/bioconda-recipes

Finished Python 3.6 migration #4888

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merged 126 commits into from Jun 3, 2017

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@johanneskoester @bioconda-bot @SoapZA @bgruening @daler
@johanneskoester
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johanneskoester commented Jun 3, 2017

  • I have read the guidelines for bioconda recipes.
  • This PR adds a new recipe.
  • This PR updates an existing recipe.
  • This PR does something else (explain below).

In the past weeks, we have migrated all existing recipes to Python 3.6 (if possible). This PR merges the required changes into master. It marks the successful completion of the migration process.

bgruening and others added some commits Jan 1, 2017

@bgruening bgruening Add python-3.6

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18a48ee
@johanneskoester johanneskoester Merge branch 'master' into python-3.6

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099f631
@johanneskoester johanneskoester Merge branch 'master' into python-3.6 e27060b
@johanneskoester johanneskoester Merged master.

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9a97f09
@bgruening @johanneskoester bgruening [ci skip] Merge pull request #4597 from kurtwheeler/more-genome-annot… 
…ations

More genome annotations
 9db94ca
@johanneskoester johanneskoester Merge pull request #4598 from bioconda/python-3.6 
Python 3.6
0e84fad
@johanneskoester johanneskoester Do not skip build for bulk updates. b3256d5
@johanneskoester johanneskoester Merge branch 'bulk' of github.com:bioconda/bioconda-recipes into bulk
e5392c7
@johanneskoester johanneskoester Fix skipping.
3f0b9ba
@johanneskoester johanneskoester Simplify filter logic.
37a7017
@johanneskoester johanneskoester Remove travis_wait, because bioconda-utils now prints a spinner for l… 
…ong-running tasks.
1692561
@johanneskoester johanneskoester Remove phonenumbers (available in conda-forge).
0b52eb3
@johanneskoester johanneskoester Skip unnecessary tests in rpy2. 852369d
@johanneskoester johanneskoester Add libgcc runtime dependency for scoop. b8992f5
@johanneskoester johanneskoester Add zlib to pytabix. Add gcc to python-igraph. 59fd303
@johanneskoester johanneskoester Add bzip2 to libsbml.
5d7da1d
@bgruening bgruening add libxml2 as dependency
65347be
@bgruening bgruening rebuild flowtools
bd4057b
@bgruening bgruening skip openbabel on py36
6332d4b
@bgruening bgruening try an other selector
d1befbd
@bgruening bgruening fix the builds a little bit, however this important package needs a s… 
…ome love
329b3fb
@bgruening bgruening fix URL 
ping @BioNinja, please don't remove tarballs :)
e3734e0
@bgruening bgruening Fix tests for mgf-formatter
4fd450c
@bgruening bgruening That is scary, the checksum changed?
1f6b266
@bgruening bgruening removed in favor of https://github.com/conda-forge/python-magic-feeds… 
…tock
ed477cd
@bgruening bgruening fix download path
a2f0e9c
@bgruening bgruening checksum incorrect :(
fd7071c
@johanneskoester johanneskoester Fix pybigwig test cases.
d0342b6
@johanneskoester johanneskoester Merge branch 'master' into bulk 60c5e1d
@johanneskoester johanneskoester Pin conda-build to a newer version.
f89b45a
@johanneskoester johanneskoester Revert conda pinning.
4744ae8
@johanneskoester johanneskoester Fix merge error.
0b298fd
@daler daler point to bioconda-utils:enable-build-ids branch
faff0c1
@bgruening bgruening remove dev version from repository
4848ed6
@bgruening bgruening add dependency on pyqt4
2d936ad
@johanneskoester johanneskoester Fix nanosimh source URL. 1b2b52f
@johanneskoester johanneskoester Add gcc/libgcc to illuminate. 61c8e77
@johanneskoester johanneskoester Removed old busco recipe because the source code is not available any… 
…more.
 7664085
@johanneskoester johanneskoester Add automake. Update numpy to 1.12, because 1.10 is not built with Py… 
…thon 3.6 support.
 475fcd5
@johanneskoester johanneskoester Remove superfluous test case. a9511e9
@johanneskoester johanneskoester Minor.
62197f3
@johanneskoester johanneskoester Fix intarna build string. 97bda3b
@johanneskoester johanneskoester Remove old prosic version. 6e89276
@johanneskoester johanneskoester Fix scipy dependency of igdiscover and cosmetic changes. 3150a62
@johanneskoester johanneskoester Add ncurses dependency. fa48dbe
@johanneskoester johanneskoester Add pyqt.
047b4ce
@johanneskoester johanneskoester Skip zeroc-ice because of segmentation fault. 087f7b6
@johanneskoester johanneskoester Try to fix selector. edae01b
@johanneskoester johanneskoester Add pyqt4 dependency. 7fd6b15
@johanneskoester johanneskoester Remove old version of bx-python. 65bb37b
@johanneskoester johanneskoester Skip python 3.6 92d9230
@johanneskoester johanneskoester Skip Python 3.6 because it is unsupported.
dcd1797
@johanneskoester johanneskoester Use bioconda-utils master again (after the merge). Suppress warnings … 
…in intarna build.
11f8f25
@johanneskoester johanneskoester Remove llvm dependency of whatshap. f2ad993
@johanneskoester johanneskoester Use debian container image in case of recipes depending on click. 
The reason is that click requires full unicode support, which is not present in the busybox image used for mulled.
dea26c5
@johanneskoester johanneskoester Merge branch 'master' into bulk e3d246c
@johanneskoester johanneskoester Fixes and blacklisting. Temporarily use a fixed branch of bioconda-ut… 
…ils.
7a84980
@johanneskoester johanneskoester Fix merge conflict in openbabel recipe.
b2b5b83
@johanneskoester johanneskoester Skip py36 because pysamstats relies on old pysam which does not build… 
… on py36.
 2a32a79
@johanneskoester johanneskoester Use debian container for ggplot. 678c5a7
@johanneskoester johanneskoester Revert skipping because of encoding errors. These should be fixed by b… 
…ioconda/bioconda-utils#116.
 6115564
@johanneskoester johanneskoester Temporarily use fixed branch of bioconda-utils.
00c479f
@johanneskoester johanneskoester Bioconda-utils fix has been merged, use master again. 87e9738
@johanneskoester johanneskoester Add missing library. 8442015
@johanneskoester johanneskoester Skip whole section outside of osx. 236c1c5
@johanneskoester johanneskoester Add missing dependency. a02369d
@johanneskoester johanneskoester Show test results of last. c3df0d2
@johanneskoester johanneskoester Fix hmmlearn dependencies. 7b1377b
@johanneskoester johanneskoester Relax setuptools dependency. bb5ac0c
@johanneskoester johanneskoester Update viral-ngs dependency in order to avoid conflict with py36. 55776fc
@johanneskoester johanneskoester Fix fsnviz dependency. 6d59640
@johanneskoester johanneskoester New garnet version. The old one was removed from pypi!! 7047c3b
@johanneskoester johanneskoester Disable make test for intarna. 6924ce6
@johanneskoester johanneskoester Add pyqt as build requirement. b46da75
@johanneskoester johanneskoester Relax bowtie dependency. 481421c
@johanneskoester johanneskoester Skip osx.
fecb972
@johanneskoester johanneskoester Pyqt is not a dependency of gseapy. 9f5336d
@johanneskoester johanneskoester Skip viral-ngs for py36. 4204350
@johanneskoester johanneskoester Relax matplotlib pinning for qiime.
1e66155
@johanneskoester johanneskoester Fix url. dbc2f7a
@johanneskoester johanneskoester Skip ig-flowtools until R dependencies have been updated. 3287601
@johanneskoester johanneskoester Omit futures in python 3k. Add missing dependency. c26fa2a
@johanneskoester johanneskoester Try simplifying osx setup for whatshap. The stdlib argument did not w… 
…ork anymore.
 50340a6
@johanneskoester johanneskoester Relax snakemake dependency. 5c5a791
@johanneskoester johanneskoester Use debian container for samsifter because it depends on X11 libs.
d465239
@johanneskoester johanneskoester Skip rapclust. b20c849
@johanneskoester johanneskoester Fix matplotlib version. 27f103e
@johanneskoester johanneskoester Skip chanjo
d6b9b19
@johanneskoester johanneskoester Fix perl dependency. c0eb897
@johanneskoester johanneskoester Fix last dependencies. b393a5b
@johanneskoester johanneskoester Use extended container for fitter.
6019f6b
@johanneskoester johanneskoester Fix args.
b4e4e37
@johanneskoester johanneskoester Fix gseapy. c728a5a
@johanneskoester johanneskoester Merge branch 'bulk' of github.com:bioconda/bioconda-recipes into bulk 74e021c
@johanneskoester johanneskoester Merge branch 'master' into bulk
5f0f993
@johanneskoester johanneskoester Handle locale in test cases of click-related recipes. Fix swarm tests. 97217e4
@johanneskoester johanneskoester Fixes.
8dced15
@johanneskoester johanneskoester Remove unnecessary dependencies. 8411440
@johanneskoester johanneskoester Use our own extended base image.
1e0952d
@johanneskoester johanneskoester Use master branch of bioconda-utils.
b463444
@johanneskoester johanneskoester Documentation and base image.
31cb51a
@johanneskoester johanneskoester Fix swarm dependencies. c7d582f
@johanneskoester johanneskoester Skip until we have completely switched to conda-forge. 4cb1c5a
@johanneskoester johanneskoester Use extended base image for dreamtools. cec3ccf
@johanneskoester johanneskoester Skip fwdpy (missing headers in own source).
da1425f
@johanneskoester johanneskoester Fixes and formatting.
a1481fb
@johanneskoester johanneskoester Skipping hlama for anything except py35. @holtgrewe this is because f… 
…or py36, you would need to depend on a current Snakemake version.

I suggest to relax this dependency since Snakemake is backwards compatible anyway.
 df4ca09
@johanneskoester johanneskoester Fixes 7614675
@johanneskoester johanneskoester Adapt container image definition to new syntax. Skip click-based reci… 
…pes on py3k.
9821831
@johanneskoester johanneskoester Add zlib to bx-python. 21ef87b
@johanneskoester johanneskoester Fixes.
364f7c2
@johanneskoester johanneskoester Add missing dependency. 57f6a1d
@johanneskoester johanneskoester Add gcc.
94f0bd7
@johanneskoester johanneskoester Add missing dependency xz. 5aaf23b
@johanneskoester johanneskoester Remove bx-python 0.7.1 because it does not build even on python 2.7 06bc570
@johanneskoester johanneskoester Use extended base image. 305cfcd
@johanneskoester johanneskoester Add missing lib.
789408f
@johanneskoester johanneskoester Use UTF-8 in test cases. 23956d1
@johanneskoester johanneskoester Debug bx-python.
7532b12
@johanneskoester johanneskoester Fix qiime. Use test branch of bioconda-utils.
cb19598
@johanneskoester johanneskoester Fix qiime. Use test branch of bioconda-utils. 9cb7c80
@johanneskoester johanneskoester Merge branch 'bulk' of github.com:bioconda/bioconda-recipes into bulk
54d6b24
@johanneskoester johanneskoester Skip cgat-scripts-devel on py36. Use master branch of bioconda-utils … 
…again after PR has been merged.
f715be6
@johanneskoester johanneskoester Merge branch 'master' into bulk

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f097818

johanneskoester referenced this pull request Jun 3, 2017

Merged

Import smallgenomeutilities 0.1 #4882

2 of 4 tasks complete
@bioconda-bot

bioconda-bot commented Jun 3, 2017

Linting

The following problems have been found

Recipe failed checks
recipes/amos missing_hash
recipes/amos uses_git_url
recipes/bcl2fastq-nextseq missing_hash
recipes/bcl2fastq-nextseq uses_git_url
recipes/biom-format/2.1.5 uses_setuptools
recipes/bx-python uses_setuptools
recipes/cgat-pipelines-nosetests uses_setuptools
recipes/cgat-scripts uses_setuptools
recipes/cgat-scripts-devel uses_setuptools
recipes/cgat-scripts-nosetests uses_setuptools
recipes/crispresso uses_javajdk
recipes/crispresso uses_setuptools
recipes/hmmlearn missing_hash
recipes/hmmlearn uses_setuptools
recipes/moca uses_setuptools
recipes/phizz uses_setuptools
recipes/planemo/0.34.1 uses_setuptools
recipes/pybigwig/0.1.11 missing_tests
recipes/python-bioext missing_hash
recipes/python-bioext uses_git_url
recipes/python-igraph in_other_channels
recipes/scikit-bio in_other_channels
recipes/spades/3.9.0 missing_hash
recipes/swga uses_setuptools
recipes/transabyss missing_hash
recipes/umis missing_hash
recipes/whatshap uses_setuptools
@SoapZA
Contributor

SoapZA commented Jun 3, 2017

@johanneskoester I see a lot of merge commits, don't you rather want to rebase to keep the history somewhat clean?
@johanneskoester johanneskoester Merge branch 'bulk' of github.com:bioconda/bioconda-recipes into bulk

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0ab0065
@johanneskoester
Contributor

johanneskoester commented Jun 3, 2017

Rebasing in a branch that has diverged since months is very dangerous in my experience (-> rebase hell). We will do a squash merge of this PR, so that the master history stays clean.
@bgruening
Contributor

bgruening commented Jun 3, 2017

Yeah, thanks a lot @johanneskoester!

@bgruening bgruening merged commit f575c10 into master Jun 3, 2017
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