[med-svn] [Git][med-team/libsbml][master] 7 commits: Add lintian-overrides for embedded-library libminizip (see...
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Feb 18 15:55:51 GMT 2026
Andreas Tille pushed to branch master at Debian Med / libsbml
Commits:
3442c055 by Andreas Tille at 2026-02-18T15:30:17+01:00
Add lintian-overrides for embedded-library libminizip (see https://github.com/sbmlteam/libsbml/issues/471 - thanks to Santiago Vila for filing it)
- - - - -
ccb2f687 by Andreas Tille at 2026-02-18T15:33:12+01:00
lintian-overrides for embedded-javascript-library please use libjs-jquery
- - - - -
ea51b6ac by Andreas Tille at 2026-02-18T15:34:45+01:00
cme fix dpkg-control
- - - - -
c28c7fb0 by Santiago Vila at 2026-02-18T16:54:06+01:00
Fix clean target.
- - - - -
61a1ab87 by Santiago Vila at 2026-02-18T16:54:26+01:00
d/salsa-ci.yml: Use the simplified version.
- - - - -
afdf358f by Andreas Tille at 2026-02-18T16:54:48+01:00
Update changelog
- - - - -
9988ce64 by Andreas Tille at 2026-02-18T16:55:17+01:00
Upload to unstable
- - - - -
11 changed files:
- debian/changelog
- + debian/clean
- debian/control
- + debian/libsbml5-doc.lintian-overrides
- debian/libsbml5-java.lintian-overrides
- + debian/libsbml5-perl-doc.lintian-overrides
- + debian/libsbml5-perl.lintian-overrides
- debian/libsbml5t64.lintian-overrides
- + debian/python3-sbml5-doc.lintian-overrides
- + debian/python3-sbml5.lintian-overrides
- debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,11 +1,21 @@
-libsbml (5.20.5+dfsg-3) UNRELEASED; urgency=medium
+libsbml (5.20.5+dfsg-3) unstable; urgency=medium
+ [ Andreas Tille ]
* Drop Build-Depends: libnewlib-dev
Closes: #1128320
* Drop Ivo Maintz from Uploaders (Thank you for your work Ivo)
* Fix doc-base files
+ * Add lintian-overrides for embedded-library libminizip
+ (see https://github.com/sbmlteam/libsbml/issues/471 - thanks to
+ Santiago Vila for filing it)
+ * lintian-overrides for embedded-javascript-library please use libjs-jquery
+ * cme fix dpkg-control
+
+ [ Santiago Vila ]
+ * Fix clean target.
+ * d/salsa-ci.yml: Use the simplified version.
- -- Andreas Tille <tille at debian.org> Wed, 18 Feb 2026 09:35:59 +0100
+ -- Andreas Tille <tille at debian.org> Wed, 18 Feb 2026 16:55:00 +0100
libsbml (5.20.5+dfsg-2) unstable; urgency=medium
=====================================
debian/clean
=====================================
@@ -0,0 +1,17 @@
+docs/src/class-list.txt
+docs/src/common-text/libsbml-downloading.html
+docs/src/common-text/libsbml-group-comp-intro.html
+docs/src/common-text/libsbml-group-distrib-intro.html
+docs/src/common-text/libsbml-group-fbc-intro.html
+docs/src/common-text/libsbml-group-groups-intro.html
+docs/src/common-text/libsbml-group-layout-intro.html
+docs/src/common-text/libsbml-group-multi-intro.html
+docs/src/common-text/libsbml-group-qual-intro.html
+docs/src/common-text/libsbml-group-render-intro.html
+docs/src/common-text/libsbml-group-spatial-intro.html
+docs/src/common-text/libsbml-installation.html
+docs/src/common-text/sbml-specifications-table.html
+docs/src/css/libsbml-package-stylesheet.css
+docs/src/doxygen-search-config.txt
+docs/src/libsbml-converters.txt
+src/sbml/test/test-data/tempOut.xml
=====================================
debian/control
=====================================
@@ -1,30 +1,32 @@
Source: libsbml
+Standards-Version: 4.7.3
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
Section: science
-Priority: optional
-Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
- dh-sequence-python3,
- cmake,
- dh-exec,
- doxygen <!nodoc>,
- swig,
- libxml2-dev,
- python3-dev,
+Build-Depends:
+ dpkg-dev (>= 1.22.5),
+ debhelper-compat (= 13),
+ dh-sequence-python3,
+ cmake,
+ dh-exec,
+ doxygen <!nodoc>,
+ swig,
+ libxml2-dev,
+ python3-dev,
# should be python3-all-dev but build system can only deal with one Python interpreter
- perl,
- libperl-dev,
- default-jdk-headless,
- default-jdk-doc,
- dh-octave,
- r-base-dev,
- r-base-core,
- graphviz <!nodoc>,
- zlib1g-dev,
- libbz2-dev,
- check,
- rdfind,
-Standards-Version: 4.7.2
+ perl,
+ libperl-dev,
+ default-jdk-headless,
+ default-jdk-doc,
+ dh-octave,
+ r-base-dev,
+ r-base-core,
+ graphviz <!nodoc>,
+ zlib1g-dev,
+ libbz2-dev,
+ check,
+ rdfind,
Vcs-Browser: https://salsa.debian.org/med-team/libsbml
Vcs-Git: https://salsa.debian.org/med-team/libsbml.git
Homepage: https://www.sbml.org/
@@ -33,9 +35,11 @@ Rules-Requires-Root: no
Package: libsbml5-dev
Architecture: any
Section: libdevel
-Depends: libsbml5t64 (= ${binary:Version}),
- ${misc:Depends}
-Provides: libsbml-dev
+Depends:
+ libsbml5t64 (= ${binary:Version}),
+ ${misc:Depends},
+Provides:
+ libsbml-dev,
Description: System Biology Markup Language library - development files
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -45,15 +49,21 @@ Description: System Biology Markup Language library - development files
This package contains files necessary for development with libsbml.
Package: libsbml5t64
-Replaces: libsbml5
-Breaks: libsbml5 (<< ${source:Version})
Architecture: any
-Section: libs
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Pre-Depends: ${misc:Pre-Depends}
-Provides: ${t64:Provides}, libsbml
Multi-Arch: same
+Section: libs
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+Pre-Depends:
+ ${misc:Pre-Depends},
+Breaks:
+ libsbml5 (<< ${source:Version}),
+Provides:
+ ${t64:Provides},
+ libsbml,
+Replaces:
+ libsbml5,
Description: 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
@@ -63,10 +73,12 @@ Description: System Biology Markup Language library
Package: python3-sbml5
Architecture: any
Section: python
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${python3:Depends},
-Provides: python3-sbml
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${python3:Depends},
+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
@@ -78,12 +90,15 @@ Description: System Biology Markup Language library - Python3 bindings
Package: libsbml5-java
Architecture: any
Section: java
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- jarwrapper,
- default-jdk-doc
-Pre-Depends: ${misc:Pre-Depends}
-Provides: libsbml-java
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ jarwrapper,
+ default-jdk-doc,
+Pre-Depends:
+ ${misc:Pre-Depends},
+Provides:
+ libsbml-java,
Description: System Biology Markup Language library - Java bindings
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -95,10 +110,12 @@ Description: System Biology Markup Language library - Java bindings
Package: libsbml5-perl
Architecture: any
Section: perl
-Depends: ${shlibs:Depends},
- ${perl:Depends},
- ${misc:Depends}
-Provides: libsbml-perl
+Depends:
+ ${shlibs:Depends},
+ ${perl:Depends},
+ ${misc:Depends},
+Provides:
+ libsbml-perl,
Description: System Biology Markup Language library - Perl bindings
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -110,10 +127,12 @@ Description: System Biology Markup Language library - Perl bindings
Package: libsbml5-octave
Architecture: any
Section: math
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${octave:Depends}
-Provides: libsbml-octave
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${octave:Depends},
+Provides:
+ libsbml-octave,
Description: System Biology Markup Language library - Octave bindings
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -124,11 +143,12 @@ Description: System Biology Markup Language library - Octave bindings
Package: libsbml5-examples
Architecture: all
-Build-Profiles: <!nodoc>
Multi-Arch: foreign
Section: doc
-Depends: ${misc:Depends}
-Suggests: libsbml5-dev (= ${binary:Version})
+Depends:
+ ${misc:Depends},
+Suggests:
+ libsbml5-dev (= ${binary:Version}),
Description: System Biology Markup Language library -- example files
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -136,15 +156,17 @@ Description: System Biology Markup Language library -- example files
but rather a library you can embed in your own applications.
.
This package contains C/C++, Java, Perl and layout examples.
+Build-Profiles: <!nodoc>
Package: libsbml5-doc
-Build-Profiles: <!nodoc>
Architecture: all
Multi-Arch: foreign
Section: doc
-Depends: ${misc:Depends},
- node-mathjax-full
-Suggests: libsbml5-dev (= ${binary:Version})
+Depends:
+ ${misc:Depends},
+ node-mathjax-full,
+Suggests:
+ libsbml5-dev (= ${binary:Version}),
Description: System Biology Markup Language library -- documentation
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -152,15 +174,17 @@ Description: System Biology Markup Language library -- documentation
but rather a library you can embed in your own applications.
.
This package contains C/C++ documentation.
+Build-Profiles: <!nodoc>
Package: libsbml5-perl-doc
-Build-Profiles: <!nodoc>
Architecture: all
-Section: doc
-Depends: ${misc:Depends},
- node-mathjax-full
-Suggests: libsbml5-dev (= ${binary:Version})
Multi-Arch: foreign
+Section: doc
+Depends:
+ ${misc:Depends},
+ node-mathjax-full,
+Suggests:
+ libsbml5-dev (= ${binary:Version}),
Description: System Biology Markup Language library -- Perl documentation
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -168,15 +192,17 @@ Description: System Biology Markup Language library -- Perl documentation
but rather a library you can embed in your own applications.
.
This package contains documentation for Perl bindings
+Build-Profiles: <!nodoc>
Package: python3-sbml5-doc
-Build-Profiles: <!nodoc>
Architecture: all
Multi-Arch: foreign
Section: doc
-Depends: ${misc:Depends},
- node-mathjax-full
-Suggests: libsbml5-dev (= ${binary:Version})
+Depends:
+ ${misc:Depends},
+ node-mathjax-full,
+Suggests:
+ libsbml5-dev (= ${binary:Version}),
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
@@ -184,3 +210,4 @@ Description: System Biology Markup Language library - Python3 documentation
but rather a library you can embed in your own applications.
.
This package contains documentation for Python3 bindings
+Build-Profiles: <!nodoc>
=====================================
debian/libsbml5-doc.lintian-overrides
=====================================
@@ -0,0 +1 @@
+libsbml5-doc: embedded-javascript-library please use libjs-jquery *
=====================================
debian/libsbml5-java.lintian-overrides
=====================================
@@ -1,3 +1,6 @@
libsbml5-java: package-name-doesnt-match-sonames
libsbml5-java: shared-library-lacks-version
libsbml5-java: hardening-no-fortify-functions
+
+# see https://github.com/sbmlteam/libsbml/issues/471
+libsbml5-java: embedded-library libminizip *
=====================================
debian/libsbml5-perl-doc.lintian-overrides
=====================================
@@ -0,0 +1 @@
+libsbml5-perl-doc: embedded-javascript-library please use libjs-jquery *
=====================================
debian/libsbml5-perl.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# see https://github.com/sbmlteam/libsbml/issues/471
+libsbml5-perl: embedded-library libminizip *
+
=====================================
debian/libsbml5t64.lintian-overrides
=====================================
@@ -1 +1,4 @@
libsbml5t64: package-name-doesnt-match-sonames libsbml5
+
+# see https://github.com/sbmlteam/libsbml/issues/471
+libsbml5t64: embedded-library libminizip *
=====================================
debian/python3-sbml5-doc.lintian-overrides
=====================================
@@ -0,0 +1 @@
+python3-sbml5-doc: embedded-javascript-library please use libjs-jquery *
=====================================
debian/python3-sbml5.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# see https://github.com/sbmlteam/libsbml/issues/471
+python3-sbml5: embedded-library libminizip *
+
=====================================
debian/salsa-ci.yml
=====================================
@@ -1,4 +1,3 @@
---
include:
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
View it on GitLab: https://salsa.debian.org/med-team/libsbml/-/compare/ab75baa283a730713e45f74542405aabc2b47500...9988ce64a5dfe6e0d3fff1ffe3176c7119ea55ed
--
View it on GitLab: https://salsa.debian.org/med-team/libsbml/-/compare/ab75baa283a730713e45f74542405aabc2b47500...9988ce64a5dfe6e0d3fff1ffe3176c7119ea55ed
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