Andreas Tille pushed to branch master at Debian Med / python-biom-format
Commits: f87001cf by Andreas Tille at 2019-01-17T19:38:22Z Do not ship *.c and *.pyx cython input files in binary packages - - - - - 9c7b4be6 by Andreas Tille at 2019-01-21T20:27:24Z Provide examples and tests in separate python-biom-format-examples package - - - - - 7 changed files: - debian/changelog - debian/control - + debian/python-biom-format-examples.docs - debian/python-biom-format-doc.examples → debian/python-biom-format-examples.examples - debian/rules - debian/tests/python2 - debian/tests/python3 Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +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 <[email protected]> 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: ${misc:Depends}, +Description: examples and test data for BIOM format + The BIOM file format (canonically pronounced biome) is designed to be a + general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth + Microbiome Project and is a Genomics Standards Consortium candidate + project. + . + The BIOM format is designed for general use in broad areas of + comparative -omics. For example, in marker-gene surveys, the primary use + of this format is to represent OTU tables: the observations in this case + are OTUs and the matrix contains counts corresponding to the number of + times each OTU is observed in each sample. With respect to metagenome + data, this format would be used to represent metagenome tables: the + observations in this case might correspond to SEED subsystems, and the + matrix would contain counts corresponding to the number of times each + subsystem is observed in each metagenome. Similarly, with respect to + genome data, this format may be used to represent a set of genomes: the + observations in this case again might correspond to SEED subsystems, and + the counts would correspond to the number of times each subsystem is + observed in each genome. + . + This package provides the examples and tests for the BIOM format Python + package. ===================================== debian/python-biom-format-examples.docs ===================================== @@ -0,0 +1 @@ +biom/tests ===================================== debian/python-biom-format-doc.examples → debian/python-biom-format-examples.examples ===================================== ===================================== debian/rules ===================================== @@ -8,6 +8,7 @@ export LC_ALL=C.UTF-8 export PYBUILD_NAME=biom-format export PYBUILD_DESTDIR_python2=debian/python-$(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 View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/compare/86f300f6f13ea4c2f7d6191c22bd96ddf8bfeab0...9c7b4be60a79f8862e0491987359e1ec456618c2 -- View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/compare/86f300f6f13ea4c2f7d6191c22bd96ddf8bfeab0...9c7b4be60a79f8862e0491987359e1ec456618c2 You're receiving this email because of your account on salsa.debian.org.
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