debian/changelog

+python-biom-format (2.1.7+dfsg-2) UNRELEASED; urgency=medium
+
+  * Do not ship *.c and *.pyx cython input files in binary packages
+  * Provide examples and tests in separate python-biom-format-examples
+    package
+    Closes: #919586
+
+ -- Andreas Tille <tille@debian.org>  Thu, 17 Jan 2019 20:34:11 +0100
+
 python-biom-format (2.1.7+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -150,3 +150,31 @@ Description: command-line tools for BIOM format
  .
  This package provides the command-line tools for the BIOM format Python
  package.
+
+Package: python-biom-format-examples
+Architecture: all
+Section: doc
+Depends: ${misc:Depends},
+Description: examples and test data for BIOM format
+ 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 examples and tests for the BIOM format Python
+ package.

debian/python-biom-format-examples.docs

+biom/tests

debian/rules

@@ -8,6 +8,7 @@ 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
 
@@ -39,11 +40,22 @@ override_dh_installdocs-indep:
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	cp -a examples $(shell pybuild --print build_dir --interpreter python)
-	cp -a examples $(shell pybuild --print build_dir --interpreter python3)
+	ln -s $(CURDIR)/examples $(shell pybuild --print build_dir --interpreter python)
+	ln -s $(CURDIR)/examples $(shell pybuild --print build_dir --interpreter python3)
 	dh_auto_test
 endif
 
 override_dh_fixperms:
 	dh_fixperms
 	find debian -name exercise_cli.sh -exec chmod +x \{\} \;
+
+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
+	if [ ! -d biom/tests ] ; then \
+	    mv `find debian/python*$(PYBUILD_NAME) -name tests -type d` biom ; \
+	else \
+	    find debian/python*$(PYBUILD_NAME) -name tests -type d | xargs rm -rf ; \
+	fi

debian/tests/python2

@@ -3,7 +3,7 @@ set -efu
 
 pys="$(pyversions -r 2>/dev/null)"
 
-cp -a ./examples ./tests "$ADTTMP"
+cp -a ./examples ./biom/tests "$ADTTMP"
 cd "$ADTTMP"
 
 export LC_ALL=C.UTF-8

debian/tests/python3

@@ -3,7 +3,7 @@ set -efu
 
 pys="$(py3versions -r 2>/dev/null)"
 
-cp -a ./examples ./tests "$ADTTMP"
+cp -a ./examples ./biom/tests "$ADTTMP"
 cd "$ADTTMP"
 
 export LC_ALL=C.UTF-8