[med-svn] [Git][med-team/libsbml][master] 9 commits: d/control: skip building mono packages for mips64el and riscv64, as...
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Mon Apr 29 22:34:50 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / libsbml
Commits:
c373b3d2 by Michael R. Crusoe at 2024-04-29T21:28:13+02:00
d/control: skip building mono packages for mips64el and riscv64, as mono-runtime is not available for those archs.
- - - - -
41a0f10c by Michael R. Crusoe at 2024-04-29T21:28:16+02:00
d/control: remove dep on swig by python3-sbml5. Closes: #1067961
- - - - -
6797a70b by Michael R. Crusoe at 2024-04-29T21:28:17+02:00
d/rules & d/cmake_opts: set Python include & binary paths dynamically.
- - - - -
786a5303 by Michael R. Crusoe at 2024-04-29T21:30:31+02:00
Add a nodoc build profile
- - - - -
19cdaae8 by Michael R. Crusoe at 2024-04-29T21:30:33+02:00
d/rules: Stop setting JDK_PATH & JAVA_INCLUDE_PATH, they aren't used.
- - - - -
c3962395 by Michael R. Crusoe at 2024-04-29T21:30:33+02:00
d/rules: unify references to the build directory; use dh_auto_configure and dh_auto_make.
This also helps with build hardening and enables parallel building
- - - - -
95a80bdf by Michael R. Crusoe at 2024-04-29T21:30:33+02:00
d/upstream/metadata: Update for their GitHub repository.
- - - - -
3b66ffee by Michael R. Crusoe at 2024-04-29T21:30:34+02:00
Build and run the tests
- - - - -
1e66a95a by Michael R. Crusoe at 2024-04-29T21:30:34+02:00
Upload 5.20.2+dfsg-4 to unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/cmake_opts
- debian/cmake_opts.matlab
- debian/control
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,21 @@
-libsbml (5.20.2+dfsg-4) UNRELEASED; urgency=medium
+libsbml (5.20.2+dfsg-4) unstable; urgency=medium
* Team upload.
* Hand write the autopkgtest to only test against the default version
of Python. Closes: #1069876
-
- -- Michael R. Crusoe <crusoe at debian.org> Mon, 29 Apr 2024 13:15:30 +0200
+ * d/control: skip building mono packages for mips64el and riscv64, as
+ mono-runtime is not available for those archs.
+ * d/control: remove dep on swig by python3-sbml5. Closes: #1067961
+ * d/rules & d/cmake_opts: set Python include and binary paths dynamically.
+ * d/rules: Stop setting JDK_PATH & JAVA_INCLUDE_PATH, they aren't
+ used.
+ * d/rules: unify references to the build directory; use
+ dh_auto_configure and dh_auto_make. This also helps with build hardening
+ and enables parallel building.
+ * d/upstream/metadata: Update for their GitHub repository.
+ * d/rules: build and run the tests.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 29 Apr 2024 16:19:36 +0200
libsbml (5.20.2+dfsg-3) unstable; urgency=medium
=====================================
debian/cmake_opts
=====================================
@@ -1,6 +1,3 @@
--DCMAKE_BINARY_DIR=build
--DCMAKE_COLOR_MAKEFILE:BOOL=ON
--DCMAKE_INSTALL_PREFIX:PATH=/usr
-DENABLE_COMP:BOOL=ON
-DENABLE_FBC:BOOL=ON
-DENABLE_GROUPS:BOOL=ON
@@ -8,10 +5,7 @@
-DENABLE_QUAL:BOOL=ON
-DENABLE_RENDER:BOOL=ON
-DWITH_BZIP2:BOOL=ON
--DWITH_CHECK:BOOL=OFF
-DWITH_CPP_NAMESPACE:BOOL=OFF
--DWITH_CSHARP:BOOL=ON
--DWITH_DOXYGEN:BOOL=ON
-DWITH_EXAMPLES:BOOL=OFF
-DWITH_EXPAT:BOOL=OFF
-DWITH_JAVA:BOOL=ON
@@ -19,7 +13,6 @@
-DWITH_OCTAVE:BOOL=ON
-DWITH_PERL:BOOL=ON
-DWITH_PYTHON:BOOL=ON
--DWITH_PYTHON_INCLUDE:PATH=/usr/include/python2.7
-DWITH_R:BOOL=OFF
-DWITH_RUBY:BOOL=OFF
-DWITH_SWIG:BOOL=ON
=====================================
debian/cmake_opts.matlab
=====================================
@@ -1,6 +1,3 @@
--DCMAKE_BINARY_DIR=build
--DCMAKE_COLOR_MAKEFILE:BOOL=ON
--DCMAKE_INSTALL_PREFIX:PATH=/usr
-DENABLE_COMP:BOOL=ON
-DENABLE_FBC:BOOL=ON
-DENABLE_GROUPS:BOOL=ON
@@ -9,10 +6,7 @@
-DENABLE_RENDER:BOOL=ON
-DMATLAB_ROOT_PATH:PATH=/usr/share/matlab
-DWITH_BZIP2:BOOL=ON
--DWITH_CHECK:BOOL=OFF
-DWITH_CPP_NAMESPACE:BOOL=OFF
--DWITH_CSHARP:BOOL=ON
--DWITH_DOXYGEN:BOOL=ON
-DWITH_EXAMPLES:BOOL=OFF
-DWITH_EXPAT:BOOL=OFF
-DWITH_JAVA:BOOL=ON
@@ -22,7 +16,6 @@
-DWITH_OCTAVE:BOOL=ON
-DWITH_PERL:BOOL=ON
-DWITH_PYTHON:BOOL=ON
--DWITH_PYTHON_INCLUDE:PATH=/usr/include/python2.7
-DWITH_R:BOOL=ON
-DWITH_RUBY:BOOL=OFF
-DWITH_SWIG:BOOL=ON
=====================================
debian/control
=====================================
@@ -5,10 +5,11 @@ Uploaders: Ivo Maintz <ivo at maintz.de>,
Section: science
Priority: optional
Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
- dh-python,
+ dh-sequence-python3,
+ dh-sequence-cli [!mips64el !riscv64],
cmake,
dh-exec,
- doxygen,
+ doxygen <!nodoc>,
swig,
libxml2-dev,
python3-dev,
@@ -16,7 +17,7 @@ Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
perl,
libperl-dev,
default-jdk-headless,
- default-jdk-doc,
+ default-jdk-doc <!nodoc>,
dh-octave,
r-base-dev,
r-base-core,
@@ -25,13 +26,9 @@ Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
libbz2-dev,
libnewlib-dev,
check,
- mono-devel,
- mono-mcs,
- cli-common-dev,
- mono-runtime-common,
- texlive-latex-base,
+ texlive-latex-base <!nodoc>,
rdfind,
- texlive-latex-extra
+ texlive-latex-extra <!nodoc>
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/libsbml
Vcs-Git: https://salsa.debian.org/med-team/libsbml.git
@@ -74,7 +71,6 @@ Section: python
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
- swig
Provides: python3-sbml
Description: System Biology Markup Language library - Python3 bindings
LibSBML is a library designed to help you read, write, manipulate,
@@ -132,7 +128,7 @@ Description: System Biology Markup Language library - Octave bindings
This package contains the Octave bindings of LibSBML.
Package: libsbml5-cil
-Architecture: any-amd64 arm64 armel armhf any-i386 loong64 mips64el ppc64el s390x ia64 ppc64 riscv64 sh4 sparc64 x32
+Architecture: any-amd64 arm64 armel armhf any-i386 loong64 ppc64el s390x ia64 ppc64 sh4 sparc64 x32
Section: cli-mono
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -149,6 +145,7 @@ Description: System Biology Markup Language library - CLI bindings
Package: libsbml5-examples
Architecture: all
+Build-Profiles: <!nodoc>
Multi-Arch: foreign
Section: doc
Depends: ${misc:Depends}
@@ -162,6 +159,7 @@ Description: System Biology Markup Language library -- example files
This package contains C/C++, Java, Perl and layout examples.
Package: libsbml5-doc
+Build-Profiles: <!nodoc>
Architecture: all
Multi-Arch: foreign
Section: doc
@@ -177,6 +175,7 @@ Description: System Biology Markup Language library -- documentation
This package contains C/C++ documentation.
Package: libsbml5-cil-doc
+Build-Profiles: <!nodoc>
Architecture: all
Multi-Arch: foreign
Section: doc
@@ -192,6 +191,7 @@ Description: System Biology Markup Language library -- CLI documentation
This package contains documentation for Mono/CLI bindings
Package: libsbml5-perl-doc
+Build-Profiles: <!nodoc>
Architecture: all
Section: doc
Depends: ${misc:Depends},
@@ -207,6 +207,7 @@ Description: System Biology Markup Language library -- Perl documentation
This package contains documentation for Perl bindings
Package: python3-sbml5-doc
+Build-Profiles: <!nodoc>
Architecture: all
Multi-Arch: foreign
Section: doc
=====================================
debian/rules
=====================================
@@ -10,6 +10,7 @@ version := $(DEB_VERSION_UPSTREAM)
libpack := libsbml
debtmp := $(CURDIR)/debian/tmp
SRC_TMP := $(CURDIR)/SRC_TMP
+PY3=$(shell py3versions -d)
# Test for matlab
CMAKE_OPTS := $(shell sed '/MATLAB/d' debian/cmake_opts)
BIND_MATLAB := $(shell which matlab | grep -q matlab && echo 'yes')
@@ -17,14 +18,30 @@ ifdef BIND_MATLAB
CMAKE_OPTS := $(shell cat debian/cmake_opts)
endif
-# seems we need to use debian/cmake_opts
-JDK_PATH:=$(shell readlink -f /usr/bin/javac | sed "s:/bin/javac::")
-JAVA_INCLUDE_PATH:=$(JDK_PATH)/include
+ifneq ($(filter nodoc,$(DEB_BUILD_PROFILES)),)
+CMAKE_OPTS += -DWITH_DOXYGEN:BOOL=OFF
+else
+CMAKE_OPTS += -DWITH_DOXYGEN:BOOL=ON
+endif
+
+ifneq ($(filter nocheck,$(DEB_BUILD_PROFILES)),)
+CMAKE_OPTS += -DWITH_CHECK:BOOL=OFF
+else
+CMAKE_OPTS += -DWITH_CHECK:BOOL=ON
+endif
ifneq (,$(filter $(DEB_HOST_ARCH), mips mipsel))
CMAKE_OPTS += -D'WITH_01_COMPILE:BOOL=ON'
endif
+CMAKE_OPTS += -DPYTHON_EXECUTABLE=/usr/bin/${PY3}
+
+ifneq (,$(filter $(DEB_HOST_ARCH), mips64el riscv64))
+CMAKE_OPTS += -DWITH_CSHARP:BOOL=OFF
+else
+CMAKE_OPTS += -DWITH_CSHARP:BOOL=ON
+endif
+
export PYBUILD_NAME=libsbml
### let's do it ###
@@ -32,10 +49,9 @@ export PYBUILD_NAME=libsbml
DEB_COMPRESS_EXCLUDE = .pdf
%:
- dh $@ --with python3,cli
+ dh $@ --builddir=build --buildsystem=cmake
-
-override_dh_auto_clean:
+execute_after_dh_auto_clean:
### the clean target of the libsbml makefile is highly b0rken ###
### the switch to cmake didn't result in great approvements ###
### still inline changes of files ###
@@ -51,33 +67,27 @@ override_dh_auto_clean:
override_dh_autoreconf:
echo "autoreconf -f -i returns exit code 1 - skip this"
-override_dh_auto_configure:
ifdef BIND_MATLAB
+execute_before_dh_auto_configure:
cat debian/control.matlab >> debian/control || true
endif
- mkdir -p build
- cd build ; cmake $(CMAKE_OPTS) ../
-override_dh_auto_build:
- cd build ; make
+override_dh_auto_configure:
+ dh_auto_configure -- $(CMAKE_OPTS)
-override_dh_auto_test:
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- echo "no tests"
-endif
-override_dh_auto_install:
- cd build ; DESTDIR=../debian/tmp make install
+execute_after_dh_auto_install:
+ifeq (,$(findstring nodoc,$(DEB_BUILD_OPTIONS)))
sed 's#formatted/##g' docs/index.html.in > $(debtmp)/usr/share/libsbml/docs/index.html
+endif
# dh_auto_install -O--buildsystem=pybuild # unfortunately there is no setup.py
set -x ; \
- for pyv in `py3versions -d` ; do \
+ for pyv in ${PY3} ; do \
if [ -d $(debtmp)/usr/lib/*/$${pyv}/site-packages/ ] ; then \
mkdir -p $(debtmp)/usr/lib/$${pyv}/dist-packages ; \
mv $(debtmp)/usr/lib/*/$${pyv}/site-packages/* $(debtmp)/usr/lib/$${pyv}/dist-packages ; \
fi ; \
done
- 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 {} +
@@ -101,8 +111,7 @@ ifdef BIND_MATLAB
dpkg-shlibdeps $(debtmp)/usr/lib/*.mex* -Tdebian/libsbml5-matlab.substvars
endif
-override_dh_installexamples:
- dh_installexamples
+execute_after_dh_installexamples:
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
done
@@ -110,17 +119,15 @@ override_dh_installexamples:
override_dh_installchangelogs:
dh_installchangelogs NEWS.txt
-override_dh_missing:
+execute_before_dh_missing:
find debian -name test.xml -delete
rm -f debian/tmp/usr/share/libsbml/*.txt \
debian/tmp/usr/share/libsbml/README*
- dh_missing
override_dh_dwz:
echo "Skip dwz: Too few files for multifile optimization"
-override_jh_installjavadoc:
- jh_installjavadoc
+execute_after_jh_installjavadoc:
rdfind -makesymlinks true -followsymlinks true \
$$(dpkg -L $$(apt-cache show default-jdk-doc | grep Depends \
| awk '{print $$2}') | grep /usr/share/doc/ \
=====================================
debian/upstream/metadata
=====================================
@@ -21,4 +21,7 @@ Registry:
Entry: NA
- Name: bio.tools
Entry: libsbml
-Repository: https://svn.code.sf.net/p/sbml/code/
+Repository: https://github.com/sbmlteam/libsbml.git
+Repository-Browse: https://github.com/sbmlteam/libsbml
+Bug-Database: https://github.com/sbmlteam/libsbml/issues
+Bug-Submit: https://github.com/sbmlteam/libsbml/issues/new
View it on GitLab: https://salsa.debian.org/med-team/libsbml/-/compare/6d99ea552c92139739788a722d9303c127e17c9a...1e66a95ab454eece8bc68bc67f94dd21bbe774aa
--
View it on GitLab: https://salsa.debian.org/med-team/libsbml/-/compare/6d99ea552c92139739788a722d9303c127e17c9a...1e66a95ab454eece8bc68bc67f94dd21bbe774aa
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