[Debian-med-packaging] r16448 - in trunk/packages/python-biopython/trunk/debian: . patches tests
Andreas Tille
andreas at an3as.eu
Sun Mar 16 10:50:34 UTC 2014
Hi Phlippp,
are you sure that you do not want to run the test on build-time as well?
IMHO running the test at build-time is in the same way important as the
autopkgtest - so I would leave all the build-depends and run the test
at package build time.
Kind regards
Andreas.
On Sat, Mar 15, 2014 at 08:36:41PM +0000, Philipp Benner wrote:
> Author: philipp
> Date: 2014-03-15 20:36:41 +0000 (Sat, 15 Mar 2014)
> New Revision: 16448
>
> Added:
> trunk/packages/python-biopython/trunk/debian/tests/
> trunk/packages/python-biopython/trunk/debian/tests/control
> trunk/packages/python-biopython/trunk/debian/tests/upstream
> Removed:
> trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch
> Modified:
> trunk/packages/python-biopython/trunk/debian/control
> trunk/packages/python-biopython/trunk/debian/patches/series
> trunk/packages/python-biopython/trunk/debian/rules
> Log:
> a very first autopkgtest
>
> Modified: trunk/packages/python-biopython/trunk/debian/control
> ===================================================================
> --- trunk/packages/python-biopython/trunk/debian/control 2014-03-15 12:07:13 UTC (rev 16447)
> +++ trunk/packages/python-biopython/trunk/debian/control 2014-03-15 20:36:41 UTC (rev 16448)
> @@ -9,45 +9,16 @@
> dpkg-dev (>= 1.16.1~),
> python-all-dev,
> python3-all-dev,
> - flex,
> - python-reportlab,
> - python-numpy,
> - python3-reportlab,
> - python3-numpy,
> - bwa [any-amd64],
> - clustalo,
> - clustalw,
> - dialign,
> - dssp,
> - emboss,
> - fasttree,
> - mafft,
> - muscle,
> - ncbi-blast+,
> - phyml,
> - prank,
> - probcons,
> - python-mysqldb,
> - python-matplotlib,
> - python3-matplotlib,
> - python-numpy,
> - python3-numpy,
> - python-pil,
> - python3-pil,
> - python-rdflib,
> - python-renderpm,
> - python3-renderpm,
> - python-psycopg2,
> - python3-psycopg2,
> - raxml,
> - t-coffee,
> - wise
> + python-numpy,
> + python3-numpy,
> + flex
> Standards-Version: 3.9.5
> Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biopython/trunk/
> Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-biopython/trunk/
> Homepage: http://biopython.org
> X-Python-Version: >= 2.5
> X-Python3-Version: >= 3.3
> +XS-Testsuite: autopkgtest
>
> Package: python-biopython
> Architecture: any
> @@ -57,14 +28,36 @@
> python-reportlab
> Recommends: python-biopython-doc (= ${source:Version})
> Suggests: python-tk,
> - wise,
> - muscle,
> + python-numpy,
> + python3-numpy,
> + bwa [any-amd64],
> + clustalo,
> clustalw,
> + dialign,
> + dssp,
> + emboss,
> + fasttree,
> mafft,
> - emboss,
> - blast2,
> + muscle,
> + ncbi-blast+,
> + phyml,
> + prank,
> + probcons,
> + python-mysqldb,
> + python-matplotlib,
> + python3-matplotlib,
> + python-numpy,
> + python3-numpy,
> + python-pil,
> + python3-pil,
> + python-rdflib,
> + python-renderpm,
> + python3-renderpm,
> python-psycopg2,
> - probcons
> + python3-psycopg2,
> + raxml,
> + t-coffee,
> + wise
> Description: Python library for bioinformatics (implemented in Python 2)
> The Biopython Project is an international association
> of developers of freely available Python tools for
> @@ -89,14 +82,37 @@
> python3-reportlab
> Recommends: python-biopython-doc (= ${source:Version})
> Suggests: python3-tk,
> - wise,
> - muscle,
> + python-reportlab,
> + python-numpy,
> + python3-numpy,
> + bwa [any-amd64],
> + clustalo,
> clustalw,
> + dialign,
> + dssp,
> + emboss,
> + fasttree,
> mafft,
> - emboss,
> - blast2,
> + muscle,
> + ncbi-blast+,
> + phyml,
> + prank,
> + probcons,
> + python-mysqldb,
> + python-matplotlib,
> + python3-matplotlib,
> + python-numpy,
> + python3-numpy,
> + python-pil,
> + python3-pil,
> + python-rdflib,
> + python-renderpm,
> + python3-renderpm,
> + python-psycopg2,
> python3-psycopg2,
> - probcons
> + raxml,
> + t-coffee,
> + wise
> Description: Python library for bioinformatics (implemented in Python 3)
> The Biopython Project is an international association
> of developers of freely available Python tools for
>
> Deleted: trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch
> ===================================================================
> --- trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch 2014-03-15 12:07:13 UTC (rev 16447)
> +++ trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch 2014-03-15 20:36:41 UTC (rev 16448)
> @@ -1,39 +0,0 @@
> -Index: python-biopython-1.63/Bio/PDB/DSSP.py
> -===================================================================
> ---- python-biopython-1.63.orig/Bio/PDB/DSSP.py 2014-03-12 17:58:51.000000000 +0000
> -+++ python-biopython-1.63/Bio/PDB/DSSP.py 2014-03-12 18:00:02.000000000 +0000
> -@@ -80,7 +80,7 @@
> - assert 0
> -
> -
> --def dssp_dict_from_pdb_file(in_file, DSSP="dssp"):
> -+def dssp_dict_from_pdb_file(in_file, DSSP="mkdssp"):
> - """
> - Create a DSSP dictionary from a PDB file.
> -
> -@@ -199,7 +199,7 @@
> - -42.399999999999999)
> - """
> -
> -- def __init__(self, model, pdb_file, dssp="dssp"):
> -+ def __init__(self, model, pdb_file, dssp="mkdssp"):
> - """
> - @param model: the first model of the structure
> - @type model: L{Model}
> -Index: python-biopython-1.63/Tests/test_DSSP_tool.py
> -===================================================================
> ---- python-biopython-1.63.orig/Tests/test_DSSP_tool.py 2014-03-12 17:59:10.000000000 +0000
> -+++ python-biopython-1.63/Tests/test_DSSP_tool.py 2014-03-12 17:59:33.000000000 +0000
> -@@ -22,10 +22,10 @@
> - try:
> - try:
> - # Newer versions of DSSP
> -- subprocess.check_call(["dssp", "--version"], **quiet_kwargs)
> -+ subprocess.check_call(["mkdssp", "--version"], **quiet_kwargs)
> - except subprocess.CalledProcessError:
> - # Older versions of DSSP
> -- subprocess.check_call(["dssp", "-h"], **quiet_kwargs)
> -+ subprocess.check_call(["mkdssp", "-h"], **quiet_kwargs)
> - except OSError:
> - raise MissingExternalDependencyError(
> - "Install dssp if you want to use it from Biopython.")
>
> Modified: trunk/packages/python-biopython/trunk/debian/patches/series
> ===================================================================
> --- trunk/packages/python-biopython/trunk/debian/patches/series 2014-03-15 12:07:13 UTC (rev 16447)
> +++ trunk/packages/python-biopython/trunk/debian/patches/series 2014-03-15 20:36:41 UTC (rev 16448)
> @@ -1,2 +1 @@
> fix_test_emboss.patch
> -fix_dssp.patch
>
> Modified: trunk/packages/python-biopython/trunk/debian/rules
> ===================================================================
> --- trunk/packages/python-biopython/trunk/debian/rules 2014-03-15 12:07:13 UTC (rev 16447)
> +++ trunk/packages/python-biopython/trunk/debian/rules 2014-03-15 20:36:41 UTC (rev 16448)
> @@ -7,13 +7,6 @@
> #export PYBUILD_DESTDIR_python2=debian/python-biopython/
> #export PYBUILD_DESTDIR_python3=debian/python3-biopython/
>
> -BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
> -ifeq ($(BUILDARCH),amd64)
> - EXCLUDEBWA=
> -else
> - EXCLUDEBWA=BWA_tool
> -endif
> -
> %:
> dh $@ --with python2,python3 --buildsystem=pybuild
>
> @@ -23,28 +16,6 @@
> dh_numpy3 -ppython3-biopython
>
> override_dh_auto_test:
> - # 1. avoid some tests which need online access
> - # 2. avoid tests needing a ready setup database server (MySQL and PostgreSQL)
> - # 3. avoid PAML_tools and EmbossPhylipNew since paml resp. embassy-phylip are non-free
> - # 4. avoid testing tools that are not packaged for Debian yet
> - # 5. avoid amd64 only tools on other architectures
> - # While 2. and 3. do not create errors there is no point in bloating
> - # the build log and this kind of documentation makes things more transparent
> - mkdir -p Tests_avoid
> - for avoid in \
> - Entrez_online HotRand NCBI_qblast SCOP_online SeqIO_online TogoWS \
> - BioSQL_MySQLdb BioSQL_psycopg2 \
> - PAML_tools EmbossPhylipNew \
> - MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool \
> - $(EXCLUDEBWA) \
> - ; do \
> - mv Tests/test_$${avoid}.py Tests_avoid ; \
> - done
> - # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir
> - # to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set
> - dh_auto_test -- --test --system=custom --test-args='env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss PYTHONPATH={build_dir} {interpreter} setup.py test'
> - mv Tests_avoid/* Tests
> - rmdir Tests_avoid
>
> override_dh_installdocs:
> dh_installdocs
>
> Added: trunk/packages/python-biopython/trunk/debian/tests/control
> ===================================================================
> --- trunk/packages/python-biopython/trunk/debian/tests/control (rev 0)
> +++ trunk/packages/python-biopython/trunk/debian/tests/control 2014-03-15 20:36:41 UTC (rev 16448)
> @@ -0,0 +1,36 @@
> +Tests: upstream
> +Depends: python-all-dev,
> + python3-all-dev,
> + flex,
> + python-reportlab,
> + python-numpy,
> + python3-reportlab,
> + python3-numpy,
> + bwa [any-amd64],
> + clustalo,
> + clustalw,
> + dialign,
> + dssp,
> + emboss,
> + fasttree,
> + mafft,
> + muscle,
> + ncbi-blast+,
> + phyml,
> + prank,
> + probcons,
> + python-mysqldb,
> + python-matplotlib,
> + python3-matplotlib,
> + python-numpy,
> + python3-numpy,
> + python-pil,
> + python3-pil,
> + python-rdflib,
> + python-renderpm,
> + python3-renderpm,
> + python-psycopg2,
> + python3-psycopg2,
> + raxml,
> + t-coffee,
> + wise
>
> Added: trunk/packages/python-biopython/trunk/debian/tests/upstream
> ===================================================================
> --- trunk/packages/python-biopython/trunk/debian/tests/upstream (rev 0)
> +++ trunk/packages/python-biopython/trunk/debian/tests/upstream 2014-03-15 20:36:41 UTC (rev 16448)
> @@ -0,0 +1,64 @@
> +#! /bin/sh
> +
> +################################################################################
> +# 1. avoid some tests which need online access
> +# 2. avoid tests needing a ready setup database server (MySQL and PostgreSQL)
> +# 3. avoid PAML_tools and EmbossPhylipNew since paml resp. embassy-phylip are non-free
> +# 4. avoid testing tools that are not packaged for Debian yet
> +# 5. avoid amd64 only tools on other architectures
> +#
> +# While 2. and 3. do not create errors there is no point in bloating
> +# the build log and this kind of documentation makes things more transparent
> +################################################################################
> +
> +# definitions
> +################################################################################
> +
> +BUILDARCH=$(dpkg-architecture -qDEB_BUILD_ARCH)
> +
> +EXCLUDE="Entrez_online"
> +EXCLUDE="$EXCLUDE:HotRand"
> +EXCLUDE="$EXCLUDE:NCBI_qblast"
> +EXCLUDE="$EXCLUDE:SCOP_online"
> +EXCLUDE="$EXCLUDE:SeqIO_online"
> +EXCLUDE="$EXCLUDE:TogoWS"
> +EXCLUDE="$EXCLUDE:BioSQL_MySQLdb"
> +EXCLUDE="$EXCLUDE:BioSQL_psycopg2"
> +EXCLUDE="$EXCLUDE:PAML_tools"
> +EXCLUDE="$EXCLUDE:EmbossPhylipNew"
> +EXCLUDE="$EXCLUDE:MSAProbs_tool"
> +EXCLUDE="$EXCLUDE:NACCESS_tool"
> +EXCLUDE="$EXCLUDE:PopGen_DFDist"
> +EXCLUDE="$EXCLUDE:PopGen_FDist"
> +EXCLUDE="$EXCLUDE:PopGen_GenePop"
> +EXCLUDE="$EXCLUDE:PopGen_GenePop_EasyController"
> +EXCLUDE="$EXCLUDE:PopGen_SimCoal"
> +EXCLUDE="$EXCLUDE:XXmotif_tool"
> +
> +if [ "x$BUILDARCH" = "xamd64" ]; then
> + EXCLUDE="$EXCLUDE:BWA_tool"
> +fi
> +
> +# move excluded tests
> +################################################################################
> +
> +mkdir -p Tests_avoid
> +for i in $(echo $EXCLUDE | tr ':' '\n'); do \
> + mv Tests/test_${i}.py Tests_avoid ; \
> +done
> +
> +# execute tests
> +################################################################################
> +# in the Debian package dialign it is not needed to set DIALIGN2_DIR but the
> +# test is verifying this dir to run the EMBOSS test
> +# test_Emboss also requires to have the environment variable EMBOSS_ROOT set
> +
> +for python in $(pyversions -i) $(py3versions -i); do
> + DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss PYTHONPATH={build_dir} python setup.py test
> +done
> +
> +# restore test directory
> +################################################################################
> +
> +mv Tests_avoid/* Tests
> +rmdir Tests_avoid
>
>
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