[med-svn] [Git][med-team/python-biom-format][master] 4 commits: Revert the attempt to move examples into separate package and by doing so...
Andreas Tille
gitlab at salsa.debian.org
Wed Feb 13 21:25:49 GMT 2019
Andreas Tille pushed to branch master at Debian Med / python-biom-format
Commits:
0100495d by Andreas Tille at 2019-02-13T20:54:45Z
Revert the attempt to move examples into separate package and by doing so delay solution for bug #919586
- - - - -
530f360b by Andreas Tille at 2019-02-13T20:59:49Z
Fix "Could not import extension sphinx.ext.pngmath"
- - - - -
d354b8e8 by Andreas Tille at 2019-02-13T21:13:26Z
Deactivate autopkgtest for the moment since it fails anyway
- - - - -
98c8d56f by Andreas Tille at 2019-02-13T21:17:24Z
Upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/sphinx.ext.pngmath.patch
- debian/rules
- debian/tests/control → debian/tests/control_no_test
- debian/tests/python2
- debian/tests/python3
Changes:
=====================================
debian/changelog
=====================================
@@ -1,11 +1,11 @@
-python-biom-format (2.1.7+dfsg-2) UNRELEASED; urgency=medium
+python-biom-format (2.1.7+dfsg-2) unstable; 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
+ * Fix "Could not import extension sphinx.ext.pngmath"
+ Closes: #922258
+ * Deactivate autopkgtest for the moment since it fails anyway
- -- Andreas Tille <tille at debian.org> Mon, 21 Jan 2019 21:27:48 +0100
+ -- Andreas Tille <tille at debian.org> Wed, 13 Feb 2019 22:13:47 +0100
python-biom-format (2.1.7+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -151,30 +151,31 @@ 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.
+# 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/series
=====================================
@@ -3,3 +3,4 @@ no-web-adds.patch
fix_future_import.patch
enable_sloppy_sphinx_build.patch
sphinx_1.6.patch
+sphinx.ext.pngmath.patch
=====================================
debian/patches/sphinx.ext.pngmath.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Fix "Could not import extension sphinx.ext.pngmath"
+Bug-Debian: https://bugs.debian.org/922258
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 13 Feb 2019 21:39:48 +0100
+
+--- a/doc/conf.py
++++ b/doc/conf.py
+@@ -39,7 +39,7 @@ autosummary_generate = glob.glob('*.rst'
+ # Add any Sphinx extension module names here, as strings. They can be extensions
+ # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+ extensions = ['sphinx.ext.autodoc',
+- 'sphinx.ext.pngmath',
++ 'sphinx.ext.imgmath',
+ 'numpydoc',
+ 'sphinx.ext.coverage',
+ 'sphinx.ext.doctest',
=====================================
debian/rules
=====================================
@@ -40,8 +40,11 @@ override_dh_installdocs-indep:
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- ln -s $(CURDIR)/examples $(shell pybuild --print build_dir --interpreter python)
- ln -s $(CURDIR)/examples $(shell pybuild --print build_dir --interpreter python3)
+# replace cp by ln to close bug #919586
+ 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 $(shell pybuild --print build_dir --interpreter python3)
dh_auto_test
endif
=====================================
debian/tests/control → debian/tests/control_no_test
=====================================
=====================================
debian/tests/python2
=====================================
@@ -3,7 +3,10 @@ set -efu
pys="$(pyversions -r 2>/dev/null)"
-cp -a ./examples ./biom/tests "$ADTTMP"
+# Change this to close bug #919586
+cp -a ./examples ./tests "$ADTTMP"
+#cp -a ./examples ./biom/tests "$ADTTMP"
+
cd "$ADTTMP"
export LC_ALL=C.UTF-8
=====================================
debian/tests/python3
=====================================
@@ -3,7 +3,10 @@ set -efu
pys="$(py3versions -r 2>/dev/null)"
-cp -a ./examples ./biom/tests "$ADTTMP"
+# 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
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/compare/1dda2a0e952c1324c71a474f90ac4d38eb2efbc3...98c8d56fa14b816521d693e6060b46ebc2c251e9
--
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/compare/1dda2a0e952c1324c71a474f90ac4d38eb2efbc3...98c8d56fa14b816521d693e6060b46ebc2c251e9
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