[med-svn] [python-biom-format] 09/11: Provide the Python 3 package.

[Ghislain Vaillant]

This is an automated email from the git hooks/post-receive script.

ghisvail-guest pushed a commit to branch master
in repository python-biom-format.

commit 1a3a637c9a182e830938a3b6c5bc2707d53059a1
Author: Ghislain Antony Vaillant <ghisvail at gmail.com>
Date:   Sat Mar 5 18:03:37 2016 +0000

    Provide the Python 3 package.
---
 debian/control       | 46 ++++++++++++++++++++++++++++++++++++++++++----
 debian/rules         |  7 +++++--
 debian/tests/control |  5 +++++
 debian/tests/python3 | 12 ++++++++++++
 4 files changed, 64 insertions(+), 6 deletions(-)

diff --git a/debian/control b/debian/control
index c4ef680..ab29c82 100644
--- a/debian/control
+++ b/debian/control
@@ -17,7 +17,16 @@ Build-Depends: debhelper (>= 9),
                python-future,
                python-nose,
                python-setuptools,
-               bash-completion
+               bash-completion,
+               cython3,
+               python3-all-dev,
+               python3-click,
+               python3-future,
+               python3-h5py,
+               python3-nose,
+               python3-numpy,
+               python3-setuptools,
+               python3-scipy
 Build-Depends-Indep: python-sphinx
 Standards-Version: 3.9.7
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-biom-format.git
@@ -31,7 +40,7 @@ Depends: ${python:Depends},
          ${misc:Depends},
          ${shlibs:Depends},
 Suggests: python-biom-format-doc
-Description: Biological Observation Matrix (BIOM) format
+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
@@ -54,6 +63,35 @@ Description: Biological Observation Matrix (BIOM) format
  .
  This package provides the BIOM format library for the Python 2 interpreter.
 
+Package: python3-biom-format
+Architecture: any
+Depends: ${misc:Depends},
+         ${python3:Depends},
+         ${shlibs:Depends},
+Suggests: python-biom-format-doc
+Description: Biological Observation Matrix (BIOM) format (Python 3)
+ 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 3 interpreter.
+
 Package: python-biom-format-doc
 Architecture: all
 Section: doc
@@ -86,8 +124,8 @@ Package: biom-format-tools
 Architecture: any
 Section: misc
 Depends: ${misc:Depends},
-         ${python:Depends},
-         python-biom-format (= ${binary:Version})
+         ${python3:Depends},
+         python3-biom-format (= ${binary:Version})
 Description: command-line tools for BIOM format
  The BIOM file format (canonically pronounced biome) is designed to be a
  general-use format for representing biological sample by observation
diff --git a/debian/rules b/debian/rules
index b803c33..f386eee 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,11 +9,13 @@ mandir  := $(CURDIR)/debian/$(pkg)/usr/share/man/man1
 
 export PYBUILD_NAME=biom-format
 export PYBUILD_DESTDIR_python2=debian/python-$(PYBUILD_NAME)
+export PYBUILD_DESTDIR_python3=debian/python3-$(PYBUILD_NAME)
 export PYBUILD_AFTER_INSTALL_python2=dh_numpy
+export PYBUILD_AFTER_INSTALL_python3=dh_numpy3
 export PYBUILD_BEFORE_TEST=cp -r {dir}/examples {dir}/tests {build_dir}
 
 %:
-	dh $@ --with python2,bash-completion --buildsystem=pybuild
+	dh $@ --with python2,python3,bash-completion --buildsystem=pybuild
 
 override_dh_auto_build-arch:
 	USE_CYTHON=true dh_auto_build
@@ -25,9 +27,10 @@ override_dh_auto_build-indep:
 override_dh_auto_install:
 	dh_auto_install
 	# Install command-line scripts in separate tools package.
-	dh_install --sourcedir=$(PYBUILD_DESTDIR_python2) \
+	dh_install --sourcedir=$(PYBUILD_DESTDIR_python3) \
 		--package=$(PYBUILD_NAME)-tools usr/bin
 	rm -rf $(PYBUILD_DESTDIR_python2)/usr/bin
+	rm -rf $(PYBUILD_DESTDIR_python3)/usr/bin
 
 override_dh_auto_clean:
 	rm -rf build/tests
diff --git a/debian/tests/control b/debian/tests/control
index 9eb6a76..dac89b8 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -2,3 +2,8 @@ Tests: python2
 Depends: python-all,
          python-biom-format,
          python-nose
+
+Tests: python3
+Depends: python3-all,
+         python3-biom-format,
+         python3-nose
diff --git a/debian/tests/python3 b/debian/tests/python3
new file mode 100644
index 0000000..fe7a0e0
--- /dev/null
+++ b/debian/tests/python3
@@ -0,0 +1,12 @@
+#!/bin/sh
+set -efu
+
+pys="$(py3versions -r 2>/dev/null)"
+
+cp -a ./examples ./tests "$ADTTMP"
+cd "$ADTTMP"
+
+for py in $pys; do
+	echo "=== $py ==="
+	$py -m nose tests 2>&1
+done

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-biom-format.git