debian/changelog

 python-biopython (1.75+dfsg-2) UNRELEASED; urgency=medium
 
+  [ Michael R. Crusoe ]
   * Team upload.
   * Skip PDB_ResidueDepth test, as http://mgltools.scripps.edu/packages/MSMS
     is not yet packaged for Debian
@@ -11,6 +12,10 @@ python-biopython (1.75+dfsg-2) UNRELEASED; urgency=medium
   * Fix the ignoring of the test errors so that the python3 tests are still
     run.
 
+  [ Andreas Tille ]
+  * Drop Python2 package
+    Closes: #937606
+
  -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 10 Dec 2019 10:12:10 +0100
 
 python-biopython (1.75+dfsg-1) unstable; urgency=medium

debian/control

@@ -6,12 +6,9 @@ Section: python
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-all-dev,
                python3-all-dev,
-               python-numpy,
                python3-numpy,
                flex,
-               python-reportlab,
                python3-reportlab,
                hevea,
                texlive-latex-base,
@@ -31,25 +28,16 @@ Build-Depends: debhelper-compat (= 12),
                phyml [any-amd64 any-i386 arm64 armhf sparc64],
                prank,
                probcons,
-               python-networkx,
                python3-networkx,
-               python-mysqldb,
                python3-mysqldb,
-               python-matplotlib,
                python3-matplotlib,
-               python-pil,
                python3-pil,
-               python-rdflib,
                python3-rdflib,
-               python-renderpm,
                python3-renderpm,
-               python-psycopg2,
                python3-psycopg2,
-               python-scipy,
                python3-scipy,
-               python-setuptools,
                python3-setuptools,
-               python-unittest2,
+               python3-unittest2,
                raxml [any-amd64 any-i386],
                samtools [alpha arm64 armel armhf hppa ia64 m68k mips mips64el mipsel powerpc powerpcspe ppc64 ppc64el s390x sh4 sparc64],
                t-coffee,
@@ -60,58 +48,6 @@ Vcs-Browser: https://salsa.debian.org/med-team/python-biopython
 Vcs-Git: https://salsa.debian.org/med-team/python-biopython.git
 Homepage: http://biopython.org
 
-Package: python-biopython
-Architecture: any
-Depends: ${python:Depends},
-         ${shlibs:Depends},
-         ${misc:Depends},
-         python,
-         python-reportlab
-Recommends: python-biopython-doc (= ${source:Version}),
-            ncbi-blast+
-Suggests: python-tk,
-          bwa [any-amd64],
-          clustalo,
-          clustalw,
-          dialign,
-          dssp,
-          emboss,
-          fasttree,
-          mafft,
-          muscle,
-          phylip,
-          phyml [any-amd64 any-i386 arm64 armhf sparc64],
-          prank,
-          probcons,
-          python-mysqldb,
-          python-matplotlib,
-          python-numpy,
-          python-pil,
-          python-rdflib,
-          python-renderpm,
-          python-psycopg2,
-          python-scipy,
-          raxml,
-          samtools,
-          t-coffee,
-          wise,
-          w3-dtd-mathml
-Description: Python library for bioinformatics (implemented in Python 2)
- The Biopython Project is an international association
- of developers of freely available Python tools for
- computational molecular biology.
- .
- It is a distributed collaborative effort to develop Python
- libraries and applications which address the needs of
- current and future work in bioinformatics. The source code
- is made available under the Biopython License, which is
- extremely liberal and compatible with almost every license in
- the world. The project works along with the Open Bioinformatics
- Foundation, who generously provide web and CVS space for
- the project.
- .
- This package is targeting Python version 2.
-
 Package: python3-biopython
 Architecture: any
 Depends: ${python3:Depends},
@@ -147,12 +83,12 @@ Suggests: python3-tk,
           t-coffee,
           wise,
           w3-dtd-mathml
-Description: Python library for bioinformatics (implemented in Python 3)
+Description: Python3 library for bioinformatics
  The Biopython Project is an international association
  of developers of freely available Python tools for
  computational molecular biology.
  .
- It is a distributed collaborative effort to develop Python
+ It is a distributed collaborative effort to develop Python3
  libraries and applications which address the needs of
  current and future work in bioinformatics. The source code
  is made available under the Biopython License, which is
@@ -160,14 +96,12 @@ Description: Python library for bioinformatics (implemented in Python 3)
  the world. The project works along with the Open Bioinformatics
  Foundation, who generously provide web and CVS space for
  the project.
- .
- This package is targeting Python version 3.
 
 Package: python-biopython-doc
 Architecture: all
 Section: doc
 Depends: ${misc:Depends}
-Recommends: python-biopython (= ${source:Version})
+Recommends: python3-biopython (= ${source:Version})
 Description: Documentation for the Biopython library
  Documentation and examples about how to use the Biopython
  library.
@@ -175,32 +109,14 @@ Description: Documentation for the Biopython library
  This package also contains the unit tests of the test suite
  to enable reproducing the test results.
 
-Package: python-biopython-sql
-# Todo: add www.biosql.org as "External Ressource" on packages.debian.org when the infrastructure will provide a way to do so.
-Architecture: all
-Depends: ${python:Depends},
-         ${misc:Depends},
-         python,
-         python-mysqldb,
-         python-biopython
-Provides: ${python:Provides}
-Description: Biopython support for the BioSQL database schema (Python 2)
- This is the Biopython interface to a BioSQL database (see www.biosql.org
- for details). BioPerl, BioJava and BioRuby also provide their own BioSQL
- interfaces onto the same shared SQL schema.
- .
- This package is targeting Python version 2.
-
 Package: python3-biopython-sql
 # Todo: add www.biosql.org as "External Ressource" on packages.debian.org when the infrastructure will provide a way to do so.
 Architecture: all
 Depends: ${python3:Depends},
          ${misc:Depends},
          python3-biopython
-Provides: ${python:Provides}
+Provides: ${python3:Provides}
 Description: Biopython support for the BioSQL database schema (Python 3)
  This is the Biopython interface to a BioSQL database (see www.biosql.org
  for details). BioPerl, BioJava and BioRuby also provide their own BioSQL
  interfaces onto the same shared SQL schema.
- .
- This package is targeting Python version 3.

debian/python-biopython-sql.install

-usr/lib/python2*/*-packages/BioSQL

debian/python-biopython.install

-usr/lib/python2*/*-packages/Bio
-usr/lib/python2*/*-packages/biopython-*.egg-info

debian/python-biopython.links

-/usr/share/xml/schema/w3c/mathml/dtd/mathml2.dtd	/usr/lib/python2.7/dist-packages/Bio/Entrez/DTDs/mathml2.dtd

debian/rules

@@ -4,8 +4,7 @@
 export DH_VERBOSE=1
 
 #export PYBUILD_NAME=biopython
-#export PYBUILD_DESTDIR_python2=debian/python-biopython/
-#export PYBUILD_DESTDIR_python3=debian/python3-biopython/
+#export PYBUILD_DESTDIR_python3=debian/python3-$(PYBUILD_NAME)/
 
 # export DEB_BUILD_MAINT_OPTIONS = hardening=+all ... does not build
 export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
@@ -45,7 +44,7 @@ EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2
 EXCLUDEFAILINGTESTS=phyml_tool
 
 %:
-	dh $@ --with python2,python3 --buildsystem=pybuild
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_clean:
 	dh_auto_clean
@@ -71,16 +70,15 @@ override_dh_auto_build:
 
 override_dh_auto_install:
 	dh_auto_install
-	dh_numpy -ppython-biopython
 	dh_numpy3 -ppython3-biopython
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 ifeq ($(BUILDARCH),mips)
+	# FIXME: Do the tests *really* fail any more?
 	echo "***************************************************************************"
 	echo "* Attention: Build time tests for mips architecture are skipped.          *"
-	echo "* The reason is that the tests are known to fail for Python3 and the      *"
-	echo "* effort to simply run only for Python 2.7 seems to be error prone.       *"
+	echo "* The reason is that the tests are known to fail for Python3              *"
 	echo "* Upstream is working on a solution so this should be dropped for         *"
 	echo "* next upstream version. See:                                             *"
 	echo "* http://mailman.open-bio.org/pipermail/biopython/2014-August/015383.html *"

debian/tests/control

 Tests: run-unit-test
-Depends: @, @builddeps@
+Depends: @, python3-setuptools
 Restrictions: allow-stderr

debian/tests/run-unit-test

@@ -10,6 +10,7 @@ mkdir -p Doc/
 cp -a /usr/share/doc/python-biopython-doc/Doc/Tutorial.tex* Doc
 cp -a /usr/share/doc/python-biopython-doc/Doc/Tutorial Doc
 cp -a /usr/share/doc/python-biopython-doc/Doc/examples Doc
+unset GZIP
 find . -name "*.gz" -exec gunzip \{\} \;
 cd Tests
 # we really need this gzipped duplicate of the example.fastq and E3MFGYR02_random_10_reads.sff files to pass the BGZF compression test
@@ -32,7 +33,7 @@ fi
 # test is verifying this dir to run the EMBOSS test
 # test_Emboss also requires to have the environment variable EMBOSS_ROOT set
 
-for pi in $(pyversions -i) $(py3versions -i); do
+for pi in $(py3versions -i); do
     LC_ALL=C.UTF-8 DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=$AUTOPKGTEST_TMP ${pi} run_tests.py --offline
 done