debian/changelog

-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@debian.org>  Mon, 21 Jan 2019 21:27:48 +0100
+ -- Andreas Tille <tille@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

+Description: Fix "Could not import extension sphinx.ext.pngmath"
+Bug-Debian: https://bugs.debian.org/922258
+Author: Andreas Tille <tille@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/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