, it is also about retrieving and _interrogating _data. Normally, this would mean querying the metadata database directly, using queries written in SPARQL. But this is not intuitive, can be inefficient (if you do things the wrong way) and error prone (oops, I messed up a parameter!

While reading the statistics for my blog, I noticed that a number of searches looked for hierarchical clustering with Python, which [I covered quite a while ago]({{ site.url }}/2007/11/data-clustering-with-python). Today I’d like to present an updated version which uses more robust techniques.

Some of the oldest readers of this blog are well aware of [a certain hobby of mine]({{ site.url }}/category/anime). Over the years I’ve always wanted to write more about that, including the stuff I’m viewing nowadays, but I found a hassle to collect snapshots from videos / DVDs, selecting them, and so on. Recently I learnt that VLC has some rather complete Python bindings, and I thought, why not make the process automated?

One of the greatest strengths of KDE is undoubtedly the asynchronous and network-transparent I/O access, employed by the so-called “I/O” slaves, part of the KIO class. If you are developing an application that requires file or network access, those classes make things incredibly simple to do, and they don’t freeze your GUI when you are in the middle of a process. In this post I’ll show how to use KIO to retrieve files from network resources using PyKDE4.

Some time has passed since I last blogged… this was not only due to lack of time but also due to motivation (writing long texts can be discouraging at times). In any case, I’d like to rectify for that. In this post, I’ll talk about Nepomuk, and in particular how to use it to tag and annotate arbitrary files using its API in PyKDE4. Before starting, let me say that creating this tutorial was only possible thanks to the help of Sebastian Trueg, who helped me by pointing out some mistakes I was doing.

The rest is up to you to figure out.

With my last entry, I announced the start of the work for an OCS library for the KDE Community Forums. Today I’d like to blog again about the recent developments. First of all, now there isn’t one, but two Python modules: _ocslib, _ a pure Python module that can be used to interface with OCS-based forum systems; ocslibkde, a PyKDE4 based module that can be used to interface with OCS-based forum system in KDE applications.

For KDE developers, web-based forums are often uncommon workflows. Indeed, for communication among developers mailing lists are much better tools, especially since you can handle everything inside a client (most of the time), compared to forums where you have to use a web browser. The ways of reading, replying and interacting with posters are dramatically different. And that is why some developers find themselves uncomfortable with the KDE Community Forums.

Recently, I investigated how to perform some checks on web addresses using KIO for Danbooru Client. My old code was synchronous, so it blocked the application while checking, thus causing all sort of troubles (UI freezing, etc.). Therefore, making the switch to KIO was the best solution. However, I had one problem: how could I check the HTTP response? I knew already that the various ioslaves can store metadata, consisting of key-value pairs which are specific on the slave used.

With my brand-new SVN account, I just committed some code to kdeexamples, KDE’s example code module. In particular, I committed a simple example which shows how to use KConfigXT via PyKDE4, a simplified version of [what I wrote about here]({{ site.url }}/2009/10/howto-kconfigxt-with-pykde4). As most of KDE is C++, and the Python API docs are translated directly from the C++ API docs, it is essential to have good examples to help newcomers learn faster.

Sometimes answering apparently harmless questions on instant messaging can have unexpected results. In particular, I was telling about Danbooru Client to someone and a question popped up “Why don’t you support pages?”. It seemed a nice idea, so I branched off the code (yay for git!) and started working on it. Well, it took me more than a month to get this thing done… I didn’t spend every day coding, but it was a challenge.

A while ago I presented [“danbooru2nepomuk”]({{ site.url }}/2009/10/danbooru2nepomuk-a-nepomuk-tagger-for-danbooru-images), a small program to tag images coming from Danbooru-based image boards. Today I want to present the evolution of that program, that is a PyKDE4 client for those boards.

If you read around the KDE Techbase, or if you develop KDE applications, you may have heard about KDE’s KConfigXT. This is an extension of KDE’s KConfig, and can be used to generate nice configure dialogs with multiple pages with minimal effort, also taking care of saving and applying settings. In short, something really neat! But there are problems when using it with interpreted language bindings (such as PyKDE, which is the one I use):

• KConfigXT requires an XML file and an INI-like file to be compiled by kconfig_compiler in order to produce C++ files
• There is no such a tool (at least to my knowledge) that does the same job for bindings

So what to do? Either give up on the niceness of KConfigXT, or work around the issue. I chose the latter.

At last, after months of inactivity, I pushed out a new release of [DataMatrix]({{ site.url }}/projects/datamatrix). Although the version bump is small (0.8) there are a lot of changes since last releases. The most notable include: Ability to apply functions to elements of the matrix Ability to filter rows by column contents Ability to transpose rows with columns An option to load text files produced by R (which are, by design, broken) Removed the getter for columns, using dictionary-like syntax directly A lot of bug fixes The download links on [the project page]({{ site.

Finally a new entry! I’ve been extremely busy with other things, that is why I did not have time to write more. One of the main reason is related to an important landmark in my professional career, but I’ll write more about it after January 1st (hint: those who follow my Twitter updates may have already understood). As a nice way to break the hiatus, I’m releasing a new version of DataMatrix, my implementation of R’s data.

Ok, ok… my definition of “tomorrow” is not like what most people use, apparently. Although I took quite a while, now [there is a static page on DataMatrix]({{ site.url }}/projects-2/datamatrix). There you will find a summary of wht I wrote in my other blog posts regarding this module. Of course, it will be kept up-to-date should I release a new version. Aside that, I put a contact form on this blog.

At last, since it’s been like ages, I decided to put out a new version of DataMatrix. For those who haven’t seen my previous post, DataMatrix is a Pythonic implementation of R’s data.frame. It enables you to manipulate a text file by columns or rows, to your liking, using a dictionary-like syntax. In this new version there have been a few improvements and correction to a couple bugs (for example saveMatrix did not really save) and the start (only a stub at the moment) of an append function to add more columns (I’ll also think about a function to add rows).

For a long time I have tried to handle text files in Python in the same way that R’s data.frame does - that is, direct access to columns and rows of a loaded text file. As I don’t like R at all, I struggled to find a Pythonic equivalent, and since I found none, I decided to eat my own food and write an implementation, which is what you’ll find below.

I’ve recently begun trying to create GUIs for my Python applications with PyQt, and I can say I’m absolutely loving the toolkit, relatively easy to use and featureful. As I’m trying to create a GUI for some module I wrote that deals with databases (using MySQLdb), I also learnt that Qt has a series of classes for dealing with databases, mainly QSql. My question, directed to whoever has experience with QSql and the Python DB-API, is: what are the advantages of one approach to the other?

While working today on an annotation class in Python I stumbled on a problem. Normally I work with lists of genes that are consistent, i.e. all Entrez Gene IDs (or RefSeq IDs, or Genome Browser IDs…), but today I had a list of mixed identifiers. The subsequent idea was “let’s implement auto-detection of common identifiers in the class”. The problem is… is there any actual documentation on how identifiers are made?

**Notice:**Just now I realized this has been linked to to a Stack Overflow question. I recently wrote a new post that uses a different technique and a combination of R and Python. [Check it out!]({{ site.url }}/2011/05/multiscale-bootstrap-clustering-with-python-and-r)

Following up my recent post, I’ve been looking for alternatives to TMeV. So far I’ve found the R package pvclust and the Pycluster library, part of BioPython. The first one also performs bootstrapping (I’m not sure if it’s similar to what support trees do, but it’s still better than no resampling at all). I’ve found another Python project but it is still too basic to perform what I need.

The other day I was thinking about how to make screencaps for the anime I watch. Windows users often use Media Player Classic, which can create a video contact sheet (i.e., a series of captures) out of a movie file. I had two problems with this: The biggest is that it runs on Windows, and I don’t use Windows; The frames needed to be manually cropped every time, which was slow.

Today I started working on a data set published on GEO. As the sample data were somehow inconsistent (they mentioned 23 controls when I found 28), I decided to parse the SOFT file from GEO in order to get the exact sample information. I did a grave mistake. First of all, Biopython’s SOFT parser is horribly broken (doesn’t work at all) and quite undocumented: I could work around the lack of documentation (API docs) but not with the fact that it wouldn’t work.

Among the different widgets I use on my desktop, there is a small one which tells me my current public IP address. The reason I’m having it is due to the fact that my own ISP uses a NAT for almost all its customers (don’t ask - long story) and so I need to keep tabs on my current IP, because it may have been blacklisted, and so on. Up to now I was using this plasmoid written in Python, but the code had several issues and used its own way of getting the public IP.

I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.

I’m often wondering why people only resort to R when working with microarrays. I can understand that Bioconductor offers a plethora of different packages and that R’s statistical functions come in handy for many applications, but still, I think people underestimate the impact of performance. R is not a performing language at all, it doesn’t parallelize well when using HPC (at least from the talks I’ve had with people studying the matter), and in general is a memory and resource hog.

**Notice:**Just now I realized this has been linked to to a Stack Overflow question. I recently wrote a new post that uses a different technique and a combination of R and Python. [Check it out!]({{ site.url }}/2011/05/multiscale-bootstrap-clustering-with-python-and-r)

Following up my recent post, I’ve been looking for alternatives to TMeV. So far I’ve found the R package pvclust and the Pycluster library, part of BioPython. The first one also performs bootstrapping (I’m not sure if it’s similar to what support trees do, but it’s still better than no resampling at all). I’ve found another Python project but it is still too basic to perform what I need.

Today I started working on a data set published on GEO. As the sample data were somehow inconsistent (they mentioned 23 controls when I found 28), I decided to parse the SOFT file from GEO in order to get the exact sample information. I did a grave mistake. First of all, Biopython’s SOFT parser is horribly broken (doesn’t work at all) and quite undocumented: I could work around the lack of documentation (API docs) but not with the fact that it wouldn’t work.

The latest release of the KDE Platform, Workspaces, and Applications (4.11) is around the corner: in fact, the last RC was recently made available. We’re almost there, but it doesn’t mean that testing and reporting should stop: on the contrary, it is needed even more to ensure that no bad bugs crawl up in the final release. As part of this effort, openSUSE packages for RC2 have been released through the OBS, and are available in the KDE:Distro:Factory repository.

As a consequence of [the recent changes in the repositories]({{ site.url }}/2013/06/upcoming-changes-to-opensuse-kde-repositories), the openSUSE KDE team is happy to announce the availability of packages containing the first beta of the KDE Platform, Workspaces and Applications 4.11. Packages are available in the KDE:Distro:Factory repository. As it is beta software, it may have not-yet-discovered bugs, and its use is recommended only if you are willing to test packaging (reporting bugs to Novell’s bugzilla) or the software (reporting bugs directly to KDE).

These posts kind of sound like a broken record, right? ;) Anyway, since KDE has released new versions of Platform, Workspaces and Applications as part of the stable release cycle, thanks to the OBS we have packages available for openSUSE 12.2 and 12.3. The 4.10.4 update will also be released as an official update for 12.3 in due time. Where you can get the packages? Two places, as usual: KDE:Distro:Factory in case you are interested in contributing to packaging for the next openSUSE release; KDE:Release:410 (openSUSE 12.

KDE released 4.10.3 versions of the Platform, Workspaces and Applications yesterday, with more than 70 bugs being fixed. Notably: Several fixes in handling encrypted mails in KMail Fixes for KDEPIM syncing and ownCloud A number of improvements in Dolphin, including crash fixes Optimizations in the Plasma Workspaces [The full list](https://bugs.kde.org/buglist.cgi?query_format=advanced&bug_status=RESOLVED&bug_status=VERIFIED&bug_status=CLOSED&bugidtype=include&chfieldfrom=2013-01-01&chfieldto=Now&chfield=cf_versionfixedin&chfieldvalue=4.10.3&order=Bug Number&list_id=638034) has other important changes. As usual, there are two different repositories from which you can get them:

KDE has released its monthly update for the 4.10 release, and after a brief wait while the Open Build Service worked over the released tarballs, the openSUSE KDE team is pleased to announce the availability of the 4.10.2 release packages for openSUSE 12.2 and 12.3. []({{ site.url }}/images/2013/04/757111961.png) Despite being a minor release, more than 100 bugs were fixed, in particular there were many KDEPIM fixes touching both the low level stack and KMail/KAddressbook/Kontact.

Hot on the heels of the announcement from KDE, the openSUSE KDE team is happy to announce the availability of packages for the latest stable release of the KDE Platform, Workspaces, and Applications. Packages are available in the KDE:Distro:Factory repository (which is where the packages to land in 12.3 are tested) for openSUSE Factory (soon to be 12.3) and openSUSE 12.2 and soon (when the Open Build Systen finishes rebuilding a number of packages) in the KDE:Release:410  repository for openSUSE 12.

As you all know, KDE 4.3.0 has been releeased today! Now it’s the time to tell the developers “thanks” for their hard work. Join us in the KDE Community Forums and spread the word!

Following up on the announcement from KDE, the openSUSE KDE team is happy to announce the availability of 4.10 RC3 packages. Remember that they are packages meant for testing and reporting bugs, so that the next release will be as polished as possible. You will find the packages in the KDE:Distro:Factory repository. An updated live media based on the upcoming openSUSE 12.3 ([see previous post]({{ site.url }}/2013/01/test-the-upcoming-opensuse-12-3-and-kde-workspace-applications-and-platform-4-10-rc2)) is also available (files named KDE4-4.

It is not news that openSUSE, through to the effort of the openSUSE community KDE team, offers several third-party repositories for those who want the latest software from KDE. Since a while, stable releases were offered in the KDE:Release:4x repositories, created with every major release of KDE software. These were meant to offer the latest and greatest to the users without having them to track KDE:Distro:Factory, which is instead used to track packaging for the next openSUSE release and is more in a state of flux.

Summer is ending soon (at least for those living in the northern hemisphere) and while usually cleaning is done during spring, the KDE team decided to do what I’d call… autumn cleaning of repositories. You may know that the KDE presence in openSUSE, aside being the default desktop, is quite a long one. In the past years different repositories were created by the members of the openSUSE KDE team (at the time mostly made up by KDE people hired by Novell) in order to review and test packages, like newer Qt versions, KDE software, and so on.

As you may know, there is an ongoing effort to rearrange and adjust the openSUSE KDE repositories. In line with the previously announced deletions, and more recent adjustments, a number of changes went into the organization and layout of the KDE repositories: KDE:Distro:Factory and KDE:Release:4xy will now hold the “core” KDE packages: this means the base Development Platform, Workspaces and Applications, and additional applications for a basic desktop experience.

As you may already know, recently the KDE sysadmins completely overhauled the commit hooks used with the Git infrastructure. Written in Python, they have already brought significant improvements to the current workflows. These hooks include keywords that when specified trigger particular actions: the most used are to CC specific email addresses (CCMAIL), to CC bug reports (CCBUG) or to close bug reports (BUG). With the adoption of Review Board to facilitate code reviews, there were also requests for a REVIEW keyword that could close the review requests without asking the submitters to do so manually (which is slow and not always effective).

This was inspired by this forum thread on the Piwigo forums. Set up rewrite rules in nginx where “piwigo” is the path the gallery lies in: location @rewrite { rewrite ^/piwigo/picture((/|$).*)$ /piwigo/picture.php$1 last; rewrite ^/piwigo/index((/|$).*)$ /piwigo/index.php$1 last; # The following is needed for batch operations which use i.php rewrite ^/piwigo/i((/|$).*)$ /piwigo/i.php$1 last; } location /piwigo { index index.php; try_files $uri $uri/ @rewrite; } location ~ ^(?

I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.

I’ve found myself in a situation where my ISP, notorious for having problems with certain online services (not to mention putting everyone under a permanent NAT) started misbehaving with Sony’s Playstation Network: I was getting timeouts of all sorts with no reason (and reading online you see all sorts of attempts from people to work around the issue). When using my phone as hotspot, everything worked, as I went through my mobile operator’s network.

I’m back from holidays, and when I got back I found the Saber Revoltech figure I had preordered in May (!) in the mail. This is the package when I pulled it out from the box it came in (apologies for the image quality, I only had my mobile phone to take it):

Because changes occur when one least expects them. This post is about one such change.

While reading the statistics for my blog, I noticed that a number of searches looked for hierarchical clustering with Python, which [I covered quite a while ago]({{ site.url }}/2007/11/data-clustering-with-python). Today I’d like to present an updated version which uses more robust techniques.

 My Akademy talk proposal was not accepted, but the organizers were kind enough to offer me the chance to hold a BoF on the same subject. Now I bet you wonder on what I’m going to discuss, and I think the title already gives you an idea: KDE and bioinformatics: the missing link Although in the KDE community we have our fair share of scientists (hey there, Stuart!

In the past months I’ve always wanted to write a small Plasma applet to aid me in some boring tasks as a bioinformatician. One example (for the non-scientific crowd out there) is when I find a specific gene out of my analysis work which I want to take a look at. I am often lazy, so instead of firing up the browser to look at the online resources, I wanted to write something which could access said resources programmatically.

Some say that all good things must come to an end. I’m not entirely sure that this is a universal truth, but I can say that at some point in life there are decisions that need to be taken. In this case I made my own: today was the last day inDr.Cristina Battaglia’s laboratory, a place where I spent my three-year Ph.D. course and one year as a post-doc research fellow.

During the course of my research work, I may obtain results that are worthy of publication in scientific journals. Since my master’s thesis I’ve been using LaTeX as my writing platform, mainly because I can concentrate on content rather than presentation (I find it useful also for writing non-scientific stuff as well). Also, I can handle bibliography (essential for a scientific publication) very well without using expensive proprietary applications (such as Endnote).

In my early days I used kLyX first, then LyX, but I found the platform to be too limited for my tastes, and also LaTeX errors were difficult to diagnose. I needed a proper editor, and that’s when I heard of kile, a KDE front-end for LaTeX. Kile is currently at version 2.0.2 and is a KDE 3 application. However, in KDE SVN work is ongoing to produce a KDE4 version (2.1) and that’s what I’ll look at in this entry.

I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.

Finally I can lift the curtain of silence and tell the reason why I’ve been very busy before Christmas: it all lies in the publication of a paper, “Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments”, which is finally out on this week’s issue of PLoS ONE. It’s different from [the previous paper I mentioned]({{ site.url }}/2008/01/phd) (which was not my first publication, either), for two main reasons:

I wanted to write this earier, but I couldn’t: I’m now in a hotel in Maastricht, Netherlands, and waiting to get back tomorrow. I’ve been attending the 4th NuGO hands-on advanced microarray data analysis course and I even wanted to blog about it… but the hotel’s connection did not resolve any non-European web page until late today.

I’ve been wondering about why FOSS is often compared to the academic world, but at least in my limited experience, I see little people that grasp its concept in the world of research. On a quick look, developing FOSS in a research environment would be very good: not only you’d get publicly available results when you publish, but at the same time you can make sure that in an extreme case your application will be carried on by someone else should you not be able to continue development.

I’m often wondering why people only resort to R when working with microarrays. I can understand that Bioconductor offers a plethora of different packages and that R’s statistical functions come in handy for many applications, but still, I think people underestimate the impact of performance. R is not a performing language at all, it doesn’t parallelize well when using HPC (at least from the talks I’ve had with people studying the matter), and in general is a memory and resource hog.

Fourteen days since my last post. Quite a while, indeed. Mostly I’ve been stumbled with work and some health related issues. Anyway, I thought I’d follow up on the meta analysis matter I discussed in my last post. It turns out that it’s a fault of both limma and the data sets, because apparently the raw data found in the Stanford Microarray Database have different length, gene-wise (a result of not all spots on the array being good?

Again in the past days I’ve been banging my head thanks to the fact that doing meta-analysis with microarray data is more difficult than what it seems. The problem sometimes lies in the data, sometimes lies in the analysis software and sometimes in a combination of factors. When doing work on a public data set (Zhao et al., 2005), I had to start analysis from raw data. Now, I tried using both the limma and marray Bioconductor packages, but both of them bail out with cryptic error messages.

The title says it all. After all these years, I was finally able to get my Ph.D. in Molecular Medicine this morning, with my thesis “Identification of disregulated metabolic pathways by transcriptomic analysis in renal carcinoma samples” (yes, that’s a long title). The defense was a success and I admit I was surprised when the commitee actually expressed a significant interest in my work. In any case, I’m happy that it’s over, as the past period has been rather hectic.

There is always a lot of talk about “brain drain” (fuga di cervelli in Italian) from my country. I keep on reading disgruntled comments of low pays and poor research, and that going abroad is the only solution for an Italian scientist to be successful.

While I believe that research done outside of my country can be handled better (but it’s impossible to know for sure: never tar everyone with the same brush), I think that, also thanks to the way the media and the scientists themselves handle it, in everyone’s view it has almost become like the El Dorado. And that, in my opinion, is incorrect.

My supervisor has given me an OK for my thesis (save for a couple of cosmetic changes), therefore now I have just to wait for the verdict of the Ph.D. council then fill in some paperwork: the next step is the defense, sometime in January. After that I’ll probably put my thesis online and post a few articles on the concept of group testing for microarray data.

Today I started working on a data set published on GEO. As the sample data were somehow inconsistent (they mentioned 23 controls when I found 28), I decided to parse the SOFT file from GEO in order to get the exact sample information. I did a grave mistake. First of all, Biopython’s SOFT parser is horribly broken (doesn’t work at all) and quite undocumented: I could work around the lack of documentation (API docs) but not with the fact that it wouldn’t work.

Today I was looking for an easy way to do some calculations of raw expression data on Affymetrix arrays, but I didn’t want to use R: I have already mentioned how I don’t like its design and implementation. While looking for some documentation, I stumbled upon this nifty little program called RMAExpress.

It turned out I forgot to add the last screencast produced by the students of Kourse 2, so I’ll fix my mistake right now. Here’s Panel settings, by Kourse student TeaAge: [blip.tv ?posts_id=1653914&dest=-1]

Students from Kourse 2 fengshaun and Primoz have prepared two nice screencasts, dealing with the Zooming User Interface (ZUI) and desktop settings respectively. Without further ado, here they are: Zooming User Interface by fengshaun [blip.tv ?posts_id=1648944&dest=-1] Desktop settings by Primoz [blip.tv ?posts_id=1646835&dest=-1] As usual, both Free and non-Free versions are available. The students are also at work on subtitled versions, without the Notes plasmoid. I’ll be sure to post them once they’re done.

Today I’m in a posting spree…This clip shows how to resize and move Plasma panels around. [youtube]http://www.youtube.com/watch?v=Rmpv-S5JJI4[/youtube]

Following up on my previous post, here is another screencast showing off how to create a sidebar panel and add a few plasmoids to it. As usual, the version on Youtube has annotations. [youtube]http://www.youtube.com/watch?v=WPeFSDdt2PY[/youtube]

Recently in the Plasma mailing list, KDE developers have discussed a new screen-locking implementation that could be added to the upcoming 4.8 release of the KDE Workspaces. The first reason to do so was to solve some security constraints of the existing implementation. As an added bonus, screen locking should be also more aestetically pleasing. There is however a trade-off: such implementation would mean that screensavers that rely on X (also called X screensavers) would not be compatible.

The other day I was thinking about how to make screencaps for the anime I watch. Windows users often use Media Player Classic, which can create a video contact sheet (i.e., a series of captures) out of a movie file. I had two problems with this: The biggest is that it runs on Windows, and I don’t use Windows; The frames needed to be manually cropped every time, which was slow.

Up to now, the main language in which KDE applications are developed is C++. This is a perfectly valid choice: however, at least for users that don’t have a computing background (I include myself in the list: I do science) C++ can be a rather steep requirement (although Hans, fellow staff member at the KDE Community forums, is doing a nice job in explaining his learning experience). Scripted language bindings (that have a lower barrier of entry) for KDE exist: on top of my memory I can list Python, Ruby, and C# (and I’ve probably missed a few).

Yesterday I’ve been in Camogli and Portofino, two small towns in the eastern part of Liguria. The weather was nice and warm, and I took the opportunity of taking a few photos: [singlepic id=328 w=320 h=240 float=] [singlepic id=331 w=320 h=240 float=] Those are samples, the rest are available [in the gallery.]({{ site.url }}/nggallery/page-494/album-1/gallery-9)

(Note: this post also appears in Planet KDE and Planet openSUSE because I thought this might be interesting to others) As I mentioned in some other posts, I have a small “server” which I use as a NAS to provide archiving for photos and other files of interest. As it runs in a remarkably small (and quiet) enclosure, I’ve managed to put it in an incospicuous part of the room it is in.

Some time has passed since I last blogged… this was not only due to lack of time but also due to motivation (writing long texts can be discouraging at times). In any case, I’d like to rectify for that. In this post, I’ll talk about Nepomuk, and in particular how to use it to tag and annotate arbitrary files using its API in PyKDE4. Before starting, let me say that creating this tutorial was only possible thanks to the help of Sebastian Trueg, who helped me by pointing out some mistakes I was doing.

I just read from Weblog Tools Collection that CollegeScholarships.org is hosting a vote for a round of $10,000 blogging scholarships. Now, I may be a little out of the “Web 2.0” trend (actually for me “2.0” does not relate to Tim O’Reilly’s buzzword, but to real and interesting technologies like the Semantic Web), but I find this absurd. I mean, I have no doubts that the people listed there have made interesting blogs.

Interested by some promotional art and by a resemblance of the main female character to my brother’s own Yumiko, I took a look at the first episode of Ookami to Koshinryo, better known as Spice and Wolf. I’m being told it is inspired by a series of novels and that there is also a manga version.

Straight out of my anime backlog, I watched the first episode of Clannad. I don’t know much about the original name (save for the time it took to be released), but I knew that the animation studio who did this series was Kyoto Animation (The Melancholy of Haruhi Suzumiya, Air, Kanon and Lucky Star).

From the already large backlog of new series, I recently watched the first episode of Prism Ark, an anime adaptation of the H-Game _PRISM ARK ~ PRISM HEART II ~ _by Pajamas Soft (I wonder how some Japanese companies get to choose their names…). It is being directed by Masami Obari, who did Dancougar Nova the last season.

Yesterday I got a few novels that I’ve been waiting for a while: _Slayers _(the last two volumes published by Tokyopop, as ) and Shakugan no Shana 2. I bought the latter as a “final warning” because I’m not very sure I’ll ever continue: the first Shana was written poorly and with a plot that didn’t make much sense (but again, I don’t think the animated version was shining in that respect).

[]({{ site.url }}/images/2008/07/slayers3.jpg)

It’s been a long time since Slayers had aired on TV, basically since Slayers TRY was released, which means more than 10 years ago. Then, this year news told that two new series were planned, and this post is about the first episode (out of 13, aired on July 2nd; the second series will start sometime around January).

Yesterday I got a few novels that I’ve been waiting for a while: _Slayers _(the last two volumes published by Tokyopop, as ) and Shakugan no Shana 2. I bought the latter as a “final warning” because I’m not very sure I’ll ever continue: the first Shana was written poorly and with a plot that didn’t make much sense (but again, I don’t think the animated version was shining in that respect).

I wanted to write this earier, but I couldn’t: I’m now in a hotel in Maastricht, Netherlands, and waiting to get back tomorrow. I’ve been attending the 4th NuGO hands-on advanced microarray data analysis course and I even wanted to blog about it… but the hotel’s connection did not resolve any non-European web page until late today.

As people who read my science-related posts know already, I’m not a big fan of {{post id=“software-and-biological-research” text=“software made just to support a publication”}}. Recently I’ve stumbled again into similar software. Namely, I’m talking about the TIGR Multiexperiment Viewer (TMeV), a Java-based program which is often used for microarray analysis. It’s not exactly “fit for publication”, because it has reached version 4 last year, but shows some of the problems ({{post id=“genbugg” text=“mentioned already”}}) with releasing bioinformatics software.

I use TMeV mostly because I didn’t find any other implementation of the hierarchical clustering algorithm with support trees. However, I’ve stumbled upon a very annoying bug in the most recent version. Normally I use average linkage clustering and as the distance metric I employ the Pearson’s correlation, and with gene and sample bootstrapping: with certain files this makes TMeV report errors at random during the iterations.

Today I started working on a data set published on GEO. As the sample data were somehow inconsistent (they mentioned 23 controls when I found 28), I decided to parse the SOFT file from GEO in order to get the exact sample information. I did a grave mistake. First of all, Biopython’s SOFT parser is horribly broken (doesn’t work at all) and quite undocumented: I could work around the lack of documentation (API docs) but not with the fact that it wouldn’t work.

[]({{ site.url }}/images/2008/04/ookami_cover.png)

A rather large number of days ago I got the first DVD of Ookami to koshinryo, better known as Spice and Wolf, which I when the first episode was released. I got the limited edition, which came in with a number of extra features (which still don’t justify its ~ ¥6800 price tag, though). The main one is the inclusion of a 300 piece puzzle, illustrated by the artist who works on the original novels.

Interested by some promotional art and by a resemblance of the main female character to my brother’s own Yumiko, I took a look at the first episode of Ookami to Koshinryo, better known as Spice and Wolf. I’m being told it is inspired by a series of novels and that there is also a manga version.

You might have heard it in the past few months: some areas of the Internet are buzzing with discussions on “generative art”, that is, artwork generated from “AI” models that were fed with an absurdly large amount of images as training as a base. There are supporters, there are critics, and techology advances: among all this, this post offers my humble experience with computer-generated imagery. In this post, you’ll be guided by Yumiko, Satsuki, and Maya: the first two are characters created by someone else I know (who wants to remain anonymous) which I then expanded, cooperating with their creator in a certain project from a few years ago; the latter is… well, a character with an interesting history, which will be explained later.

A rather big change has gone into KDE’s SVN recently: Ben Cooksley (bcooksley) and Mathias Soeken (msoeken) have committed a complete rework of System Settings.

Compared to the previous implementation, System Settings now has two operational modes, one being the current icon-based view since KDE 4 (and also seen in Kubuntu prior to KDE 4), and a second view, named “Classic”, which reimplements the old KControl look and feel. The latter change is probably very welcome to anyone who found System Settings less useful than the old KControl. The current view used can be changed in the configuration options. In addition, upon hovering an icon or module that show if there are any sub-modules associated.

Recently I’ve been testing out murmur, http://wiki.mumble.info/wiki/Main_Page server component, on my CentOS 7 server. Murmur requires specific ports being open to operate, and when using it I would open them manually, and close them after the session had been completed. I found it pretty tedious: I wanted to wrap it into a single call to the service, so I could enable my user (via sudoers) to be able to start and stop the service without worrying about elevating permissions to start and stop the firewall.

openSUSE is migrating to the use of systemd for the upcoming 12.3 version, given the difficulties that emerged in trying to co-maintain two different init systems (SysV + systemd). While I am not going into the details of this choice (I leave this to more informed people), this has some consequences for software higher in the stack. As ConsoleKit is deprecated, systemd offers its own daemon to keep track of sessions and assigned seats in a system.

Today, after some customs delay and courier problems, I finally received the first volume of Tears to Tiara. Having got a PS3, I chose the Blu-Ray version (priced 8,192 yen, quite steep if you hear me): as I preordered it soon enough, I got the first presse edition, which, according to CDJapan, was comprised of a “deluxe outer case”, a “stick poster” and a booklet, in addition to the Blu-ray itself.


So I’ve heard that _Tears to Tiara _is coming in animated form. Being in the middle of playing its PS3 incarnation, Tears to Tiara - Kaikan no Daichi, I decided to take a look at some images that have been recently published on news.dengeki.com. It was already known that the anime would be an adaptation of the PS3 game, which is a good thing (I didn’t like the original character design). Animation is done by _Oriental Light and _Magic (OLM), and the same staff who adapted another Aquaplus game, Utawarerumono (or should I say Underwater Ray Romano ? snicker).

During the discussions for the release of openSUSE 12.3, the topic of update notifications and applets was brought up again. Originally openSUSE shipped with a custom update applet, but since it was basically unmaintained, the decision was made to switch to Apper for openSUSE 12.2 The original Apper used in that version had a number of issues, which the upstream developer (Daniel Nicoletti) fixed in a newer version, which also had a lot of other improvments.

Following up on my previous post, a different type of image has been made by the openSUSE KDE community members. In particular, alin has created images sporting the same software from KDE (4.10 RC2) but using the upcoming openSUSE 12.3 as base. Download links: 32 bit version 64 bit version Release directory (in case the above links go 404; the files are named KDE4-.4.10.RC2-Live) These images are provided not only to test 4.

Following up my [earlier post]({{ site.url }}/2012/10/whats-cooking-for-kde-in-opensuse-12-3-theming), the new openSUSE 12.3 theme has finally landed into the official openSUSE repositories  and will be part of the upcoming 12.3. A lot of work has gone into the new theme since I last posted about it, so this post will show how things look at the moment.

A few caveats:

• The theme targets the 4.10 release of the KDE Workspaces, so it may be not be perfect under 4.9;

• The default wallpaper has not been chosen yet.

Without further ado, let’s get down to seeing what’s improved.

Although the release of openSUSE 12.3 is yet to come, the people of the openSUSE community contributing to KDE are already at work to bring the best possible KDE experience for the new release.

The title says it all. After all these years, I was finally able to get my Ph.D. in Molecular Medicine this morning, with my thesis “Identification of disregulated metabolic pathways by transcriptomic analysis in renal carcinoma samples” (yes, that’s a long title). The defense was a success and I admit I was surprised when the commitee actually expressed a significant interest in my work. In any case, I’m happy that it’s over, as the past period has been rather hectic.

My supervisor has given me an OK for my thesis (save for a couple of cosmetic changes), therefore now I have just to wait for the verdict of the Ph.D. council then fill in some paperwork: the next step is the defense, sometime in January. After that I’ll probably put my thesis online and post a few articles on the concept of group testing for microarray data.

I’m aching all over but I managed to write this entry. Today I went to the Ueno area first, hoping to go to the National Museum: however I forgot it was closed on Mondays, so I had to go to the National Science Museum instead. It turned out that it wasn’t a bad choice after all, as the museum is rich with exhibits and has a very good presentation. After that we moved to the Toshogu Shrine in Ueno Park, a shrine that was dedicated to the shogun Ieyasu Tokugawa.

When Tokyopop announced _Slayers, Kino no Tabi _and _Scrapped Princess _my interest was piqued: even more when I read about Seikai no Monsho. After getting what was available (three volumes of Scrapped Princess, the whole Seikai no Monsho trilogy and the single volume of Kino no Tabi) I waited for the rest.

Today we went to Nar, site of the first capital of Japan, especially to see the Todaiji Temple, designated as a World Heritage site by UNESCO. We used an express train to get to Nara and then a bus to get to the Todaiji itself (actually it’s a quick walk, I just didn’t know the distance was so short). The temple lies inside the Nara-koen, or Nara park, which is famous for its 1200 tame sacred deers.

It’s been a hot day here in Kyoto. And I don’t mean lame second meanings, just that the temperature was really over the top. As a consequence, we changed our plans: we were supposed to visit the so-called “path of the philosophy” but instead we set for Nijo Castle. Nijo Castle was the Kyoto residence of Ieyasu Tokugawa (I suspect to tell the emperor who was the real person in power) and it can be visited.

I was too tired to write an entry yesterday, so I’ll just sum things up here. Yesterday we went to Nikko, home of the Rinnoji Temple, the Toshogu Shrine and the Futarasan Shrine. We decided to visit it to see the tomb of Ieyasu Tokugawa. We took the Tobu Railways SPACIA train to Nikko then used a special pass I had bought beforehand online (the World Heritage Pass) to see the places.

I’m aching all over but I managed to write this entry. Today I went to the Ueno area first, hoping to go to the National Museum: however I forgot it was closed on Mondays, so I had to go to the National Science Museum instead. It turned out that it wasn’t a bad choice after all, as the museum is rich with exhibits and has a very good presentation. After that we moved to the Toshogu Shrine in Ueno Park, a shrine that was dedicated to the shogun Ieyasu Tokugawa.

I didn’t get time to write before about it, but I and my brother went to Japan for a 10-day holiday there, starting on yesterday. After a 12 hour trip, we arrived in Narita Airport and I took the chance of getting an IC card (prepaid subway/bus card) plus a shinkansen reservation I could only make in Japan (and that cost me “just” 27,000 yen). Once that was settled, we boarded the Japan Rail (JR) Narita Express and arrived in Tokyo.

No, it’s not_ _a teen-like “I hate my life, I’m going to die tomorrow” post. I’m actually referring to the comments of a person nicknamed “I Love” that are popping up in almost all blogs that are linked to PlanetKDE which deal with Plasma or KDE4 adoption. The name “I Love” contrasts with an attitude that is unconstructive and rather trollish. This wouldn’t be such a big problem, if not for the fact that posts from said individual have had a rather negative effect: for example Aaron was forced to turn comment moderation on on his blog, Jos’ entry on the new Plasma in the upcoming KDE 4.

As KDE software (be it the Frameworks libraries, the Plasma 5 workspace, or the Applications) develops during a normal release cycle, a lot of things happen. New and exciting features emerge, bugs get fixed, and the software becomes better and more useful than it was before. Thanks to code review and continuous integration, the code quality of KDE software has also tremendously improved. Given how things are improving, it is tempting to follow development as it happens.

Omnia? The Turris Omnia is quite a nice (although a little pricey) OpenWRT-based router from CZ.NIC. It provides a fairly powerful CPU, relatively unconstrained eMMC space, and quite a lot of hackability (some revisions even have GPIO ports to play with). It runs a modified version of OpenWRT, named TurrisOS. The problem A few years ago, I built a custom NAS for my storage needs, using a cheap Intel SoC (J1900 chipset) and a (much pricier) mini-ITX small form factor server tower.

The migration happened and well… it turns out that it was not as smooth as I expected. In particular, comments weren’t working at all due to a filesystem permission on the database (which meant nothing would get written at all). That is now fixed. Sorry for the problems. To add problems over problems, I had a hardware failure (RAID card) last June, which wrecked the root filesystem and I had to reinstall everything from scratch.

You might have noticed that the blog has a markedly different look than before. It has not only changed visually, but also under the hood. This (brief) post summarizes the reasons behind the change. Why? Simply put, the previous solution was unmaintainable. “But,” you might say, “it was a static site generator! How could it become unmaintainable?”. It can. You might recall I moved from Wordpress to Jekyll about six years ago.

As you have noticed, I have upgraded FailWordpress to version 2.7, getting also a new theme in the process. The header image is temporary, until I or someone else gets it fixed. The gallery has also changed: I ditched WPG2 and Gallery 2 because they kept on breaking every time I upgraded Wordpress (of course it’s probably Wordpress’s API and schema instability to blame). Therefore, the gallery had been organized and most likely older posts won’t show images anymore (I’ll get to fix those eventually).

Some of the oldest readers of this blog are well aware of [a certain hobby of mine]({{ site.url }}/category/anime). Over the years I’ve always wanted to write more about that, including the stuff I’m viewing nowadays, but I found a hassle to collect snapshots from videos / DVDs, selecting them, and so on. Recently I learnt that VLC has some rather complete Python bindings, and I thought, why not make the process automated?

As you may already know (if you don’t, please check these older posts) openQA, the automated testing system used by openSUSE runs daily tests on the latest KDE software from git. It works well and uncovered a number of bugs. However, it only tested X11. With Wayland starting to become usable, and some developers even switching to Wayland full time, it was a notable shortcoming. Until now. Why would openQA not run on Wayland?

I just read from Weblog Tools Collection that CollegeScholarships.org is hosting a vote for a round of $10,000 blogging scholarships. Now, I may be a little out of the “Web 2.0” trend (actually for me “2.0” does not relate to Tim O’Reilly’s buzzword, but to real and interesting technologies like the Semantic Web), but I find this absurd. I mean, I have no doubts that the people listed there have made interesting blogs.

While I’m waiting for KDE 4.0 to compile, I just wanted to share a small clip of my brother’s character doing the Drain Samba animation. A bit of background: he has leveled Dancer up to level 7, and now he stopped because there is no artifact armor available yet (probably out in February) and because he’s also leveling another job, monk. Given how people rushed to get Dancer to 75 in less than a week (comments are left to the reader) it is a nice change.

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Finally my copy of Wings of the Goddess has arrived. It was just a matter of putting the DVD in the drive and let install the measly 350+ Mb of update (rather low for a DVD). As usual, Square Enix’s installation program is greedy with regards to information. Once it was installed, I enabled the expansion in PlayOnline and was good to go (save a 20,000+ file check).

With the new version update, these strange portals have been appearing throughout Vana’diel. They’re supposedly the gateways to the past, but since I don’t have Wings of the Goddess yet I can’t really see what will they do. Nevertheless, I was curious and went to take a look at them. They’re **huge. **I estimate at least twice the height of my character. For those curious, here are two photos (one is of my brother’s character, the other is mine):

And so I’m reading that the FFXI Fan Festival has kicked off yesterday (I wish I could have been there). Naturally, reports have been flowing. The FFXI Encyclopedia has a good report of what has been said so far. 1up, the online branch of EGM, has also covered the event, but the article is only focusing on the new jobs (talk about explaining something no one else will ask… not to mention the attitude of that “journalist”).

As you have noticed, I have upgraded FailWordpress to version 2.7, getting also a new theme in the process. The header image is temporary, until I or someone else gets it fixed. The gallery has also changed: I ditched WPG2 and Gallery 2 because they kept on breaking every time I upgraded Wordpress (of course it’s probably Wordpress’s API and schema instability to blame). Therefore, the gallery had been organized and most likely older posts won’t show images anymore (I’ll get to fix those eventually).

Yesterday I updated _The S.T.E.A.L. Saga _to Wordpress 2.5.1. I thought the upgrade would be painless, but I was wrong. First of all, the auto plugin updater kind of confused between the various plugins, so it marked some as updateable although they weren’t. Then, some plugins (albeit incompatible), disappeared from the plugin list (the fix was downloading a more recent version). The biggest issue was, however, the mangling of my .

I have upgraded this blog to Wordpress 2.5. As a result, there are some functions, such as the image gallery, that have been disabled due to the annoying habit of the Wordpress developers of making core changes in very little time. Please report any problems you find, and notice that although the thumbnails look truncated in the new gallery, the full images are actually displayed correctly. I had to fiddle a bit wit the “new media manager”, not only because it’s in Flash, but because at least on Linux it gives odd results (apparently no one from the WP team bothered to check past Win and OSX?

After some thoughts, I switched dennogumi.org to the dKret theme. Please report any errors you may find. The header is the default image, but it will be changed soon (hint: Melissa, you already know what to do…).

I’ve recently upgraded this blog to Wordpress 2.3. While I’m interested in the new changes this release brings (like tagging support) I question the way the transition to the new version was handled. In particular, I am referring to the (questionable) idea of breaking the database schema three weeks before the release. Given the amount of breakage that brought upon plugins, it should have been announced at the start of the 2.

Sadly (for me) I’m back from the holidays. For those of you who wondered why the updates on Japan stopped: when I got back to Tokyo I didn’t have an Internet connection, so I had no means to update. The whole holiday was a blast, though, and we’re considering getting back in two years. Aside from that, work has picked up a really fast pace immediately (why on Earth journals don’t accept LaTeX-produced PDFs?

Since my work schedule is bordering on the hectic, I was thinking on buying something to get me more organized. Rather than a PDA, I’ve been rather interested in the Asus Eee PC: small form factor, SSDs and Linux preinstalled are definitely pluses. It’s too bad that at least in Italy Asus sells only the 512M RAM version (when there are more powerful options available elsewhere). I’d like to get impressions on the Asus Eee, before considering a purchase (€ 300 are still a lot): did you try it?

If you look through this blog’s archives, you may notice that although Free and Open Source Software is what I write most about, it is not the exclusive topic. I’ve written on science (my day job) as well as other interests. And today I’d like to lift the wraps on another project which I take part on, unrelated to the above. Notice for those who read my blog coming from FOSS aggregators like Planet KDE: this is fairly different than most recent topics from me, so be warned before you continue reading.

I’ve put together a small video that shows what you can do with zooming in and out with Plasma’s Zooming User Interface (ZUI). Enjoy. (note: the version on Youtube has also annotations that explain better what is going on) [youtube]http://www.youtube.com/watch?v=EhODrJkoidA[/youtube] If you can, please spread the link to the video. We need more correct information out there.