[med-svn] [Git][med-team/python-ruffus][master] 9 commits: Remove Python2 module

Andreas Tille gitlab at salsa.debian.org
Sun Dec 22 20:51:44 GMT 2019 


Andreas Tille pushed to branch master at Debian Med / python-ruffus


Commits:
ab77b638 by Andreas Tille at 2019-12-22T18:12:35Z
Remove Python2 module

- - - - -
bc4d36ab by Andreas Tille at 2019-12-22T18:12:47Z
routine-update: debhelper-compat 12

- - - - -
efe9d53b by Andreas Tille at 2019-12-22T18:12:52Z
routine-update: Standards-Version: 4.4.1

- - - - -
a92d3b43 by Andreas Tille at 2019-12-22T18:12:52Z
R-U: rename d/tests/control.autodep8 to d/tests/control

- - - - -
33613004 by Andreas Tille at 2019-12-22T18:12:52Z
R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g

- - - - -
1daa74b3 by Andreas Tille at 2019-12-22T18:12:56Z
Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.
- - - - -
a31619fa by Andreas Tille at 2019-12-22T18:37:46Z
Fiy doc-base file

- - - - -
4acf6976 by Andreas Tille at 2019-12-22T19:03:46Z
Run only Python3 testscript in autopkgtest

- - - - -
4d8c6b82 by Andreas Tille at 2019-12-22T19:11:35Z
Upload to unstable

- - - - -


9 changed files:

- debian/changelog
- − debian/compat
- debian/control
- debian/python-ruffus-doc.doc-base.html
- debian/python-ruffus-doc.doc-base.pdf
- debian/rules
- debian/tests/control.autodep8 → debian/tests/control
- debian/tests/run-unit-test
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+python-ruffus (2.8.1-5) unstable; urgency=medium
+
+  * Remove Python2 module
+    Closes: #938152
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * rename debian/tests/control.autodep8 to debian/tests/control
+  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
+  * Set upstream metadata fields: Bug-Database, Repository, Repository-
+    Browse.
+
+ -- Andreas Tille <tille at debian.org>  Sun, 22 Dec 2019 20:04:05 +0100
+
 python-ruffus (2.8.1-4) unstable; urgency=medium
 
   * Enable reproducible build by removing non-deterministic temporary temp


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -4,40 +4,19 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: python
 Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-all,
-               python-setuptools,
-               python-pytest,
                python3-all,
                python3-setuptools,
                python3-sphinx,
                python3-sphinx-rtd-theme,
                python3-pytest,
                graphviz
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-ruffus
 Vcs-Git: https://salsa.debian.org/med-team/python-ruffus.git
 Homepage: http://www.ruffus.org.uk/
 
-Package: python-ruffus
-Architecture: all
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-         ${python:Depends},
-         graphviz
-Suggests: python-drmaa
-Description: Python computation pipeline library widely used in bioinformatics
- Ruffus is designed to allow scientific and other analyses to be automated
- with the minimum of fuss and the least effort.
- .
-  * Lightweight: Suitable for the simplest of tasks
-  * Scalable: Handles even fiendishly complicated pipelines which would cause
-    make or scons to go cross-eyed and recursive.
-  * Standard Python: No "clever magic", no pre-processing.
-  * Unintrusive: Unambitious, lightweight syntax which tries to do this one
-    small thing well.
-
 Package: python3-ruffus
 Architecture: all
 Depends: ${shlibs:Depends},


=====================================
debian/python-ruffus-doc.doc-base.html
=====================================
@@ -14,5 +14,5 @@ Abstract: Python computation pipeline library widely used in bioinformatics
 Section: Science/Biology
 
 Format: html
-Files: /usr/share/doc/python-ruffus/html
-Index: /usr/share/doc/python-ruffus/html/index.html
+Files: /usr/share/doc/python-ruffus-doc/html
+Index: /usr/share/doc/python-ruffus-doc/html/index.html


=====================================
debian/python-ruffus-doc.doc-base.pdf
=====================================
@@ -14,4 +14,4 @@ Abstract: Python computation pipeline library widely used in bioinformatics
 Section: Science/Biology
 
 Format: pdf
-Files: /usr/share/doc/python-ruffus/ruffus.pdf.gz
+Files: /usr/share/doc/python-ruffus-doc/ruffus.pdf.gz


=====================================
debian/rules
=====================================
@@ -9,7 +9,7 @@ docpkg:=$(DEB_SOURCE)-doc
 export PYBUILD_NAME=ruffus
 
 %:
-	dh $@ --with python2,python3,sphinxdoc --buildsystem=pybuild
+	dh $@ --with python3,sphinxdoc --buildsystem=pybuild
 
 override_dh_auto_build:
 	dh_auto_build
@@ -18,6 +18,7 @@ override_dh_auto_build:
 override_dh_installdocs:
 	dh_installdocs -ppython-ruffus-doc doc/_build/html
 	dh_installdocs -A
+	find debian -name run_all_unit_tests.cmd -delete
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
@@ -60,7 +61,6 @@ override_dh_install:
 	find debian/python3-$(PYBUILD_NAME)/usr/lib/python3*/dist-packages/ruffus/test -name "*.py" -exec sed -i 's+^\(#!/usr/bin/.*python\)[[:space:]]*$$+\13+' \{\} \;
 	# leave only the test starter that fits Python version
 	find debian/python3-$(PYBUILD_NAME) -name run_all_unit_tests.cmd -delete
-	find debian/python-$(PYBUILD_NAME) -name run_all_unit_tests3.cmd -delete
 	sed -i '1s?^#! */usr/bin/env *python *$$?#!/usr/bin/python3?' `grep -Rl '^#! */usr/bin/env *python *$$' debian/python3-$(PYBUILD_NAME)`
 
 override_dh_fixperms:


=====================================
debian/tests/control.autodep8 → debian/tests/control
=====================================


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,23 +1,17 @@
 #!/bin/sh -e
 
 pkg=python-ruffus
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
 mkdir ruffus
 cd ruffus
 cp -a /usr/share/doc/python-ruffus-doc/test .
 cd test
 find . -type f -name "*.gz" -exec gunzip \{\} \;
-# mod +x [a-z]*.py
 
 export LC_ALL=C.UTF-8
-export HOME=$ADTTMP
-for testscript in run_all_unit_tests*.cmd ; do
-    # exclude tests with known issues ... should not be needed any more since fix_test.patch
-#    sed -i -e 's/\(unittest test_file_name_parameters.*\)\\/\1 true/' \
-#           -e 's/\(unittest test_ruffus_utility.*\)\\/\1 true/' \
-#        $testscript
-    bash $testscript
-done
+export HOME=$AUTOPKGTEST_TMP
+bash run_all_unit_tests3.cmd


=====================================
debian/upstream/metadata
=====================================
@@ -1,23 +1,24 @@
 Reference:
- Author: Leo Goodstadt
- Title: "Ruffus: A Lightweight Python Library for Computational Pipelines"
- Journal: Bioinformatics
- Year: 2010
- Volume: 26
- Number: 21
- Pages: 2778-9
- DOI: 10.1093/bioinformatics/btq524
- PMID: 20847218
- URL: "http://bioinformatics.oxfordjournals.org/content/early/\
-  2010/09/16/bioinformatics.btq524"
- ePrint: "http://bioinformatics.oxfordjournals.org/content/early/\
-  2010/09/16/bioinformatics.btq524.full.pdf+html"
+  Author: Leo Goodstadt
+  Title: 'Ruffus: A Lightweight Python Library for Computational Pipelines'
+  Journal: Bioinformatics
+  Year: 2010
+  Volume: 26
+  Number: 21
+  Pages: 2778-9
+  DOI: 10.1093/bioinformatics/btq524
+  PMID: 20847218
+  URL: http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524
+  ePrint: http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524.full.pdf+html
 Registry:
- - Name: OMICtools
-   Entry: OMICS_07398
- - Name: SciCrunch
-   Entry: NA
- - Name: bio.tools
-   Entry: NA
- - Name: conda:bioconda
-   Entry: ruffus
+- Name: OMICtools
+  Entry: OMICS_07398
+- Name: SciCrunch
+  Entry: NA
+- Name: bio.tools
+  Entry: NA
+- Name: conda:bioconda
+  Entry: ruffus
+Bug-Database: https://github.com/bunbun/ruffus/issues
+Repository: https://github.com/bunbun/ruffus.git
+Repository-Browse: https://github.com/bunbun/ruffus



View it on GitLab: https://salsa.debian.org/med-team/python-ruffus/compare/8d9294dc2e3535ca60869d08d483b3699d54576c...4d8c6b825b2d3359ce394d0c29328bbe950244f5

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View it on GitLab: https://salsa.debian.org/med-team/python-ruffus/compare/8d9294dc2e3535ca60869d08d483b3699d54576c...4d8c6b825b2d3359ce394d0c29328bbe950244f5
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