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 apbs (3.4.1-5.1) unstable; urgency=medium . * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. Closes: #1061891 apbs (3.4.1-5.1~exp2) experimental; urgency=medium . * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. * Fix uninstallable packages from the previous upload. apbs (3.4.1-5.1~exp1) experimental; urgency=medium . * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. 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. 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 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. 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. 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 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 apbs (3.0.0+dfsg1-2) unstable; urgency=medium . * Team upload. * reinstate debian patch python3.patch (to specify python executable as python3) 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 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 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) . 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 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 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. 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. 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. 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. 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. 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. apbs (0.4.0-1) unstable; urgency=low * Initial release. dbus (1.15.90-1) unstable; urgency=medium . * New upstream release candidate (effectively 1.16.0 rc1) * Switch packaging branch to debian/unstable. dbus 1.15.90 is a release candidate for 1.16.0, so it can go to testing/unstable. * d/salsa-ci.yml: Use recommended recipe * Drop patches, applied upstream * d/libdbus-1-3.symbols.in: Stop distinguishing between development versions. Behave as though all symbols added in a development branch had been added in the stable release that followed it, instead. This simplifies the generated dependency. Leave the one symbol that was added during 1.15.x as-is, since we have not yet reached 1.16.0. * Add references to #1072756, #1085407 in the 1.14.10-5 changelog entry dbus (1.15.12-1) experimental; urgency=medium . * New upstream development release * Merge packaging changes from unstable * d/p/doc-Substitute-DBUS_APIDOC_LINK-from-Meson-build-not-just.patch, d/p/tests-Only-check-whether-the-first-1024-fds-are-close-on-.patch: Drop patches that are included in the new upstream release * Update doc-base registration and documentation symlinks for new layout * d/p/doc-Use-api-html-to-link-to-Doxygen-docs-in-Devhelp-index.patch, d/p/doc-Use-the-top-level-index.html-as-the-table-of-contents.patch: Add proposed patches to fix the Devhelp documentation index * Enable assertions for the debug build. These were always meant to be enabled in the debug build (and disabled in the normal and udeb builds), but were accidentally disabled when switching from Autotools to Meson. dbus (1.15.10-1) experimental; urgency=medium . * New upstream release * Merge packaging changes from unstable - No functional change, all changes were already in experimental * d/copyright: Update for deletion of m4/ * Standards-Version: 4.7.0 (no changes required) * Refresh patch series (no functional change) * d/p/doc-Substitute-DBUS_APIDOC_LINK-from-Meson-build-not-just.patch: Add proposed patch to fix missing link from index to API docs dbus (1.15.8-4) experimental; urgency=medium . * Move the shared library from /lib/MULTIARCH to /usr/lib/MULTIARCH * Merge packaging changes from unstable - dbus depends on usr-is-merged (>= 38~) (Closes: #1054650) - all other changes were already present in the experimental branch dbus (1.15.8-3) experimental; urgency=medium . * Install systemd system units into /usr/lib/systemd/system. This was allowed by TC resolution #1053901. The shared library is still in /lib, for now. Build-depend on debhelper 13.11.6~ to ensure that the units are still picked up by dh_installsystemd. * Merge 1.14.10-1 packaging from unstable - No functional changes, equivalent fixes were already included in 1.15.8 (for the upstream parts) and 1.15.8-2 (for the packaging) * Build-depend on pkgconf rather than pkg-config dbus (1.15.8-2) experimental; urgency=medium . * dbus-x11: Don't copy XDG_SEAT_PATH, XDG_SESSION_PATH to activation environment. These variables are specific to a single login session. * dbus-user-session: Copy XDG_CURRENT_DESKTOP to activation environment. This is needed by various freedesktop.org specifications, in particular for xdg-desktop-portal (>= 1.17) to choose the correct portal backend for a desktop session. Some session managers like gnome-session and plasma-workspace already upload this into the activation environment, but many older or simpler session managers do not. dbus (1.15.8-1) experimental; urgency=medium . * New upstream development release * d/copyright: Update * d/rules: Pass the correct private library directory to dh_shlibdeps dbus (1.15.6-2) experimental; urgency=medium . * Merge packaging from unstable (Closes: #1040790) dbus (1.15.6-1) experimental; urgency=medium . [ Simon McVittie ] * New upstream development release - Fixes a denial of service issue if the root or messagebus user is monitoring messages on the system bus with the Monitoring interface (dbus-monitor, busctl monitor, gdbus monitor or similar) (Closes: #1037151) * d/rules: Tell dh_shlibdeps where to find dbus-tests' private libraries dbus-tests contains an instrumented/debug build of libdbus in a private directory, which has more ABI than the production build, and a second set of tests which depend on that debug build. * d/rules: Extend arbitrary timeout for tests. Some mipsel buildds are very slow and have seen the hash test time out after 30 seconds (it normally takes about 10 on slower machines). . [ Helmut Grohne ] * Mark dbus-daemon and dbus-bin Multi-Arch: foreign (Closes: #1033056) dbus (1.15.4-1) experimental; urgency=medium . * New upstream development release - Fixes a denial of service issue that is not relevant for the way we compile dbus in Debian * d/copyright: Update * d/rules: Explicitly enable the message bus and tools, which are now compile-time optional * Merge packaging changes from unstable dbus (1.15.2-1) experimental; urgency=medium . * New upstream development release - Fix several denial of service issues where an authenticated attacker can crash the system bus by sending crafted messages (CVE-2022-42010, CVE-2022-42011, CVE-2022-42012) - Use a path-based Unix socket for the session bus, avoiding sandbox escape for Flatpak apps with network access (dbus#416) * Merge packaging from unstable dbus (1.15.0-1) experimental; urgency=medium . [ Simon McVittie ] * New upstream development release * Drop most patches, applied upstream * d/copyright: Update . [ Dave Jones ] * Make autopkgtest cross-friendly dbus (1.14.99~git20220715-1) experimental; urgency=medium . * d/control, d/gbp.conf, d/watch: Branch for experimental * New upstream snapshot with Meson build system * Build with Meson instead of Autotools * d/copyright: Update * libdbus-1-dev: Depend on libsystemd-dev. Autotools represented the libsystemd dependency as Libs.private, which meant we would only have needed libsystemd-dev for static linking, but Meson uses Requires.private. * d/p/activation-helper-Never-crash-if-unable-to-write-oom_scor.patch, d/p/sysdeps-Only-open-oom_score_adj-read-write-if-we-need-to-.patch: Add proposed patches to make oom_score_adj handling more robust * d/p/test-bus-Factor-out-common-setup-teardown-code.patch, d/p/test-bus-Break-up-dispatch-test-into-three-separate-tests.patch, d/p/dispatch-test-Pass-in-test-data-directory-as-a-C-string.patch: Add proposed patches to speed up build-time testing * d/rules: Run all tests, even the slow ones. They're a lot less slow now.