[med-svn] [Git][med-team/python-biom-format][master] 11 commits: debhelper-compat 12
Andreas Tille
gitlab at salsa.debian.org
Tue Aug 6 09:39:20 BST 2019
Andreas Tille pushed to branch master at Debian Med / python-biom-format
Commits:
81d0e0a4 by Andreas Tille at 2019-08-06T06:30:23Z
debhelper-compat 12
- - - - -
6e97f0e5 by Andreas Tille at 2019-08-06T06:33:14Z
Standards-Version: 4.3.0
- - - - -
2fa53562 by Andreas Tille at 2019-08-06T07:21:06Z
Drop biom-format-tools package - wrapper script is in Python3 package
- - - - -
e092ab41 by Andreas Tille at 2019-08-06T07:22:12Z
Do not copy build time tests to doc directory
- - - - -
5932f88b by Andreas Tille at 2019-08-06T07:38:01Z
Fix provides
- - - - -
4fb50386 by Andreas Tille at 2019-08-06T07:38:21Z
Examples should be in python3-biom-format package
- - - - -
77fbab33 by Andreas Tille at 2019-08-06T07:51:37Z
Provide valid autopkgtest for Python3 module based on upstreams CI test
- - - - -
3686ff0c by Andreas Tille at 2019-08-06T07:52:50Z
Provide autopkgtest script as user example
- - - - -
64b57e5e by Andreas Tille at 2019-08-06T07:57:40Z
MOre of upstream tests
- - - - -
18e648c6 by Andreas Tille at 2019-08-06T08:11:20Z
Fix shell syntax
- - - - -
97a40855 by Andreas Tille at 2019-08-06T08:16:04Z
Upload to unstable
- - - - -
15 changed files:
- + debian/README.test
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/posix_shell.patch
- debian/patches/series
- − debian/python-biom-format-examples.docs
- + debian/python3-biom-format.docs
- debian/python-biom-format-examples.examples → debian/python3-biom-format.examples
- debian/rules
- + debian/tests/control
- − debian/tests/control_no_test
- − debian/tests/python2
- − debian/tests/python3
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+python-biom-format (2.1.7+dfsg-3) unstable; urgency=medium
+
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * executable /usr/bin/biom in Python3 package
+ * Examples in Python3 package to support testing
+ * Do not copy build time tests to doc directory
+ Closes: #919586
+ * Drop biom-format-tools package - wrapper script is in Python3 package
+ * Provide valid autopkgtest for Python3 module based on upstreams CI test
+ Closes: #896953
+
+ -- Andreas Tille <tille at debian.org> Tue, 06 Aug 2019 10:11:48 +0200
+
python-biom-format (2.1.7+dfsg-2) unstable; urgency=medium
* Do not ship *.c and *.pyx cython input files in binary packages
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>
Section: python
Testsuite: autopkgtest-pkg-python
Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
dh-python,
cython,
python-dev,
@@ -30,7 +30,7 @@ Build-Depends: debhelper (>= 12~),
python3-setuptools,
python3-scipy,
python3-sphinx
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
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/
@@ -70,6 +70,9 @@ Depends: ${misc:Depends},
${python3:Depends},
${shlibs:Depends}
Suggests: python-biom-format-doc
+Breaks: biom-format-tools (<< 2.1.7+dfsg-3)
+Replaces: biom-format-tools (<< 2.1.7+dfsg-3)
+Provides: biom-format-tools
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
@@ -120,62 +123,3 @@ Description: documentation for BIOM format
observed in each genome.
.
This package provides the documentation for the BIOM format Python package.
-
-Package: biom-format-tools
-Architecture: any-amd64 any-arm64 armel armhf any-i386 any-mips64el mipsel any-ppc64el
-Section: misc
-Depends: ${misc:Depends},
- ${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
- 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 command-line tools for the BIOM format Python
- package.
-
-# This is needed to close bug #919586
-#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/patches/posix_shell.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 06 Aug 2019 08:30:23 +0200
+Description: Fix shell syntax
+
+--- a/biom/assets/exercise_cli.sh
++++ b/biom/assets/exercise_cli.sh
+@@ -3,7 +3,7 @@ set -xe
+
+ table=examples/min_sparse_otu_table_hdf5.biom
+ obsmd=examples/obs_md.txt
+-if [[ ! -f ${table} ]];
++if [ ! -f ${table} ] ;
+ then
+ echo "This script expects to operate in the base repository directory"
+ exit 1
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ fix_future_import.patch
enable_sloppy_sphinx_build.patch
sphinx_1.6.patch
sphinx.ext.pngmath.patch
+posix_shell.patch
=====================================
debian/python-biom-format-examples.docs deleted
=====================================
@@ -1 +0,0 @@
-biom/tests
=====================================
debian/python3-biom-format.docs
=====================================
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/run-unit-test
=====================================
debian/python-biom-format-examples.examples → debian/python3-biom-format.examples
=====================================
=====================================
debian/rules
=====================================
@@ -28,11 +28,8 @@ override_dh_auto_build:
override_dh_auto_install:
dh_auto_install
- # Install command-line scripts in separate tools package.
- dh_install --sourcedir=$(PYBUILD_DESTDIR_python3) \
- --package=$(PYBUILD_NAME)-tools usr/bin
+ # Install command-line scripts into Python3 package only
rm -rf $(PYBUILD_DESTDIR_python2)/usr/bin
- rm -rf $(PYBUILD_DESTDIR_python3)/usr/bin
override_dh_installdocs-indep:
dh_installdocs --indep
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/control_no_test deleted
=====================================
@@ -1,9 +0,0 @@
-Tests: python2
-Depends: python-all,
- python-biom-format,
- python-nose
-
-Tests: python3
-Depends: python3-all,
- python3-biom-format,
- python3-nose
=====================================
debian/tests/python2 deleted
=====================================
@@ -1,17 +0,0 @@
-#!/bin/sh
-set -efu
-
-pys="$(pyversions -r 2>/dev/null)"
-
-# Change this to close bug #919586
-cp -a ./examples ./tests "$ADTTMP"
-#cp -a ./examples ./biom/tests "$ADTTMP"
-
-cd "$ADTTMP"
-
-export LC_ALL=C.UTF-8
-
-for py in $pys; do
- echo "=== $py ==="
- $py -m nose tests 2>&1
-done
=====================================
debian/tests/python3 deleted
=====================================
@@ -1,17 +0,0 @@
-#!/bin/sh
-set -efu
-
-pys="$(py3versions -r 2>/dev/null)"
-
-# Change this to close bug #919586
-cp -a ./examples ./tests "$ADTTMP"
-#cp -a ./examples ./biom/tests "$ADTTMP"
-
-cd "$ADTTMP"
-
-export LC_ALL=C.UTF-8
-
-for py in $pys; do
- echo "=== $py ==="
- $py -m nose tests 2>&1
-done
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,31 @@
+#!/bin/bash
+set -e
+
+pkg=python3-biom-format
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+biom show-install-info
+# we can only validate the tables if we have H5PY
+for table in examples/*hdf5.biom; do
+ biom validate-table -i ${table}
+done
+
+# validate JSON formatted tables
+for table in examples/*table.biom; do
+ biom validate-table -i ${table}
+done
+
+python3 /usr/lib/python3/dist-packages/biom/assets/exercise_api.py examples/rich_sparse_otu_table_hdf5.biom sample
+python3 /usr/lib/python3/dist-packages/biom/assets/exercise_api.py examples/rich_sparse_otu_table_hdf5.biom observation
+sh /usr/lib/python3/dist-packages/biom/assets/exercise_cli.sh
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/compare/98c8d56fa14b816521d693e6060b46ebc2c251e9...97a40855a6d7dc07400c099c78a818a2ab5fef62
--
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/compare/98c8d56fa14b816521d693e6060b46ebc2c251e9...97a40855a6d7dc07400c099c78a818a2ab5fef62
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