Finished Python 3.6 migration (#4888)

* Add python-3.6

* Merged master.

* Do not skip build for bulk updates.

* Fix skipping.

* Simplify filter logic.

* Remove travis_wait, because bioconda-utils now prints a spinner for long-running tasks.

* Remove phonenumbers (available in conda-forge).

* Skip unnecessary tests in rpy2.

* Add libgcc runtime dependency for scoop.

* Add zlib to pytabix. Add gcc to python-igraph.

* Add bzip2 to libsbml.

* add libxml2 as dependency

* rebuild flowtools

* skip openbabel on py36

* try an other selector

* fix the builds a little bit, however this important package needs a some love

* fix URL

ping @BioNinja, please don't remove tarballs :)

* Fix tests for mgf-formatter

* That is scary, the checksum changed?

* removed in favor of  https://github.com/conda-forge/python-magic-feedstock

* fix download path

* checksum incorrect :(

* Fix pybigwig test cases.

* Pin conda-build to a newer version.

* Revert conda pinning.

* Fix merge error.

* point to bioconda-utils:enable-build-ids branch

* remove dev version from repository

* add dependency on pyqt4

* Fix nanosimh source URL.

* Add gcc/libgcc to illuminate.

* Removed old busco recipe because the source code is not available anymore.

* Add automake. Update numpy to 1.12, because 1.10 is not built with Python 3.6 support.

* Remove superfluous test case.

* Minor.

* Fix intarna build string.

* Remove old prosic version.

* Fix scipy dependency of igdiscover and cosmetic changes.

* Add ncurses dependency.

* Add pyqt.

* Skip zeroc-ice because of segmentation fault.

* Try to fix selector.

* Add pyqt4 dependency.

* Remove old version of bx-python.

* Skip python 3.6

* Skip Python 3.6 because it is unsupported.

* Use bioconda-utils master again (after the merge). Suppress warnings in intarna build.

* Remove llvm dependency of whatshap.

* 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.

* Fixes and blacklisting. Temporarily use a fixed branch of bioconda-utils.

* Fix merge conflict in openbabel recipe.

* Skip py36 because pysamstats relies on old pysam which does not build on py36.

* Use debian container for ggplot.

* Revert skipping because of encoding errors. These should be fixed by bioconda/bioconda-utils#116.

* Temporarily use fixed branch of bioconda-utils.

* Bioconda-utils fix has been merged, use master again.

* Add missing library.

* Skip whole section outside of osx.

* Add missing dependency.

* Show test results of last.

* Fix hmmlearn dependencies.

* Relax setuptools dependency.

* Update viral-ngs dependency in order to avoid conflict with py36.

* Fix fsnviz dependency.

* New garnet version. The old one was removed from pypi!!

* Disable make test for intarna.

* Add pyqt as build requirement.

* Relax bowtie dependency.

* Skip osx.

* Pyqt is not a dependency of gseapy.

* Skip viral-ngs for py36.

* Relax matplotlib pinning for qiime.

* Fix url.

* Skip ig-flowtools until R dependencies have been updated.

* Omit futures in python 3k. Add missing dependency.

* Try simplifying osx setup for whatshap. The stdlib argument did not work anymore.

* Relax snakemake dependency.

* Use debian container for samsifter because it depends on X11 libs.

* Skip rapclust.

* Fix matplotlib version.

* Skip chanjo

* Fix perl dependency.

* Fix last dependencies.

* Use extended container for fitter.

* Fix args.

* Fix gseapy.

* Handle locale in test cases of click-related recipes. Fix swarm tests.

* Fixes.

* Remove unnecessary dependencies.

* Use our own extended base image.

* Use master branch of bioconda-utils.

* Documentation and base image.

* Fix swarm dependencies.

* Skip until we have completely switched to conda-forge.

* Use extended base image for dreamtools.

* Skip fwdpy (missing headers in own source).

* Fixes and formatting.

* Skipping hlama for anything except py35. @holtgrewe this is because for py36, you would need to depend on a current Snakemake version.
I suggest to relax this dependency since Snakemake is backwards compatible anyway.

* Fixes

* Adapt container image definition to new syntax. Skip click-based recipes on py3k.

* Add zlib to bx-python.

* Fixes.

* Add missing dependency.

* Add gcc.

* Add missing dependency xz.

* Remove bx-python 0.7.1 because it does not build even on python 2.7

* Use extended base image.

* Add missing lib.

* Use UTF-8 in test cases.

* Debug bx-python.

* Fix qiime. Use test branch of bioconda-utils.

* Fix qiime. Use test branch of bioconda-utils.

* Skip cgat-scripts-devel on py36. Use master branch of bioconda-utils again after PR has been merged.

* Skip linting when PR comes from the special bulk branch.

.travis.yml

@@ -11,7 +11,7 @@ services:
 
 install: scripts/travis-setup.sh
 
-script: travis_wait 119 scripts/travis-run.sh
+script: scripts/travis-run.sh
 
 env:
   global:

recipes/amos/build.sh

@@ -1,8 +1,20 @@
+# fix automake
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/aclocal
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/automake
+
+# fix autoconf
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autom4te
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoheader
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoreconf
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/ifnames
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoscan
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoupdate
+
 rm -r test tutorial
 export LDFLAGS="-L$PREFIX/lib"
 export CPPFLAGS="-I$PREFIX/include"
 ./bootstrap
 ./configure \
-    --prefix=$PREFIX 
+    --prefix=$PREFIX
 make
 make install

recipes/amos/meta.yaml

@@ -14,8 +14,7 @@ source:
 build:
   number: 3
   # OSX failing due to missing dependencies in OSX branch
-  skip: True # [osx]
-
+  skip: true  # [osx]
 
 test:
   commands:
@@ -25,11 +24,12 @@ requirements:
   build:
     - gcc
     - zlib
-    - boost 
+    - boost
     - autoconf
+    - automake
     - blat
     - mummer
-    - perl-threaded
+    - perl
     - perl-statistics-descriptive
     - perl-xml-parser
     - perl-dbi
@@ -38,7 +38,7 @@ requirements:
 
   run:
     - mummer
-    - perl-threaded
+    - perl
     - perl-statistics-descriptive
     - perl-xml-parser
     - perl-dbi

recipes/bcbio-nextgen/meta.yaml

@@ -84,9 +84,10 @@ test:
     #     Reason: image not found
     #- bcbio.distributed.ipython
   commands:
-    - bcbio_nextgen.py -h
-    - bcbio_setup_genome.py -h
-    - bcbio_prepare_samples.py -h
+    # click requires a unicode locale
+    - LANG=C.UTF-8 bcbio_nextgen.py -h
+    - LANG=C.UTF-8 bcbio_setup_genome.py -h
+    - LANG=C.UTF-8 bcbio_prepare_samples.py -h
 
 about:
   home: https://github.com/chapmanb/bcbio-nextgen

recipes/bcl2fastq-nextseq/meta.yaml

@@ -30,7 +30,8 @@ requirements:
 
 test:
   commands:
-    - bcl_to_fastq -h &> /dev/null
+    # click requires a unicode locale
+    - LANG=C.UTF-8 bcl_to_fastq -h &> /dev/null
 
 about:
   home: https://github.com/brwnj/bcl2fastq

recipes/biokit/meta.yaml

@@ -6,13 +6,10 @@ source:
   fn: biokit-0.4.1.tar.gz
   url: https://pypi.python.org/packages/e3/fe/9bc827910cbd19a1a03bb5b0a1c4aa583903696526d7f6e51fbc9f849e28/biokit-0.4.1.tar.gz
   md5: 755efcfa4982fd23d31d1ebdd4972c22
-#  patches:
-   # List any patch files here
-   # - fix.patch
 
 build:
   skip: True # [py34]
-  number: 2
+  number: 4
 
 # Set xmltodict >= 0.10.2 to use conda-forge version instead of bioconda
 # Same with easydev
@@ -25,6 +22,9 @@ requirements:
     - colormap
     - scipy
     - xmltodict
+    - numpydoc
+    - bioservices
+    - mesalib
 
   run:
     - python
@@ -34,25 +34,21 @@ requirements:
     - colormap
     - scipy
     - xmltodict
-    #- matplotlib 
-    #- libgcc # [not osx]
-    #- glib
+    - numpydoc
+    - bioservices
+    - matplotlib
+    - libgcc
+    - mesalib
     #- xz
     #- libxcb
 
 # Could not manage to import it without an libXext issue from conda-forge ? and
-# matplotlib v1.5.3 or v2.0.0. Hopefully, this will be resolved in the future 
+# matplotlib v1.5.3 or v2.0.0. Hopefully, this will be resolved in the future
 test:
-  # Python imports
-  # imports:
-  #- biokit
+  imports:
+    - biokit
 
 about:
   home: ['http://pypi.python.org/pypi/biokit']
   license: BSD
   summary: 'Set of visualisation and analysis tools for biological data sets'
-
-
-extra:
-  recipe-maintainers:
-    - cokelaer

recipes/biom-format/2.1.5/meta.yaml

@@ -9,19 +9,12 @@ source:
 
 
 build:
-  # noarch_python: True
   preserve_egg_dir: True
   entry_points:
-    # Put any entry points (scripts to be generated automatically) here. The
-    # syntax is module:function.  For example
-    #
-    # - biom-format = biom-format:main
-    #
-    # Would create an entry point called biom-format that calls biom-format.main()
-
     - biom=biom.cli:cli
-
   number: 3
+  # click needs to be patched in order to properly detect unicode in py3k
+  skip: true  # [py3k]
 
 requirements:
   build:
@@ -43,6 +36,8 @@ requirements:
     - numpy >=1.3.0
     - future >=0.15.0
     - scipy >=0.13.0
+    # missing scipy dependency
+    - libgcc
 
 test:
   # Python imports
@@ -51,9 +46,8 @@ test:
     - biom.cli
 
   commands:
-    # You can put test commands to be run here.  Use this to test that the
-    # entry points work.
-    - biom --help
+    # click requires a unicode locale
+    - LANG=C.UTF-8 biom --help
 
 about:
   home: http://www.biom-format.org

recipes/biomaj/meta.yaml

@@ -48,6 +48,5 @@ test:
 about:
   home: http://biomaj.genouest.org
   license: GNU Affero General Public License v3 or later (AGPLv3+)
-  summary: 'BioMAJ'
   license_family: AGPL
   summary: Automates the update cycle and the supervision of the locally mirrored databank repository

recipes/biopython/1.65/build.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-$PYTHON setup.py install 

recipes/biopython/1.65/meta.yaml

@@ -1,113 +0,0 @@
-{% set name = "biopython" %}
-{% set version = "1.65" %}
-{% set sha256 = "6d591523ba4d07a505978f6e1d7fac57e335d6d62fb5b0bcb8c40bdde5c8998e" %}
-
-
-package:
-  name: {{ name|lower }}
-  version: {{ version }}
-
-source:
-  fn: {{ name }}-{{ version }}.tar.gz
-  url: https://pypi.python.org/packages/4e/77/8590d61dcda439d83f378106954e748db1a71e565335168a966642133ef8/biopython-1.65.tar.gz
-  sha256: {{ sha256 }}
-
-about:
-  home: http://www.biopython.org/
-  license: Biopython License Agreement
-  license_file: LICENSE
-  summary: 'Freely available tools for computational molecular biology.'
-
-build:
-  number: 0
-  skip: True # [py34]
-
-requirements:
-  build:
-    - python
-    - numpy x.x
-    - reportlab
-    - mmtf-python
-
-  run:
-    - python
-    - numpy x.x
-    - reportlab
-    - mmtf-python
-
-test:
-  imports:
-    - Bio
-    - Bio.Align
-    - Bio.Align.Applications
-    - Bio.AlignIO
-    - Bio.Alphabet
-    - Bio.Application
-    - Bio.Blast
-    - Bio.CAPS
-    - Bio.Compass
-    - Bio.Crystal
-    - Bio.Data
-    - Bio.Emboss
-    - Bio.Entrez
-    - Bio.ExPASy
-    - Bio.FSSP
-    - Bio.GA
-    - Bio.GA.Crossover
-    - Bio.GA.Mutation
-    - Bio.GA.Repair
-    - Bio.GA.Selection
-    - Bio.GenBank
-    - Bio.Geo
-    - Bio.Graphics
-    - Bio.Graphics.GenomeDiagram
-    - Bio.HMM
-    - Bio.KEGG
-    - Bio.KEGG.Compound
-    - Bio.KEGG.Enzyme
-    - Bio.KEGG.KGML
-    - Bio.KEGG.Map
-    - Bio.Medline
-    - Bio.NMR
-    - Bio.NeuralNetwork
-    - Bio.NeuralNetwork.BackPropagation
-    - Bio.NeuralNetwork.Gene
-    - Bio.Nexus
-    - Bio.PDB
-    - Bio.PDB.QCPSuperimposer
-    # - Bio.PDB.mmtf  Introduced in 1.68
-    - Bio.Pathway
-    - Bio.Pathway.Rep
-    - Bio.Phylo
-    - Bio.Phylo.Applications
-    - Bio.Phylo.PAML
-    - Bio.PopGen
-    - Bio.PopGen.Async
-    - Bio.PopGen.FDist
-    - Bio.PopGen.GenePop
-    - Bio.PopGen.SimCoal
-    - Bio.Restriction
-    - Bio.SCOP
-    - Bio.SVDSuperimposer
-    - Bio.SearchIO
-    - Bio.SearchIO.BlastIO
-    - Bio.SearchIO.ExonerateIO
-    - Bio.SearchIO.HmmerIO
-    - Bio.SearchIO._model
-    - Bio.SeqIO
-    - Bio.SeqUtils
-    - Bio.Sequencing
-    - Bio.Sequencing.Applications
-    - Bio.Statistics
-    - Bio.SubsMat
-    - Bio.SwissProt
-    - Bio.TogoWS
-    - Bio.UniGene
-    - Bio.UniProt
-    - Bio.Wise
-    - Bio._py3k
-    - Bio.codonalign
-    - Bio.motifs
-    - Bio.motifs.applications
-    - Bio.motifs.jaspar
-    - BioSQL

recipes/busco/1.2/build.sh

@@ -1,5 +0,0 @@
-#!/bin/bash
-
-mkdir -p $PREFIX/bin/
-cp BUSCO_v1.2.py $PREFIX/bin
-ln -s $PREFIX/bin/BUSCO_v1.2.py $PREFIX/bin/busco

recipes/busco/1.2/meta.yaml

@@ -1,33 +0,0 @@
-package:
-  name: busco
-  version: "1.2"
-
-build:
-  number: 1
-
-source:
-  fn: busco-v1.2.tar.gz
-  url: http://busco.ezlab.org/files/BUSCO_v1.2.tar.gz
-  md5: 4b4551ccdbc8e64d18295fc8d8729d84
-
-requirements:
-  build:
-    - python  
-  run:
-    - python
-    - blast
-    - hmmer
-      #    - emboss
-
-about:
-  home: http://busco.ezlab.org/
-  license: GPL
-  summary: BUSCO provides measures for quantitative assessment of genome 
-           assembly, gene set, and transcriptome completeness based on 
-           evolutionarily informed expectations of gene content from 
-           near-universal single-copy orthologs selected from OrthoDB. 
-
-test:
-  commands:
-    - BUSCO_v1.2.py -h > /dev/null
-    - busco -h > /dev/null

recipes/bx-python/0.7.1/build.sh

@@ -1,2 +0,0 @@
-#!/bin/sh
-$PYTHON setup.py install