astropy (7.0.0-1) unstable; urgency=medium . * New upstream version 7.0.0 * Rediff patches * Drop Mark-two-future-test-as-remote_data.patch: fixed upstream * Make some more tests xfail that sometimes fail under mips64el * Mark one test as xfail that sometimes fails on i386 (Closes: #1087612) astropy (7.0.0~rc1-1) experimental; urgency=medium . * New upstream release candidate 7.0.0~rc1. Switch to experimental. * Rediff patches * Skip system_info doctest that fails during build * Mark three future test as remote_data cwltest (2.5.20240906231108-1) unstable; urgency=medium . * New upstream version cwltest (2.5.20240714110256-1) unstable; urgency=medium . * New upstream version cwltest (2.5.20240425111257-1) unstable; urgency=medium . * d/control: build-dep on setuptools-scm to set the version correctly. * d/{rules,control,manpages}: use help2man to generate a manual page * New upstream version cwltest (2.5.20240304113812-1) unstable; urgency=medium . * New upstream version cwltest (2.4.20240129145612-1) unstable; urgency=medium . * New upstream version cwltest (2.4.20231222081524-1) unstable; urgency=medium . * New upstream version cwltest (2.3.20230825125225-1) unstable; urgency=medium . * New upstream version * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * remove patch, it was applied upstream. cwltest (2.3.20230607140609-1) experimental; urgency=medium . * Initial release. (Closes: #1037201) elpa-snakemake (2.0.0+git20231210.4ad41da-3) unstable; urgency=medium . * Team upload. * Rebuild against dh-elpa 2.1.5. Upload pushed to dgit-repos but not salsa. See . elpa-snakemake (2.0.0+git20231210.4ad41da-2) unstable; urgency=medium . * Team upload. * Rebuild against dh-elpa 2.1.3. Upload pushed to dgit-repos but not salsa. See . elpa-snakemake (2.0.0+git20231210.4ad41da-1) unstable; urgency=medium . [ Xiyue Deng ] * Team upload * Sync to latest upstream snapshot (4ad41da) (Closes: #1068956) * Disable autopkgtest as the ERT tests require a writable $HOME * Modernize d/watch with substitute strings to be more robust * Add a version header in snakemake.el to workaround dh-elpa upstream version handling limitation * d/control: Trim trailing whitespace * Set upstream metadata fields: Repository * Update standards version to 4.7.0, no changes needed elpa-snakemake (2.0.0-3) unstable; urgency=medium . * Add emacs-el >= 1:28 | elpa-transient Dependency to elpa-snakemake (Closes: #1024648) * Add elpa-snakemake-mode dependency to elpa-snakemake (Closes: #1025876) elpa-snakemake (2.0.0-2) unstable; urgency=medium . * Rebuild to create source only uploade elpa-snakemake (2.0.0-1) unstable; urgency=medium . * Initial release. (Closes: #1016769) kallisto (0.48.0+dfsg-4) unstable; urgency=medium . [ Vagrant Cascadian ] * Remove quant_out/run_info.json to enable reproducible-builds Closes: #1004053 kallisto (0.48.0+dfsg-3) unstable; urgency=medium . * Packaging update * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) kallisto (0.48.0+dfsg-2) unstable; urgency=medium . * Team upload. * Preventing volatile test outputs from appearing in kallisto-examples binary package (Closes: #1004053). Thanks Vagrant Cascadian. * Limiting kallisto builds to 64bit architectures as 32bit are not supported. kallisto (0.48.0+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version 0.48.0+dfsg * Enabling function and snakemake tests. * Bumping copyright years. * Refreshing patches, disabling Check_busOptions.seq_length_before_accessing.patch (integrated upstream). kallisto (0.46.2+dfsg-3) unstable; urgency=medium . * Team Upload. * debian/patches/gcc11.patch: Fix gcc-11 FTBFS (Closes: #984073) kallisto (0.46.2+dfsg-2) unstable; urgency=medium . * Team upload * Patch to avoid segfault (Closes: #960368) kallisto (0.46.2+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.5.0 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright). kallisto (0.46.1+dfsg-2) unstable; urgency=medium . * Team upload. * mark kallisto-examples as Multi-Arch: foreign * debian/patches/spelling: fix typo * debian/patches/htslib1.3: use kseq.h from htslib, not the bundled version kallisto (0.46.1+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version kallisto (0.46.0+dfsg-1) unstable; urgency=medium . * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.0 kallisto (0.45.1+dfsg-1) unstable; urgency=medium . * Initial release (Closes: #925417) numexpr (2.10.2-1) unstable; urgency=medium . * New upstream release. * Standards version bumped to 4.7.0, no changes. * debian/patches: - Drop 0002-Fix-test_max_threads_unset.patch, applied upstream. pizzly (0.37.3+ds-9) unstable; urgency=medium . * Team upload. * Really fix watch file pizzly (0.37.3+ds-8) unstable; urgency=medium . * Team upload. * Fix watch file pizzly (0.37.3+ds-7) unstable; urgency=medium . * Team upload * Add a build-dependency on kallisto to avoid building on architectures where pizzly will not be installable * Bump Standards-Version to 4.6.1, no changes pizzly (0.37.3+ds-6) unstable; urgency=medium . * Team upload. . [ Steffen Moeller ] * Fix watchfile to detect new versions on github (routine-update) . [ Andreas Tille ] * Standards-Version: 4.6.0 (routine-update) * Avoid explicitly specifying -Wl,--as-needed linker flag. * Lintian-overrides: - drop unused override - add script-with-language extension * DEP3 pizzly (0.37.3+ds-5) unstable; urgency=medium . * Regression in i386, run on arm64 instead pizzly (0.37.3+ds-4) unstable; urgency=medium . * Tests for pizzly does not run properly on 32-bit arches pizzly (0.37.3+ds-3) unstable; urgency=medium . [ Andreas Tille ] * Debian Med team as maintainer * debhelper-compat 12 * Set upstream metadata fields: Bug-Database, Bug-Submit. * debian/control: reformatting using `cme fix dpkg-control` * Simplify watch file * Fix Vcs fields . [ Nilesh Patra ] * Add autopkgtest * Add myself to uploaders * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Enhance metadata pizzly (0.37.3+ds-2) unstable; urgency=medium . * Reacted to 2nd iteration of FTP masters' comments and extended copyright info for files imported from Ensembl (Closes: #929939) * Bumped standard to 4.5.0 rust-debian-changelog (0.2.0-2) unstable; urgency=high . * Team upload * Package debian-changelog 0.2.0 from crates.io using debcargo 2.7.0 * Build using rust-rowan 0.16 rust-debian-control (0.1.39-1) unstable; urgency=medium . * Package debian-control 0.1.39 from crates.io using debcargo 2.7.4 rust-debian-watch (0.2.8-1) unstable; urgency=medium . * Package debian-watch 0.2.8 from crates.io using debcargo 2.7.2 rust-makefile-lossless (0.1.6-1) unstable; urgency=medium . * Package makefile-lossless 0.1.6 from crates.io using debcargo 2.7.2 rust-rowan (0.16.0-1) unstable; urgency=medium . * Package rowan 0.16.0 from crates.io using debcargo 2.7.4 trinityrnaseq (2.15.2+dfsg-1) unstable; urgency=medium . * New upstream version * Delete patch R_4.2_fix, it was applied upstream. trinityrnaseq (2.15.1+dfsg-5) unstable; urgency=medium . * Team upload. * Add support for loong64 Closes: #1059072 trinityrnaseq (2.15.1+dfsg-4) unstable; urgency=medium . * d/control: also restrict architectures for the -examples binary package. trinityrnaseq (2.15.1+dfsg-3) unstable; urgency=medium . * d/control: tighten architecture list to those with necessary dependencies. trinityrnaseq (2.15.1+dfsg-2) unstable; urgency=medium . * d/control: move many deps of the binary package to recommends/suggests. As not all deps are needed for all usages, this enables usage on architectures where some deps are not available. trinityrnaseq (2.15.1+dfsg-1) unstable; urgency=medium . [ Michael R. Crusoe ] * d/watch: update for GitHub API breakage . [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) . [ Michael R. Crusoe ] * d/control: update homepage * d/control: remove unused test-deps * d/source/lintian-overrides: note that we clean up the config.{log,status} automatically. * d/patches/R_4.2_fix: fix for R 4.2.x+. Closes: #1006336, #1004773 trinityrnaseq (2.13.2+dfsg-3) unstable; urgency=medium . * Team upload * Applying a new patch to build against newest libjung-free-java, adding a versioned dependency trinityrnaseq (2.13.2+dfsg-2) unstable; urgency=medium . * debian/javabuild: updated to correct path to the Butterfly source * debian/copyright: Now that the Butterfly source is back in the upstream tarball, adjust the paths accordingly here as well. * debian/patches: forwarded many patches upstream trinityrnaseq (2.13.2+dfsg-1) unstable; urgency=medium . * New upstream version * watch file standard 4 (routine-update) * Freshen patches * debian/tests/control: dep on libpicard-java * debian/rules: adjust cmake invocation * new patch: debian/patches/which_command_v to use 'command -v' instead of which * New upstream version * Standards-Version: 4.6.0 (routine-update) * Refresh patches trinityrnaseq (2.11.0+dfsg-6) unstable; urgency=medium . * fix typo in debian/test/control. trinityrnaseq (2.11.0+dfsg-5) unstable; urgency=medium . * Add r-bioc-dexseq to the deps for the trinityrnaseq binary package. * Standards-Version: 4.5.1 (routine-update) trinityrnaseq (2.11.0+dfsg-4) unstable; urgency=medium . * Add patch to remove m64 flag. Hopefully helps arm64 to compile. trinityrnaseq (2.11.0+dfsg-3) unstable; urgency=medium . * debian/tests/control: adjust so that the tests don't have to pass on archs where we don't build trinityrnaseq (2.11.0+dfsg-2) unstable; urgency=medium . * debian/patches/STAR_genomeSAindexNbases: Attempt to fix the DTU STAR test error * debian/patches/skip_DTU_STAR_test: skip the test until a better fix is found trinityrnaseq (2.11.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Fix gcc-10 build issue Closes: #966876 * debhelper-compat 13 (routine-update) * Review Files-Excluded for moved and removed files as well as new binary *.jars * Remove redundant debian/gbp.conf * Remove __pycache__ from installed package . [ Michael R. Crusoe ] * Correct location of bamsifter installation * debian/patches/fix_system_paths: fix expected path for ParaFly * debian/patches/update-paths: fix paths to Butterfly.jar * Enable more features and tests with r-cran-{argparse,dexseq} & tabix trinityrnaseq (2.10.0+dfsg-1) unstable; urgency=medium . * Eliminate warning about missing hardening flags * New upstream version * debhelper-compat 12 * debian/control: Added python3-htseq, rna-star, picard-tools, gmap, histat2, subread, kallisto, r-bioc-{edger,deseq2,rots,ctc,biobase,qvalue,goseq,tximport,dexseq,glimma}, r-cran-{ape,fastcluster,gplots,argparse,goplot,readr,tidyverse}, liburi-perl deps, and python3-hisat2 * Standards-Version: 4.5.0 (routine-update) * Refresh patches * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Use secure URI in Homepage field. * debian/rules: seqtk-trinity now has a unversioned path * debian/patches/butterfly: restore missing Butterfly sources * debian/patches/submake: use $(MAKE) consistently * Install the new bamsfilter plugin * Install trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl * Install trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py * Install PyLib/Pipeliner.py * Set PICARD_HOME default of /usr/share/java * Skip tests that require GATK4 until it gets packaged * Skip tests that require r-bioc-tximportdata * Skip the remaining tests waiting for new packages * debian/tests/runtests: s/ADTTMP/AUTOPKGTEST_TMP/g * Remove trailing whitespace in debian/changelog (routine-update) * debian/upstream/metadata: add Repository{,-Browse}, Bug-{Database,Submit} trinityrnaseq (2.6.6+dfsg-6) unstable; urgency=medium . * -examples: Don't hardcode number of --CPU (especially above 2). Fixes the autopkgtests when the number of CPUs/cores is less than 4 and blastn's intransigency to accept a larger value to -num_threads. trinityrnaseq (2.6.6+dfsg-5) unstable; urgency=medium . * Added missing dependency on ncbi-blast+ to the binary package. trinityrnaseq (2.6.6+dfsg-4) unstable; urgency=medium . * Default to Python 3, as needed. * Use better Java version check from upstream trinityrnaseq (2.6.6+dfsg-3) unstable; urgency=medium . * debian/control: add numpy dependency, required for Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py trinityrnaseq (2.6.6+dfsg-2) unstable; urgency=medium . * debian/trinityrnaseq.install: Add BubbleUpClustering binary trinityrnaseq (2.6.6+dfsg-1) unstable; urgency=medium . * Team upload. . [ Michael R. Crusoe ] * New upstream release, now with the sample data returned Closes: #897877 * Build and ship seqtk-trinity . [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Secure URI in copyright format * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target * Remove trailing whitespace in debian/changelog * Remove trailing whitespace in debian/copyright * Fix permissions and Perl interpreter path trinityrnaseq (2.5.1+dfsg-2) unstable; urgency=medium . * Team upload. . [ Aurelien Jarno ] * Build with glibc 2.27 (fix for cannot find -lieee) trinityrnaseq (2.5.1+dfsg-1) unstable; urgency=medium . * New upstream release. Updated watch file. * NeedlemanWunschGotohBanded.java moved into trinityrnasq_jaligner package * Much of the sample data is missing from upstream's tarball, so some tests have been turned off trinityrnaseq (2.2.0+dfsg-4) unstable; urgency=medium . [ Steffen Moeller ] * debian/upstream/metadata - Completed references to registries - yamllint clean * debian/copyright - Corrected upstream-name to 'Trinity' . [ Michael R. Crusoe ] * Removed unneeded dependency on r-bioc-edger trinityrnaseq (2.2.0+dfsg-3) unstable; urgency=medium . * Team upload . [ Gert Wollny ] * Fix build gcc 7 Closes: #853687 . [ Andreas Tille ] * debhelper 10 Closes: #865262 * Standards-Version: 4.1.0 (no changes needed) * hardening=+all * remove unused lintian override * Build-Depends: bowtie2, yellyfish Closes: #860645 trinityrnaseq (2.2.0+dfsg-2) unstable; urgency=medium . * Team upload. * Fix build on GCC 6 (Closes: #831110) trinityrnaseq (2.2.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Team upload * d/watch: Use xz compression for upstream source . [ Michael R. Crusoe ] * new upstream version * prune d/copyright excludes * refresh patches, drop a few included upstream * Standards-Version: '3.9.7' -> '3.9.8' trinityrnaseq (2.1.1+dfsg2-1) unstable; urgency=low . * Properly harden Chrysalis binaries * Drop Galaxy plugin * Increment dfsg version for the above trinityrnaseq (2.1.1+dfsg-2) unstable; urgency=medium . * Split install of arch-dependent & arch-independent files, fixes FTBFS (Closes: #813958) trinityrnaseq (2.1.1+dfsg-1) unstable; urgency=low . * Initial release (Closes: #777697) REMOVED: prime-phylo 1.0.11-12 REMOVED: yarsync 0.2.1-3 REMOVED: kmetronome 1.4.0-1 REMOVED: python-pydub 0.25.1-1 REMOVED: vmpk 0.9.0-1 REMOVED: rust-debian-analyzer 0.158.8-1 REMOVED: trac-customfieldadmin 0.4.0+svn18456-2 REMOVED: sdml 0.3.1+20241014-3 REMOVED: pwdsphinx 1.0.19-1 REMOVED: pandoc-filter-diagram 0.2.1-5 REMOVED: spyder-line-profiler 0.3.2-2 REMOVED: digikam 4:8.4.0-3 REMOVED: python-wsgilog 0.3.1-4 REMOVED: libregf 20201007-2.1 REMOVED: trac-wysiwyg 0.12.0.7+svn18546-2 REMOVED: todoman 4.4.0-1 REMOVED: libdrumstick 2.9.0-1.1 REMOVED: stopt 5.12+dfsg-2