ERROR-mk_matrix with conda packaged version of release 0.9.1

[guillaumecharbonnier]

The first conda package for pygtftk is out: https://anaconda.org/guillaumecharbonnier/pygtftk I am not able to pass tests requiring this file though: ERROR-mk_matrix : Not a bigwig file :pygtftk/data/simple/simple.bw

Maybe an issue with the version of pyBigWig?

            bigwig = pyBigWig.open(big_wig)
            if not bigwig.isBigWig():
                message("Not a bigwig file :" + big_wig, type="ERROR")

Version of pybigwig in packaged environment: https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.2.8-py27_0.tar.bz2

Version of pybigwig in working unpackaged environment: https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.3.10-np113py27_0.tar.bz2

Currently rebuilding with higher-version requirement to see if it solves the issue.

[guillaumecharbonnier]

Adding pybigwig >= 0.3.1 in meta.yaml, I got https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.3.6-np112py27_0.tar.bz2 which allows to pass all tests except this one:

not ok 7 random_tx_7
# (in test file random_tx.bats, line 27)
#   `[ "$result" = "ENST00000378016,107" ]' failed
make: *** [random_tx.completed] Error 1

It also fails in my unpackaged pygtftk installation. @dputhier do you pass it on 0.9.1?

[dputhier]

Hi Guillaume, I also had issues recently with pybigwig when packaging for Pypi. In 0.9.3 (whose release is ungoing) I have updated the env.yaml to get pybigwig >=0.3.12. It won't install directly from a conda repo but should be instruct by conda to install through pip (seems to work with conda create). Regarding the last test that fail I think I have fixed this one in the upcoming release (0.9.3). This last release should be Pypiable, condable (I hope), should support Python 2/3 and should fixe last warning upon compilation that may encounter on Py3. It should be available soon (Fafa@13 should fix the compilation warnings soon). Note that 0.9.2 suffers from a problem with the profile command (the user-choosen colors are not applied to the diagrams). So my hope is that this 0.9.3 should be close to a release (and not pre-release) version. Note that the last env.yaml will rely on Python 3.6.

[dputhier]

0.9.4 is out. Pygtftk now requires pyBigWig 0.3.12. I think it would fix this issues... Let see. Test 'random_tx_7' passed on both OSX and Ubuntu 12.04.