Travis ci

[johanneskoester]

Hi guys,
I have finished the work on automatic builds and tests with Travis CI.
This pull request introduces the following changes:

• all recipes are moved to the recipes subfolder
• the Docker image is modified to include a build script that uses conda to build all recipes
• conda is configured to skip packages that are already present in bioconda in the same version
• if executed on the master branch, the script uploads all successful builds to our channel (using a private token instead of username and password)
• all failed builds/tests are reported at the end
• Travis is configured to build for both Python 3.4 and Python 2.7 and Numpy 1.8. This can be easily extended in the future.

This approach allows us to test any branch or pull request. Further the master branch will always be in sync with the bioconda channel.

Everything works now, but the pysam test fails for Python 2.7 while importing htslib. This is not really related to this branch, we just did not have a Python 2.7 build of pysam before.

[johanneskoester]

Ok, I have "fixed" the pysam test, by removing some import checks that seem to be Python version specific. The simple pysam import works. Ryan, are you ok with that change?
Now the tests only fail because pybedtools cannot be compiled on Python 2.7. Looks like a __future__ import is misplaced.

[daler]

Very nice!

Honestly compiling pysam has been giving me a lot of trouble recently, esp on Mac. I will need to do some more testing to see if those other imports are needed when actually using pysam. Hopefully the simpler import test will be fine.

I think one reason pybedtools failed is because it needed pysam built for py27 (see this line). But I guess since pysam comes later alphabetically, it wasn't built yet.

However, it looks like pysam for py27 was successfully uploaded now, so maybe a re-run of the Travis tests will work.

[daler]

Also a thought on dependencies, like pybedtools depending on pysam:

If B depends on A, then perhaps the workflow should be

• open a PR to build A
• ensure test passes, and therefore A gets uploaded to conda
• then open a PR to build B

[johanneskoester]

Exactly.
After restarting the build, there is still this import error in pybedtools:

Using /tmp/conda-build/anaconda/envs/_build/lib/python2.7/site-packages
Finished processing dependencies for pybedtools==0.7.0
Compiling /tmp/conda-build/anaconda/envs/_build/lib/python2.7/site-packages/pybedtools-0.7.0-py2.7-linux-x86_64.egg-info/scripts/pbt_plotting_example.py ...
  File "/tmp/conda-build/anaconda/envs/_build/lib/python2.7/site-packages/pybedtools-0.7.0-py2.7-linux-x86_64.egg-info/scripts/pbt_plotting_example.py", line 5
    from __future__ import print_function
SyntaxError: from __future__ imports must occur at the beginning of the file

Easy to fix though.

[daler]

Ah thanks. Yep, just saw that upon trying to build it myself. Building to the latest tag (0.7.1) should fix this, but I'm testing locally first. I'll push to this branch when it's done.

[johanneskoester]

I have implemented the OSX building and think the changes are ready for merging now.

[daler]

Wow, this is fantastic!

[chapmanb]

Johannes;
This is so incredible. Thanks for putting all the Travis pieces together. Brilliant.

[johanneskoester]

Thanks :-).