Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a10d2c51d3e29ceef17b056992f04f98b0f8472c https://github.com/galaxyproject/galaxy/commit/a10d2c51d3e29ceef17b056992f04... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Add/pin configurable node version to 18.09. Backport/tweak of https://github.com/galaxyproject/galaxy/pull/7220) Commit: 9f501bb2b0bfa5193cd908d5f43bdca9a4bc5a2d https://github.com/galaxyproject/galaxy/commit/9f501bb2b0bfa5193cd908d5f43bd... Author: Matt Chambers <matt.chambers42@gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar Log Message: ----------- Add datatypes and sniffers for several directory-based mass spectrometry formats: Bruker BAF, Agilent/Bruker YEP, Bruker TDF, Agilent MassHunter, and Waters MassLynx Commit: 68a66f462e007fdbcf8e966fc5cc1a7ea06a8527 https://github.com/galaxyproject/galaxy/commit/68a66f462e007fdbcf8e966fc5cc1... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- update h5py dependency Commit: d79514b823371c36c12dcbb6aef25a4490cd50ca https://github.com/galaxyproject/galaxy/commit/d79514b823371c36c12dcbb6aef25... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/__init__.py Log Message: ----------- allow assertions on binary inputs Commit: e37036af04ac34dd7c865f5f11ccaa0ee4e17e9a https://github.com/galaxyproject/galaxy/commit/e37036af04ac34dd7c865f5f11cca... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A lib/galaxy/tools/verify/asserts/hdf5.py Log Message: ----------- add hdf5 assert tests Commit: db2987b2b21fefad9feb2af0bd4f93b7d490361f https://github.com/galaxyproject/galaxy/commit/db2987b2b21fefad9feb2af0bd4f9... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A test/functional/tools/validation_hdf5.xml Log Message: ----------- add test tool for new assertions Commit: d4420b75662b7667d430f78be67b09e69037a77b https://github.com/galaxyproject/galaxy/commit/d4420b75662b7667d430f78be67b0... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- register new test tool Commit: a00fd508b758fc73aeb537ca98156fff1c7ac14d https://github.com/galaxyproject/galaxy/commit/a00fd508b758fc73aeb537ca98156... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- adopt XSD for new syntax Commit: cb13e56e6bd00a932e9594241fe043f845d4f815 https://github.com/galaxyproject/galaxy/commit/cb13e56e6bd00a932e9594241fe04... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A test-data/matrix.cool Log Message: ----------- add test-data for new hdf5 based tool test Commit: e9f40f2f95a611f0fab6d81bb225cf409b86f353 https://github.com/galaxyproject/galaxy/commit/e9f40f2f95a611f0fab6d81bb225c... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py Log Message: ----------- fix pep8 Commit: 2a97f726cc86d44610738d04755622e8e4b8342a https://github.com/galaxyproject/galaxy/commit/2a97f726cc86d44610738d0475562... Author: John Chilton <jmchilton@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- Tweaks to hdf5 testing. - This is in galaxy-lib so h5py import should probably be conditional. - Namespace very generic test functions a bit by adding h5 into the names. - Stricter validation of XSD (the other assertions don't have this but that is problematic on their part), I'm not sure if the docs will render unevenly now though - we may want to revisit that and do this for all the assertions. Commit: 3d4ff4fc372bc6b44b384af944b548915427fda4 https://github.com/galaxyproject/galaxy/commit/3d4ff4fc372bc6b44b384af944b54... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #41 from jmchilton/hdf5_tests Tweaks to hdf5 testing. Commit: 365ac400ae629b415b8ec11a364ec0e4465d1c7f https://github.com/galaxyproject/galaxy/commit/365ac400ae629b415b8ec11a364ec... Author: Matt Chambers <matt.chambers42@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix lint errors Commit: 413af14bb55d890ca053d08877cee98ab440008f https://github.com/galaxyproject/galaxy/commit/413af14bb55d890ca053d08877cee... Author: Matt Chambers <matt.chambers42@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix lint errors Commit: d30852b286b9baba5cf6faffa389db8ec2837114 https://github.com/galaxyproject/galaxy/commit/d30852b286b9baba5cf6faffa389d... Author: Matt Chambers <matt.chambers42@gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/some.wiff.tar Log Message: ----------- Add wiff.tar extension and sniffer Commit: 0a7583b6de024d02b7063fa3f59c7febe63df5f5 https://github.com/galaxyproject/galaxy/commit/0a7583b6de024d02b7063fa3f59c7... Author: Helena Rasche <hxr@hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- More contrast Commit: 87c82595771438b0e8244b32885430e4fe1bab6e https://github.com/galaxyproject/galaxy/commit/87c82595771438b0e8244b3288543... Author: Helena Rasche <hxr@hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Add box-shadow Commit: 12fde52494541d73da42a41d026c8a0217d7533c https://github.com/galaxyproject/galaxy/commit/12fde52494541d73da42a41d026c8... Author: Helena Rasche <hxr@hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- remove inaccurate comment Commit: dc303f004fc5254f6de14bc29084532d3db98912 https://github.com/galaxyproject/galaxy/commit/dc303f004fc5254f6de14bc290845... Author: Matt Chambers <matt.chambers42@gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Remove try/except in sniffers Add .d/.raw to file_ext Commit: d36cf51f6b63407fd96e49918fe6092d993275a9 https://github.com/galaxyproject/galaxy/commit/d36cf51f6b63407fd96e49918fe60... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- change "name" to "key" Commit: b59d76eb4a928af8866275cb91afd583a82fee99 https://github.com/galaxyproject/galaxy/commit/b59d76eb4a928af8866275cb91afd... Author: Helena Rasche <hxr@hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix emoji tags Commit: dd917099ba43b3d9638c16623ca45bc13edfc9c5 https://github.com/galaxyproject/galaxy/commit/dd917099ba43b3d9638c16623ca45... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Only block the single category of C characters that is problematic Co-Authored-By: erasche <hxr@hx42.org> Commit: e3f1234b2c1359e4d5353ba0e0b56834a964bb28 https://github.com/galaxyproject/galaxy/commit/e3f1234b2c1359e4d5353ba0e0b56... Author: Martin Cech <marten@bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #7310 from erasche/fix-emoji-tags [19.01] Fix emoji tags Commit: 23d4af5dafbb768ba61c6cf8849cd17087f31520 https://github.com/galaxyproject/galaxy/commit/23d4af5dafbb768ba61c6cf8849cd... Author: Helena Rasche <hxr@hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Revert "Add box-shadow" This reverts commit 87c82595771438b0e8244b32885430e4fe1bab6e. Commit: 8f7263a1dcce4a2d3e5c251e4253dece2998e61d https://github.com/galaxyproject/galaxy/commit/8f7263a1dcce4a2d3e5c251e4253d... Author: John Chilton <jmchilton@gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd A test-data/matrix.cool M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #7301 from bgruening/hdf5_tests Add new test syntax specific for HDF5 files Commit: f0026962219ebad2177f57ebee5ae9b837882e60 https://github.com/galaxyproject/galaxy/commit/f0026962219ebad2177f57ebee5ae... Author: Nate Coraor <nate@bx.psu.edu> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Merge pull request #7309 from erasche/more-contrast [19.01] More contrast in CSS Commit: f7322d85a317614de1a745da57d5e394b5eb8041 https://github.com/galaxyproject/galaxy/commit/f7322d85a317614de1a745da57d5e... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar A lib/galaxy/datatypes/test/some.wiff.tar Log Message: ----------- Merge pull request #7299 from chambm/feature/rawtar-datatypes Add datatypes and sniffers for tar archives of directory-based MS formats and WIFF/SCAN pairs Commit: 9c9c8a5d50d7c8ae68f34712d0e9b053aed33ea2 https://github.com/galaxyproject/galaxy/commit/9c9c8a5d50d7c8ae68f34712d0e9b... Author: Martin Cech <marten@bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7239 from dannon/node_ver_pin_18.09 [18.09] Add/pin configurable node version Commit: b33b06440ffdd7e58b6172315df1e015e4ac0e52 https://github.com/galaxyproject/galaxy/commit/b33b06440ffdd7e58b6172315df1e... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 21ce99e231af7eaa0c81e3fcc9dae1f857ab1e1c https://github.com/galaxyproject/galaxy/commit/21ce99e231af7eaa0c81e3fcc9dae... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar A lib/galaxy/datatypes/test/some.wiff.tar M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M scripts/common_startup.sh A test-data/matrix.cool M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge branch 'release_19.01' into dev Commit: 2f1a0cd2581ced221e8d4d9264cfe386642bdf73 https://github.com/galaxyproject/galaxy/commit/2f1a0cd2581ced221e8d4d9264cfe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Use brand-secondary for tool form titles in canvas (the workflow editor) Commit: 0e03aea084d05405a2b6c296877dc8513714e004 https://github.com/galaxyproject/galaxy/commit/0e03aea084d05405a2b6c296877dc... Author: Dannon <dannon.baker@gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar A lib/galaxy/datatypes/test/some.wiff.tar M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M scripts/common_startup.sh A test-data/matrix.cool M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #7350 from nsoranzo/merge_19.01 Merge 19.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/4b92f95e87b1...0e03aea084d0