[med-svn] [Git][med-team/libsbml][master] 10 commits: Provide Python3 instead of Python2 bindings (SBML can only provide either…
Andreas Tille
gitlab at salsa.debian.org
Mon Dec 3 17:41:59 GMT 2018
Andreas Tille pushed to branch master at Debian Med / libsbml
Commits:
04b51d36 by Andreas Tille at 2018-12-03T15:14:47Z
Provide Python3 instead of Python2 bindings (SBML can only provide either Python2 or Python3 - lets do the switch now)
- - - - -
42249124 by Andreas Tille at 2018-12-03T15:15:26Z
Standards-Version: 4.2.1
- - - - -
eaf1e9ce by Andreas Tille at 2018-12-03T15:17:20Z
Do not mention unneeded autoconf, automake in Build-Depends
- - - - -
8d6219a0 by Andreas Tille at 2018-12-03T15:23:41Z
Testsuite: autopkgtest-pkg-python
- - - - -
1b6953ef by Andreas Tille at 2018-12-03T15:23:42Z
Secure URI in copyright format
- - - - -
324c7821 by Andreas Tille at 2018-12-03T15:23:42Z
Drop useless get-orig-source target
- - - - -
25610739 by Andreas Tille at 2018-12-03T15:27:46Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
9ce22ebf by Andreas Tille at 2018-12-03T15:27:46Z
Remove trailing whitespace in debian/changelog
- - - - -
122874c9 by Andreas Tille at 2018-12-03T15:32:43Z
Do not parse d/changelog
- - - - -
97adce58 by Andreas Tille at 2018-12-03T17:41:48Z
Build-Depends: libnewlib-dev
- - - - -
12 changed files:
- + debian/NEWS.Debian
- debian/changelog
- debian/control
- debian/copyright
- − debian/libsbml5-python-doc.links
- − debian/libsbml5-python.install
- − debian/libsbml5-python.lintian-overrides
- debian/libsbml5-python-doc.doc-base → debian/python3-libsbml5-doc.doc-base
- debian/libsbml5-python-doc.docs → debian/python3-libsbml5-doc.docs
- + debian/python3-libsbml5-doc.links
- + debian/python3-libsbml5.install
- debian/rules
Changes:
=====================================
debian/NEWS.Debian
=====================================
@@ -0,0 +1,6 @@
+libsbml (5.17.0+dfsg-1) unstable; urgency=medium
+
+ Python3 API was requested in bug #847013. Since libsbml can only provide
+ either Python2 or Python3 the switch to Python3 is done with this release.
+
+ -- Andreas Tille <tille at debian.org> Mon, 03 Dec 2018 16:11:35 +0100
=====================================
debian/changelog
=====================================
@@ -6,11 +6,21 @@ libsbml (5.17.0+dfsg-1) UNRELEASED; urgency=medium
[ Andreas Tille ]
* Point Vcs fields to salsa.debian.org
- * Standards-Version: 4.1.4
+ * Standards-Version: 4.2.1
* Deal with issue in doclets by removing docs/src/SBMLDoclet.java
* Remove libsbml-java-doc since doc does not build properly
-
- -- Andreas Tille <tille at debian.org> Mon, 14 May 2018 10:55:58 +0200
+ * Provide Python3 instead of Python2 bindings (SBML can only provide
+ either Python2 or Python3 - lets do the switch now)
+ Closes: #847013
+ * Testsuite: autopkgtest-pkg-python
+ * Secure URI in copyright format
+ * Drop useless get-orig-source target
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+ * Remove trailing whitespace in debian/changelog
+ * Do not parse d/changelog
+ * Build-Depends: libnewlib-dev
+
+ -- Andreas Tille <tille at debian.org> Mon, 03 Dec 2018 16:11:35 +0100
libsbml (5.16.0+dfsg-2) unstable; urgency=medium
@@ -200,11 +210,11 @@ libsbml (5.4.1-4) UNRELEASED; urgency=low
[ Steffen ]
* Removed everyone from Uploaders except Ivo
- - Ivo also builds the libsbml5-matlab package, the
+ - Ivo also builds the libsbml5-matlab package, the
control file is changed dynamically when the Matlab
development environment is detected.
- Matlab creator Mathworks provides their development
- package to help us.
+ package to help us.
[ Andreas Tille ]
* debian/upstream: Make author field BibTeX compliant
=====================================
debian/control
=====================================
@@ -3,15 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Ivo Maintz <ivo at maintz.de>,
Andreas Tille <tille at debian.org>
Section: science
+Testsuite: autopkgtest-pkg-python
Priority: optional
-Build-Depends: autoconf,
- automake,
- debhelper (>= 11~),
+Build-Depends: debhelper (>= 11~),
cmake,
doxygen,
swig,
libxml2-dev,
- python-dev,
+ python3-dev,
perl,
libperl-dev,
default-jdk,
@@ -21,12 +20,13 @@ Build-Depends: autoconf,
graphviz,
zlib1g-dev,
libbz2-dev,
+ libnewlib-dev,
mono-devel,
mono-mcs,
cli-common-dev,
mono-runtime-common,
texlive-latex-base
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/libsbml
Vcs-Git: https://salsa.debian.org/med-team/libsbml.git
Homepage: http://www.sbml.org/
@@ -34,6 +34,7 @@ Homepage: http://www.sbml.org/
Package: libsbml5-dev
Architecture: any
Section: libdevel
+Testsuite: autopkgtest-pkg-python
Depends: libsbml5 (= ${binary:Version}),
${misc:Depends}
Provides: libsbml-dev
@@ -48,6 +49,7 @@ Description: System Biology Markup Language library - development files
Package: libsbml5
Architecture: any
Section: libs
+Testsuite: autopkgtest-pkg-python
Depends: ${shlibs:Depends},
${misc:Depends}
Pre-Depends: ${misc:Pre-Depends}
@@ -58,26 +60,27 @@ Description: System Biology Markup Language library
application itself (though it does come with many example programs),
but rather a library you can embed in your own applications.
-Package: libsbml5-python
+Package: python3-libsbml5
Architecture: any
Section: python
+Testsuite: autopkgtest-pkg-python
Depends: ${shlibs:Depends},
${misc:Depends},
- ${python:Depends},
+ ${python3:Depends},
swig2.0 | swig
-Provides: python-sbml,
- libsbml-python
-Description: System Biology Markup Language library - Python bindings
+Provides: python3-sbml
+Description: System Biology Markup Language library - Python3 bindings
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
application itself (though it does come with many example programs),
but rather a library you can embed in your own applications.
.
- This package contains the Python bindings of LibSBML.
+ This package contains the Python3 bindings of LibSBML.
Package: libsbml5-java
Architecture: any
Section: java
+Testsuite: autopkgtest-pkg-python
Depends: ${shlibs:Depends},
${misc:Depends},
jarwrapper
@@ -94,6 +97,7 @@ Description: System Biology Markup Language library - Java bindings
Package: libsbml5-perl
Architecture: any
Section: perl
+Testsuite: autopkgtest-pkg-python
Depends: ${shlibs:Depends},
${perl:Depends},
${misc:Depends}
@@ -109,6 +113,7 @@ Description: System Biology Markup Language library - Perl bindings
Package: libsbml5-octave
Architecture: any
Section: math
+Testsuite: autopkgtest-pkg-python
Depends: ${shlibs:Depends},
${misc:Depends},
${octave:Depends}
@@ -124,6 +129,7 @@ Description: System Biology Markup Language library - Octave bindings
Package: libsbml5-cil
Architecture: any
Section: cli-mono
+Testsuite: autopkgtest-pkg-python
Depends: ${shlibs:Depends},
${misc:Depends},
${cli:Depends},
@@ -140,6 +146,7 @@ Description: System Biology Markup Language library - CLI bindings
Package: libsbml5-examples
Architecture: all
Section: doc
+Testsuite: autopkgtest-pkg-python
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
Description: System Biology Markup Language library -- example files
@@ -153,6 +160,7 @@ Description: System Biology Markup Language library -- example files
Package: libsbml5-doc
Architecture: all
Section: doc
+Testsuite: autopkgtest-pkg-python
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
Description: System Biology Markup Language library -- documentation
@@ -166,6 +174,7 @@ Description: System Biology Markup Language library -- documentation
Package: libsbml5-cil-doc
Architecture: all
Section: doc
+Testsuite: autopkgtest-pkg-python
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
Description: System Biology Markup Language library -- CLI documentation
@@ -179,6 +188,7 @@ Description: System Biology Markup Language library -- CLI documentation
Package: libsbml5-perl-doc
Architecture: all
Section: doc
+Testsuite: autopkgtest-pkg-python
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
Description: System Biology Markup Language library -- Perl documentation
@@ -189,15 +199,16 @@ Description: System Biology Markup Language library -- Perl documentation
.
This package contains documentation for Perl bindings
-Package: libsbml5-python-doc
+Package: python3-libsbml5-doc
Architecture: all
Section: doc
+Testsuite: autopkgtest-pkg-python
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- Python documentation
+Description: System Biology Markup Language library - Python3 documentation
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
application itself (though it does come with many example programs),
but rather a library you can embed in your own applications.
.
- This package contains documentation for Python bindings
+ This package contains documentation for Python3 bindings
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: libsbml
Source: http://www.sbml.org/software/libsbml/
Files-Excluded:
=====================================
debian/libsbml5-python-doc.links deleted
=====================================
@@ -1 +0,0 @@
-usr/share/doc/libsbml5-python-doc/python-api usr/share/doc/libsbml5/python-api
=====================================
debian/libsbml5-python.install deleted
=====================================
@@ -1 +0,0 @@
-usr/lib/python2*
=====================================
debian/libsbml5-python.lintian-overrides deleted
=====================================
@@ -1 +0,0 @@
-libsbml5-python: hardening-no-fortify-functions
\ No newline at end of file
=====================================
debian/libsbml5-python-doc.doc-base → debian/python3-libsbml5-doc.doc-base
=====================================
@@ -1,5 +1,5 @@
-Document: libsbml5-python
-Title: libsbml5 Python API
+Document: python3-libsbml5
+Title: libsbml5 Python3 API
Abstract: System Biology Markup Language library
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -8,5 +8,5 @@ Abstract: System Biology Markup Language library
Section: Programming/Python
Format: HTML
-Files: /usr/share/doc/libsbml5-python/python-api/*.html
-Index: /usr/share/doc/libsbml5-python/python-api/index.html
+Files: /usr/share/doc/python3-libsbml5/python-api/*.html
+Index: /usr/share/doc/python3-libsbml5/python-api/index.html
=====================================
debian/libsbml5-python-doc.docs → debian/python3-libsbml5-doc.docs
=====================================
=====================================
debian/python3-libsbml5-doc.links
=====================================
@@ -0,0 +1 @@
+usr/share/doc/python3-libsbml5-doc/python-api usr/share/doc/libsbml5/python-api
=====================================
debian/python3-libsbml5.install
=====================================
@@ -0,0 +1 @@
+usr/lib/python*
=====================================
debian/rules
=====================================
@@ -5,8 +5,8 @@
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
### define the VARS ###
-version := $(shell dpkg-parsechangelog | grep Version | cut -d\ -f2 | cut -d- -f1)
-major := $(shell dpkg-parsechangelog | grep Version | cut -d\ -f2 | cut -d. -f1)
+include /usr/share/dpkg/default.mk
+version := $(DEB_VERSION_UPSTREAM)
libpack := libsbml
debtmp := $(CURDIR)/debian/tmp
SRC_TMP := $(CURDIR)/SRC_TMP
@@ -30,10 +30,8 @@ endif
DEB_COMPRESS_EXCLUDE = .pdf
%:
- dh $@ --with python2,cli
+ dh $@ --with python3,cli
-get-orig-source:
- uscan --verbose --download-current-version --force-download --repack --compression xz
override_dh_auto_clean:
### the clean target of the libsbml makefile is highly b0rken ###
@@ -68,7 +66,9 @@ override_dh_auto_build:
cd build ; make
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
echo "no tests"
+endif
override_dh_auto_install:
cd build ; DESTDIR=../debian/tmp make install
@@ -78,7 +78,7 @@ override_dh_auto_install:
find $(debtmp)/usr -type f -name "*.js" -delete
find $(debtmp)/usr -type f -name "*.md5" -delete
find $(debtmp)/usr -type f -exec chmod 644 {} +
- for pyv in `pyversions -s` ; do \
+ for pyv in `py3versions -s` ; do \
test -e $(debtmp)/usr/lib/$${pyv}/site-packages && mv $(debtmp)/usr/lib/python$${pyv}/site-packages $(debtmp)/usr/lib/python$${pyv}/dist-packages || true ; \
done
find $(debtmp)/usr/lib -name "*.mex*" -exec strip --strip-unneeded {} + || true
View it on GitLab: https://salsa.debian.org/med-team/libsbml/compare/a547decda7971828d6520cae2f2b2ea874ea1d93...97adce5890d26fc279912abc63096bfdbbe42e48
--
View it on GitLab: https://salsa.debian.org/med-team/libsbml/compare/a547decda7971828d6520cae2f2b2ea874ea1d93...97adce5890d26fc279912abc63096bfdbbe42e48
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