debian/NEWS.Debian

+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@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@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@debian.org>  Mon, 03 Dec 2018 16:11:35 +0100
 
 libsbml (5.16.0+dfsg-2) unstable; urgency=medium
 

debian/control

@@ -3,15 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Ivo Maintz <ivo@maintz.de>,
            Andreas Tille <tille@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

-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

-usr/share/doc/libsbml5-python-doc/python-api usr/share/doc/libsbml5/python-api

debian/libsbml5-python.install

-usr/lib/python2*

debian/libsbml5-python.lintian-overrides

-libsbml5-python: hardening-no-fortify-functions
\ No newline at end of file

debian/libsbml5-python-doc.doc-base → debian/python3-libsbml5-doc.doc-base

-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/python3-libsbml5-doc.links

+usr/share/doc/python3-libsbml5-doc/python-api usr/share/doc/libsbml5/python-api

debian/python3-libsbml5.install

+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