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.

(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.

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?

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.

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.

(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.

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.

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.

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 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 ~ ^(?

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.

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:

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.

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.

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.

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.

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.

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).

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.

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.

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.

Hello people! Yes, it’s been a while but I haven’t forgotten about it… with the Brainstorm’s new look and most technical issues resolved, I’m able to make Brainstorm Digests more often (hopefully!) Issue 3 - Special summary issue Since we have skipped a few months, what I’d like to present today (aside the usual data about the past month), is a general overview of the state of Brainstorm since the start of the initiative a while ago.

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!).

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.

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 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”.

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.

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.

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).

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).

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.

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.

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.

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?

To me nowadays reading KDE Dot News is a bother. Not because of the news, which are always high quality, but the comments leave a lot to be desired. Let’s take for example the recent news about Nokia buying Trolltech: 99% of the comments talk doom and gloom. This is not bad per se, but most of them bring absolutely nothing to the discussion. Truth is, it’s too early to say, so we’ll have to wait and see.

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.

**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.

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).

At the time of writing, a lot of people (even in bioinformatics) uses Microsoft Word to write their papers. I personally think it’s not a good idea, and not just for the file formats (like Microsoft lobbying semi-legally to get OOXML approved by ISO), but because for scientific papers the WYSIWYG paradigm is not appropriate.

The title comes from some random thoughts I had while reading aseigo’s latest entry on Plasma. I was thinking about the line “who uses KDE for his/her day job, and why?”, but related perhaps to people who don’t code for a living. Here I will illustrate my point of view on why I chose KDE as my day to day desktop environment.

The reason for this post is the time I wasted this afternoon to enable DMA for a DVD burner in Windows, in order to burn a backup DVD at a decent speed. Apparently, the two optical drives are IDE while the HD is on a SATA controller. For no reason, DMA got turned off on the DVD burner (but not on the other drive). Of course I tried everything I could, of course.

Looks like my laptop doesn’t really want to keep its data in stable form. Like [I have blogged previously]({{ site.url }}/2007/05/31/borked/), the bus-reset issue apparently trashed my root partition again. I do not know the cause as it seemed a normal shutdown… but the moment I rebooted I had lost a lot of files (thankfully not on /home: I’m glad I keep data separated from the rest). Reinstalling proved less difficult, thanks to a Kubuntu DVD I burnt with my other computer.

Recently, I had to do a few scans with my old but trusty BenQ 640BU. Given that I could not use any GUI due to a long-standing Feisty bug, I tried to settle for command line scanning with the scanimage command from SANE. The main problem is that scanimage only saves images in PNM or TIFF formats. I wanted to use JPEG or PNG, but apparently that looked impossible to do.

The title will already give an idea of what happened to my laptop two days ago. Due to a bus problem and a forced reboot, my root partition got corrupted. Luckily no data was lost as I keep /usr and /home separated from the rest. However reinstalling proved to be a very difficult task. First of all, my DVD drive has some problems, and so it wouldn’t read the Kubuntu Feisty install disk I had brought from work.

Today I made a simple sed script that converts a tab-delimited text file to a format that can be pasted into a DokuWiki wiki. There is a plugin that permits to read CSV files directly, however: It doesn’t support tab-delimited text files; It’s incompatible with some plugins (one being DokuTexit, which I need). Hence the need for this script. To use it, just copy and paste the code (see below) into a new file, make it executable (chmod +x) and then invoke it with

While working through large text files for work, I found several command line tools whose existence was unknown to me before. Their usefulness is great however, expecially if you deal with comma or tab delimited files (I do, and a great deal).

On a recent dotKDE article about the weekly commit digest, someone brought up again the issue of Plasma, a component of KDE 4 whose object is to bring “revolution” to the current desktop paradigm. However, I think that many in the community had unrealistic expectations, so some people even started to think it was vaporware, like in some comments in the aforementioned article. I’ll say it again, people had unrealistic expectations.

As I’ve been working to get some results done for my Ph.D. thesis, I’ve stumbled across the problem of having different data obtained through different software. Even if it’s just a matter of text files, the fields are all different and even if dealing with the same data, trying to infer relationships is a pain.

[code lang=“bash”] lb@hardin:~$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 7.04 Release: 7.04 Codename: feisty [/code]

I just read on Slashdot that the famous RMS has now sung something against the prisoners in Guantanamo Bay (no link, I’m not giving it hits). All this while being in Cuba, for all heavens, that’s not even remotely a democracy. I don’t deny the fact that that place may have been ground for abuses, but I find it hypocritical that RMS did that in a place where people are imprisoned on a whim and human rights are not upheld constantly.

I’ve again seen how useful and powerful Python can be. The other day I had to prepare an Excel spreadsheet (sadly) which among other things needed to contain links to the GeneCards database for each gene listed. There were more than 2900 genes listed, so adding links by hand would have been suicidal. That’s when Python, through its Windows extensions, comes into play. First of all I created a module for COM objects using the makepy utility.

Recently (before my tendinitis forced me to avoid using my desktop computer) I installed the beta version of Kubuntu 7.04 (Feisty Fawn).

As I anticipated, I can finally release this small script. Its purpose is to build BED files out of tab-delimited text files. I made this because I had several files to make and moving columns left and right (not to mention writing a heading line for the Genome Browser) was becoming annoying. Its use is fairly straightforward, as the help itself says:

Today I decided to give the new Oxygen icon theme (the default icon theme for KDE 4, as Troy Unrau explains effectively on dot.kde.org) a spin. Since it’s not (obviously) available for KDE 3.x, I had to do a checkout from SVN (from trunk/KDE/kdelibs/pics, since they were recently moved there). Then it was a matter of moving the oxygen folder to /usr/share/icons and selecting the theme in kcontrol.

A recent article on dotKDE caused really a stir and a rather long (more than 430 comments!) debate. What is the reason? The decision to use the [Dolphin file manager](The Road to KDE 4: Dolphin and Konqueror) instead of Konqueror as default file manager. I found myself rather surprised at such a reaction. After all, Dolphin and Konqueror will share much of the code base (which means that they will improve both) and Konqueror won’t be removed and will be available as default file manager through configuration.

No, I’m not talking about his looks. I’m talking about him being morally disgusting. The reason? The fact that he went to Cuba and convinced them to switch to FOSS. You may want to know, why is that a bad thing? Easy answer: Cuba isn’t a democracy. Think what you want, blame the United States for the embargo how much you like, but you won’t be able to hide the fact that it is a totalitarian, oppressive regime.

Yesterday I and another person went to the server room to do the basic configuration of the Apple Xserve we have bought, along with its Xserve RAID unit. Despite the general “idea” that anything Apple does is user-friendly, our experience was plagued by problems.

In the past two days, aside studying the Python basics, I’ve been looking to find a decent GUI toolset to develop user interfaces in Python.

Reading Wesley J. Chun’s excellent Core Python Programming I realized I could definitely improve [my wallpaper checker]({{ site.url }}/2006/12/23/wallpaper-size-checker/), at least internally. That’s what I did today, and aside that, I added an option to view a thumbnail of the images contained in the lists. Note that it is not meant to be an image viewer, just a way to show the images in the list (and I suggest you filter it first if it’s long).

I’ve decided to update the wp_filter.py script. I fixed a good deal of bugs and at the same time I added a simple text-driven menu in order to simplify the program use, and I also added a readme file that describes operation and other requirements. You can download the program in [tar.gz format]({{ site.url }}/files/wp_filter.tar.gz) or in [zip format]({{ site.url }}/files/wp_filter.zip). For basic requirements, refer to my [previous blog post]({{ site.

UPDATE: Some stupid bugs had crept in the code, so I updated the archives. Sorry for the inconvenience.

I’ve writtern a small Python script to find wallpapers with right size or aspect ratio I needed, and now I’m releasing it to the public. It may come in handy especially when you download lots of desktop wallpapers (archives, torrents) and you don’t know which ones are suited for your monitor.

Two days ago I decided to install Linux on the new computer I had obtained, so I just got a Kubuntu 6.10 alternate CD and went through the steps. THe network card was not detected, but by reading around I found it was just a matter of the r1000 module not being present in the installation kernel. The problems arose when GRUB was installed. Actually, that part of the installation went fine, but once rebooted I got “error 21”, which meant “disk not found”.

I’m really saddened by the fanatic tone that a part of FOSS community is using to criticize the Novell-Microsoft deal. It should be noted that personally I don’t like the deal at all, since Microsoft has a good history of stomping on its partners when they’re no loner needed. But still, the reactions from the community are too strong, sometimes leading to (involuntary) disinformation.

In the past two days I’ve written a simple annotator program, that given an input list of RefSeq genes, automatically determines the relevant Entrez Gene IDs and annotates them using the flat files provided by the NCBI. A direct conversion was not possible due to limitations in Biopython’s parsers, but I managed to use the GenBank parser to identify and extract the references to the Gene IDs (and putting them in a list).

Finally I cleaned up my code enough to post it here. It’s probably still ugly, but not as ugly as when I wrote it down the first time. It’s all about manipulating text files, to be precise tab-delimited files. All the snippets are published under the GNU GPL v2 (not that I think that anyone would use them, but just in case…).

I’ve upgraded both leon (one of my computers at home) and quant (my work machine) to Kubuntu Edgy Eft (now in Release Candidate status, screenshots here). Leon’s upgrade went perfectly, while quant gave me some headaches. First of all there was a conflict between packages, then the nvidia module for legacy hardware wouldn’t load: $ modprobe nvidia_legacy FATAL: Module nv not found. In the end I manually compiled the nvidia module, and had to insert it via insmod or it would give out a cryptic error message (“error running install for module nvidia”).

Although I’m still studying the language, finally I managed to create a program that actually does something I need. The need arose from a gene list I was given, made up by Entrez Gene IDs. I need to annotate it, but in a form that wasn’t able to be produced by the usual functional annotation tools I have. Actually it could have been done, but what I needed was to make something that I could automate.

WARNING: This entry is somewhat political in nature.

Given the recent controversies about the GPL v3 draft, I thought I’d give my insight on the Free Software Foundation and especially its founder, Richard M. Stallman, better known as RMS. I won’t cover the GPL v3 debate as I haven’t read the license draft, though I think that the kernel developers’ standing must be at least given attention.

Jucato has some screenshots of the recently released Kubuntu Edgy Eft Knot 3. I like very much the new artwork, but it doesn’t seem that there’ll be Oxygen icons, at least from what I can gather. In any case I will try to play with it as soon as it hits a beta stage. On unrelated news, I still have got some RSI issues, so I’ll have to slow down posting.

Recently I decided to update the fglrx driver (ATI’s proprietary driver for Linux) to the latest version. I wanted to do that because the old version made switching between virtual consoles and X impossible (X would lose the correct timing of the screen, distorting it and forcing a kill to reset the settings). Also I was hoping on finally solving the hibernate issue that has been plaguing the driver for months.

A lot of my bioinformatics work involves performing functional annotation on genes. This means that given lits of genes I need to resolve their known function, or if they’re part or some metabolic pathways and so on. Even with the current trend in our laboratory, that is investigating DNA copy number changes using SNP microarrays (it’s a rather new form of analysis, but some relevant papers are out already), in the end we have to go back to the genes affected by such changes (in order to find interesting/marker genes - we study solid tumors).

I learnt recently that the Kile LaTeX environment had a new release (1.9.2) on 26th August. It is mainly a bugfix release. However no packages for Ubuntu and Kubuntu exist yet, so I decided to fill the gap by building one, as I also use Kile for S.T.E.A.L.. It is based on the packages made by Harald Sitter and Marcus Czeslinski, whom should take most of the credit, as I merely recompiled the already debianized source with the new version.

[code]lb@hardin:~$ uname -a Linux hardin 2.6.17-emission7 [/code] (the rest of the output was truncated) Thanks to some folks over at the Ubuntu Web Forums I’ve been working into rolling in my own kernel trying to solve the fact that when I’m shutting down I always get drives in an unclean state (actually only the root partition), giving rise to several errors. I wasn’t content with a vanilla kernel so I decided to use the emission patchset.

Yesterday I was trying to adjust some files in order to make a program use Affymetrix SNP arrays data (instead of arrayCGH data like the program was designed for). I had a big (116,000 rows) tab-delimited text file and I needed to use only part of the columns there.

I’ve already explained in a previous entry that I like to tweak images, extract them from backgrounds and so on. However I didn’t like that I needed Windows to perform my actions, as I want to use that operating system as less as possible. I tried then to use FOSS (Free and Open Source Software) tools available on Linux to see if I could do the same job.

305 Yesterday when I went at work I found an envelope coming from Canonical. Inside, there were the five Kubuntu 6.06 “Dapper Drake” LTS CDs I ordered from Shipit. Those are Live CDs that will run Kubuntu without any needs for installing (though I’d have preferred real install CDs). 307 I will probably try to hand out a few of those: there are already a few people using Linux where I work.

I got upgrade hardin (my laptop)’s memory at least, bringing it to 1Gb, at last. However I had two 256 Mb modules installed, that means I had to buy two 512 Mb ones. Oh well, I’ll just try to sell those ones. Everything seems snappier now, and even Firefox seems not to clog the CPU when loading pages (I need to experiment more, since I have no clue why that should have changed).

Today I’ve been trying to set up suspend to RAM and suspend to disk (also known as hibernate) on my laptop using Kubuntu 6.06 LTS. Both tries failed miserably, sadly. The machine would suspend and also wake up, but I’d get only a garbled screen. This means that the video driver failed to wake up properly: this is the well known fglrx driver, the binary only driver that ATI made for Linux.

Finally, the new version of Kubuntu 6.06 LTS (Long Term Support) is out! Not that I noticed many differences since I kept it constantly dist-upgraded since I put the beta on the desktop and the RC on the laptop. I really like it so far (save minor nags with 3D acceleration that I solved by issuing a couple of shell commands). Also, KDE 3.5.3 packages are already available from 3rd-party repositories. I will be upgrading them soon.

Yesterday I updated my laptop to Kubuntu Dapper RC. Overall the (long) process was quite smooth save a couple of problems (the use of NetworkManager for exaple, that caused me headaches to make wireless work) including the fact that the ATI drivers were looking in the wrong location (/usr/X11/lib/modules/dri instead of /usr/lib/dri) so 3D acceleration wasn’t working. It seems smooth so far, though I think the idea of NetworkManager needs polishing, as some services that are started before it connects will fail (such as autofs).

Today I found out that a computer running Windows had been “self-writing” words when an Internet Explorer window was open. This obviously led to the conclusion that there was some kind of malware running. I immediately unplugged the network cable but the typing continued - this is a good sign meaning that it was just some random program doing it. It only affected IE, no other programs. I wonder how it got there, I can only suspect the current user, as I never do any network-based activity there, only analysis (and I run a much safer Linux box - no Windows for me).

I’ve been playing a bit with Ubuntu on two computers. On the laptop, I have managed to make the email led blink when I get new mail (thanks to a tip I found online involving the use of the acerhk driver). I still need to find a way to turn it off (actually I can turn it off, just not automatically after I finish reading my mails).

Today was much more tiring than yesterday. It was a full day with courses, and especially the ones in the afternoon were rather heavy on the subjects. First of all there were some talks on networks and promoter site prediction (I liked a lot the second one) , followed by some talks on microarray data analysis (I knew a bit already of this stuff). The afternoon talks featured more statistics for bioinformatics (ugghhhh) followed by a nearly non-understandable talk that lasted for almost two hours and really drained the life out of me.

I haven’t blogged in a while, mostly because I’m either doing something else, or when I want to, I find out I’m really tired (this and the past week have been very tiring for me). In any case, I’ll make a big, random entry. I’ll start saying that I’m amazed at how badly software can be written. In the life sciences field you see very clear examples. Horrible UIs and poor documentation mostly (while the algorithms and methods implemented are usually very solid).

I’ve been migrating settings and files from the old router to the new one (check my brother’s blog to understand better what I’m talking about). I noticed the free space already dropped significantly, as you can see from this: [code] lb@hari:~$ df -h Filesystem Size Used Avail Use% Mounted on /dev/hda1 9,2G 859M 7,9G 10% / tmpfs 43M 0 43M 0% /dev/shm tmpfs 43M 13M 30M 30% /lib/modules/2.6.12-10-386/volatile /dev/hda6 83G 8,5G 70G 11% /home

As today was almost completely uneventful (and kept on raining), I’m putting together an all-in-one entry. First of all I played more with the webcam on Linux. The exposure setting and some other gamma corrections can’t be really set in real-time yet, so it tends to get a little dark. Nevertheless I can get some decent results, here’s an example picture of my desk: general/desktop.jpg I also tried to update my old Mandriva 2006.

I’ve just upgraded my blog to WP 2.0.1. Aside a little problem with the gallery images (easily fixed) everything seems to run smooth for now. If you notice any glitches please post a comment and I’ll get it fixed.

Yesterday I tried to run an electronic Italian-English dictionary I own. As I write my novel using LaTeX and I have an environment on Linux, I thought it would good to use WINE to read it. I was wrong. Wine has progressed immensely and the commercial offerings (for example CodeWeavers) are even capable of running Office in its latest incarnation: however they are totally useless in front of the extremely bad quality of those dictionaries (from a programming point of view).

I’ve just wasted an expensive DVD+R dual layer thanks to some bugs in the burning program. My laptop could handle the burning fine (hopefully) but I couldn’t read the source DVD because of the crappy quality of the DVD reader inside (I had the same exact problem with my old laptop), and on my desktop (MDV 2006.0) k3b refuses to burn, and growisofs borks mid-way with a generic error, in any case the DVD is wasted, bah.

The two items in the title aren’t really related but they sum up today’s entry. My cat had to be visited by the vet, that diagnoesed renal insufficiency and strong dehydration. Something to be worry about, but it will be at lest kept under control soon. The second part of the entry deals with the fact that I’m trying to find a decent finance program that works under Linux (no thanks to any program on Windows, sorry): I tried KMyMoney but aside the fact that it doesn’t have any Italian template, it’s a little confusing.

Recently my hosting service has been boasting service upgrades. However I didn’t see any changes in my control panel. So, I emailed them, and their reply was that it was valid only for customers signing up from November 9th (because they had set up new servers). However, I find it quite unfair, since I pay the same price as the people who will sign up, and get less. Looks like I’ll have to change hosting again in the future…