debian/changelog

+python-biom-format (2.1.7+dfsg-4) UNRELEASED; urgency=medium
+
+  [ Steve Langasek ]
+  * Drop Python2 package
+    Closes: #934864
+
+  [ Andreas Tille ]
+  * Fix doc-base control file
+
+ -- Andreas Tille <tille@debian.org>  Fri, 16 Aug 2019 22:02:14 +0200
+
 python-biom-format (2.1.7+dfsg-3) unstable; urgency=medium
 
   * debhelper-compat 12

debian/control

@@ -7,17 +7,7 @@ Priority: optional
 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-Browser: https://salsa.debian.org/med-team/python-biom-format
 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},

debian/python-biom-format-doc.doc-base

@@ -10,5 +10,5 @@ Abstract:  Biological Observation Matrix (BIOM) format
 Section: Science/Biology
 
 Format: html
-Index: /usr/share/doc/python-biom-format/html/index.html
-Files: /usr/share/doc/python-biom-format/html/
+Index: /usr/share/doc/python-biom-format-doc/html/index.html
+Files: /usr/share/doc/python-biom-format-doc/html/

debian/rules

@@ -6,10 +6,8 @@ export DH_VERBOSE=1
 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 PYBUILD_AFTER_INSTALL_python3=dh_numpy3
 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 @@ override_dh_auto_build:
 	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 $(PYBUILD_DESTDIR_python2)/usr/bin
-
 override_dh_installdocs-indep:
 	dh_installdocs --indep
 	dh_sphinxdoc --indep
@@ -53,7 +46,7 @@ override_dh_installexamples:
 	dh_installexamples
 	find debian -name "*.c" -delete
 	find debian -name "*.pyx" -delete
-	# remove tests from Python2 package, move tests from Python3 package to examples package
+	# move tests from Python3 package to examples package
 	if [ ! -d biom/tests ] ; then \
 	    mv `find debian/python*$(PYBUILD_NAME) -name tests -type d` biom ; \
 	else \