apbs (3.4.1-6) unstable; urgency=medium
* Team upload.
[ Drew Parsons ]
* fix build with gcc-14. Closes: #1077646.
- patch vf2c in debian/external_deps/fetk
- debian patch gcc14.patch reverts an upstream hack in vfetk
function definitions that prevent building with gcc-14.
* add hashbang to debian/tests/test-apbs. Thanks Simon Chopin.
Closes: #1033528.
* Build-Depends: pkgconf not pkg-config
* mark apbs-doc Multi-Arch: foreign
* Standards-Version: 4.7.0
-- Drew Parsons <dparsons@debian.org> Thu, 31 Oct 2024 14:24:17 +0100
apbs (3.4.1-5.1) unstable; urgency=medium
* Non-maintainer upload.
* Rename libraries for 64-bit time_t transition. Closes: #1061891
-- Steve Langasek <vorlon@debian.org> Wed, 28 Feb 2024 01:04:53 +0000
apbs (3.4.1-5) unstable; urgency=medium
* Team upload.
* Add patch to drop obsolete "U" mode passed to open(), which causes runtime
errors with python 3.11, by Steve Langasek. Closes: #1028354.
-- Michael Banck <mbanck@debian.org> Tue, 10 Jan 2023 21:56:38 +0100
apbs (3.4.1-4) unstable; urgency=medium
* Team upload.
* update patch on FETK punc component vf2c/uninit.c to test for
availability of _FPU_MASK_IM rather than __mips to allow riscv64
to build.
* patch FETK punc component vf2c/uninit.c to define Masks for
riscv64 interrupts. Thanks Bo YU. Closes: #1012302.
* Standards-Version: 4.6.1
-- Drew Parsons <dparsons@debian.org> Sat, 04 Jun 2022 09:58:09 +0200
apbs (3.4.1-3) unstable; urgency=medium
* Team upload.
* patch FETK punc component vf2c/uninit.c to use specific MIPS fpu
masks with _FPU_SETCW. Closes: #1012177.
-- Drew Parsons <dparsons@debian.org> Wed, 01 Jun 2022 13:43:34 +0200
apbs (3.4.1-2) unstable; urgency=medium
* Team upload.
* Build-Depends-Indep: python3-yaml (to build docs)
* add specific copyright entries for FETK components
punc/src/pmg (GPL) and punc/src/vf2c (AT&T)
* patch FETK punc component vf2c/uninit.c to not run __mips block on
linux
* don't double-up bin dir in path for apbs tools. Closes: #979339.
* debian/rules: run build-time tests after dh_auto_install
* FETK is now provided (built against system SuperLU), and debci
tests pass. Closes: #1006382, #1008726.
-- Drew Parsons <dparsons@debian.org> Tue, 31 May 2022 02:52:47 +0200
apbs (3.4.1-1) unstable; urgency=medium
* Team upload.
* New upstream release.
- requires FETK
- Build-Depends: pybuild-plugin-pyproject, python3-pybind11
- drop deprecated debian patches debian_make.patch and
link_libapbs_routines.patch
* provide FETK external source as a git subtree in
debian/external_deps/fetk. Source is pulled from
https://github.com/Electrostatics/FETK, the required
version is specified in the toplevel apbs CMakeLists.txt
- pull FETK 1.9.3 (commit 57195e5) to use system SuperLU
- patch to use system maloc (don't build local maloc)
- patch mc and punc with BLA_STATIC OFF to used BLAS shared
libraries, and don't specify BLA_VENDOR OpenBLAS (use generic
blas to allow for alternative optimised BLASes)
- build FETK libraries (libmc.so, libgamer.so, libpunc.so,
also punc components libcgcode.so, libvf2c.so)
with soname set by FETK project minor version (currently 1.9)
- provide FETK libraries in libfetk-dev and libfetk1.9 packages.
- FETK copyright licence is LGPL-2.1+
- Build-Depends: libsuitesparse-dev (for libumfpack),
libarpack2-dev
* python3-apbslib provides both apbs and apbslib python modules
* update debian/rules
- specify cmake build with source at top level
- specify APBS_STATIC_BUILD=Off
* update debian patch python3.patch to fix check of PYTHON_MAX_VERSION
and only copy python library files to a pdb2pka dir it exists
* add debian patch cmake.patch
- adjusts upstream cmake files to install headers in
/usr/include/apbs, and don't install (unformed) docs
- add RPC_CFLAGS (/usr/include/tirpc) to CFLAGS in
ImportFETK.cmake to include FETK RPC support.
Build-Depends: libtirpc-dev (using pkg-config)
- treat PYTHON_VERSION (3.6) as minimum not exact version
- skip RPATH in shared library build (CMAKE_SKIP_RPATH=ON)
* provide apbs-doc package
- build user docs with sphinxdoc, libjs-mathjax
- Build-Depends-Indep: python3-sphinx-rtd-theme
* fix ©,Å symbols with UTF-8 via debian patch
fix_spelling_errors.patch and direct in FETK
* add apbs_check_intermediate_energies.py to
debian patch wrong-path-for-interpreter.patch and replace with
"env python3" as needed (following upstream more closely)
* update upstream source to https://github.com/Electrostatics/apbs
* upstream source no longer includes pdb2pqr, don't need to
exclude it and repackage the source (drop +dfsg1)
* Standards-Version: 4.6.0
* lintian updates
-- Drew Parsons <dparsons@debian.org> Sun, 29 May 2022 10:42:09 +0200
apbs (3.0.0+dfsg1-3) unstable; urgency=medium
* Team upload.
* use -fcommon in CFLAGS to aid build with gcc-10
(managing multiple definitions of common variables).
Closes: #956998.
* provide python path to inputgen for build-time tests
-- Drew Parsons <dparsons@debian.org> Thu, 23 Jul 2020 17:35:23 +0800
apbs (3.0.0+dfsg1-2) unstable; urgency=medium
* Team upload.
* reinstate debian patch python3.patch
(to specify python executable as python3)
-- Drew Parsons <dparsons@debian.org> Wed, 24 Jun 2020 03:37:37 +0800
apbs (3.0.0+dfsg1-1) experimental; urgency=medium
* Team upload.
* New upstream release.
- now supports Python 3. Drop debian patch python3.patch.
- bump to soname 3 (provide libapbs3)
* update debian/watch to catch new releases
* debhelper compatibility level 13
* update debian/not-installed for unused files installed by build
system
* lintian lib overrides moved to libapbs3.lintian-overrides
* mark libapbs-dev and libapbs3 Multi-Arch: same,
apbs-data Multi-Arch: foreign
-- Drew Parsons <dparsons@debian.org> Thu, 18 Jun 2020 16:05:52 +0800
apbs (1.5+dfsg1-3) unstable; urgency=medium
* Team upload.
* python3.patch, wrong-path-for-interpreter.patch: use python3 as
python executable for tests and scripts, fix print statements
-- Drew Parsons <dparsons@debian.org> Fri, 03 Apr 2020 12:05:58 +0800
apbs (1.5+dfsg1-2) unstable; urgency=medium
* Team upload.
* Split package into component packages supporting shared libraries
and python module: libapbs-dev, libapbs1, python3-apbslib.
Python 3 support Closes: #936124
* debian patch link_libapbs_routines.patch links libapbs_routines
to libapbs_generic and libapbs_mg (providing internal symbols)
* debian/not-installed marks components of usr/share/apbs/tools
which are deliberately not installed (matlab, windows, osx, etc)
-- Drew Parsons <dparsons@debian.org> Mon, 30 Mar 2020 12:08:59 +0800
apbs (1.5+dfsg1-1) unstable; urgency=medium
* Team upload.
[ Daniel Leidert ]
* debian/apbs-data.install: Fix brace-expansion-in-debhelper-config-file.
* debian/compat: Increase dh level to 12.
* debian/copyright: Minor update. Use HTTPS. Fix license short name.
* debian/rules: Fix debian-rules-uses-unnecessary-dh-argument.
(override_dh_install): Remove deprecated options. Make scripts executable.
* debian/patches/debian_testfiles.patch (Description): Fix typo.
* debian/patches/wrong-path-for-interpreter.patch: Added.
- Fix wrong-path-for-interpreter in examples/protein-rna/apbs_unix_dx.py.
* debian/patches/series: Adjusted.
* debian/upstream: Rename to debian/upstream/metadata. Use HTTPS.
[ Drew Parsons ]
* update Homepage to http://www.poissonboltzmann.org/
* update debian/watch to track https://github.com/Electrostatics/apbs-pdb2pqr
* exclude pdb2pqr from source tarball (reversion with +dfsg1) since
pdb2pqr is currently packaged separately.
* New upstream release (+dfsg1 excluding pdb2pqr).
* provide binary mesh tools in /usr/lib/apbs/tools/bin (linked from share)
* activate Python support (uses shared libs)
* add debian patches
- shared_library_soname.patch assigns a soversion to shared libs
- use major version as soname (until ABI proves unstable in the
minor version). Requires cmake policy to set CMP0048 as NEW.
- python3.patch enables tests to run in python3
* modernize debhelper compatibility with
Build-Depends: debhelper-compat (= 12)
* Standards-Version: 4.5.0
-- Drew Parsons <dparsons@debian.org> Sun, 29 Mar 2020 23:54:29 +0800
apbs (1.4.2.1-1) unstable; urgency=medium
* New upstream release.
* debian/patches/debian_testfiles.patch: Updated.
* debian/patches/debian_testfiles.patch: Remove geoflow testcase, no longer
working.
* debian/patches/debian_testfiles.patch: Include test_cases.cfg in binary
package.
* debian/control (Build-Depends): Added swig3.0.
* debian/rules (override_dh_auto_configure): Removed -DBUILD_SHARED_LIBS and
switched -DENABLE_PYTHON to Off.
* debian/patches/debian_testfiles.patch: Add /usr/share/apbs/tools/manip/ to
python search path.
* debian/tests/control: Added needs-root to system-wide test.
* debian/patches/debian_make.patch: Updated.
* debian/gitlab-ci.yml: New file.
-- Michael Banck <mbanck@debian.org> Fri, 19 Jul 2019 21:20:55 -0300
apbs (1.4-2) UNRELEASED; urgency=medium
* Team upload.
* fix spelling-error-in-binary lintian warnings
* add debian/tests/control for autopkgtest
* cme fix dpkg-control
* update debhelper to >= 9
* fix hardening-no-pie and hardening-no-bindnow lintian warnings
* make debian/copyright machine-readable and check with
"cme fix dpkg-copyright"
* split to apbs and apbs-data, install examples/ and tests/ to apbs-data
* fix script-not-executable lintian warnings
* add allow-stderr restriction to debian/tests/control
* add tests to debian/tests/control to check the same test when installed,
install tools/manip/ to /usr/share/apbs (this is used with tests/)
* add debian/README.test and debian/docs
-- Tatiana Malygina <merlettaia@gmail.com> Wed, 03 Aug 2016 16:46:10 +0300
apbs (1.4-1) unstable; urgency=low
* New upstream release.
[ Daniel Leidert ]
* debian/control (Uploaders): Removed myself.
(Standards-Version): Bumped to 3.9.4.
(Vcs-Browser, Vcs-Svn): Fixed vcs-field-not-canonical.
(DM-Upload-Allowed): Dropped.
(Build-Depends): Dropped all autotools related build dependencies,
libarpack2-dev, libblas-dev and bc. Added cmake, libpython-dev
and zlib1g-dev.
* debian/copyright: Updated.
* debian/rules: Enable hardening. Dropped all autotools related stuff and
rewrote it for cmake build system.
* debian/watch: Make regex case insensitive.
* debian/patches/03_skip_expensive_tests.patch: Dropped. Upstream changed
to cmake.
* debian/patches/06_quicktest.patch: Ditto.
* debian/patches/07_destdir.patch: Ditto.
* debian/patches/08_distclean.patch: Ditto.
* debian/patches/09_acinclude_fix.patch: Ditto.
* debian/patches/debian_make.patch: Added.
- Compile internal libraries statically into apbs.
* debian/patches/debian_testfiles.patch: Added.
- Skip expensive tests (see 03_skip_expensive_tests.patch).
* debian/patches/series: Adjusted.
[ Andreas Tille ]
* debian/upstream: Author field in BibTeX syntax
-- Debichem Team <debichem-devel@lists.alioth.debian.org> Thu, 08 Aug 2013 18:21:30 +0200
apbs (1.3.0-2) unstable; urgency=low
* debian/apbs.install: Adjusted.
* debian/apbs.manpages: Added to fix binary-without-manpage.
* debian/compat: Increased dh level to 7.
* debian/control: Used wrap-and-sort.
(Standards-Version): Bumped to recent 3.9.3.
(Build-Depends): Removed unused cdbs. Added autotools-dev version
requirements. Lowered required debhelper version.
(Vcs-Browser): Fixed.
* debian/copyright: Updated. Removed BSD license file reference to fix
copyright-refers-to-deprecated-bsd-license-file.
* debian/rules: Run autotools_dev template. Added override target for
dh_install. Added target to install upstream changelog file.
* debian/upstream: Added.
* debian/README.source: Dropped obsolete file.
* debian/patches/*.patch: Updated for quilt.
* debian/patches/04_remove_install-exec-am_rule.patch: Dropped. Moved
patch content to 07_destdir.patch.
* debian/patches/series: Adjusted.
-- Daniel Leidert (dale) <daniel.leidert@wgdd.de> Sun, 29 Apr 2012 23:35:09 +0200
apbs (1.3.0-1) unstable; urgency=low
* New upstream release.
[ Daniel Leidert (dale) ]
* debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Don't build nor link against
shipped copy of zlib.
[ Michael Banck ]
* Switch packaging to "3.0 (quilt)" format.
* debian/rules: Rewritten for dh.
* debian/control (Build-Depends): Removed quilt, bumped required debhelper
version to 8.
* debian/apbs.install: Install apbs executable explicitly.
* debian/patches/07_destdir.patch: New patch, fixes DESTDIR in python
setup.py installation in a contributed module.
* debian/control (Build-Depends): Added dh-autoreconf, autoconf and
automake.
* debian/rules: Use --with autoreconf.
* debian/rules (override_dh_auto_clean): Run make distclean in examples
directory and remove all uncleaned Makefiles.
* debian/patches/08_distclean.patch: New patch, fixes Makefile.am in various
directories to clean all relevant files on make distclean.
* debian/patches/09_acinclude_fix.patch: New patches, rewrites some m4
macros so that recent autoconf versions do not produce faulty shell code,
taken from Gentoo.
* debian/control (Build-Depends): Added python-setuptools.
-- Michael Banck <mbanck@debian.org> Sun, 11 Mar 2012 19:12:24 +0100
apbs (1.2.1b-1) unstable; urgency=low
* New upstream (bugfix) release.
* debian/control (Standards-Version): Bumped to 3.8.3.
(Build-Depends): Replace libmpich1.0-dev with mpi-default-dev.
* debian/rules: Added list-missing target.
(DEB_CONFIGURE_EXTRA_FLAGS, DEB_CONFIGURE_SCRIPT_ENV): Use the default
MPI implementation for the architecture.
* debian/watch: Slightly adjusted for upstream version schema.
-- Daniel Leidert (dale) <daniel.leidert@wgdd.de> Sun, 13 Dec 2009 15:59:00 +0100
apbs (1.1.0-1) unstable; urgency=low
* New upstream release.
* debian/apbs.1: Added citation section.
(SEE ALSO): User guide is not available locally anymore.
* debian/apbs.doc-base,
debian/apbs.dirs: Dropped useless files.
* debian/apbs.install: Removed documentation files, because the user guide
is not shipped anymore (closes: #508980). The lintian overrides are
considered by dh_lintian.
* debian/control (Uploaders): Removed LI as requested. Thanks for your work!
(Build-Depends): Re-added arpack, which is back in main.
(Standards-Version): Bumped to 3.8.2 (no other changes).
(Vcs-Svn): Fixed vcs-field-uses-not-recommended-uri-format.
* debian/copyright: Updated and completed.
* debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Build with arpack.
* debian/README.source: Added to comply to policy.
* debian/lintian-overrides/apbs: Dropped. License file is not installed
anymore.
* debian/patches/01_html_documentation.dpatch: Dropped, as there is no
documentation installed anymore.
* debian/patches/04_remove_install-exec-am_rule.dpatch: Updated/adjusted.
* debian/patches/05_reduce_test_suite.dpatch: Dropped (cannot be applied
anymore).
* debian/patches/00list: Adjusted.
-- Daniel Leidert (dale) <daniel.leidert@wgdd.de> Fri, 17 Jul 2009 19:06:05 +0200
apbs (1.0.0-2) unstable; urgency=low
* debian/patches/06_quicktest.dpatch: New patch, add a `quicktest' target
which only runs a couple of small tests.
* debian/rules (DEB_MAKE_CHECK_TARGET): Run quicktest instead of test for
now.
* debian/control (Build-Depends): Removed libarpack2-dev. (closes: #497722)
* debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Removed --with-arpack.
-- Michael Banck <mbanck@debian.org> Thu, 04 Sep 2008 00:00:41 +0200
apbs (1.0.0-1) unstable; urgency=low
* New upstream release.
+ No longer contains a corrupted tarball (closes: #473822).
* debian/patches/04_remove_install-exec-am_rule.dpatch: Refreshed.
* debian/patches/05_reduce_test_suite.dpatch: New patch, remove most of the
coordinates for the ion test to save time (closes: 475064).
-- Michael Banck <mbanck@debian.org> Tue, 10 Jun 2008 14:25:47 +0200
apbs (0.5.1-2) unstable; urgency=low
* Acknowledge NMU 0.5.1-1.1 (closes: #462263). Thanks to Colin Tuckley.
[ Daniel Leidert ]
* debian/apbs.1: Added.
* debian/apbs.doc-base (Section): Adjusted accordingly to latest doc-base
policy.
* debian/apbs.install: Install lintian override.
* debian/compat: Raised to level 5.
* debian/control: Homepage field transition. Added Vcs fields. Added
DM-Upload-Allowed field for DM status.
(Maintainer): Set to the debichem team address. Moved Michael to
Uploaders.
(Uploaders): Added myself and LI Daobing.
(Standards-Version): Updated to latest 3.7.3 (no other changes).
(Build-Depends): Raised debhelper to v5. Added libarpack2-dev. Added
libmpich1.0-dev for MPI support. Added python-minimal for some tests.
* debian/copyright: Fixed old-fsf-address-in-copyright-file issue. Updated
copyright information. Added exception.
* debian/rules: Install the newly added apbs.1 manpage.
(DEB_CONFIGURE_EXTRA_FLAGS): Enable building with arpack (not useful atm
without tools). Set prefix.
(DEB_CONFIGURE_EXTRA_FLAGS, DEB_CONFIGURE_SCRIPT_ENV): Enable MPI.
(DEB_MAKE_INSTALL_TARGET): Only install from bin/ as long as we don't use
the rest.
* debian/watch: Updated to fit new source archive naming.
* debian/lintian-overrides/apbs: Added. The documentation contains the
license in several formats.
[ LI Daobing ]
* FTBFS if built twice in a row (Closes: #424100)
-- Daniel Leidert (dale) <daniel.leidert@wgdd.de> Mon, 10 Mar 2008 08:46:53 +0100
apbs (0.5.1-1.1) unstable; urgency=low
* Non-maintainer upload
* Build depend on libblas-dev instead of refblas3-dev (closes: #462263)
* Add gfortran to Build Depends: to fix FTBFS in clean chroot
-- Colin Tuckley <colint@debian.org> Mon, 28 Jan 2008 11:05:21 +0000
apbs (0.5.1-1) unstable; urgency=low
* New upstream release.
[ Daniel Leidert ]
* debian/control (Build-Depends): Added dpatch and autotools-dev.
(Standards-Version): Changed to latest standards version 3.7.2.
(Description): Added Homepage field.
* debian/copyright: Fixed download location after apbs has been moved to
sourceforge.net.
* debian/rules: Changed to use dpatch.mk instead of simple-patchsys.mk.
Added buildcore.mk ruleset. Added FFLAGS flags to configure.
* debian/watch: Added.
* debian/patches/01_html_documentation.dpatch: Added. Replaces
debian/patches/01_html_docu.patch.
* debian/patches/02_remove_vf2c.dpatch: Added. Replaces
debian/patches/02_remove_vf2c.patch.
* debian/patches/90_autoreconf.dpatch: Added. Replaces
debian/patches/90_autoreconf.patch. Probably closes: #424100.
* debian/patches/00list: Added.
[ Michael Banck ]
* debian/patches/01_html_documentation: Updated.
* debian/patches/02_remove_vf2c: Removed; no longer needed.
* debian/patches/90_autoreconf: Likewise.
* debian/control (Build-Depends): Added bc, needed for the test suite.
* debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Added
--with-fetk-include=/usr/include --with-fetk-library=/usr/lib
--with-blas=-lblas.
* debian/rules (DEB_MAKE_CHECK_TARGET): New target, run the test suite.
* debian/patches/03_skip_expensive_tests.dpatch: New patch, skip tests which
take a lot of memory and CPU.
* debian/patches/04_remove_install-exec-am_rule.dpatch: New patch, remove
the install-exec-am rule from the top-level Makefile. We can just install
that data manually and it does not support DESTDIR anyway.
* debian/apbs.install: Updated location of the user's guide and tutorial in
the source tree. Install license.html as well.
-- Michael Banck <mbanck@debian.org> Wed, 18 Jul 2007 15:48:58 +0200
apbs (0.4.0-2) unstable; urgency=low
* debian/patches: New directory, manage changes to upstream with
simple-patchsys.mk.
* debian/patches/01_html_docu.patch: New patch, supress link to the
programmer's manual we don't ship for now.
* debian/patches/02_remove_vf2c.patch: New patch, remove MALOC's own
-lvf2c f2c fork from linking.
* debian/patches/90_autoreconf.patch: Update libtool; closes: #378211.
-- Michael Banck <mbanck@debian.org> Sun, 10 Sep 2006 19:14:24 +0200
apbs (0.4.0-1) unstable; urgency=low
* Initial release.
-- Michael Banck <mbanck@debian.org> Thu, 29 Jun 2006 17:10:18 +0200