[med-svn] [Git][med-team/macsyfinder][master] 5 commits: Use unittests for autopkgtests
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Feb 6 14:36:10 GMT 2021
Michael R. Crusoe pushed to branch master at Debian Med / macsyfinder
Commits:
153545ee by Michael R. Crusoe at 2021-02-06T14:21:39+01:00
Use unittests for autopkgtests
- - - - -
3e1dacaf by Michael R. Crusoe at 2021-02-06T14:50:59+01:00
Fix conffile placement
- - - - -
905685e6 by Michael R. Crusoe at 2021-02-06T14:56:09+01:00
Make sure no build paths are embedded
- - - - -
4447898f by Michael R. Crusoe at 2021-02-06T15:31:03+01:00
Build the docs
- - - - -
609d9859 by Michael R. Crusoe at 2021-02-06T15:35:04+01:00
routine-update: Ready to upload to unstable
- - - - -
13 changed files:
- debian/changelog
- + debian/clean
- debian/control
- debian/docs
- debian/macsyfinder.doc-base
- + debian/macsyfinder.docs
- + debian/macsyfinder.lintian-overrides
- + debian/patches/debian_path
- + debian/patches/privacy
- debian/patches/series
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-macsyfinder (2.0~rc1-1) UNRELEASED; urgency=medium
+macsyfinder (2.0~rc1-1) unstable; urgency=medium
* Team upload
@@ -16,8 +16,12 @@ macsyfinder (2.0~rc1-1) UNRELEASED; urgency=medium
[ Michael R. Crusoe ]
* debian/patches/allow_setuptools: added to fix build. Closes: #933928
+ * Use unittests for autopkgtests
+ * Fix conffile placement
+ * Make sure no build paths are embedded
+ * Build the docs
- -- Andreas Tille <tille at debian.org> Fri, 06 Sep 2019 10:40:05 +0200
+ -- Michael R. Crusoe <crusoe at debian.org> Sat, 06 Feb 2021 15:35:04 +0100
macsyfinder (1.0.5-3) unstable; urgency=medium
=====================================
debian/clean
=====================================
@@ -0,0 +1,3 @@
+uninstall.cfg
+uninstall_files
+doc/_build/
=====================================
debian/control
=====================================
@@ -28,6 +28,7 @@ Rules-Requires-Root: no
Package: macsyfinder
Architecture: all
Depends: ${python3:Depends},
+ ${sphinxdoc:Depends},
${misc:Depends},
python3-networkx,
python3-yaml,
@@ -36,6 +37,7 @@ Depends: ${python3:Depends},
ncbi-blast+,
libjs-jquery,
libjs-underscore
+Built-Using: ${sphinxdoc:Built-Using}
Description: detection of macromolecular systems in protein datasets
MacSyFinder is a program to model and detect macromolecular systems,
genetic pathways... in protein datasets. In prokaryotes, these systems
=====================================
debian/docs
=====================================
@@ -1,2 +1,2 @@
-debian/README.test
-debian/tests/run-unit-test
+#debian/README.test
+#debian/tests/run-unit-test
=====================================
debian/macsyfinder.doc-base
=====================================
@@ -16,4 +16,4 @@ Files: /usr/share/doc/macsyfinder/html/*
Index: /usr/share/doc/macsyfinder/html/index.html
Format:pdf
-Files: /usr/share/doc/macsyfinder/pdf/Macsyfinder.pdf.gz
+Files: /usr/share/doc/macsyfinder/macsyfinder.pdf.gz
=====================================
debian/macsyfinder.docs
=====================================
@@ -0,0 +1,2 @@
+doc/build/latex/macsyfinder.pdf
+doc/build/html/
=====================================
debian/macsyfinder.lintian-overrides
=====================================
@@ -0,0 +1 @@
+macsyfinder: package-contains-documentation-outside-usr-share-doc usr/share/macsyfinder/data/models/readme
=====================================
debian/patches/debian_path
=====================================
@@ -0,0 +1,16 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Use the final Debian paths
+Forwarded: not-needed
+--- macsyfinder.orig/setup.py
++++ macsyfinder/setup.py
+@@ -61,8 +61,8 @@
+
+ inst = self.distribution.command_options.get('install', {})
+ _file = os.path.join('macsypy', '__init__.py')
+- subst_file(_file, {'MACSYDATA': os.path.join(get_install_data_dir(inst), 'macsyfinder'),
+- 'MACSYCONF': os.path.join(get_install_conf_dir(inst), 'macsyfinder')})
++ subst_file(_file, {'MACSYDATA': os.path.join('/usr/share', 'macsyfinder'),
++ 'MACSYCONF': os.path.join('/etc/', 'macsyfinder')})
+
+ _install_lib.run(self)
+
=====================================
debian/patches/privacy
=====================================
@@ -0,0 +1,19 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Fix privacy-breach-generic due to external image
+Forwarded: not-needed
+--- macsyfinder.orig/doc/source/_templates/layout.html
++++ macsyfinder/doc/source/_templates/layout.html
+@@ -3,10 +3,7 @@
+ {% block footer %}
+
+ <a href="https://github.com/gem-pasteur/macsyfinder">
+- <img style="position: absolute; top: 0; right: 0; border: 0;"
+- src="https://camo.githubusercontent.com/38ef81f8aca64bb9a64448d0d70f1308ef5341ab/68747470733a2f2f73332e616d617a6f6e6177732e636f6d2f6769746875622f726962626f6e732f666f726b6d655f72696768745f6461726b626c75655f3132313632312e706e67"
+- alt="Fork me on GitHub"
+- data-canonical-src="https://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png">
++Fork me on GitHub
+ </a>
+
+-{% endblock %}
+\ No newline at end of file
++{% endblock %}
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,4 @@
skip_failing_test.patch
allow_setuptools
+debian_path
+privacy
=====================================
debian/rules
=====================================
@@ -3,36 +3,12 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-%:
- dh $@ --with python3 --buildsystem=pybuild
-
-_override_dh_auto_install:
- cd doc && make html
- cd doc && make latexpdf
- # ln -sf $(shell pybuild --print build_dir --interpreter python3) build/lib.$(shell dpkg-architecture -qDEB_BUILD_ARCH_OS)-$(shell dpkg-architecture -qDEB_BUILD_GNU_CPU)-$(shell py3versions -vs)
- python3 setup.py install --prefix=debian/macsyfinder/usr/ --install-conf=debian/macsyfinder/etc/ --no-viewer
- # The better solution would be to use
- # dh_auto_install -- --prefix=/usr --install-conf=/etc --no-viewer
- # and fiy setup.py to use --root as install location (which is ignored unfortunately)
- # Since I have no idea how to fix setup.py here the broken config files are hacked afterwards
- for conffile in \
- etc/macsyfinder/macsyfinder.conf.new \
- usr/lib/python3*/site-packages/macsypy/config.py \
- usr/lib/python3*/site-packages/macsypy/registries.py \
- ; do \
- sed -i 's:debian/macsyfinder::g' debian/macsyfinder/$${conffile} ; \
- done
- mv debian/macsyfinder/etc/macsyfinder/macsyfinder.conf.new debian/macsyfinder/etc/macsyfinder/macsyfinder.conf
- rm debian/macsyfinder/usr/share/doc/macsyfinder/html/_static/jquery.js
- rm debian/macsyfinder/usr/share/doc/macsyfinder/html/_static/underscore.js
- rm -Rf debian/macsyfinder/usr/share/macsyfinder/macsyview
+export PYBUILD_AFTER_INSTALL=mv {destdir}/usr/etc {destdir}/etc && cd {dir}/doc && make html latexpdf
-override_dh_clean:
- rm -Rf doc/_build
- rm -f uninstall.cfg
- rm -f uninstall_files
- dh_clean
+%:
+ dh $@ --with python3,sphinxdoc --buildsystem=pybuild
override_dh_fixperms:
dh_fixperms
find debian -name "test_*.fa" -executable -exec chmod -x \{\} \;
+ find debian -name "*.prt" -executable -exec chmod -x \{\} \;
=====================================
debian/tests/control
=====================================
@@ -1,4 +1,3 @@
Tests: run-unit-test
-Depends: @
-Restrictions:
-
+Depends: @, python3-setuptools
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,17 +1,19 @@
#!/bin/bash
set -e
pkg="macsyfinder"
-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
-AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
-fi
-cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
-cd $AUTOPKGTEST_TMP
-find . -name "*.gz" -exec gunzip \{\} \;
+# if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+# AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+# fi
+# cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+# cd $AUTOPKGTEST_TMP
+# find . -name "*.gz" -exec gunzip \{\} \;
+#
+# echo "TEST START"
+#
+# /usr/bin/macsyfinder --db-type unordered --sequence-db test_base.fa all
+#
+# /usr/bin/macsyfinder --db-type ordered_replicon --sequence-db ordered_replicon_base all
+#
+# echo "PASS"
-echo "TEST START"
-
-/usr/bin/macsyfinder --db-type unordered --sequence-db test_base.fa all
-
-/usr/bin/macsyfinder --db-type ordered_replicon --sequence-db ordered_replicon_base all
-
-echo "PASS"
+python3 setup.py test
View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/compare/421623a15e365930a72f4c874d378db053db05c3...609d985930fc5ba1ea9da68a3c202bf2f47f86ba
--
View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/compare/421623a15e365930a72f4c874d378db053db05c3...609d985930fc5ba1ea9da68a3c202bf2f47f86ba
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