Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3650d9fb6b2c422d62db1c10c4bfffe425e5f36 https://github.com/galaxyproject/galaxy/commit/c3650d9fb6b2c422d62db1c10c4bf... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst Log Message: ----------- add initial release notes Commit: 1fe0f2f76b67bbb034af48e0ee963da4dd176284 https://github.com/galaxyproject/galaxy/commit/1fe0f2f76b67bbb034af48e0ee963... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- bring in @nsoranzo's comments Commit: 47863ff13444b1596e12fb4903229717593bdea4 https://github.com/galaxyproject/galaxy/commit/47863ff13444b1596e12fb4903229... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/_thanks.rst Log Message: ----------- more work towards reasonable release notes Commit: 21525ee25ef2b7b49733d845affe6fd9ede5b7b2 https://github.com/galaxyproject/galaxy/commit/21525ee25ef2b7b49733d845affe6... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- clarify fastq compression handling Commit: e0d2f6dbc8b8bc5d96855cc74bf62fa56c731fd6 https://github.com/galaxyproject/galaxy/commit/e0d2f6dbc8b8bc5d96855cc74bf62... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- clarify how to prevent unpacking of archives Commit: 2d2e7ddc958f9908fa72caca540c333929e8b517 https://github.com/galaxyproject/galaxy/commit/2d2e7ddc958f9908fa72caca540c3... Author: John Chilton <jmchilton@gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Don't encourage uploads of fastq in release notes. My understanding is nearly all data now produced is fastqsanger. Commit: 32e624195b827b1e3ba607337c1b87067651b0c2 https://github.com/galaxyproject/galaxy/commit/32e624195b827b1e3ba607337c1b8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst Log Message: ----------- Add all PRs and authors for compressed fastq support Commit: 76076dfeff8de4eb9509e60563a6cc905d2b5b22 https://github.com/galaxyproject/galaxy/commit/76076dfeff8de4eb9509e60563a6c... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- remove jmchilton from credits the Galaxy-lab members are explicitly omitted from RN mentions Commit: 9217889d2e23d339665a95a06d97112a28e91b2b https://github.com/galaxyproject/galaxy/commit/9217889d2e23d339665a95a06d971... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Add ashvark to author list Commit: 2f0a635e9f270007ec1da64b7ed054ff47cbb35e https://github.com/galaxyproject/galaxy/commit/2f0a635e9f270007ec1da64b7ed05... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- Various improvements to the release notes. - Rewording things to focus on reader concerns. - Grouping things into single bullets (like testing stuff) and close to similar topics (like Conda stuff). - Eliminated some things which should have been marked #minor Commit: e3f50e90f8ab9e8313d077da2961a81bafb7c90a https://github.com/galaxyproject/galaxy/commit/e3f50e90f8ab9e8313d077da2961a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst Log Message: ----------- More work on 17.01 release notes. Commit: f985b613ea1002a6595e073dfb459880ad7fdfdf https://github.com/galaxyproject/galaxy/commit/f985b613ea1002a6595e073dfb459... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix new history naming for batchmode workflow runs Commit: 639e2e5b2c4631901450a58710acbee373b498d8 https://github.com/galaxyproject/galaxy/commit/639e2e5b2c4631901450a58710acb... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- minor tweaks of RN Commit: 715e73adc97ea2c88639a50d1aaf88b9a1f3bcdc https://github.com/galaxyproject/galaxy/commit/715e73adc97ea2c88639a50d1aaf8... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- minor changes thanks to @nsoranzo Commit: 4df803a930c1546d41e4adeef9a0cc286cf6ada0 https://github.com/galaxyproject/galaxy/commit/4df803a930c1546d41e4adeef9a0c... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Merge pull request #3532 from guerler/fix_new_history_naming [16.10] Fix new history naming for batchmode workflow runs Commit: f9edf39f58b9942b461e5238c9df60ab5765faea https://github.com/galaxyproject/galaxy/commit/f9edf39f58b9942b461e5238c9df6... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Migrate galaxy_utils to a wheel. Alternative approach to #3542 which was not future proof with Conda dependencies. I think this should be now. xref #3364 #2994 http://dev.list.galaxyproject.org/Tools-using-Galaxy-s-Python-library-td4670... Rebased with fixes from @nsoranzo and @mvdbeek. Commit: 934bf6b056bc2475b217d62524e95de564c7a7a8 https://github.com/galaxyproject/galaxy/commit/934bf6b056bc2475b217d62524e95... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Ensure toolbox conf watcher updates cached hash when config change is detected Commit: b41b8e305bac3425b9bd20cda43936b23bd02abd https://github.com/galaxyproject/galaxy/commit/b41b8e305bac3425b9bd20cda4393... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3558 from natefoo/toolconf-watch-hash [16.10] Ensure toolbox conf watcher updates cached hash when config change is detected Commit: 43873b8a6de5a6f1669f8364fff54c206b5f2f84 https://github.com/galaxyproject/galaxy/commit/43873b8a6de5a6f1669f8364fff54... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3560 from galaxyproject/release_16.10 [17.01] Merge 16.10 into 17.01 Commit: 16a97e47c70f544d7acd30aac107a6687f01b736 https://github.com/galaxyproject/galaxy/commit/16a97e47c70f544d7acd30aac107a... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #3551 from jmchilton/galaxy_utils_external [17.01] Migrate galaxy_utils to a wheel. Commit: 9feb8b3f02038c5cadad858d4b4675467ec90616 https://github.com/galaxyproject/galaxy/commit/9feb8b3f02038c5cadad858d4b467... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst Log Message: ----------- Merge pull request #3497 from martenson/17.01_release_notes [17.01] add release notes Commit: 440c75fe589d3c92e6837bdd244490dc29003e45 https://github.com/galaxyproject/galaxy/commit/440c75fe589d3c92e6837bdd24449... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge branch 'release_17.01' into dev Commit: 6fc64f6f46f16efb45450cf4597d5e86dec865b5 https://github.com/galaxyproject/galaxy/commit/6fc64f6f46f16efb45450cf4597d5... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #3565 from dannon/merge_1701_dev Merge 1701 to dev Compare: https://github.com/galaxyproject/galaxy/compare/ed98b1b75aac...6fc64f6f46f1