debian/README.test

+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

+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@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

-12

debian/control

@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@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

+Author: Andreas Tille <tille@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

-biom/tests

debian/python3-biom-format.docs

+debian/README.test
+debian/tests/run-unit-test

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

+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr

debian/tests/control_no_test

-Tests: python2
-Depends: python-all,
-         python-biom-format,
-         python-nose
-
-Tests: python3
-Depends: python3-all,
-         python3-biom-format,
-         python3-nose

debian/tests/python2

-#!/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

-#!/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

+#!/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