- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 27a341: resolve missing closing div and three extra closin...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27a34151887a65bc24a44b33bf06280339f6e710 https://github.com/galaxyproject/galaxy/commit/27a34151887a65bc24a44b33bf06… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M templates/base/base_panels.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- resolve missing closing div and three extra closing divs with net of two extra closing divs this used to work Commit: 1f9894069c7424dd202fbaeb562f9d71a86564d7 https://github.com/galaxyproject/galaxy/commit/1f9894069c7424dd202fbaeb562f… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M templates/base/base_panels.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #6445 from martenson/mako-crazy fix TS: resolve missing closing div and three extra closing divs Compare: https://github.com/galaxyproject/galaxy/compare/82523528f2b9...1f9894069c74 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6654a8: Hack around #6299.
by GitHub 01 Jul '18

01 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 6654a837527797971b28fd2cbb092d7081c918b9 https://github.com/galaxyproject/galaxy/commit/6654a837527797971b28fd2cbb09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Hack around #6299. Commit: 39d7cf2eb73177532237ad38a8a75095d1be4428 https://github.com/galaxyproject/galaxy/commit/39d7cf2eb73177532237ad38a8a7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6433 from jmchilton/hack_6299 [18.05] decode potential encoded id Compare: https://github.com/galaxyproject/galaxy/compare/e0c269291a20...39d7cf2eb731 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a45b30: Fix panel drag resize.
by GitHub 01 Jul '18

01 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a45b30e97e5b680709d3f67f56d10c649da8f25c https://github.com/galaxyproject/galaxy/commit/a45b30e97e5b680709d3f67f56d1… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/scripts/layout/panel.js Log Message: ----------- Fix panel drag resize. The mouse position and dragging were out of sync, sometimes even resizing in the wrong direction (when dragging slowly). This switches from a relative calculation to an absolute one which solves the problem. Might have been events out of order or dropped. Commit: 82523528f2b90447df5c47cbfc54bf03f462961c https://github.com/galaxyproject/galaxy/commit/82523528f2b90447df5c47cbfc54… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/layout/panel.js Log Message: ----------- Merge pull request #6421 from jxtx/fix-panel-drag Fix panel drag resize. Compare: https://github.com/galaxyproject/galaxy/compare/fcdd1a42451f...82523528f2b9 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 41f25b: fix a few tool_deps test errors
by GitHub 01 Jul '18

01 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 41f25b928afbf849e94c3c3b5ca222253d778abb https://github.com/galaxyproject/galaxy/commit/41f25b928afbf849e94c3c3b5ca2… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- fix a few tool_deps test errors Commit: fcdd1a42451f02fa97349b6213c44e55676071ad https://github.com/galaxyproject/galaxy/commit/fcdd1a42451f02fa97349b6213c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #6436 from bgruening/lint-fixes fix a few tool_deps test errors Compare: https://github.com/galaxyproject/galaxy/compare/01ba96a7acda...fcdd1a42451f **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] dceee9: Citation style overhaul
by GitHub 01 Jul '18

01 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dceee9bc1b496a1d28f63f2906660b1170898b62 https://github.com/galaxyproject/galaxy/commit/dceee9bc1b496a1d28f63f290666… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue Log Message: ----------- Citation style overhaul Commit: 01ba96a7acda5f321e3f3f0975909615122a7880 https://github.com/galaxyproject/galaxy/commit/01ba96a7acda5f321e3f3f097590… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue Log Message: ----------- Merge pull request #6427 from dannon/citations_style_fix Citation style work Compare: https://github.com/galaxyproject/galaxy/compare/e0721ac85451...01ba96a7acda **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 29cf68: Do not encode a rendered Mako template
by GitHub 01 Jul '18

01 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29cf68f0b07d1342fdd1e8f00c1bf751de6b581c https://github.com/galaxyproject/galaxy/commit/29cf68f0b07d1342fdd1e8f00c1b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/webapp.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Do not encode a rendered Mako template Fix 1 error and 2 failures in unit tests under Python 3, e.g.: ``` FAIL: test_render (unit.visualizations.plugins.test_VisualizationPlugin.VisualizationsPlugin_TestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/travis/build/galaxyproject/galaxy/test/unit/visualizations/plugins/test_VisualizationPlugin.py", line 180, in test_render self.assertIsInstance(response, string_types) AssertionError: b'\nTrue\n' is not an instance of (<class 'str'>,) ``` Commit: e0721ac8545107bd0eb0194f131bbb687cfcc18f https://github.com/galaxyproject/galaxy/commit/e0721ac8545107bd0eb0194f131b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/webapp.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge pull request #6431 from nsoranzo/python3 Do not encode a rendered Mako template Compare: https://github.com/galaxyproject/galaxy/compare/af26564559f9...e0721ac85451 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 0c20f5: python3 get_file_peek doctest fix
by GitHub 01 Jul '18

01 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c20f523fec2d38680b81969937157aee6acf1a6 https://github.com/galaxyproject/galaxy/commit/0c20f523fec2d38680b819699371… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- python3 get_file_peek doctest fix Commit: d961f9ca6cff533eaf578dda6b44612340d5e8e5 https://github.com/galaxyproject/galaxy/commit/d961f9ca6cff533eaf578dda6b44… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- python3 FilePrefix line_iterator StringIO issue StringIO no longer has len and pos properties. Using len(getvalue()) and tell() instead. Commit: 2237bd4648e8595f9e52696a82253e56a4872892 https://github.com/galaxyproject/galaxy/commit/2237bd4648e8595f9e52696a8225… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- sniff open/write doctest fixes consume return value from write so docktest doesn't complain Commit: e7d7b72665b64538d4967048cedb5fc2a48794a1 https://github.com/galaxyproject/galaxy/commit/e7d7b72665b64538d4967048cedb… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- tools/parameters/basic doctests assert fixes Commit: 14f81bc2152d33909e761b146e263ba402061ced https://github.com/galaxyproject/galaxy/commit/14f81bc2152d33909e761b146e26… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- additional tools/parameters/basic doctests assert fix Commit: ee4baea86542226d723a3098114459de212c2d62 https://github.com/galaxyproject/galaxy/commit/ee4baea86542226d723a30981144… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- maf_utilities python3 compatible maketrans Commit: b05bd2ab98073d19dea221b8e2e5242de389bdf9 https://github.com/galaxyproject/galaxy/commit/b05bd2ab98073d19dea221b8e2e5… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- change to fix flake8 blank line issue Commit: b47be025c43b1620d2da638ad38de53860155a92 https://github.com/galaxyproject/galaxy/commit/b47be025c43b1620d2da638ad38d… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- create maketrans function in maf_utilities Trying to get flake8 to pass. flake8 didn't like way I assigned str.maketrans. Createing a function now that checks python version. Commit: 23079a0c947f25284e8ff54df77338f9f02379e4 https://github.com/galaxyproject/galaxy/commit/23079a0c947f25284e8ff54df773… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- add back extra blank line wanted by flake8 Commit: 97f356b1b6cde2cc1772edaf1461a358a9b8a8ac https://github.com/galaxyproject/galaxy/commit/97f356b1b6cde2cc1772edaf1461… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- simplify maf_utilities maketrans import Commit: 7cc2e6d48c2f43a76abf909d6fdb226560841cfa https://github.com/galaxyproject/galaxy/commit/7cc2e6d48c2f43a76abf909d6fdb… Author: John Bradley <johnbradley2008(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- remove unused variable in map_utilities Commit: 329374622c82b2d25b6d49468e1f2f28f75c5d96 https://github.com/galaxyproject/galaxy/commit/329374622c82b2d25b6d49468e1f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Use `with` statement in doctests Commit: af26564559f9c558ceb892f32a464a0c54a4046f https://github.com/galaxyproject/galaxy/commit/af26564559f9c558ceb892f32a46… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- Merge pull request #6429 from johnbradley/python3-fixes Python 3 fixes from GCC-BOSC-2018 Compare: https://github.com/galaxyproject/galaxy/compare/c980d348f4d4...af26564559f9 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a221a3: Fixed comparison with binary string
by GitHub 01 Jul '18

01 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a221a37af33616114c8721120c1bfe2b4c844aa2 https://github.com/galaxyproject/galaxy/commit/a221a37af33616114c8721120c1b… Author: Nic Herndon <nic.herndon(a)uconn.edu> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fixed comparison with binary string Commit: d95c32f4b830303a232de9901841c259a1d0bf2f https://github.com/galaxyproject/galaxy/commit/d95c32f4b830303a232de9901841… Author: Nic Herndon <nic.herndon(a)uconn.edu> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- Fixed comparison with binary string Commit: 03a4172680ced1a5667d7308fbc13dc50998209c https://github.com/galaxyproject/galaxy/commit/03a4172680ced1a5667d7308fbc1… Author: Nic Herndon <nic.herndon(a)uconn.edu> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/util/checkers.py M test/unit/jobs/test_runner_params.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Fixed bugs with unit test on Python 3 Commit: c980d348f4d45b4042387c086cb4a34370dd219f https://github.com/galaxyproject/galaxy/commit/c980d348f4d45b4042387c086cb4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/util/checkers.py M test/unit/jobs/test_runner_params.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Merge pull request #6430 from NicHerndon/dev Unit testing with Python 3 Compare: https://github.com/galaxyproject/galaxy/compare/6e718e98eb6f...c980d348f4d4 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2d8f09: Remove installation of python-lzo system dependenc...
by GitHub 30 Jun '18

30 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2d8f09e605050c64459cc3f53d75f8ba71730bba https://github.com/galaxyproject/galaxy/commit/2d8f09e605050c64459cc3f53d75… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M .travis.yml Log Message: ----------- Remove installation of python-lzo system dependencies for testing under Python 3. We have Python 3 wheels now, thanks @natefoo ! Commit: b3cf4480cc44fc25cbc00d84bb76859155ba546e https://github.com/galaxyproject/galaxy/commit/b3cf4480cc44fc25cbc00d84bb76… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M .travis.yml Log Message: ----------- Revert "Speedup the py34-first_startup TravisCI job" This reverts commit e49ee433e82a31f4d0560bb4727cd5b80aefd8e9. This was not making py34-first_startup faster because it was creating a Python2 virtual environment just for the final database migrations. It is probably useful to test all the database migrations somewhere anyway. Commit: 6e718e98eb6fc410f9e2f6d8b6230624a7284c7b https://github.com/galaxyproject/galaxy/commit/6e718e98eb6fc410f9e2f6d8b623… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #6425 from nsoranzo/python-lzo_py3_wheel Remove installation of python-lzo system dependencies Compare: https://github.com/galaxyproject/galaxy/compare/c09a771a0002...6e718e98eb6f **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c5fb75: Hide empty message view instead of fading it out
by GitHub 30 Jun '18

30 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5fb753aceadf3b155c99ee99979c721e09bf7ae https://github.com/galaxyproject/galaxy/commit/c5fb753aceadf3b155c99ee99979… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Hide empty message view instead of fading it out Commit: db3b7676dcd94e3026f0c3e9dee9d0b500de5b33 https://github.com/galaxyproject/galaxy/commit/db3b7676dcd94e3026f0c3e9dee9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove style dependent message hiding Commit: c09a771a00024fb9984f046c86eec16829395144 https://github.com/galaxyproject/galaxy/commit/c09a771a00024fb9984f046c86ee… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6424 from guerler/fix_message_fadeout Fix message fadeout by relying on hiding the message instead Compare: https://github.com/galaxyproject/galaxy/compare/60470c05f825...c09a771a0002 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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