[med-svn] [Git][med-team/ghmm][master] 8 commits: d/rules: fix FTBFS with setuptools installing plain files
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon Oct 19 19:45:12 BST 2026
Andreas Tille pushed to branch master at Debian Med / ghmm
Commits:
7fd39519 by Andreas Tille at 2026-10-19T14:58:04+02:00
d/rules: fix FTBFS with setuptools installing plain files
Newer setuptools no longer creates a ghmmwrapper egg during setup.py
install; it installs the Python modules as plain files instead. Handle
that layout in addition to the legacy egg, fixing the build.
Closes: #1149420
- - - - -
8c98b3cc by Andreas Tille at 2026-10-19T14:58:45+02:00
Packaging update (routine-update)
- - - - -
4c4a15c8 by Andreas Tille at 2026-10-19T14:58:48+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
379a0754 by Andreas Tille at 2026-10-19T15:00:16+02:00
Changes made by cme
- - - - -
50c1b340 by Andreas Tille at 2026-10-19T14:00:22+01:00
Set upstream metadata fields: Bug-Database.
Changes-By: lintian-brush
- - - - -
cb42aa3a by Andreas Tille at 2026-10-19T15:00:24+02:00
debputy lint --auto-fix (routine-update)
- - - - -
32a408af by Andreas Tille at 2026-10-19T18:07:11+02:00
d/copyright:
* d/copyright:
- Fix License
- Add missing File
* Added d/lrc.config
- - - - -
c874dbb7 by Andreas Tille at 2026-10-19T18:09:17+02:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/lrc.config
- debian/rules
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,24 @@
+ghmm (0.9~rc3-14) unstable; urgency=medium
+
+ * Packaging update (routine-update)
+ * Standards-Version: 4.7.4 (routine-update)
+ * Reflow Uploaders field (cme)
+ * Set upstream metadata fields: Bug-Database.
+ * debputy lint --auto-fix (routine-update)
+ * d/copyright:
+ - Fix License
+ - Add missing File
+ * Added d/lrc.config
+
+ -- Andreas Tille <tille at debian.org> Mon, 19 Oct 2026 18:07:22 +0200
+
+ghmm (0.9~rc3-13) unstable; urgency=medium
+
+ * d/rules: support setuptools installing Python modules as plain files
+ instead of an egg, fixing the FTBFS. (Closes: #1149420)
+
+ -- Andreas Tille <tille at debian.org> Mon, 19 Oct 2026 14:35:00 +0200
+
ghmm (0.9~rc3-12) unstable; urgency=medium
* d/control: hardcode conflicting libghmm1 version.
=====================================
debian/control
=====================================
@@ -1,32 +1,37 @@
Source: ghmm
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>,
- Étienne Mollier <emollier at debian.org>
+Uploaders:
+ Steffen Moeller <moeller at debian.org>,
+ Étienne Mollier <emollier at debian.org>,
Section: science
-Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
- dh-sequence-python3,
- d-shlibs (>= 0.106~),
- python3-dev,
- python3-setuptools,
- pkgconf,
- libxml2-dev,
- libgsl-dev,
- liblapacke-dev,
- zlib1g-dev,
- swig
-Standards-Version: 4.7.3
+Build-Depends:
+ debhelper-compat (= 14),
+ dh-sequence-python3,
+ d-shlibs (>= 0.106~),
+ dpkg-dev (>= 1.22.5),
+ libgsl-dev,
+ liblapacke-dev,
+ libxml2-dev,
+ pkgconf,
+ python3-dev,
+ python3-setuptools,
+ swig,
+ zlib1g-dev,
Vcs-Browser: https://salsa.debian.org/med-team/ghmm
Vcs-Git: https://salsa.debian.org/med-team/ghmm.git
Homepage: https://sourceforge.net/p/ghmm/wiki/Home/
Package: ghmm
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${python3:Depends},
- python3,
- libghmm1t64
-Recommends: libopenblas0 | libblis4
+Depends:
+ libghmm1t64,
+ python3,
+ ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends},
+Recommends:
+ libopenblas0 | libblis4,
Description: General Hidden-Markov-Model library - tools
The General Hidden Markov Model Library (GHMM) is a C library with
additional Python3 bindings implementing a wide range of types of
@@ -38,10 +43,11 @@ Description: General Hidden-Markov-Model library - tools
Package: libghmm-dev
Architecture: any
Section: libdevel
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- libghmm1t64 (>= ${source:Upstream-Version}),
- libghmm1t64 (<< ${source:Upstream-Version}+1)
+Depends:
+ libghmm1t64 (<< ${source:Upstream-Version}+1),
+ libghmm1t64 (>= ${source:Upstream-Version}),
+ ${misc:Depends},
+ ${shlibs:Depends},
Description: General Hidden-Markov-Model library - header files
The General Hidden Markov Model Library (GHMM) is a C library with
additional Python3 bindings implementing a wide range of types of
@@ -51,14 +57,18 @@ Description: General Hidden-Markov-Model library - header files
Header files and static library to compile against the library.
Package: libghmm1t64
-Provides: ${t64:Provides}
-Replaces: libghmm1
-Conflicts: libghmm1 (<< 0.9~rc3-9)
Architecture: any
Section: libs
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- python3
+Depends:
+ python3,
+ ${misc:Depends},
+ ${shlibs:Depends},
+Conflicts:
+ libghmm1 (<< 0.9~rc3-9),
+Provides:
+ ${t64:Provides},
+Replaces:
+ libghmm1,
Description: General Hidden-Markov-Model library
The General Hidden Markov Model Library (GHMM) is a C library with
additional Python3 bindings implementing a wide range of types of
=====================================
debian/copyright
=====================================
@@ -28,21 +28,50 @@ Contributors:
Marie Hoffmann
Marko Briesemann
Markus Schueler
-License: GPL-2.0+
+License: LGPL-2+
Files: ghmm/ghmm.h
Copyright: 1998-2004 Alexander Schliep <schliep at ghmm.org>
1998-2001 ZAIK/ZPR, Universitaet zu Koeln
2002-2004 Max-Planck-Institut fuer Molekulare Genetik, Berlin
-License: LGPL-2.0+
- On Debian systems you can find a full copy of the Library General Public
- License at /usr/share/common-licenses/LGPL-2.
+License: LGPL-2+
+
+Files: ghmm/mt19937ar.c
+Copyright: 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
+ 2005, Mutsuo Saito,
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ .
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ .
+ 3. The names of its contributors may not be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Files: debian/*
Copyright: 2018 Steffen Moeller <moeller at debian.org>
-License: GPL-2.0+
+License: GPL-2+
-License: GPL-2.0+
+License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
@@ -58,3 +87,7 @@ License: GPL-2.0+
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+License: LGPL-2+
+ On Debian systems you can find a full copy of the Library General Public
+ License at /usr/share/common-licenses/LGPL-2.
=====================================
debian/lrc.config
=====================================
@@ -0,0 +1,7 @@
+aclocal.m4
+configure
+INSTALL
+install-sh
+ltmain.sh
+GPL.txt
+LGPL.txt
=====================================
debian/rules
=====================================
@@ -38,8 +38,19 @@ override_dh_install:
$(CURDIR)/debian/ghmm/usr/bin/ghmm-config
find debian -name libghmm.la -delete
# temporarily copy over ghmmwrapper to the pybuild created dir
- mkdir -p debian/python3-HMMEd/usr/lib/python3/dist-packages
- mv debian/tmp/usr/local/lib/python3.*/dist-packages/ghmmwrapper-0.8-py3*.egg debian/python3-HMMEd/usr/lib/python3/dist-packages/ghmm
+ mkdir -p debian/python3-HMMEd/usr/lib/python3/dist-packages/ghmm
+# newer setuptools installs plain files instead of an egg
+ if ls debian/tmp/usr/local/lib/python3.*/dist-packages/ghmmwrapper-*.egg >/dev/null 2>&1; then \
+ mv debian/tmp/usr/local/lib/python3.*/dist-packages/ghmmwrapper-*.egg/* \
+ debian/python3-HMMEd/usr/lib/python3/dist-packages/ghmm/; \
+ else \
+ for f in ghmm.py ghmmhelper.py modhmmer.py class_change.py ghmmwrapper.py; do \
+ mv debian/tmp/usr/local/lib/python3.*/dist-packages/$$f \
+ debian/python3-HMMEd/usr/lib/python3/dist-packages/ghmm/; \
+ done; \
+ mv debian/tmp/usr/local/lib/python3.*/dist-packages/_ghmmwrapper*.so \
+ debian/python3-HMMEd/usr/lib/python3/dist-packages/ghmm/; \
+ fi
rm -rf debian/tmp/usr/local
find debian -type d -name __pycache__ | xargs rm -rf
=====================================
debian/upstream/metadata
=====================================
@@ -8,4 +8,5 @@ Registry:
- Name: conda:bioconda
Entry: ghmm
Archive: SourceForge
+Bug-Database: 'http://sourceforge.net/tracker/?func=add&group_id=67094&atid=516866'
Repository: https://svn.code.sf.net/p/ghmm/code/
=====================================
debian/watch
=====================================
@@ -2,4 +2,4 @@ Version: 5
Source: https://sf.net/ghmm/
Matching-Pattern: ghmm- at ANY_VERSION@@ARCHIVE_EXT@
-UVersion-Mangle: auto
+Uversion-Mangle: auto
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/2305da0cedaeefcf769dd39d03ddb16203d678b3...c874dbb7130c7d09753177decfd0ccf63576316a
--
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/2305da0cedaeefcf769dd39d03ddb16203d678b3...c874dbb7130c7d09753177decfd0ccf63576316a
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