bioperl-run (1.7.3-13) unstable; urgency=medium . * Revert "skip_tests_for_ncbi-blast+.patch: remove." * Revert "d/control: remove build dependency on ncbi-blast+-legacy." * update-blastdbcmd-error-output.patch: fix test regression. This patch updates the expected blastdbcmd error output parsed by the StandAloneBlastPlus.pm runner, fixing the corresponding test item in the maneuver. Thanks to Aaron M. Ucko (Closes: #1077454) bioperl-run (1.7.3-12) unstable; urgency=medium . * d/control: remove build dependency on ncbi-blast+-legacy. This skips the failing test reported in bug #1077454. * skip_tests_for_ncbi-blast+.patch: remove. The workaround in this patch gets to interfere with the test run once ncbi-blast+-legacy is not available anymore. * d/control: declare compliance to standards version 4.7.0. bioperl-run (1.7.3-11) unstable; urgency=medium . * d/control: restrict emboss build-dependency. emboss is not available anymore on 32-bit and big endian architectures. It is thus not possible anymore to test it in such context. * d/control: demote bioperl-run recommends to suggestions. emboss, hmmer and infernal are currently not available on some release architectures. Demoting them helps getting the autodep8 perl test back on tracks at least on s390x. * d/control: demote tigr-glimmer to suggestion. * d/control: also restrict tigr-glimmer build-deps architecture set. bioperl-run (1.7.3-10) unstable; urgency=medium . * d/control: restrict some build-deps to amd64. Following 64-bit time_t transition, ncbi tools have been limited to 64-bit architectures. This fixes package building aod one of the autodep8 perl autopkgtests. This change is intended to facilitate the transition timely. * d/control: demote several packages as suggestions. This fixes autodep8 perl autopkgtest base checking the installability of recommendations; it could have been better to skip it but the mecanisme to proceed to the skip occurs after the failure to install missing recommends on architectures not supporting them. bioperl-run (1.7.3-9) unstable; urgency=medium . [ Andreas Tille ] * Fix test data in BEDtools test * Fix upstream source download name in watch file * Standards-Version: 4.6.2 (routine-update) * Update lintian override info format in d/bioperl-run.lintian-overrides on line 2-6. . [ Étienne Mollier ] * d/control: depend on libsoap-lite-perl. * d/t/p/smoke-skip: skip test only suitable for build time. bioperl-run (1.7.3-8) unstable; urgency=medium . * Replace skip_tests_for_muscle.patch by adjust-muscle-test.patch. Integration of newer muscle version in debian changed the code path in the way the test may be skipped, breaking autopkgtest of bioperl-run. * Move libmodule-build-perl from Build-Depends-Indep to Build-Depends. bioperl-run (1.7.3-7) unstable; urgency=medium . * d/watch: fix broken link to github and adjust version mangling to fit upstream's tagging convention (tag "release-x-y-z" for version "x.y.z") * adjust lintian override on bp_bioperl_application_installer.pl file extension, which is not provided anymore * add fix-whatis-entries.patch; fixes lintian warnings on bad-whatis-entry by providing a convenient description in the NAME field where needed * add unscramble-erpin.patch; fixes a kind of typo in ERPIN.pm documentation, flagged by lintian warning national-encoding * add fix-pod-conversion.patch; address the lintian warning pod-conversion-message affecting Bio::DB::SoapEUtilities::Result. * d/control: add myself to uploaders * Standards-Version: 4.6.0 (routine-update) bioperl-run (1.7.3-6) unstable; urgency=medium . * Team upload. * d/control: restrict build-dependencies to their supported architectures. * added skip-test-for-kalign.patch bioperl-run (1.7.3-5) unstable; urgency=medium . * Team upload. . [ Michael R. Crusoe ] * Add build-dep on libfile-sort-perl as that has arrived in Debian * debian/upstream/metadata: Add Repository & Repository-Browse . [ Pranav Ballaney ] * Disable tests for RemoteBlast * Disable tests for RemoteBlast_rpsblast * Extract BEDTools version properly . [ Andreas Tille ] * Depends: libfile-sort-perl Closes: #974168 * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Remove trailing whitespace in debian/control (routine-update) . [ Étienne Mollier ] * Add get-overlap.patch to map to the proper "getOverlap" wrapper. * Add build time test dependencies to get BEDtools test data sets. * Add alternate-data.patch to use a dataset available in the Debian archive during build time testings. * Suppress retries when attempting to access remote Blast resources, this prevents hogging autopkgtest runners ten more minutes. bioperl-run (1.7.3-4) unstable; urgency=medium . [ Michael R. Crusoe ] * Team upload. * Fix the autopkgtests * Set 'Bio::Factory::EMBOSS' as the main module name for the purpose of the use.t autopkgtest * fix hyphympi autopkgtests * libipc-run-perl is needed for Bio::Tools::Run::BEDTools * drawgram is pary of the phylip package . [ Pranav Ballaney ] * Change kalign command string to input via stdin It fails to take input via the -in flag during testing * Revert changes made outside of debian/ * Update quilt version * Kalign takes input via a pipe * Extract Kalign version properly (Closes: #954511) . [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Wrap long lines in changelog entries: 1.7.2-1. * Set upstream metadata fields: Bug-Submit. bioperl-run (1.7.3-3) unstable; urgency=medium . * Team upload. * Depends: libbio-tools-run-alignment-clustalw-perl (Closes: #948323) * Depends: libbio-featureio-perl bioperl-run (1.7.3-2) unstable; urgency=medium . * Depends: libbio-tools-run-alignment-clustalw * Build-Depends / Recommends: s/blast2/ncbi-blast+-legacy/ Closes: #948082 * debhelper-compat 12 * Standards-Version: 4.4.1 * Remove trailing whitespace in debian/changelog * Remove trailing whitespace in debian/copyright * Set upstream metadata fields: Bug-Database. bioperl-run (1.7.3-1) unstable; urgency=medium . * New upstream version * debhelper 12 * Standards-Version: 4.3.0 * Drop dependencies: bowtie, bwa, maq, t-coffee, gmap, paml Thanks for the hint to Carnë Draug ) * Versioned (Build-)Depends: bioperl (>= 1.7.4) bioperl-run (1.7.2-4) unstable; urgency=medium . * (Build-)Depends: ncoils * do not run tests parallel to get sensibly sorted output * Allow MPI oversubscription (as in phyml build since phyml caused problems inside build time tests) This is also not reliable - skip phyml test at all Closes: #906337 * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Fix Homepage * Lintian-override for script-with-language-extension bioperl-run (1.7.2-3) unstable; urgency=medium . * Drop adjust_bowtie_tests.patch, Closes: #887578 * Bump Standards-Version to 4.1.3 (no changes needed) bioperl-run (1.7.2-2) unstable; urgency=medium . * Team upload * Add adjust_bowtie_tests.patch fixing failing tests for Bowtie Closes: #880347 * Bump Standards-Version to 4.1.2, apply cme fix dpkg bioperl-run (1.7.2-1) unstable; urgency=medium . * New upstream version * Convert packaging from SVN to Git * For some reason Ensembl.t test is executed in autopkgtest run even if it should be skipped due to missing preconditions (http://search.cpan.org/~cjfields/Bio-EUtilities-1.72/lib/Bio/DB/EUtilities.pm) The test will now be fully removed to make sure it is skipped. * Standards-Version: 4.1.0 (no changes needed) * Do not try to run bowtie tests with wrong bowtie call Closes: #868073 bioperl-run (1.7.1-3) unstable; urgency=medium . * s/Conflicts/Breaks/ Closes: #850029 bioperl-run (1.7.1-2) unstable; urgency=medium . * Conflicts: libbio-perl-perl (<< 1.7.1-1) Closes: #850029 bioperl-run (1.7.1-1) unstable; urgency=medium . * New upstream version * Testsuite: autopkgtest-pkg-perl * cme fix dpkg-control * Enable lots of tests * Module Bio::Tools::Run::WrapperBase was taken over from BioPerl into bioperl-run in commit acd57a7d14112c5fd2cd979005b072efdaf57679 which is taken over in quilt patch * Fix homepage * d/watch: - version=4 - Fix versionmangling * Build-Depends: raxml * Update copyright * debhelper 10 bioperl-run (1.6.9-3) unstable; urgency=medium . [ Charles Plessy ] * Build-depend on libmodule-build-perl, Closes: #788888. . [ Andreas Tille ] * Compliant with Standards-Version: 3.9.6 bioperl-run (1.6.9-2) unstable; urgency=low . * debian/source/format: 3.0 (quilt) * debian/control: - cme fix dpkg-control - canonical Vcs URLs - debhelper 9 * debian/README.source: removed because redundant * debian/copyright: DEP5 * debian/watch: Point download location to github which provides more reliable version numbering than CPAN which would have needed a more complex version mangling * refreshed quilt patches to get rid of fuzz bioperl-run (1.6.9-1) unstable; urgency=low * New upstream release. * Converted and validated debian/copyright to latest machine-readable format. * debian/control: - Refreshed the list of packages for which wrappers are provided, in the Suggests field as well as in an experimental Build-Recommends field. - Incremented Standards-Version to reflect conformance with Policy 3.9.2. No other changes needed. - Vcs-Browser URL made redirectable to viewvc. - Removed useless ‘svn’ in the Vcs-Svn URL. * Point debian/watch to CPAN. * Tiny style with Debhelper 8 (debian/rules, debian/compat, debian/control). * Split scripts in bioperl-run and modules in libbio-perl-run-perl. (debian/rules, debian/control, debian/bioperl-run.install, debian/libbio-perl-run-perl.install) * debian/rules, debian/patches/series, debian/control: - debian/patches/install-scripts.patch for non-interactive script install. - debian/patches/Use-system-s-Perl.patch against /usr/local/bin/perl. - debian/patches/Some-spellchecking.patch. * Trigger network tests with DEB_MAINTAINER_MODE (debian/rules, debian/README.test). bioperl-run (1.6.1-1) unstable; urgency=low * New upstream release. * debian/patches/10-wrong-path-for-interpreter.patch: removed (fixed upstream). * debian/watch updated (bioperl -> BioPerl). * debian/rules refreshed with dh-make-perl 0.53. - Disabled installation of examples (removed upstream). - Removed the correction of file permission of Pise documentation (removed upstream). - Removed patching facilities (no patches anymore). - Disabled tests as I experience failures with t/Eponine.t despite this program is not installed. * debian/copyright: - Removed vanity lines about debianization and debian copyright. - Incremented years to 2009. - Updated to latest experimentation of the machine-readable license summary. * debian/control: - Incremented Standards-Version to reflect conformance on new Policy (dropped versionned build-dependancy on Perl). - Removed build-dependancy on quilt (no patches anymore). - Depend and Build-Depend on bioperl versions superior or equal to 1.6.0. - Build-depends on, and Recommdnes libalgorithm-diff-perl, libipc-run-perl, libio-string-perl and libxml-twig-perl, that are listed in DEPENDANCIES. - Build-depends on libarray-compare-perl and libtree-dagnode-perl (otherwise tests fail). - Depend on amap-align instead of amap (Closes: #541274). glbinding (3.3.0-3) unstable; urgency=medium . * Team upload. * Migrate debian/watch to version 5 format * Fix FTBFS with CMake 4 (Closes: #1112958) * Fix autopkgtest golang-github-prometheus-client-golang (1.23.0-2) unstable; urgency=medium . * Team upload. * Disable tests that break with golang 1.25, Closes: #1117401 jdupes (1.31.1-1) unstable; urgency=medium . * New upstream version 1.31.1. libbio-primerdesigner-perl (0.07-8) unstable; urgency=medium . * Team upload. * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine- update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) libbio-primerdesigner-perl (0.07-6) unstable; urgency=medium . * Team upload. . [ Salvatore Bonaccorso ] * Update Vcs-* headers for switch to salsa.debian.org . [ Andreas Tille ] * debhelper 11 * Standards-Version: 4.1.5 libbio-primerdesigner-perl (0.07-5) unstable; urgency=medium . [ gregor herrmann ] * debian/rules: use 'wildcard' instead of 'shell echo'. . [ Salvatore Bonaccorso ] * debian/control: Use HTTPS transport protocol for Vcs-Git URI . [ gregor herrmann ] * Change bugtracker URL(s) to HTTPS. * debian/copyright: change Copyright-Format 1.0 URL to HTTPS. * Remove Jonathan Yu from Uploaders. Thanks for your work! * Remove Ryan Niebur from Uploaders. Thanks for your work! * Skip t/remote.t during autopkgtest as well. (Closes: #843993) * Declare compliance with Debian Policy 3.9.8. * Bump debhelper compatibility level to 9. * Turn off DNS queries during build and autopkgtests completely. * Add a patch to fix spelling mistakes. libbio-primerdesigner-perl (0.07-4) unstable; urgency=medium . * Team upload. . [ gregor herrmann ] * Strip trailing slash from metacpan URLs. . [ Salvatore Bonaccorso ] * Update Vcs-Browser URL to cgit web frontend . [ Niko Tyni ] * Declare the package autopkgtestable * Update to Standards-Version 3.9.6 * Add explicit build dependency on libmodule-build-perl libbio-primerdesigner-perl (0.07-3) unstable; urgency=low . * Team upload . * add patch fixing hash manipulation inside each. Fixes test failures with perl 5.18 (Closes: #711426) libbio-primerdesigner-perl (0.07-2) unstable; urgency=low . [ Ryan Niebur ] * Email change: Jonathan Yu -> jawnsy@cpan.org * Email change: Ryan Niebur -> ryan@debian.org . [ gregor herrmann ] * debian/control: Changed: (build-)depend on perl instead of perl- modules. * Re-wrap long description. * Don't install empty Bio::PrimerDesigner::Config.3pm manpage; thanks lintian. * Remove alternative (build) dependencies that are already satisfied in oldstable. . [ Ansgar Burchardt ] * debian/control: Convert Vcs-* fields to Git. . [ gregor herrmann ] * debian/control: update {versioned,alternative} (build) dependencies. . [ Salvatore Bonaccorso ] * Change search.cpan.org based URIs to metacpan.org based URIs . [ gregor herrmann ] * Switch to "3.0 (quilt)" source format. * Add a patch to use Module::Build's args() instead of Getopt::Long. (Closes: #718120) * debian/copyright: switch formatting to Copyright-Format 1.0. * Update debian/rules and remove debian/clean. * Bump debhelper compatibility level to 8. * Declare compliance with Debian Policy 3.9.4. libbio-primerdesigner-perl (0.07-1) unstable; urgency=low * New upstream release (no changes on Linux systems). [ Jonathan Yu ] * Standards-Version 3.8.2 * Added myself to Uploaders. * Do real clean to clean things up (get rid of the generated Makefile) [ Nathan Handler ] * debian/watch: Update to ignore development releases. [ Charles Plessy ] * Refreshed and prettified debian/copyright. * Restored the skipping of the remote.t test in debian/rules after it was factorised using Debhelper’s ”dh” command. [ Ryan Niebur ] * Use --buildsystem=perl_build in debian/rules. * Test if Build is present before calling dh_auto_clean in debian/rules. (Temporary workaround for debhelper bug #539848.) * Add myself to Uploaders libbio-primerdesigner-perl (0.04-1) unstable; urgency=low * Initial Release (Closes: #512718). libbio-tools-phylo-paml-perl (1.7.3-4) unstable; urgency=medium . [ Debian Janitor ] * Update standards version to 4.5.1, no changes needed. * Remove constraints unnecessary since buster * Update standards version to 4.6.0, no changes needed. libbio-tools-phylo-paml-perl (1.7.3-3) unstable; urgency=medium . * Team upload. . [ gregor herrmann ] * debian/watch: use uscan version 4. . [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) libbio-tools-phylo-paml-perl (1.7.3-2) unstable; urgency=medium . * This package also breaks/replaces bioperl << 1.7.2 Closes: #903456 * Bump Standards-Version to 4.1.5 (no changes needed) libbio-tools-phylo-paml-perl (1.7.3-1) unstable; urgency=low . * Initial Release. (Closes: #902849) libbio-tools-run-alignment-clustalw-perl (1.7.4-4) unstable; urgency=medium . * Team upload . [ Debian Janitor ] * Set upstream metadata fields: Bug-Database. * Update standards version to 4.6.2, no changes needed. . [ Andreas Tille ] * Add debian/salsa.ci to exclude i386 builds * Update lintian-overrides libbio-tools-run-alignment-clustalw-perl (1.7.4-3) unstable; urgency=medium . * Remove constraints unnecessary since buster: + libbio-tools-run-alignment-clustalw-perl: Drop versioned constraint on libbio-perl-run-perl in Replaces. + libbio-tools-run-alignment-clustalw-perl: Drop versioned constraint on libbio-perl-run-perl in Breaks. libbio-tools-run-alignment-clustalw-perl (1.7.4-2) unstable; urgency=medium . * Team upload. * Source-only upload. . [ gregor herrmann ] * debian/watch: use uscan version 4. . [ Debian Janitor ] * Bump debhelper from old 10 to 12. * Set debhelper-compat version in Build-Depends. . [ gregor herrmann ] * Declare compliance with Debian Policy 4.5.0. * Set Rules-Requires-Root: no. * Annotate test-only build dependencies with . * Bump debhelper-compat to 13. libbio-tools-run-alignment-clustalw-perl (1.7.4-1) unstable; urgency=low . * Initial Release. (Closes: #903569) libbio-tools-run-alignment-tcoffee-perl (1.7.4-3) unstable; urgency=medium . [ Debian Janitor ] * Remove constraints unnecessary since buster * Update standards version to 4.6.0, no changes needed. libbio-tools-run-alignment-tcoffee-perl (1.7.4-2) unstable; urgency=medium . * Team upload. * Source-only upload. * debian/*: replace ADTTMP with AUTOPKGTEST_TMP. * debian/watch: use uscan version 4. * Declare compliance with Debian Policy 4.5.0. * Set Rules-Requires-Root: no. * Annotate test-only build dependencies with . * Bump debhelper-compat to 13. * debian/rules: remove manual handling of HOME. debhelper 13 does this for us. libbio-tools-run-alignment-tcoffee-perl (1.7.4-1) unstable; urgency=low . * Initial Release. (Closes: #902984) lua-busted (2.2.0-3) unstable; urgency=medium . * Team upload * Drop lua5.2 support lua-system (0.6.3-1) unstable; urgency=medium . * New upstream version 0.6.3 * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository. phcpack (2.4.91+dfsg-1) unstable; urgency=medium . * New upstream release. * debian/patches/hardening.patch - Refresh for new upstream release. * debian/patches/is-zero.patch - Remove patch; applied upstream. poedit (3.8-1) unstable; urgency=medium . * New upstream version 3.8 * Update copyright file primer3 (2.6.1-6) unstable; urgency=medium . * Team upload. * gcc15.patch: new: remove SunOS workaround. This allows fixing a build failure with gcc-15. (Closes: #1097649) * d/copyright: remove the old fsf address. * d/watch: convert to v5 github template. * d/control: declare compliance to standards version 4.7.2. * d/control: drop redundant Rules-Requires-Root: no. primer3 (2.6.1-5) unstable; urgency=medium . * Team upload. * Clean up source directory properly (Closes: #1045454) * Use execute_after hook over overrides in d/rules * Bump standards version to 4.7.0 (no changes needed) * Correct patch header metadata * Drop deprecated an-trap macro from manpage primer3 (2.6.1-4) unstable; urgency=medium . * Team upload. . [ Lukas Märdian ] * d/t/run-unit-test: fix autopkgtest sed commands on s390x. (Closes: #1023823) primer3 (2.6.1-3) unstable; urgency=medium . * Team upload. . [ Steve Langasek ] * d/rules: fix handling of big-endian archs. (Closes: #1014626) . [ Étienne Mollier ] * Standards-Version: 4.6.1 (routine-update) * d/primer3-examples.lintian-overrides: refresh override. * d/rules: remove executable bit to samples. * Add buildflags.patch: propagate Debian build flags. primer3 (2.6.1-2) unstable; urgency=medium . * Run dh_auto_test with --no-parallel primer3 (2.6.1-1) unstable; urgency=medium . * New upstream version primer3 (2.5.0-1) unstable; urgency=medium . * Fix watchfile to detect new versions on github * New upstream version * Standards-Version: 4.6.0 (routine-update) * Apply multi-arch hints. + primer3-examples: Add Multi-Arch: foreign. * Fix PREFIX primer3 (2.4.0-4) unstable; urgency=medium . * Team upload * Fixup syntax skip for big endian platforms. primer3 (2.4.0-3) unstable; urgency=medium . [ Gianfranco Costamagna ] * Also skip autopkgtests that fail on big endian (see: 890993) Closes: #962190 . [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Secure URI in copyright format (routine-update) * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine- update) * Remove trailing whitespace in debian/changelog (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * debian/copyright: use spaces rather than tabs to start continuation lines. * Set fields Upstream-Name, Upstream-Contact in debian/copyright. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright). * Fix day-of-week for changelog entry 0.9-0.2. primer3 (2.4.0-2) unstable; urgency=medium . [ Liubov Chuprikova ] * Team upload. * Skip tests that fail on big endian Closes: #890993 * Added d/README.source with explanation why some tests are skipped * debian/patches/p3test_fix_exit_status.patch: Fix test to show correct exit status . [ Andreas Tille ] * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 primer3 (2.4.0-1) unstable; urgency=medium . * New upstream version * Secure URI in watch file * Standards-Version: 4.1.3 * debhelper 11 primer3 (2.3.7-4) unstable; urgency=medium . * Fix build with gcc-7 Closes: #853621 * Standards-Version: 4.1.0 (no changes needed) * d/rules: use DEB_SOURCE * hardening=+all primer3 (2.3.7-3) unstable; urgency=medium . [ Andreas Tille ] * debhelper 10 * d/watch: version=4 . [ Helmut Grohne ] * Fix FTCBFS: Pass CXX as CPP (Closes: #851230) primer3 (2.3.7-2) unstable; urgency=medium . * Team Upload [ Andreas Tille ] * Moved packaging from SVN to Git * cme fix dpkg-control * better hardening * split example data for test into separate arch all package * add lintian override for empty directories . [ Canberk Koç ] * Autopkgtest added * debian/rules: - added dh_clean to override_dh_auto_test section - sed perl interpreter path primer3 (2.3.7-1) unstable; urgency=medium . * New upstream version * Moved debian/upstream to debian/upstream/metadata * cme fix dpkg-control primer3 (2.3.6-1) unstable; urgency=low . [ Charles Plessy ] * New upstream release. * Install configuration files in /etc (first step to fix bug 702693). * Normalised debian/control with config-model-edit. * Use canonical VCS URLs. . [ Andreas Tille ] * Fix watch file * replace cdbs by dh * debian/patches/hardening.patch: Propagate hardening options * Standards-Version: 3.9.5 (no changes needed) * debian/patches/primer_thermodynamic_parameters_path_2_etc.patch: Make sure config files will be searched for in /etc/primer3_config/ instead of /opt/primer3_config/ Closes: #702693 * Verified that new upstream Closes: #716151, #716213 * New executable: ntthal (including manpage) * Removed *.xml variants of manpages to reduce redundancy primer3 (2.3.5-1) unstable; urgency=low . New upstream release. . [ Andreas Tille ] * debian/upstream: - Remove duplicated entry for PMID - Added Volume, fixed Number - Added URL+eprint * debian/control: - Removed DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) * debhelper 9 (control+compat) * debian/copyright: PD License should be avoided - bumped packaging to same license as program itself primer3 (2.3.2-1) unstable; urgency=low * New upstream release changing some default values. * Refreshed debian/copyright to machine-readable format version 1.0. Note that the license of Primer3 version 2.x changed to the GPLv2 or higher. * Spellchecked manual pages (Closes: #650477, thanks to A. Costa). * Using Debhelper 8 (debian/control, debian/compat). * Renamed debian/README.Debian debian/README.test as it is all about tests. * Conforms to Policy 3.9.3 (debian/control, no other changes needed). primer3 (2.2.3-1) unstable; urgency=low * New upstream version * debian/primer3.docs: s/README.txt/primer3_manual.htm/ * debian/compat: 7 * debian/control: - Build-Depends: debhelper (>= 7) - Standards-Version: 3.9.1 (no changes needed * debian/source/format: 3.0 (quilt) * debian/README.source * debian/primer3.doc-base primer3 (1.1.1-1) unstable; urgency=low * New upstream release. Closes: #427235. * Enhances: emboss because EMBOSS has a wrapper for primer3_core. * Add Subversion repository URL to debian/control. * Updated the manpages primer3 (1.1.0~beta-1) experimental; urgency=low * New upstream release. - Some part of primer3 is now licenced under the GNU GPL. - The oligtotm() function is now provided as a library, liboligotm. - The oligotm executable now takes additional arguments. - Non-backward compatible change: removed support of flag -2x_compat. * Added a watch file now that the sources are hosted on SourceForge.net. * Updated manpages. primer3 (1.0b-1) unstable; urgency=low * Initial release. (Closes: #241235) * New upstream version released under a revised BSD licence. * Swiching to collaborative maintainance: Maintainer is a mailing-list, Uploaders are real people. * Using debhelper v5 and conforming to policy 3.7.2. * Relicencing the manpage of Primer3 (thanks to Steffen Moeller), adding one for ntdpal and oligotm. * Extensive tests during bulding, except on slow architectures. psortb (3.0.6+dfsg-4) unstable; urgency=medium . [ Andreas Tille ] * Add missing header file Closes: #1070459 * Standards-Version: 4.7.0 (routine-update) . [ Étienne Mollier ] * add_missing_header.patch: supplement to finish fixing ftbfs. * d/control: add myself to uploaders. * d/control: migrate to pkgconf. psortb (3.0.6+dfsg-3) unstable; urgency=medium . * Team upload. * d/control: psortb now depends on libbio-perl-run-perl, fixing autopkgtest failures. * Standards-Version: 4.6.0 (routine-update) * debhelper-compat 13 (routine-update) psortb (3.0.6+dfsg-2) unstable; urgency=medium . * Team Upload. . [ Steffen Möller ] * Update metadata with ref to conda . [ Nilesh Patra ] * Update "Depends" * Fix module path to fix tests * Drop compat, switch to debhelper-compat * Add "Rules-Requires-Root: no" * Switch to https * Bump standards version to 4.5.0 . [ Andreas Tille ] * Remove trailing whitespace in debian/changelog (routine-update) * Add salsa-ci file (routine-update) psortb (3.0.6+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.2.1 psortb (3.0.5+dfsg-2) unstable; urgency=medium . [ Steve Langasek ] * Enable build with -Wl, --as-needed Closes: #895344 . [ Andreas Tille ] * Standards-Version: 4.1.4 * Point Vcs fields to salsa.debian.org psortb (3.0.5+dfsg-1) unstable; urgency=medium . * New upstream version . [ Carnë Draug ] * d/control: enable autopkgtest with pkg-perl default tests; add missing runtime dependencies on bioperl and Algorithm::SVM. . [ Steffen Moeller ] * d/upstream/metadata: - Added references to registries - yamllint cleanliness * d/copyright: removed tailing ":" from upstream name . [ Andreas Tille ] * cme fix dpkg-control * debhelper 11 * d/rules: do not parse d/changelog psortb (3.0.4+dfsg-2) unstable; urgency=medium . * Fix root dir in config file * Add pftools to Build-Depends since it is checked in build process psortb (3.0.4+dfsg-1) unstable; urgency=medium . * Initial release (Closes: #861081) qutip (5.2.1-4) unstable; urgency=medium . * debian patch fix_tests_PR2753.patch applies upstream PR#2753 to fix tests (updating tolerances) qutip (5.2.1-3) unstable; urgency=medium . * debian patch test_prony_BLAS_PR2759.patch fixes prony environment tests to pass with generic (netlib) BLAS. Closes: #1118028. qutip (5.2.1-2) unstable; urgency=medium . * skip test_fixed_prony_fit (core/test_environment.py) in build tests (fails in temporary build time environment, passes at runtime) * report qutip.about() with tests. If we need to report issues upstream, they will want to know the environment. * stop ignoring test errors at build time (drop || /bin/true) * run debian/tests on all architectures not only amd64. Run tests from $AUTOPKGTEST_TMP since `import qutip` fails from source dir (tries to access module from source). qutip (5.2.1-1) unstable; urgency=medium . * New upstream release * Build-Depends: python3-numpy-dev (for dh_numpy3) * Standards-Version: 4.7.2 r-cran-spacetime (1.3-3-2) unstable; urgency=medium . * d/watch: version=5 * d/tests/control: Do not test on architecture s390x Closes: #1112007 * Standards-Version: 4.7.2 (routine-update) * dh-update-R to update Build-Depends (routine-update) * debputy lint --auto-fix (routine-update) sumo (1.24.0+dfsg1-1) unstable; urgency=medium . * [238db3e] Update excluded files in copyright file. (Closes: #1104207) * [cee5024] New upstream version 1.24.0+dfsg1. (Closes: #1097947, #1113546) * [708f3b1] Apply patches for FTBFS, Python 3, and GUI scaling. (Closes: #1087104) * [bface43] Add lintian override for missing soname. sumo (1.18.0+dfsg-4) unstable; urgency=medium . * Team upload. . [ Bas Couwenberg ] * Mark keyword-argument-repeated.patch as Applied-Upstream. . [ Santiago Vila ] * Remove bashism from CMakeLists.txt. Closes: #1082135. * Update upstream metadata. sumo (1.18.0+dfsg-3) unstable; urgency=medium . * Team upload. * Disable Salsa CI, doesn't support large source packages. * Update keyword-argument-repeated.patch to also fix another script. sumo (1.18.0+dfsg-2) unstable; urgency=medium . * Team upload. * Add patch to fix 'SyntaxError: keyword argument repeated'. sumo (1.18.0+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream release. (closes: #1041637) * Export DEB_PYTHON_INSTALL_LAYOUT=deb_system instead of patching `setup.py install` to use --install-layout=deb. * Drop gtest-1.13.patch, included upstream. Refresh remaining patches. sumo (1.17.0+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream release. * Add patch to fix FTBFS with googletest 1.13. (closes: #1038897) * Update copyright file. * Refresh patches. * Exclude Windows devel file from repacked upstream release. * Bump Standards-Version to 4.6.2, no changes. * Add patch to not used deprecated distutils module. sumo (1.15.0+dfsg-1) unstable; urgency=medium . * Team upload. * Move from experimental to unstable. sumo (1.15.0+dfsg-1~exp2) experimental; urgency=medium . * Team upload. * Add gbp.conf to use pristine-tar & --source-only-changes by default. * Add patch to fix syntax issues with Python 3. sumo (1.15.0+dfsg-1~exp1) experimental; urgency=medium . * Team upload. * New upstream release. * Add patch to fix installation with setuptools 65.3.0. (closes: #1023520) * Reorder dependencies. * Replace python3 dependencies with ${python3:Depends} substvar. * Update watch file to handle common issues. * Bump Standards-Version to 4.6.1, no changes. * Update copyright file. * Add py3dist-overrides for sumolib & traci. * Add dh_python3 overrides for sumo-tools. * Use dh_python3 for shebang changes instead of patches. * Remove executable bit from Python files that aren't scripts. * Drop Homepage field from upstream metadata. * Remove extra license file * Update lintian overrides. * Check DEB_BUILD_OPTIONS for nocheck in dh_auto_test override * Add Rules-Requires-Root to control file. * Add Keywords to desktop file. * Remove spare manual page. * Fix jquery symlink in sumo-doc. * Refresh patches. * Move JNI libraries. sumo (1.12.0+dfsg1-1) unstable; urgency=medium . * [e174ad9] Fix typo * [0162713] New upstream version 1.12.0+dfsg1 * [4554e20] Minor update of d-files * [ffcccc0] Set compat-level 13 * [9dbf6ae] Avoid explicitly specifying -Wl,--as-needed linker flag. sumo (1.8.0+dfsg2-5) unstable; urgency=medium . * [4a4b462] Add Breaks+Replaces: sumo (<< 1.8) for sumo-tools. (Closes: #980845) * [ee90f08] Allow reprotest to fail sumo (1.8.0+dfsg2-4) unstable; urgency=medium . * [2d44042] Fix d/rules sumo (1.8.0+dfsg2-3) unstable; urgency=medium . * [3c87058] No debug info for mipsel sumo (1.8.0+dfsg2-2) unstable; urgency=medium . * [e62ac20] Do not run autotests in indep-mode * [6836a98] No debug info for mip* to avoid out of memory sumo (1.8.0+dfsg2-1) unstable; urgency=medium . * [e563f46] New upstream version 1.8.0+dfsg2 * [567c39a] Refresh patches * [16b858e] Update d/copyright * [c482b16] Remove d/clean * [7158927] Fix test * [6a5c16a] Update d/control * [71e2d68] Update d/rules * [f4f4e02] Add .gitlab-ci.yml * [a2fc178] Remove dh_make template from debian watch. * [2ca5f9b] Use secure URI in Homepage field. * [f890de3] Remove deprecated Encoding key from desktop file debian/sumo.desktop. * [fdd3cbe] Update standards version to 4.5.0, no changes needed. * [cbcd430] Set Standards-Version to 4.5.1 sumo (1.4.0+dfsg1-1) unstable; urgency=medium . * [cfb6793] New upstream version 1.4.0+dfsg1 * [55b1f2f] Refresh patches * [9f7b1a6] Remove libxerces-c2-dev from build-depends * [262513e] Set upstream metadata fields: Bug-Submit, Repository, Repository-Browse. * [1a77a39] Remove python from depends in sumo-tools. (Closes: #948931) * [1826942] Suppress python-script-but-no-python-dep lintian warning (should be clarified with upstream) * [70c62c4] Exclude min.js files * [c025637] Exclude some more files from the tarball * [fad823b] Add +dfsg1 suffix * [1c5a8e7] Update d/copyright sumo (1.3.1-5) unstable; urgency=medium . * [12e5965] Set SUMO_HOME to escape network usage during build. (Closes: #945343) * [33f60f2] Let autopkgtests be built without network * [fd3c58c] Set Standards-Version to 4.4.1 * [89e5a7f] Set upstream metadata fields: Repository. sumo (1.3.1-4) unstable; urgency=medium . * [a8daad4] Fix some lintian warnings/errors sumo (1.3.1-3) unstable; urgency=medium . * [bea99fe] Use python3 instead of python2. (Closes: #938597) sumo (1.3.1-2) unstable; urgency=medium . [ Anton Gladky ] * [4471ca1] Remove Build-Depends-Indep section . [ Wookey ] * [b28a361] Clean docs after build. (Closes: #925273) * [eddc3af] Do not clean webWizard index.html. (Closes: #925272) sumo (1.3.1-1) unstable; urgency=medium . * [93410cf] Update d/copyright * [3768348] Update d/watch * [443a78d] Refresh patches * [bb26543] Minor update in d-files * [26cd9ee] Move test-file into the d/tests * [6b981ec] Update autopkgtests * [a444fea] Set compat-level to 12 * [aaa2b7e] Set Standards-version to 4.4.0 * [483bcb4] Remove obsolete fields Name from debian/upstream/metadata. * [38f14bd] Update d/upstream/metadata * [bf6aeec] New upstream version 1.3.1. (Closes: #931940) sumo (1.1.0+dfsg1-1) unstable; urgency=medium . [ Michael Behrisch ] * [b063b03] Update d/copyright . [ Anton Gladky ] * [a9773da] Update patches * [d520897] Use libxerces-c2-dev as build-depends * [88bcbf6] Update install files * [e0d8261] Use compat-level 11 * [23d078f] Remove some files from the source * [2372382] Minor fixes * [cc81cb9] Trim trailing whitespace. * [c2b2305] Use secure copyright file specification URI. * [14aae51] Drop unnecessary dependency on dh-autoconf. * [f16a0e7] New upstream version 1.1.0+dfsg1 sumo (0.32.0+dfsg1-2) unstable; urgency=medium . * [6b65aa2] Fix FTBFS with GCC-8. (Closes: #897872) * [a1ad134] Update VCS-field * [005fdea] Set Standards-Version to 4.2.0 sumo (0.32.0+dfsg1-1) unstable; urgency=medium . * [74d6c2b] New upstream version 0.32.0+dfsg1 * [e861a46] Refresh patches * [750e89d] Remove unneeded lines from d/rules * [f104b53] Set Standards-Version: 4.1.2. No changes * [0cd6e98] Remove testsuite-fiels in d/control sumo (0.30.0+dfsg1-1) unstable; urgency=medium . * [78f2092] New upstream version 0.30.0+dfsg1 * [07cc5b1] Refresh patches. * [c29b854] Bump Standards-Version: 4.0.0 sumo (0.28.0+dfsg1-1) unstable; urgency=medium . * [ca1e1eb] Exclude some bimary files. * [e4f942c] New upstream version 0.28.0+dfsg1 * [66fa6c3] Refresh patches. * [58d6734] Apply cme fix dpkg. sumo (0.27.1+dfsg1-1) unstable; urgency=medium . * [0622343] Imported Upstream version 0.27.1+dfsg1 * [e550fac] Refresh patches. * [03913ad] Apply cme fix dpkg-copytight. sumo (0.26.0+dfsg1-1) unstable; urgency=medium . * [08a309b] Refresh patches. * [e9c4564] Minor fixes in d/rules. * [5bdf3b9] Remove pycache-files. * [dbf9954] Set Standards-Version to 3.9.8. No changes. * [933fda6] Remove dpkg-dev from build-depends. * [4218818] Update d/copyright. * [d7c2d92] Update autopkgtest. * [a3f3e74] Fix unit-test * [98423f7] Imported Upstream version 0.26.0+dfsg1 sumo (0.25.0+dfsg1-3) unstable; urgency=medium . [ Anton Gladky ] * [584dfb1] Apply cme fix dpkg. * [80de93e] Update sumo-doc dependency. . [ Santiago Vila ] * [cf767d8] Force Makefile check for errors. (Closes: #817033) * [5f3f351] Add python-matplotlib to the BD-Indep. sumo (0.25.0+dfsg1-2) unstable; urgency=medium . * [e0c661b] Add marouter and netedit to usr/bin. Thanks to Jakob Erdmann sumo (0.25.0+dfsg1-1) unstable; urgency=medium . * [c4a28a0] Imported Upstream version 0.25.0+dfsg1. (Closes: #802470) * [cf1cc2a] Refresh patches. * [f37c4fd] Refresh d/rules. * [566cd3b] Apply cme fix dpkg. * [8c9ea7f] Drop menu-file. * [05ad9d7] Add proper python-dependencies. * [21a0ed4] Update d/copyright. * [5e839de] Use system packaged OpenLayers.js. sumo (0.23.0+dfsg1-2) unstable; urgency=medium . * Move package from experimental to unstable sumo (0.23.0+dfsg1-2~exp1) experimental; urgency=medium . * [de8037f] Drop msse2 buildfpags, unsupported by some platforms sumo (0.23.0+dfsg1-1~exp1) experimental; urgency=medium . * [aad3ecb] Update d/copyright. * [f68572e] Imported Upstream version 0.23.0+dfsg1 * [006ec0e] Refresh patches. * [d6fdb64] Apply cme fix for d/control. * [51222ad] Update d/copyright. sumo (0.22.0+dfsg-1~exp1) experimental; urgency=medium . * [08bef65] Add Files-Excluded to d/copyright. * [01c89e5] Imported Upstream version 0.22.0+dfsg * [f73a708] Remove gl2ps from d/copyright. * [785774f] Refresh patches. * [b196497] Set Standards-Version: 3.9.6. No changes. * [923a4d9] Update homepage. * [34a84c3] Move d/upstream to d/upstream/metadata. Update it. * [b0c3f64] Fix lintian warnings in d/copyright. sumo (0.21.0+dfsg-1) unstable; urgency=medium . * [d7097c6] Imported Upstream version 0.21.0+dfsg * [655607d] Refresh patches. * [04454ca] Add autopkgtest. sumo (0.20.0+dfsg-1) unstable; urgency=medium . * [83c56d0] Remove debian/README.source * [fd5408c] Imported Upstream version 0.20.0+dfsg * [0c91c63] Refresh patches. sumo (0.19.0+dfsg-2) unstable; urgency=medium . * [b7da9b1] Replace libxerces-c2-dev by libxerces-c-dev. (Closes: #732217) sumo (0.19.0+dfsg-1) unstable; urgency=low . * [24595ef] Imported Upstream version 0.19.0+dfsg * [a2ba852] Refresh patch. * [0dc4baf] Set Standards-Version: 3.9.5. No changes. sumo (0.18.0+repack+dfsg-1) unstable; urgency=high . * [4da44c5] Add script, which removes *.jar files. (Closes: #728777) * [7870538] Imported Upstream version 0.18.0+repack+dfsg * [401d451] Enable eulerspiral, as it was relicensed under LGPL. sumo (0.18~dfsg-1) unstable; urgency=low . * [3a366bf] Use hardening=+all parameter on all archs except mips. * [d014241] Update homepage. * [23e6778] Imported Upstream version 0.18~dfsg * [5b43e89] Refresh patches. * [b27582b] Minor fix in debian/rules. * [6b5053e] Change section for sumo-tools package from "doc" to "science". (Closes: #717393) sumo (0.17.1~dfsg-6) unstable; urgency=low . * [0f04b59] Use autotools-dev again on all platforms. sumo (0.17.1~dfsg-5) unstable; urgency=low . * [bff2b7d] Do not use autoreconf on mips. sumo (0.17.1~dfsg-4) unstable; urgency=low . * [3a52bc9] Add freeglut3-dev to BD to fix FTBFS on mips*. * [2d47a7a] Add keyword-entry into desktop-file. sumo (0.17.1~dfsg-3) unstable; urgency=low . * [f7f8e0d] Use autoreconf. sumo (0.17.1~dfsg-2) unstable; urgency=low . [ Daniel T Chen ] * [1ff46ca] Added missing libs to link, fixing FTBFS. . [ Julian Taylor ] * [5961f4c] Fix FTBFS with ld --no-add-needed. (Closes: #710373) . [ Anton Gladky ] * [ec4054e] Use canonical VCS-field. * [ec9218d] Update fix_scripts_headers.patch. * [431de9e] Do not install .gitignore file. * [c45ac64] Add autotools-dev to BD. * [891e775] Update fix_headers-patch. * [ff138d5] Use wrap-and-sort. sumo (0.17.1~dfsg-1) unstable; urgency=low . * [1a2a17f] Imported Upstream version 0.17.1~dfsg * [1543af7] Remove obsolete DM-Upload-Allowed flag. * [f4521cb] Minor update in copyright file. * [74e45db] Bumper Standards-Version 3.9.4 (no changes). * [d29e6e2] Refresh patches. sumo (0.16.0~dfsg-1~exp1) experimental; urgency=low . * [771d69c] Imported Upstream version 0.16.0~dfsg * [5da3835] Update/remove patches. * [caa9ffa] Rename netgensumo to netgenerate (upstream decision). sumo (0.15.0~dfsg-3) unstable; urgency=low * [6ae8190] Use compat level 9. Apply hardening of buildflags. * [daa56b5] Remove from compilation embedded copy of gl2ps, use packaged version instead. * [8c08de0] Add upstream file sumo (0.15.0~dfsg-2) unstable; urgency=low * [5813a09] Update fix_headers_of_scripts.patch. * [956cf12] Replace /usr/bin/netgen binary on /usr/bin/netgensumo. (Closes: #673931) sumo (0.15.0~dfsg-1) unstable; urgency=low * Initial packaging in Debian. (Closes: #669160) zope.testrunner (8.1-1) unstable; urgency=medium . * New upstream release: - Remove run-time dependency on setuptools (closes: #1084020).