[Debian-med-packaging] Bug#934864: python-biom-format: Please drop python2 support

[Steve Langasek]

Package: python-biom-format
Version: 2.1.7+dfsg-3
Severity: normal
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu eoan ubuntu-patch

Hi Andreas,

We are of course in the process of deprecating python2 in Debian for the
next release.  In Ubuntu, I've identified that it may be useful to
accelerate this deprecation for pandas and its reverse-dependencies, because
the pandas tests appear to have bit-rotted for python2 on one architecture,
and it would be better to remove the python2 bits rather than invest in
fixing them.

python-biom-format is a package that (build-)depends on python-pandas, so
I've gone ahead and uploaded the attached patch to Ubuntu which drops the
python2 module.  python-biom-format does still have one reverse-dependency
in the archive - metaphlan2 - which should also be fixed before this change
is made in Debian (bug #933661).

Thanks for considering,
-- 
Steve Langasek                   Give me a lever long enough and a Free OS
Debian Developer                   to set it on, and I can move the world.
Ubuntu Developer                                   https://www.debian.org/
slangasek at ubuntu.com                                     vorlon at debian.org
-------------- next part --------------
diff -Nru python-biom-format-2.1.7+dfsg/debian/control python-biom-format-2.1.7+dfsg/debian/control
--- python-biom-format-2.1.7+dfsg/debian/control	2019-08-06 01:11:48.000000000 -0700
+++ python-biom-format-2.1.7+dfsg/debian/control	2019-08-15 17:54:38.000000000 -0700
@@ -7,17 +7,7 @@
 Build-Depends: debhelper-compat (= 12),
                dh-python,
                cython,
-               python-dev,
-               python-numpy,
-               python-scipy,
-               python-h5py,
                help2man,
-               python-click,
-               python-cogent,
-               python-future,
-               python-nose,
-               python-pandas,
-               python-setuptools,
                bash-completion,
                cython3,
                python3-all-dev,
@@ -35,35 +25,6 @@
 Vcs-Git: https://salsa.debian.org/med-team/python-biom-format.git
 Homepage: http://biom-format.org/
 
-Package: python-biom-format
-Architecture: any-amd64 any-arm64 armel armhf any-i386 any-mips64el mipsel any-ppc64el
-Depends: ${python:Depends},
-         ${misc:Depends},
-         ${shlibs:Depends}
-Suggests: python-biom-format-doc
-Description: Biological Observation Matrix (BIOM) format (Python 2)
- The BIOM file format (canonically pronounced biome) is designed to be a
- general-use format for representing biological sample by observation
- contingency tables. BIOM is a recognized standard for the Earth
- Microbiome Project and is a Genomics Standards Consortium candidate
- project.
- .
- The BIOM format is designed for general use in broad areas of
- comparative -omics. For example, in marker-gene surveys, the primary use
- of this format is to represent OTU tables: the observations in this case
- are OTUs and the matrix contains counts corresponding to the number of
- times each OTU is observed in each sample. With respect to metagenome
- data, this format would be used to represent metagenome tables: the
- observations in this case might correspond to SEED subsystems, and the
- matrix would contain counts corresponding to the number of times each
- subsystem is observed in each metagenome. Similarly, with respect to
- genome data, this format may be used to represent a set of genomes: the
- observations in this case again might correspond to SEED subsystems, and
- the counts would correspond to the number of times each subsystem is
- observed in each genome.
- .
- This package provides the BIOM format library for the Python 2 interpreter.
-
 Package: python3-biom-format
 Architecture: any-amd64 any-arm64 armel armhf any-i386 any-mips64el mipsel any-ppc64el
 Depends: ${misc:Depends},
diff -Nru python-biom-format-2.1.7+dfsg/debian/rules python-biom-format-2.1.7+dfsg/debian/rules
--- python-biom-format-2.1.7+dfsg/debian/rules	2019-08-06 01:11:48.000000000 -0700
+++ python-biom-format-2.1.7+dfsg/debian/rules	2019-08-15 17:54:38.000000000 -0700
@@ -6,10 +6,8 @@
 export LC_ALL=C.UTF-8
 
 export PYBUILD_NAME=biom-format
-export PYBUILD_DESTDIR_python2=debian/python-$(PYBUILD_NAME)
 export PYBUILD_DESTDIR_python3=debian/python3-$(PYBUILD_NAME)
 export examplepkg=python-$(PYBUILD_NAME)-examples
-export PYBUILD_AFTER_INSTALL_python2=dh_numpy
 export PYBUILD_AFTER_INSTALL_python3=dh_numpy3
 
 ## When trying better hardening the build fails
@@ -17,7 +15,7 @@
 export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
 
 %:
-	dh $@ --with python2,python3,bash-completion,sphinxdoc --buildsystem=pybuild
+	dh $@ --with python3,bash-completion,sphinxdoc --buildsystem=pybuild
 
 override_dh_auto_build:
 	# arch
@@ -26,11 +24,6 @@
 	PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html
 	PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b man doc build/man
 
-override_dh_auto_install:
-	dh_auto_install
-	# Install command-line scripts into Python3 package only
-	rm -rf $(PYBUILD_DESTDIR_python2)/usr/bin
-
 override_dh_installdocs-indep:
 	dh_installdocs --indep
 	dh_sphinxdoc --indep
@@ -53,7 +46,7 @@
 	dh_installexamples
 	find debian -name "*.c" -delete
 	find debian -name "*.pyx" -delete
-	# remove tests from Python2 package, move tests from Python3 package to examples package
+	# move tests from Python3 package to examples package
 	if [ ! -d biom/tests ] ; then \
 	    mv `find debian/python*$(PYBUILD_NAME) -name tests -type d` biom ; \
 	else \