Lennart's weblog

Notes about open source software, computers, other stuff.

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Subversion: merging updates in trunk to a branch

Yesterday I was working on ProbABEL, an open source package for running GWAS (genome-wide association studies). We use R-Forge and they provide us with a Subversion (SVN) server for revision control.

Some time ago we created a branch in which one of the co-developers is doing some major refactoring of the code. In the mean time I have been fixing bugs and adding new features to trunk. Now that the work in the refactoring branch comes to an end I thought it was high time to integrate the changes in trunk with the changes in the branch so that we can later promote the branch to trunk.

Since I had never done this before I decided to try the merge in the doc directory first, because I knew that in that directory nothing had changes since the branch was created, so all changes from trunk should be imported. At first I followed the SVN book instructions so I went into the doc dir in the branch and ran

$ svn merge ^/pkg/ProbABEL/doc

Unfortunately that didn’t work out. For some reasons conflicts appeared as wel as files that weren’t supposed to be there at all.

Thanks to Google and this blog post I found a solution. It boils down to explicitly telling SVN which revisions to use for the merge.

First I used

$ svn log | grep -C3 branch

to find out at which revision I created the branch:

------------------------------------------------------------------------
r864 | lckarssen | 2012-03-27 17:38:05 +0200 (Tue, 27 Mar 2012) | 1 line

Creating ProbABEL branch for code refactoring

Next I went to trunk and ran

$ svn update
At revision 987.

to find out at which revision trunk currently was. Back in the doc directory in the brach I ran

svn merge -r 864:987 ^/pkg/ProbABEL/doc

to merge al the changes since the branch was split off and it worked like a charm! All changes in trunk applied cleanly.

I then id the same for the other directories which also had changes in the branch. It turns out that when SVN find a conflict it is easier to postpone resolving the conflict because Emacs has a great SVN merge minor mode called SMerge! It highlights your changes vs. the incoming ones and allows you to select a resolution and move to the next conflict with a few easy keystrokes. After all conflicts have been resolved Emacs automtically removes the intermediate files SVN created and you are ready to commit.

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Ubuntu 12.04: LaTeX siunitx package and the correct font in beamer

When writing scientific text I normally use the siunitx package to typeset numbers (using \num{}) and numbers with units (e.g. \SI{4.0}{TB}) in LaTeX.
Something that bothered me for a while was the fact that when making presentations in Beamer, numbers and units would be typeset in a serif font, whereas beamer uses sans-serif fonts.
The solution is actually documented in the manual, but what to me a while to figure out was that in Ubuntu 12.04 (and therefore in Debian as well, I presume) the version of the siunitx package is lagging compared to what is available on CTAN. Ubuntu 12.04 still has version 1.3a of the siunitx package, which was released in September 2009. For this version the solution is to add the following to the preamble of your document:

\sisetup{obeyfamily=false,mathrm=mathsf,textrm=sffamily}

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Using Plugwise adapters with Linux

Yesterday I received a small package I had ordered: the Plugwise Home Start kit. According to the box it is an energy management and control system. The idea is that you insert a sort of adaptor between a power socket and a device and using the Plugwise Source software you can monitor the power usage of the device. Furthermore, you can use the software to create schedule to turn the device on and off at a specific time.

The package contains the following:

  • a USB adapter (called the Stick)
  • a Circle+, the master adaptor that keeps track of the other devices in the network
  • a Circle, the regular members of the Plugwise network

The Circles communicate to each other using the ZigBee protocol in the 2.4GHz range. According to the documentation, the range of each Circle is about 5m.

Unfortunately the Source software only runs on windows. Luckily some people have already analysed the protocol and written some software to control the Plugwise devices (see links below).

First steps

Plugging the USB dongle in gives the following output in /var/log/syslog:

Nov 19 12:20:37 barabas kernel: [  182.855742] usb 1-1.6.1.1.3: new full speed USB device number 14 using ehci_hcd
Nov 19 12:20:37 barabas mtp-probe: checking bus 1, device 14: "/sys/devices/pci0000:00/0000:00:1a.0/usb1/1-1/1-1.6/1-1.6.1/1-1.6.1.1/1-1.6.1.1.3"
Nov 19 12:20:37 barabas mtp-probe: bus: 1, device: 14 was not an MTP device
Nov 19 12:20:37 barabas kernel: [  183.169370] usbcore: registered new interface driver usbserial
Nov 19 12:20:37 barabas kernel: [  183.169389] USB Serial support registered for generic
Nov 19 12:20:37 barabas kernel: [  183.169431] usbcore: registered new interface driver usbserial_generic
Nov 19 12:20:37 barabas kernel: [  183.169434] usbserial: USB Serial Driver core
Nov 19 12:20:37 barabas kernel: [  183.171310] USB Serial support registered for FTDI USB Serial Device
Nov 19 12:20:37 barabas kernel: [  183.171552] ftdi_sio 1-1.6.1.1.3:1.0: FTDI USB Serial Device converter detected
Nov 19 12:20:37 barabas kernel: [  183.171588] usb 1-1.6.1.1.3: Detected FT232RL
Nov 19 12:20:37 barabas kernel: [  183.171591] usb 1-1.6.1.1.3: Number of endpoints 2
Nov 19 12:20:37 barabas kernel: [  183.171595] usb 1-1.6.1.1.3: Endpoint 1 MaxPacketSize 64
Nov 19 12:20:37 barabas kernel: [  183.171598] usb 1-1.6.1.1.3: Endpoint 2 MaxPacketSize 64
Nov 19 12:20:37 barabas kernel: [  183.171602] usb 1-1.6.1.1.3: Setting MaxPacketSize 64
Nov 19 12:20:37 barabas kernel: [  183.171975] usb 1-1.6.1.1.3: FTDI USB Serial Device converter now attached to ttyUSB0
Nov 19 12:20:37 barabas kernel: [  183.171998] usbcore: registered new interface driver ftdi_sio
Nov 19 12:20:37 barabas kernel: [  183.172002] ftdi_sio: v1.6.0:USB FTDI Serial Converters Driver
Nov 19 12:20:37 barabas modem-manager[901]: <info>  (ttyUSB0) opening serial port...
Nov 19 12:20:49 barabas modem-manager[901]: <info>  (ttyUSB0) closing serial port...
Nov 19 12:20:49 barabas modem-manager[901]: <info>  (ttyUSB0) serial port closed
Nov 19 12:20:49 barabas modem-manager[901]: <info>  (ttyUSB0) opening serial port...
Nov 19 12:20:55 barabas modem-manager[901]: <info>  (ttyUSB0) closing serial port...
Nov 19 12:20:55 barabas modem-manager[901]: <info>  (ttyUSB0) serial port closed

lsusb gives:

Bus 001 Device 014: ID 0403:6001 Future Technology Devices International, Ltd FT232 USB-Serial (UART) IC

I couldn’t get the pairing to work under Linux (with the PlugwiseOnLinux scripts), Even though I corrected the MAC address in the python code. I then tried it in Windows where I failed at first also. After resetting the Circle+ and the Circle (removing/inserting them into the power outlet with 3 second intervals, as mentioned in the FAW on the plugwise website) I managed to pair the Circles. Looking back, I think I didn’t wait long enough for the pairing to work under Linux. During the trials in Windows I noticed that the pairing can take up to about 5 minutes…

Back in Linux I used python-plugwise (see links below) to turn the Circles on and off, e.g. this is how I turn my Circle+ off (note that I am a member of the dialout group, which is needed to communicate with /dev/ttyUSB0):

$ plugwise_util -d /dev/ttyUSB0 -m 000D6F0000B1C117 -s off

This is what I want! The only minor downside of python-plugwise is that it depends on the crcmod python library, which apparently is not package for Debian/Ubuntu. So installing using the python-setup framework as mentioned in the README is necessary.

Reading out the current power usage of my Circle works also:

$ plugwise_util -d /dev/ttyUSB0 -m 000D6F0000B85134 -p
power usage: 2.27W

So, no that it works, what am I going to do with the Plugwise modules? I’m going to use them in my backup scripts to switch the power to my external hard drives.

Making a .deb

I used checkinstall to make a package of python-plugwise. In a working directory, first check out the source code of python-plugwise using mercurial, as mentioned on the web site:

$ hg clone https://bitbucket.org/hadara/python-plugwise

Then run checkinstall and don’t forget to fill in the details correctly. For example, the package name is ‘python’ by default, which you definitely don’t want, since that would overwrite Ubuntu’s default ‘python’ package. Also make sure that you remove the crcmod python library if you installed python-plugwise before, otherwise it won’t get packaged. The output below shows the final values, after I changed them.

$ sudo checkinstall -D python setup.py install
 
checkinstall 1.6.2, Copyright 2009 Felipe Eduardo Sanchez Diaz Duran
	      This software is released under the GNU GPL.
 
 
 
*****************************************
**** Debian package creation selected ***
*****************************************
 
This package will be built according to these values:
 
0 -  Maintainer: [ lennart@karssen.org ]
1 -  Summary: [ python-plugwise is used to control the Plugwise power switches as well as read out information on power usage. ]
2 -  Name:    [ python-plugwise ]
3 -  Version: [ 0.2-hg-20111120 ]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ amd64 ]
8 -  Source location: [ python-plugwise ]
9 -  Alternate source location: [  ]
10 - Requires: [ python ]
11 - Provides: [ python-plugwise ]
12 - Conflicts: [  ]
13 - Replaces: [  ]
 
Enter a number to change any of them or press ENTER to continue:

You can check the contents of the package to make sure the crcmod
files are included using dpkg:

$ dpkg --contents python-plugwise_0.2-hg-20111120-1_amd64.deb

An idea for later: make an SNMP module that calls plugwise_util to get the power usage so that I can monitor the power usage of a device using Cacti.

Links

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BluePad and Ubuntu 11.10

Over the last few years I’ve always used BluePad (the author’s blog, source and packages available at sf.net) when I had to do a presentation. BluePad allows me to use my Nokia 6230i to send PgUp and PgDn signals to my laptop via bluetooth and thus control my presentation without standing next to laptop all the time.

Unfortunately the author hasn’t updates his .deb packages in a long time, so trying to install the BluePad .deb on a recent Debian or Ubuntu machine will fail due to missing dependencies. I work around this issue by installing BluePad only when I need it and removing it afterwards. Here is how to install it.

dpkg -i --force-depends bluepad_0.4_all.deb

In older Ubuntu installations this was enough, but with Ubuntu’s Unity interface replacing Gnome the BluePad icon doesn’t appear in the top menu bar anymore and as a result it isn’t possible anymore to interact with it. So you’ll have no way of connecting the laptop to the phone.

To remedy this use the following command to allow all applications to show up in the system tray:

gsettings set com.canonical.Unity.Panel systray-whitelist "['all']"

Restart Unity or log out and back in to get the changes accepted.

After the presentation is over and the BluePad removed, use this line to reset the system tray settings:

gsettings set com.canonical.Unity.Panel systray-whitelist "['']"

(That’s two single quotes within the brackets).

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Installing Loggerhead behind Apache on Ubuntu 11.04

Introduction

Loggerhead is a webfrontend for Bazaar (usually abbreviated as bzr) repositories. Bazaar is a so-called distributed version control system. So, if you have one or more bzr repositories you can use Loggerhead to look at the files, read the change logs and see the differences between revisions from within your web browser.

The main purpose of this post is to document the steps needed to configure Loggerhead and Apache to work together to publish your bzr repos on the web. The need for this post arose when I tried to get this setup to work and found that there isn’t a lot of documentation on how to get this done and most of it is out of date. The folowing steps were performed on a Linux server with Ubuntu 11.04 installed.

Basic Loggerhead configuration

First, let’s install Loggerhead:

$ aptitude install loggerhead

Although the package is called loggerhead, the actual binary that is run is called serve-branches. The package provides start and stop scripts for the service (/etc/init.d/loggerhead), but to start successfully the file /etc/serve-branches.conf needs to exist. Older documentation I found on the web refers to the file /etc/loggerhead.conf, but that file has become obsolete.

The serve-branches.conf file contains three lines:

served_branches=/home/bzr
prefix=
port=8080

Here, the line served_branches points to the directory under which you store your bzr repositories. Each repo needs to be stored in its own directory. So in this example all the repos are in subdirectories of /home/bzr/.

You have to make sure that loggerhead can read the files in that directory. Loggerhead runs as the loggerhead user but I made the directories readable and accessible by all users:

$ chmod -R a+rx /home/bzr/

If you now start Loggerhead:

$ service start loggerhead

you should be able to visit http://localhost:8080 in your browser and see your repositories.
NOTE for Ubuntu 12.04 and 12.10: There seems to be a bug in Loggerhead for these Ubuntu releases (see the link to the Launchpad bug report at the end of this post). In order to start the Loggerhead daemon correctly in these Ubuntu releases the file /etc/init.d/loggerhead must be edited. The line

start-stop-daemon -p $PIDFILE -S --startas /usr/bin/serve-branches --chuid loggerhead --make-pidfile --background --chdir $served_branches -- --prefix=$prefix --port=$port --host=$host --log-folder /var/log/loggerhead 2>/dev/null

must be changed to

start-stop-daemon -p $PIDFILE -S --startas /usr/bin/serve-branches --chuid loggerhead --make-pidfile --background -- file://$served_branches --prefix=$prefix --port=$port --log-folder /var/log/loggerhead 2>/dev/null

Once this is done run restart the Loggerhead service as stated above and it should work again (if you run Loggerhead behind an Apache webserver as detailed below, don’t forget to restart Apache also).

How to publish your branch to this shared repository?

Now that our repository browser is set up, how do we publish our branches to it so that there actually is something to browse through? Here is how you publish your branch to the server, assuming that you are in a directory that contains a branch and want to publish it as myTests:

$ bzr push --create-prefix sftp://username@server.yourdomain.com/home/bzr/myTests

As you probably suspected, the --create-prefix option is only necessary the first time you push your branch. Note that we are using sftp here. Loggerhead itself doesn’t allow writes to the published repos. So, every user that want to push his/her changes to this repository needs to have sftp access to the /home/bzr directory. I solved that problem by adding all people that need to be able to push changes to a Linux group called vcs (for Version Control Systems) and then set the primary group of /home/bzr/ to vcs as well as giving group write permissions to this directory:

$ ls -ld /home/bzr/
drwxrwxr-x 4 root vcs 4096 2011-08-16 23:10 /home/bzr/

Adding Apache to the mix

In my case I already have a web server (Apache) running on port 80. Since I’d rather not open yet another port (8080 in this case) on my router, I wanted to use Apache to hand over the requests for bzr page to Loggerhead. For that I needed to install the following packages:

$ aptitude install python-pastedeploy

Next, I needed to change the contents of the /etc/serve-branches.conf file to this:

served_branches=/home/bzr
prefix=/bzr
port=8080

The prefix indicates the location in the URL where Apache will serve the repos. In this case that will be http://server.yourdomain.com/bzr/.

And finally I needed to configure Apache. First, make sure that the proxy and proxy-http modules are loaded:

$ a2enmod proxy proxy_http

Next, create a file /etc/apache/conf.d/sites-available/loggerhead with the following contents:

# Configuration for browsing of Bazaar repos. Make sure loggerhead is running.
<Location "/bzr/">
    ProxyPass http://127.0.0.1:8080/
    ProxyPassReverse http://127.0.0.1:8080/
</Location>

Note that Loggerhead and Apache run on the same host, that’s why I set the IP to 127.0.0.1.

Finally it’s time to enable the site and restart Apache:

$ a2ensite loggerhead
$ service apache2 restart

Now it should be possible to browse your repos at http://server.yourdomain.com/bzr/. Note the final /, it’s important.

Securing access with an LDAP connection

I have stored all my Unix user and group information in an LDAP server. To make sure that only people in the Unix group vcs are allowed access to the loggerhead pages, change the Apache configuration file loggerhead to the following:

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# Configuration for browsing of Bazaar repos. Make sure loggerhead is running.
<Location "/bzr/">
    ProxyPass http://127.0.0.1:8080/
    ProxyPassReverse http://127.0.0.1:8080/
 
    # LDAP authentication
    AuthType Basic
    AuthName "Karssen.org VCS users"
    AuthBasicProvider ldap
    AuthLDAPURL "ldap://ldap.yourdomain.com/ou=Users,dc=yourdomain,dc=com?uid"
    AuthLDAPGroupAttribute memberUid
    AuthLDAPGroupAttributeIsDN off
    Order Allow,Deny
    Allow From All
    Require ldap-group cn=vcs,ou=Groups,dc=yourdomain,dc=com
</Location>

Lines 11 and 12 are needed because the vcs group is not an LDAP group. I store my Unix (POSIX) groups in a separate OU in the LDAP tree (see line 15).
Don’t forget to restart Apache after making these changes.

References

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RefTeX, how could I have missed this?

I’ve been using Emacs and LaTeX for more than ten years now and still I keep learning. For example, last Friday I came across Stephen Eglen’s ESS (Emacs Speaks Statistics) tutorial. In his slides he mentioned RefTeX. I had heard of it before, but for some reason I thought it was either a set of LaTeX styles or an AUCTeX replacement and consequently, I never looked into it.

This time, however, I made the small effort of looking up RefTeX’s website and lo and behold, it’s neither of the two things I thought it was. Instead, it is an extension to LaTeX that makes inserting citation, references, index entries and labels a breeze. Even if you don’t (want to) use all its capabilities, the following keystrokes are worth the effort:

C-c = Show table of contents of the document (also a great way to walk through your document)

C-c ( Insert a label at point
C-c ) Insert a reference to some label
C-c [ Search in your bibliography (either BibTeX or thebibliography environment) to insert citations

To start using RefTeX in a document you are already editing simple run

M-x reftex-mode

Insert the following in .emacs file if you want to load RefTeX on startup

;; Enable RefTeX
(add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
(add-hook 'latex-mode-hook 'turn-on-reftex)   ; with Emacs latex mode

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Overwriting selected text in Emacs

I learned something new in Emacs (my favourite text editor) today. Normally in Emacs, if you start typing while having some text selected will not overwrite this text. This is contrary to what most people are used to in other editors. It turns out that Emacs has a minor mode that fixes this: delete-selection-mode. Add the following to your .emacs file to have it loaded by default:

(delete-selection-mode t)

Since delete-selection-mode enables transient-mark-mode I commented the line

(setq transient-mark-mode t)

in my .emacs

References:

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Embedding album art in FLAC files

I recently wanted to add cover art to my collection of FLAC-encoded audio files. I wrote the following simple script to help me automate the process. Running this script in a given directory (I group my music in directories per artist, followed by a subdirectory for each album) with the name of the album art image file name as argument then automatically embeds the image in the FLAC/Vorbis tag.

#!/bin/bash
#
# This script embeds a given image (usually .jpg) as album art in the
# FLAC files in the present directory (and its subdirectories).
#
# Time-stamp: <2011-07-31 20:43:23 (lennart)>
 
coverart=$1
 
find . -name "*.flac" -print0 |xargs -0 metaflac --import-picture-from="$coverart"

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