Shallow Thoughts : tags : open source

Akkana's Musings on Open Source Computing and Technology, Science, and Nature.

Thu, 22 Dec 2016

Tips on Developing Python Projects for PyPI

I wrote two recent articles on Python packaging: Distributing Python Packages Part I: Creating a Python Package and Distributing Python Packages Part II: Submitting to PyPI. I was able to get a couple of my programs packaged and submitted.

Ongoing Development and Testing

But then I realized all was not quite right. I could install new releases of my package -- but I couldn't run it from the source directory any more. How could I test changes without needing to rebuild the package for every little change I made?

Fortunately, it turned out to be fairly easy. Set PYTHONPATH to a directory that includes all the modules you normally want to test. For example, inside my bin directory I have a python directory where I can symlink any development modules I might need:

mkdir ~/bin/python
ln -s ~/src/metapho/metapho ~/bin/python/

Then add the directory at the beginning of PYTHONPATH:

export PYTHONPATH=$HOME/bin/python

With that, I could test from the development directory again, without needing to rebuild and install a package every time.

Cleaning up files used in building

Building a package leaves some extra files and directories around, and git status will whine at you since they're not version controlled. Of course, you could gitignore them, but it's better to clean them up after you no longer need them.

To do that, you can add a clean command to

from setuptools import Command

class CleanCommand(Command):
    """Custom clean command to tidy up the project root."""
    user_options = []
    def initialize_options(self):
    def finalize_options(self):
    def run(self):
        os.system('rm -vrf ./build ./dist ./*.pyc ./*.tgz ./*.egg-info ./docs/sphinxdoc/_build')
(Obviously, that includes file types beyond what you need for just cleaning up after package building. Adjust the list as needed.)

Then in the setup() function, add these lines:

          'clean': CleanCommand,

Now you can type

python clean
and it will remove all the extra files.

Keeping version strings in sync

It's so easy to update the __version__ string in your module and forget that you also have to do it in, or vice versa. Much better to make sure they're always in sync.

I found several version of that using system("grep..."), but I decided to write my own that doesn't depend on system(). (Yes, I should do the same thing with that CleanCommand, I know.)

def get_version():
    '''Read the pytopo module versions from pytopo/'''
    with open("pytopo/") as fp:
        for line in fp:
            line = line.strip()
            if line.startswith("__version__"):
                parts = line.split("=")
                if len(parts) > 1:
                    return parts[1].strip()

Then in setup():


Much better! Now you only have to update __version__ inside your module and will automatically use it.

Using your README for a package long description

setup has a long_description for the package, but you probably already have some sort of README in your package. You can use it for your long description this way:

# Utility function to read the README file.
# Used for the long_description.
def read(fname):
    return open(os.path.join(os.path.dirname(__file__), fname)).read()

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[ 10:15 Dec 22, 2016    More programming | permalink to this entry | comments ]

Sat, 17 Dec 2016

Distributing Python Packages Part II: Submitting to PyPI

In Part I, I discussed writing a to make a package you can submit to PyPI. Today I'll talk about better ways of testing the package, and how to submit it so other people can install it.

Testing in a VirtualEnv

You've verified that your package installs. But you still need to test it and make sure it works in a clean environment, without all your developer settings.

The best way to test is to set up a "virtual environment", where you can install your test packages without messing up your regular runtime environment. I shied away from virtualenvs for a long time, but they're actually very easy to set up:

virtualenv venv
source venv/bin/activate

That creates a directory named venv under the current directory, which it will use to install packages. Then you can pip install packagename or pip install /path/to/packagename-version.tar.gz

Except -- hold on! Nothing in Python packaging is that easy. It turns out there are a lot of packages that won't install inside a virtualenv, and one of them is PyGTK, the library I use for my user interfaces. Attempting to install pygtk inside a venv gets:

* Building PyGTK using distutils is only supported on windows. *
* To build PyGTK in a supported way, read the INSTALL file.    *

Windows only? Seriously? PyGTK works fine on both Linux and Mac; it's packaged on every Linux distribution, and on Mac it's packaged with GIMP. But for some reason, whoever maintains the PyPI PyGTK packages hasn't bothered to make it work on anything but Windows, and PyGTK seems to be mostly an orphaned project so that's not likely to change.

(There's a package called ruamel.venvgtk that's supposed to work around this, but it didn't make any difference for me.)

The solution is to let the virtualenv use your system-installed packages, so it can find GTK and other non-PyPI packages there:

virtualenv --system-site-packages venv
source venv/bin/activate

I also found that if I had a ~/.local directory (where packages normally go if I use pip install --user packagename), sometimes pip would install to .local instead of the venv. I never did track down why this happened some times and not others, but when it happened, a temporary mv ~/.local ~/old.local fixed it.

Test your Python package in the venv until everything works. When you're finished with your venv, you can run deactivate and then remove it with rm -rf venv.

Tag it on GitHub

Is your project ready to publish?

If your project is hosted on GitHub, you can have pypi download it automatically. In your, set


Check that in. Then make a tag and push it:

git tag 0.1 -m "Name for this tag"
git push --tags origin master

Try to make your tag match the version you've set in and in your module.

Push it to pypitest

Register a new account and password on both pypitest and on pypi.

Then create a ~/.pypirc that looks like this:

index-servers =



Yes, those passwords are in cleartext. Incredibly, there doesn't seem to be a way to store an encrypted password or even have it prompt you. There are tons of complaints about that all over the web but nobody seems to have a solution. You can specify a password on the command line, but that's not much better. So use a password you don't use anywhere else and don't mind too much if someone guesses.

Update: Apparently there's a newer method called twine that solves the password encryption problem. Read about it here: Uploading your project to PyPI. You should probably use twine instead of the commands discussed in the next paragraph.

Now register your project and upload it:

python register -r pypitest
python sdist upload -r pypitest

Wait a few minutes: it takes pypitest a little while before new packages become available. Then go to your venv (to be safe, maybe delete the old venv and create a new one, or at least pip uninstall) and try installing:

pip install -i YourPackageName

If you get "No matching distribution found for packagename", wait a few minutes then try again.

If it all works, then you're ready to submit to the real pypi:

python register -r pypi
python sdist upload -r pypi

Congratulations! If you've gone through all these steps, you've uploaded a package to pypi. Pat yourself on the back and go tell everybody they can pip install your package.

Some useful reading

Some pages I found useful:

A great tutorial except that it forgets to mention signing up for an account: Python Packaging with GitHub

Another good tutorial: First time with PyPI

Allowed PyPI classifiers -- the categories your project fits into Unfortunately there aren't very many of those, so you'll probably be stuck with 'Topic :: Utilities' and not much else.

Python Packages and You: not a tutorial, but a lot of good advice on style and designing good packages.

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[ 16:19 Dec 17, 2016    More programming | permalink to this entry | comments ]

Sun, 11 Dec 2016

Distributing Python Packages Part I: Creating a Python Package

I write lots of Python scripts that I think would be useful to other people, but I've put off learning how to submit to the Python Package Index, PyPI, so that my packages can be installed using pip install.

Now that I've finally done it, I see why I put it off for so long. Unlike programming in Python, packaging is a huge, poorly documented hassle, and it took me days to get a working.package. Maybe some of the hints here will help other struggling Pythonistas.

Create a

The file is the file that describes the files in your project and other installation information. If you've never created a before, Submitting a Python package with GitHub and PyPI has a decent example, and you can find lots more good examples with a web search for "", so I'll skip the basics and just mention some of the parts that weren't straightforward.

Distutils vs. Setuptools

However, there's one confusing point that no one seems to mention. examples all rely on a predefined function called setup, but some examples start with

from distutils.core import setup
while others start with
from setuptools import setup

In other words, there are two different versions of setup! What's the difference? I still have no idea. The setuptools version seems to be a bit more advanced, and I found that using distutils.core , sometimes I'd get weird errors when trying to follow suggestions I found on the web. So I ended up using the setuptools version.

But I didn't initially have setuptools installed (it's not part of the standard Python distribution), so I installed it from the Debian package:

apt-get install python-setuptools python-wheel

The python-wheel package isn't strictly needed, but I found I got assorted warnings warnings from pip install later in the process ("Cannot build wheel") unless I installed it, so I recommend you install it from the start.

Including scripts has a scripts option to include scripts that are part of your package:

    scripts=['script1', 'script2'],

But when I tried to use it, I had all sorts of problems, starting with scripts not actually being included in the source distribution. There isn't much support for using scripts -- it turns out you're actually supposed to use something called console_scripts, which is more elaborate.

First, you can't have a separate script file, or even a __main__ inside an existing class file. You must have a function, typically called main(), so you'll typically have this:

def main():
    # do your script stuff

if __name__ == "__main__":

Then add something like this to your

          'console_scripts': [

There's a secret undocumented alternative that a few people use for scripts with graphical user interfaces: use 'gui_scripts' rather than 'console_scripts'. It seems to work when I try it, but the fact that it's not documented and none of the Python experts even seem to know about it scared me off, and I stuck with 'console_scripts'.

Including data files

One of my packages, pytopo, has a couple of files it needs to install, like an icon image. has a provision for that:

      data_files=[('/usr/share/pixmaps',      ["resources/appname.png"]),
                  ('/usr/share/applications', ["resources/appname.desktop"]),
                  ('/usr/share/appname',      ["resources/pin.png"]),

Great -- except it doesn't work. None of the files actually gets added to the source distribution.

One solution people mention to a "files not getting added" problem is to create an explicit MANIFEST file listing all files that need to be in the distribution. Normally, setup generates the MANIFEST automatically, but apparently it isn't smart enough to notice data_files and include those in its generated MANIFEST.

I tried creating a MANIFEST listing all the .py files plus the various resources -- but it didn't make any difference. My MANIFEST was ignored.

The solution turned out to be creating a file, which is used to generate a MANIFEST. It's easier than creating the MANIFEST itself: you don't have to list every file, just patterns that describe them:

include packagename/*.py
include resources/*
If you have any scripts that don't use the extension .py, don't forget to include them as well. This may have been why scripts= didn't work for me earlier, but by the time I found out about I had already switched to using console_scripts.


Once you have a, use it to generate a source distribution with:

python sdist
(You can also use bdist to generate a binary distribution, but you'll probably only need that if you're compiling C as part of your package. Source dists are apparently enough for pure Python packages.)

Your package will end up in dist/packagename-version.tar.gz so you can use tar tf dist/packagename-version.tar.gz to verify what files are in it. Work on your until you don't get any errors or warnings and the list of files looks right.

Congratulations -- you've made a Python package! I'll post a followup article in a day or two about more ways of testing, and how to submit your working package to PyPI.

Update: Part II is up: Distributing Python Packages Part II: Submitting to PyPI.

Tags: , ,
[ 12:54 Dec 11, 2016    More programming | permalink to this entry | comments ]

Fri, 27 Nov 2015

Getting around make clean or make distclean aclocal failures

Keeping up with source trees for open source projects, it often happens that you pull the latest source, type make, and get an error like this (edited for brevity):

$ make
cd . && /bin/sh ./missing --run aclocal-1.14
missing: line 52: aclocal-1.14: command not found
WARNING: aclocal-1.14' is missing on your system. You should only need it if you modified acinclude.m4' or'. You might want to install the Automake' and Perl' packages. Grab them from any GNU archive site.

What's happening is that make is set up to run ./ (similar to running ./configure except it does some other stuff tailored to people who build from the most current source tree) automatically if anything has changed in the tree. But if the version of aclocal has changed since the last time you ran or configure, then running configure with the same arguments won't work.

Often, running a make distclean, to clean out all local configuration in your tree and start from scratch, will fix the problem. A simpler make clean might even be enough. But when you try it, you get the same aclocal error.

Whoops! make clean runs make, which triggers the rule that configure has to run before make, which fails.

It would be nice if the make rules were smart enough to notice this and not require configure or autogen if the make target is something simple like clean or distclean. Alas, in most projects, they aren't.

But it turns out that even if you can't run with your usual arguments -- e.g. ./ --prefix=/usr/local/gimp-git -- running ./ by itself with no extra arguments will often fix the problem.

This happens to me often enough with the GIMP source tree that I made a shell alias for it:

alias distclean="./ && ./configure && make clean"

Saving your configure arguments

Of course, this wipes out any arguments you've previously passed to autogen and configure. So assuming this succeeds, your very next action should be to run autogen again with the arguments you actually want to use, e.g.:

./ --prefix=/usr/local/gimp-git

Before you ran the distclean, you could get those arguments by looking at the first few lines of config.log. But after you've run distclean, config.log is gone -- what if you forgot to save the arguments first? Or what if you just forget that you need to re-run again after your distclean?

To guard against that, I wrote a somewhat more complicated shell function to use instead of the simple alias I listed above.

The first trick is to get the arguments you previously passed to configure. You can parse them out of config.log:

$ egrep '^  \$ ./configure' config.log
  $ ./configure --prefix=/usr/local/gimp-git --enable-foo --disable-bar

Adding a bit of sed to strip off the beginning of the command, you could save the previously used arguments like this:

    args=$(egrep '^  \$ ./configure' config.log | sed 's_^  \$ ./configure __')

(There's a better place for getting those arguments, config.status -- but parsing them from there is a bit more complicated, so I'll follow up with a separate article on that, chock-full of zsh goodness.)

So here's the distclean shell function, written for zsh:

distclean() {
    setopt localoptions errreturn

    args=$(egrep '^  \$ ./configure' config.log | sed 's_^  \$ ./configure __')
    echo "Saved args:" $args
    make clean

    echo "==========================="
    echo "Running ./ $args"
    sleep 3
    ./ $args

The setopt localoptions errreturn at the beginning is a zsh-ism that tells the shell to exit if there's an error. You don't want to forge ahead and run configure and make clean if your didn't work right. errreturn does much the same thing as the && between the commands in the simpler shell alias above, but with cleaner syntax.

If you're using bash, you could string all the commands on one line instead, with && between them, something like this: ./ && ./configure && make clean && ./ $args Or perhaps some bash user will tell me of a better way.

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[ 13:33 Nov 27, 2015    More programming | permalink to this entry | comments ]

Thu, 22 Oct 2015

Non-free software can mean unexpected surprises

I went to a night sky photography talk on Tuesday. The presenter talked a bit about tips on camera lenses, exposures; then showed a raw image and prepared to demonstrate how to process it to bring out the details.

His slides disappeared, the screen went blank, and then ... nothing. He wrestled with his laptop for a while. Finally he said "Looks like I'm going to need a network connection", left the podium and headed out the door to find someone to help him with that.

I'm not sure what the networking issue was: the nature center has open wi-fi, but you know how it is during talks: if anything can possibly go wrong with networking, it will, which is why a good speaker tries not to rely on it. And I'm not blaming this speaker, who had clearly done plenty of preparation and thought he had everything lined up.

Eventually they got the network connection, and he connected to Adobe. It turns out the problem was that Adobe Photoshop is now cloud-based. Even if you have a local copy of the software, it insists on checking in with Adobe at least every 30 days. At least, that's the theory. But he had used the software on that laptop earlier that same day, and thought he was safe. But that wasn't good enough, and Photoshop picked the worst possible time -- a talk in front of a large audience -- to decide it needed to check in before letting him do anything.

Someone sitting near me muttered "I'd been thinking about buying that, but now I don't think I will." Someone else told me afterward that all Photoshop is now cloud-based; older versions still work, but if you buy Photoshop now, your only option is this cloud version that may decide ... at the least opportune moment ... that you can't use your software any more.

I'm so glad I use Free software like GIMP. Not that things can't go wrong giving a GIMP talk, of course. Unexpected problems or bugs can arise with any software, and you take that risk any time you give a live demo.

But at least with Free, open source software like GIMP, you know you own the software and it's not suddenly going to refuse to run without a license check. That sort of freedom is what makes the difference between free as in beer, and Free as in speech.

You can practice your demo carefully before the talk to guard against most bugs and glitches; but all the practice in the world won't guard against software that won't start.

I talked to the club president afterward and offered to give a GIMP talk to the club some time soon, when their schedule allows.

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[ 10:24 Oct 22, 2015    More gimp | permalink to this entry | comments ]

Mon, 16 May 2011

How to make a patch that might get accepted into Ubuntu, using bzr

Update and warning: My bzr diff was not accepted. It turns out this particular package doesn't accept that format. Apparently different packages within Ubuntu require different types of patches, and there's no good way to find out besides submitting one type of patch and seeing if it's rejected or ignored. In the end, I did get a patch accepted, and will write up separately how that patch was generated.

The process of submitting bugs and patches to Ubuntu can be deeply frustrating. Even if you figure out how to fix a bug and attach a patch, the patch can sit in Launchpad for years with no attention, as this ubuntu-devel-discuss thread attests.

The problem is that there are a lot of bugs and not enough people qualified to review patches and check them in. To make things easier for the packagers, sometimes people are told to "make a debdiff" or "make a ppa". But it's tough to find good instructions on how to do these things. There are partial instructions at Contributing and on the Packaging Guide -- but both pages are aimed at people who want to become regular packagers of new apps, not someone who just has one patch for a specific bug, and they're both missing crucial steps. Apparently there's a new and better packaging guide being written, but it's not publically available yet.

These days, Bazaar (bzr), not debdiff, is considered the best way to make a patch easy for Ubuntu developers to review. With a lot of help from #ubuntu-women, and particularly Maco (THANKS!), I worked through the steps to submit a patch I'd posted to bug 370735 two years ago for gmemusage. Here's what I needed to do.

Set up the tools

First, install some build tools you'll need, if you don't already have them:

sudo apt-get install bzr bzr-builddeb pbuilder

You will also need a Launchpad account:

and connect bzr to your Launchpad account:
bzr whoami "Firstname Lastname <>"
bzr launchpad-login your-acct

Check out the code

Create a directory where you'll do the work:

mkdir pkgname
cd pkgname

Check out the source from bzr:

bzr branch lp:ubuntu/pkgname pkgname

Make a bzr branch for your fixes. It's probably a good idea to include the bug number or other specifics in the branch name:

bzr branch pkgname pkgname-fix-bugnum
cd pkgname-fix-bugnum

Now you can apply the patch, e.g. patch <../mypatch.diff, or edit source files directly.

Make a package you can test

Making a package from a bzr directory requires several steps.

Making a source package is easy:

bzr bd -S -- -uc -us
This will show up as ../pkgname_version.dsc.

But if you want something you can install and test, you need a binary package. That's quite a bit more trouble to generate. You'll be using pbuilder to create a minimal install of Ubuntu in a chroot environment, so the build isn't polluted by any local changes you have on your own machine.

First create the chroot: this takes a while, maybe 10 minutes or so, or a lot longer if you have a slow network connection. You'll also need some disk space: on my machine it used 168M in /var/cache (plus more for the next step). Since it uses /var/cache, it needs sudo to write there:

sudo pbuilder --create natty

Now build a .deb binary package from your .dsc source package:

sudo pbuilder --build ../pkgname_version.dsc
pbuilder will install a bunch of additional packages, like X and other libraries that are needed to build your package but weren't included in the minimal pbuilder setup.

And then once it's done with the build, it removes them all again. Apparently there's a way to make it cache them so you'll have them if you need to build again, but I'm not sure how.

pbuilder --build gives lots of output, but none of that output tells you where it's actually creating the .deb. Look in /var/cache/pbuilder/result for it.

And now you can finally try installing it:

sudo  dpkg -i /var/cache/pbuilder/result/pkgname_blahblah.deb

You can now test your fix, and make sure you fixed the problem and didn't break anything else.

Check in your bzr branch

Once you're confident your fix is good. it's time to check it in.

Make a new changelog entry:

dch -i
This will open your editor of choice, where you should explain briefly what you changed and why. If it's a fix for a Launchpad bug, list the bug number like this: (LP: #370735).

If you're proposing a fix for an Ubuntu that's already released, you also need to add -proposed to the release name in the top line in the changelog, e.g.:

pkgname (0.2-11ubuntu1) natty-proposed; urgency=low

Also, pay attention to that ubuntu1 part of the version string if the entry prior to yours doesn't include "ubuntu" in the version. If you're proposing a change to a stable release, change that to ubuntu0.1; if it's for the current development release, it's okay to leave it at ubuntu1 (more details on this Packaging page).

Finally, you can check it in to your local repository:

and push it to Launchpad:
bzr push lp:~yourname/ubuntu/natty/pkgname/pkgname-fix-bugnum

Notify possible sponsors

You'll want to make sure your patch gets on the sponsorship queue, so someone can review it and check in the fix.

bzr lp-open
(For me, this opened chromium even though firefox is my preferred browser. To use Firefox, I had to: sudo update-alternatives --config x-www-browser first. Boo chromium for making itself default without asking me.)

You should now have a launchpad page open in your browser. Click on "Propose for merging into another branch" and include a description of your change and why it should be merged. This, I'm told, notifies potential sponsors who can review your patch and approve it for check-in.

Whew! That's a lot of steps. You could argue that it's harder to prepare a patch for Ubuntu than it was to fix the bug in the first place. Stay tuned ... I'll let you know when and if my patch actually gets approved.

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[ 15:38 May 16, 2011    More linux | permalink to this entry | comments ]

Sat, 06 Feb 2010

Making "Citizen Science" compelling

I had the opportunity to participate in a focus group on NASA's new "citizen science" project, called Moon Zoo, with a bunch of other fellow lunatics, amateur astronomers and lunar enthusiasts.

Moon Zoo sounds really interesting. Ordinary people will analyze high-resolution photos of the lunar surface: find out how many boulders and craters are there. I hope it will also include more details like crater type and size, rilles and so forth, though that wasn't mentioned. These are all tasks that are easy for a human and hard for a computer: perfect for crowdsourcing. Think Galaxy Zoo for the moon. The resulting data will be used for planning future lunar missions as well as for general lunar science.

It sounds like a great project and I'm excited about it. But I'm not going to write about Moon Zoo today -- it doesn't exist yet (current estimate is mid-March), though there is a preliminary PDF. Instead, I want to talk about some of the great ideas that came out of the focus group.

The primary question: How do we get people -- both amateur astronomers and the general public, people of all ages -- interested in contributing to a citizen science project like Moon Zoo?

Here are some of the key ideas:

Make the data public

This was the most important point, echoed by a lot of participants. Some people felt that many of the existing "citizen science" projects project the attitude "We want something from you, but we're not going to give you anything in return." If you use crowdsourcing to create a dataset, make it available to the crowd.

Opening the data has a lot of advantages:

Projects like Wikipedia and Open Street Map, as well as Linux and the rest of the open source movement, show how much an open data model can inspire contributions.

Give credit to individuals and teams

People cited the example of SETI@Home, where teams of contributors can compete to see who's contributed the most. Show rankings for both individuals and groups, so they can track their progress and maybe get a bit competitive with other groups. Highlight groups and individuals who contribute a lot -- maybe even make it a formal competition and offer inexpensive prizes like T-shirts or mugs.

A teenaged panel member had the great suggestion of making buttons that said "I'm a Moon Zookeeper." Little rewards like that don't cost much but can really motivate people.

Offer an offline version

They wanted to hear ideas for publicizing Moon Zoo to groups like our local astronomy clubs.

I mentioned that I've often wanted to spread the word about Galaxy Zoo, but it's entirely a web-based application and when I give talks to clubs or school groups, web access is never an option. (Ironically, the person leading the focus group had planned to demonstrate Galaxy Zoo to us but couldn't get connected to the wi-fi at the Lawrence Hall of Science.)

Projects are so much easier to evangelize if you can download an offline demo.

And not just a demo, either. There should be a way to download a real version, including a small data set. Imagine if you could grab a Moon Zoo pack and do a little classifying whenever you got a few spare minutes -- on the airplane or train, or in a hotel room while traveling.

Important note: this does not mean you should write a separate Windows app for people to download. Keep it HTML, Javascript and cross platform so everyone can run it. Then let people download a local copy of the same web app they run on your site.

Make sure it works on phones and game consoles

Lots of people use smartphones more than they use a desktop computer these days. Make sure the app runs on all the popular smartphones. And lots of kids have access to handheld web-enabled game consoles: you can reach a whole new set of kids by supporting these platforms.

Offer levels of accomplishment, like a game

Lots of people are competitive by nature, and like to feel they're getting better at what they're doing. Play to that: let users advance as they get more experienced, and give them the option of doing harder projects. "I'm up to level 7 in Moon Zoo!"

Use social networking

Facebook. Twitter. Nuff said.

Don't keep results a secret

Quite a few scientific publications have arisen out of Galaxy Zoo -- yet although most of us were familiar with Galaxy Zoo, few of us knew that. Why so secretive? They should be trumpeting achievements like that.

How many times have you volunteered for a survey or study, then wondered for years afterward how the results came out? Researchers never contact the volunteers when the paper is finally published. It's frustrating and demotivating; it makes you not want to volunteer again. Lots of us sign up because we're curious about the science -- but that means we're also curious about the results.

With citizen science projects, this is particularly easy. Set up a mailing list or forum (or both) to discuss results and announce when papers are published. Set up a Twitter account and a Facebook group to announce new papers to anyone who wants to follow. This is the age of Web 2.0, folks -- there's no excuse for not communicating.

I don't know if NASA will listen to our ideas. But I hope they do. Moon Zoo promises to be a terrific project ... and the more of these principles they follow, the more dedicated volunteers they'll get and that will make the project even better.

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[ 20:25 Feb 06, 2010    More science/astro | permalink to this entry | comments ]

Sun, 06 Sep 2009

Using apt-file to track down build errors

Someone was asking for help building XEphem on the XEphem mailing list. It was a simple case of a missing include file, where the only trick is to find out what package you need to install to get that file. (This is complicated on Ubuntu, which the poster was using, by the way they fragment the X developement headers into a maze of a xillion tiny packages.)

The solution -- apt-file -- is so simple and easy to use, and yet a lot of people don't know about it. So here's how it works.

The poster reported getting these compiler errors:

ar rc libz.a adler32.o compress.o crc32.o uncompr.o deflate.o trees.o zutil.o inflate.o inftrees.o inffast.o
ranlib libz.a
make[1]: Leaving directory `/home/gregs/xephem-3.7.4/libz'
gcc -I../../libastro -I../../libip -I../../liblilxml -I../../libjpegd -I../../libpng -I../../libz -g -O2 -Wall -I../../libXm/linux86 -I/usr/X11R6/include   -c -o aavso.o aavso.c
In file included from aavso.c:12:
../../libXm/linux86/Xm/Xm.h:56:27: error: X11/Intrinsic.h: No such file or directory
../../libXm/linux86/Xm/Xm.h:57:23: error: X11/Shell.h: No such file or directory
../../libXm/linux86/Xm/Xm.h:58:23: error: X11/Xatom.h: No such file or directory
../../libXm/linux86/Xm/Xm.h:59:34: error: X11/extensions/Print.h: No such file or directory
In file included from ../../libXm/linux86/Xm/Xm.h:60,
                 from aavso.c:12:
../../libXm/linux86/Xm/XmStrDefs.h:1373: error: expected `=', `,', `;', `asm' or `__attribute__' before `char'
In file included from ../../libXm/linux86/Xm/Xm.h:60,
                 from aavso.c:12:
../../libXm/linux86/Xm/XmStrDefs.h:5439:28: error: X11/StringDefs.h: No such file or directory
In file included from ../../libXm/linux86/Xm/Xm.h:61,
                 from aavso.c:12:
../../libXm/linux86/Xm/VirtKeys.h:108: error: expected `)' before `*' token
In file included from ../../libXm/linux86/Xm/Display.h:49,
                 from ../../libXm/linux86/Xm/DragC.h:48,
                 from ../../libXm/linux86/Xm/Transfer.h:44,
                 from ../../libXm/linux86/Xm/Xm.h:62,
                 from aavso.c:12:
../../libXm/linux86/Xm/DropSMgr.h:88: error: expected specifier-qualifier-list before `XEvent'
../../libXm/linux86/Xm/DropSMgr.h:100: error: expected specifier-qualifier-list before `XEvent'
How do you go about figuring this out?

When interpreting compiler errors, usually what matters is the *first* error. So try to find that. In the transcript above, the first line saying "error:" is this one:

../../libXm/linux86/Xm/Xm.h:56:27: error: X11/Intrinsic.h: No such file or directory

So the first problem is that the compiler is trying to find a file called Intrinsic.h that isn't installed.

On Debian-based systems, there's a great program you can use to find files available for install: apt-file. It's not installed by default, so install it, then update it, like this (the update will take a long time):

$ sudo apt-get install apt-file
$ sudo apt-file update
Once it's updated, you can now find out what package would install a file like this:
$  apt-file search Intrinsic.h
libxt-dev: /usr/include/X11/Intrinsic.h
tendra: /usr/lib/TenDRA/lib/include/x5/t.api/X11/Intrinsic.h

In this case two two packages could install a file by that name. You can usually figure out from looking which one is the "real" one (usually the one with the shorter name, or the one where the package name sounds related to what you're trying to do). If you're stil not sure, try something like apt-cache show libxt-dev tendra to find out more about the packages involved.

In this case, it's pretty clear that tendra is a red herring, and the problem is likely that the libxt-dev package is missing. So apt-get install libxt-dev and try the build again.

Repeat the process until you have everything you need for the build.

Remember apt-file if you're not already using it. It's tremendously useful in tracking down build dependencies.

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[ 11:25 Sep 06, 2009    More linux | permalink to this entry | comments ]

Fri, 12 Jun 2009

A Table of Closed versus Open Formats

My last Toastmasters speech was on open formats: why you should use open formats rather than closed/proprietary ones and the risks of closed formats.

To make it clearer, I wanted to print out handouts people could take home summarizing some of the most common closed formats, along with open alternatives.

Surely there are lots of such tables on the web, I thought. I'll just find one and customize it a little for this specific audience.

To my surprise, I couldn't find a single one. Even didn't have very much.

So I started one: Open vs. Closed Formats. It's far from complete, so I hope I'll continue to get contributions to flesh it out more.

And the talk? It went over very well, and people appreciated the handout. There's a limit to how much information you can get across in under ten minutes, but I think I got the point across. The talk itself, such as it is, is here: Open up!

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[ 11:37 Jun 12, 2009    More tech | permalink to this entry | comments ]

Sat, 03 Jan 2009

OpenStreetMap mapping parties

Latest obsession: mapping with OpenStreetMap.

Last month, OpenStreetMap and its benefactor company CloudMade held a "mapping party" in Palo Alto. I love maps and mapping (I wrote my own little topographic map viewer when I couldn't find one ready-made) and I've been wanting to know more about the state of open source mapping. A mapping party sounded perfect.

The party was a loosely organized affair. We met at a coffeehouse and discussed basics of mapping and openstreetmap. The hosts tried to show us newbies how OSM works, but that was complicated by the coffeehouse's wireless net being down. No big deal -- turns out the point of a mapping party is to hand out GPSes to anyone who doesn't already have one and send us out to do some mapping.

I attached myself to a couple of CloudMade folks who had some experience already and we headed north on a pedestrian path. We spent a couple of hours walking urban trails and marking waypoints. Then we all converged on a tea shop (whose wireless worked a little better than the one at the coffeehouse, but still not very reliably) for lunch and transfer of track and waypoint files.

This part didn't work all that well. It turned out the units we were using (Garmin Legend HCx) can transfer files in two modes, USB mass storage (the easy way, just move files as if from an external disk) or USB Garmin protocol (the hard way: you have to use software like gpsbabel, or the Garmin software if you're on Windows). And in mass storage mode, you get a file but the waypoints aren't there.

The folks running the event all had Macs, and there were several Linux users there as well, but no Windows laptops. By the time the Macs both had gpsbabel downloaded over the tea shop's flaky net, it was past time for me to leave, so I never did get to see our waypoint files. Still, I could see it was possible (and one of the Linux attendees assured me that he had no trouble with any of the software; in fact, he found it easier than what the Mac people at the party were going through).

But I was still pretty jazzed about how easy OpenStreetMap is to use. You can contribute to the maps even without a GPS. Once you've registered on the site, you just click on the Edit tab on any map, and you see a flash application called "Potlatch" that lets you mark trails, roads or other features based on satellite images or the existing map. I was able to change a couple of mismarked roads near where I live, as well as adding a new trail and correcting the info on an existing one for one of the nearby parks.

If you prefer (as, I admit, I do) to work offline or don't like flash, you can use a Java app, JOSM, or a native app, merkaartor. Very cool! Merkaartor is my favorite so far (because it's faster and works better in standalone mode) though it's still fairly rough around the edges. They're all described on the OSM Map Editing page.

Of course, all this left me lusting after a GPS. But that's another story, to be told separately.

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[ 13:00 Jan 03, 2009    More mapping | permalink to this entry | comments ]

Fri, 04 Jul 2008

Learning about Firefox 3 extensions

Oops! Right after I posted that last entry, I discovered that my little kitfox extension wasn't working as well as I'd thought. And the more I hacked it, the less well it worked, and the more I discovered was missing, like a chrome.manifest file (which firefox 2 hadn't seemed to need).

Eventually some very helpful folks on #extdev pointed me to Ted Mielczarek's excellent Extension Wizard. Give it some details about your extension (its name and version, your name, and a couple things you might want like a toolbar button, a prefs panel and a context menu) and it generates a zipped directory containing a bare bones extension, even including niceties like internationalized strings.

Even better, your new extension skeleton includes a readme that tells you how to leave the extension expanded while you work on it. That's quite a bit easier than building the XPI file and installing it each time.

So kitfox has a 0.3 version (in the unlikely event that anybody besides me wants it).

There's a project called fizzypop to develop and extend useful Mozilla dev tools like the Extension Wizard ... watch that space for more details.

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[ 21:12 Jul 04, 2008    More tech/web | permalink to this entry | comments ]