[med-svn] [Git][med-team/python-biom-format][master] 3 commits: Apply patch from Steve Langasek
Andreas Tille
gitlab at salsa.debian.org
Fri Aug 16 21:13:33 BST 2019
Andreas Tille pushed to branch master at Debian Med / python-biom-format
Commits:
cfc20311 by Andreas Tille at 2019-08-16T20:02:03Z
Apply patch from Steve Langasek
- - - - -
49c8e4a2 by Andreas Tille at 2019-08-16T20:02:57Z
Drop Python2 package
- - - - -
cdcb6435 by Andreas Tille at 2019-08-16T20:10:59Z
Fix doc-base control file
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/python-biom-format-doc.doc-base
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+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 at 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 \
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/compare/97a40855a6d7dc07400c099c78a818a2ab5fef62...cdcb64355b065005b1c0e0f41ec2bc5814621198
--
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/compare/97a40855a6d7dc07400c099c78a818a2ab5fef62...cdcb64355b065005b1c0e0f41ec2bc5814621198
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