galaxy-commits February 2019

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[galaxyproject/galaxy] ae8bf6: Release notes raw.
by Martin Cech 20 Feb '19

20 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: ae8bf6f793edda9211b59c68d6c029b9fa74154a https://github.com/galaxyproject/galaxy/commit/ae8bf6f793edda9211b59c68d6c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst Log Message: ----------- Release notes raw. Commit: b5713ca170cfeb574063a2ec9dca8adbee1f7d74 https://github.com/galaxyproject/galaxy/commit/b5713ca170cfeb574063a2ec9dca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst M doc/source/releases/index.rst Log Message: ----------- Progress on 19.01 release notes... Commit: 16af73423f2c5a1181b016dcc01955c1c2ab037a https://github.com/galaxyproject/galaxy/commit/16af73423f2c5a1181b016dcc019… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- Update doc/source/releases/19.01.rst Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: 072b8d73eca68201bcf691c7dc9fa22272433ac3 https://github.com/galaxyproject/galaxy/commit/072b8d73eca68201bcf691c7dc9f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- Update doc/source/releases/19.01.rst Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: 2a3555d9d73e4a9f72b003a319698f7e8fb01d3c https://github.com/galaxyproject/galaxy/commit/2a3555d9d73e4a9f72b003a31969… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst Log Message: ----------- Better Singularity summary thanks to @mvdbeek. Commit: 94bcb8d00f3fc8817cdca5ef3ab383e705b950d6 https://github.com/galaxyproject/galaxy/commit/94bcb8d00f3fc8817cdca5ef3ab3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- More fixes to 19.01 release notes. Commit: ca4acf78df6cfc89f76b0f09143d0301aac234b4 https://github.com/galaxyproject/galaxy/commit/ca4acf78df6cfc89f76b0f09143d… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01_announce.rst Log Message: ----------- Sort PR numbers Small fixes. Commit: 37a93972d59459ffd50d340d53c5f278b3e15dae https://github.com/galaxyproject/galaxy/commit/37a93972d59459ffd50d340d53c5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- Fix PR link Commit: 015ce5cedc21c1a318d6455534f52f8acc3d36ca https://github.com/galaxyproject/galaxy/commit/015ce5cedc21c1a318d6455534f5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #7308 from jmchilton/19.01_release_notes [19.01] Release notes for 19.01. Compare: https://github.com/galaxyproject/galaxy/compare/ac9b300df66b...015ce5cedc21

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[galaxyproject/galaxy] 57af07: Update application documentation
by Martin Cech 20 Feb '19

20 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 57af0738139db28939d83f1ae76b981eeb77b530 https://github.com/galaxyproject/galaxy/commit/57af0738139db28939d83f1ae76b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M doc/source/api/guidelines.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.managers.rst A doc/source/lib/galaxy.metadata.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.verify.asserts.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst Log Message: ----------- Update application documentation with: ``` make -C doc/ updaterst ``` Also fix 2 links in `doc/source/api/guidelines.rst` . Commit: 3c3d36c62b445daaa30ea6448b45184583c0b89f https://github.com/galaxyproject/galaxy/commit/3c3d36c62b445daaa30ea6448b45… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M doc/source/api/guidelines.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.managers.rst A doc/source/lib/galaxy.metadata.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.verify.asserts.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst Log Message: ----------- Merge pull request #7391 from nsoranzo/api_doc_update Update application documentation Compare: https://github.com/galaxyproject/galaxy/compare/394ce04c37ba...3c3d36c62b44

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[galaxyproject/galaxy] 203353: Fix HDF5 test assert docs
by Nicola Soranzo 20 Feb '19

20 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 203353597671ec7c3daa02791705ebb921fb28ad https://github.com/galaxyproject/galaxy/commit/203353597671ec7c3daa02791705… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix HDF5 test assert docs Alternative to https://github.com/galaxyproject/galaxy/pull/7382, fix documentation without giving up better validation one gets with actual types for assertion XML elements. Commit: 7abd448cbe64e64758e476d0e78921288663abd4 https://github.com/galaxyproject/galaxy/commit/7abd448cbe64e64758e476d0e789… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/anvio.py Log Message: ----------- Add datatypes for Anvi'o Commit: 948cdb251a500a41b8b6c81891868e0b0bbec070 https://github.com/galaxyproject/galaxy/commit/948cdb251a500a41b8b6c8189186… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/datatypes/anvio.py Log Message: ----------- cleanup anvio.py Commit: cf31e330e8575ccc6635dfd1c9c2c1cc95454e1f https://github.com/galaxyproject/galaxy/commit/cf31e330e8575ccc6635dfd1c9c2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/datatypes/anvio.py Log Message: ----------- Decrease readability. Commit: 51280fbf7d345deb6d2cc0aefd4f0bbe598a92c1 https://github.com/galaxyproject/galaxy/commit/51280fbf7d345deb6d2cc0aefd4f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/datatypes/anvio.py Log Message: ----------- flip a line Commit: 737bae8f9b920ec9bed43a2d25378b19ace12f58 https://github.com/galaxyproject/galaxy/commit/737bae8f9b920ec9bed43a2d2537… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Reword HDF5 attribute test docs Commit: 35529a05fb9210bd2f7fce3f91418cdf95cebb2f https://github.com/galaxyproject/galaxy/commit/35529a05fb9210bd2f7fce3f9141… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #7384 from jmchilton/fix_h5_assertion_docs [19.01] Fix HDF5 test assert docs Commit: ac9b300df66bc696a7e2c3a2093ded02222ac1e4 https://github.com/galaxyproject/galaxy/commit/ac9b300df66bc696a7e2c3a2093d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/anvio.py Log Message: ----------- Merge pull request #7385 from blankenberg/19.01-anvio-datatypes [19.01] Add datatypes for Anvi'o Commit: 394ce04c37baf1f6d912c9a78eb8740474fb0b89 https://github.com/galaxyproject/galaxy/commit/394ce04c37baf1f6d912c9a78eb8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M doc/parse_gx_xsd.py A lib/galaxy/datatypes/anvio.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b8a98687a9ef...394ce04c37ba

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[galaxyproject/galaxy] a22142: Use mysqlclient instead of mysql-python as conditi...
by Marius van den Beek 20 Feb '19

20 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a22142437df527342d72cde51f2f79c667fe0da4 https://github.com/galaxyproject/galaxy/commit/a22142437df527342d72cde51f2f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Use mysqlclient instead of mysql-python as conditional dependency MySQL-python is legacy and unmaintained. xref. https://github.com/galaxyproject/starforge-recipes/issues/22 Commit: c6f1183939cf8b9897357e4506bfc6d438067f36 https://github.com/galaxyproject/galaxy/commit/c6f1183939cf8b9897357e4506bf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M client/README.md M doc/source/admin/framework_dependencies.rst M scripts/common_startup.sh Log Message: ----------- Update documentation about dependencies Commit: b84c61a12a4e6c2aac6c223d668dae4a722cbf60 https://github.com/galaxyproject/galaxy/commit/b84c61a12a4e6c2aac6c223d668d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Remove pin on Sphinx. Update all dependencies with `make update-dependencies` using pipenv 2018.11.26 . Important updates: - Cheetah3 3.2.0 has now x86_64 wheels on PyPI - `sphinx-rtd-theme` 0.4.3 has integrated Google Analytics support that we can use for the docs website - Fix environment markers for `configparser`, `functools32` and `more-itertools` Commit: b8a98687a9efefadb1606537ee3797c8cec54a9a https://github.com/galaxyproject/galaxy/commit/b8a98687a9efefadb1606537ee37… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M client/README.md M doc/source/admin/framework_dependencies.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #7365 from nsoranzo/update_deps Remove pin on Sphinx. Update all dependencies Compare: https://github.com/galaxyproject/galaxy/compare/ff962b158425...b8a98687a9ef

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[galaxyproject/galaxy]
by Nicola Soranzo 20 Feb '19

20 Feb '19

Branch: refs/heads/afgane-patch-1 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 000ba8: Fix link doc syntax
by Nicola Soranzo 20 Feb '19

20 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 000ba82895bb6d0309575cabd15d6ed245343e97 https://github.com/galaxyproject/galaxy/commit/000ba82895bb6d0309575cabd15d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Fix link doc syntax Commit: ff962b158425e297681fb1c1418b687c38826473 https://github.com/galaxyproject/galaxy/commit/ff962b158425e297681fb1c1418b… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #7388 from galaxyproject/afgane-patch-1 Fix link doc syntax Compare: https://github.com/galaxyproject/galaxy/compare/f3d711c13bf0...ff962b158425

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[galaxyproject/galaxy] 000ba8: Fix link doc syntax
by Enis Afgan 20 Feb '19

20 Feb '19

Branch: refs/heads/afgane-patch-1 Home: https://github.com/galaxyproject/galaxy Commit: 000ba82895bb6d0309575cabd15d6ed245343e97 https://github.com/galaxyproject/galaxy/commit/000ba82895bb6d0309575cabd15d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Fix link doc syntax

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[galaxyproject/galaxy] e9aba7: Restore gray scale difference between panel vs por...
by Dannon 19 Feb '19

19 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9aba7b260d9ae6a7e434adece9d1c306f922ab7 https://github.com/galaxyproject/galaxy/commit/e9aba7b260d9ae6a7e434adece9d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Restore gray scale difference between panel vs portlet background color for contrast Commit: f3d711c13bf05f08c04119d9468f6dd1dd198af0 https://github.com/galaxyproject/galaxy/commit/f3d711c13bf05f08c04119d9468f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Merge pull request #7387 from guerler/use_brighter_backgrounds Restore gray scale difference between panel vs portlet background color for contrast Compare: https://github.com/galaxyproject/galaxy/compare/6b1b71425c68...f3d711c13bf0

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[galaxyproject/usegalaxy-playbook] 265c13: Install wrapper version 1.16.5 for cutadapt on test.
by Dave B. 19 Feb '19

19 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 265c1367122d918669a3fc70195b1dfbf0ab2c24 https://github.com/galaxyproject/usegalaxy-playbook/commit/265c1367122d9186… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Install wrapper version 1.16.5 for cutadapt on test.

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[galaxyproject/galaxy] 7abd44: Add datatypes for Anvi'o
by Martin Cech 19 Feb '19

19 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 7abd448cbe64e64758e476d0e78921288663abd4 https://github.com/galaxyproject/galaxy/commit/7abd448cbe64e64758e476d0e789… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/anvio.py Log Message: ----------- Add datatypes for Anvi'o Commit: 948cdb251a500a41b8b6c81891868e0b0bbec070 https://github.com/galaxyproject/galaxy/commit/948cdb251a500a41b8b6c8189186… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/datatypes/anvio.py Log Message: ----------- cleanup anvio.py Commit: cf31e330e8575ccc6635dfd1c9c2c1cc95454e1f https://github.com/galaxyproject/galaxy/commit/cf31e330e8575ccc6635dfd1c9c2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/datatypes/anvio.py Log Message: ----------- Decrease readability. Commit: 51280fbf7d345deb6d2cc0aefd4f0bbe598a92c1 https://github.com/galaxyproject/galaxy/commit/51280fbf7d345deb6d2cc0aefd4f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M lib/galaxy/datatypes/anvio.py Log Message: ----------- flip a line Commit: ac9b300df66bc696a7e2c3a2093ded02222ac1e4 https://github.com/galaxyproject/galaxy/commit/ac9b300df66bc696a7e2c3a2093d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/anvio.py Log Message: ----------- Merge pull request #7385 from blankenberg/19.01-anvio-datatypes [19.01] Add datatypes for Anvi'o Compare: https://github.com/galaxyproject/galaxy/compare/35529a05fb92...ac9b300df66b

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galaxy-commits February 2019