- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 8b90cd: Encode JSON encoder output
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b90cd997fb485045ab4384d96149e89891b29aa https://github.com/galaxyproject/galaxy/commit/8b90cd997fb485045ab4384d9614… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Encode JSON encoder output Commit: 44300668d4e479b3f7f6e6928fd82c5517f1c556 https://github.com/galaxyproject/galaxy/commit/44300668d4e479b3f7f6e6928fd8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Fix registry import in test_galaxy_mapping.py Commit: f93b3e09862bbda6d7a7c358f414d847bd6c2238 https://github.com/galaxyproject/galaxy/commit/f93b3e09862bbda6d7a7c358f414… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Unicodify _sniffnfix_pg9_hex output Commit: 75511506a8828e922c8b12f91af4637c5db3b778 https://github.com/galaxyproject/galaxy/commit/75511506a8828e922c8b12f91af4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/model/custom_types.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #6439 from mvdbeek/py3_db_interaction Python3: Encode return values of JSON encoder Compare: https://github.com/galaxyproject/galaxy/compare/a51ad0fc5204...75511506a882 **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] 590607: replace the administration header in admin menu wi...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59060783a9e169496548ae38766f04cd94eb54a3 https://github.com/galaxyproject/galaxy/commit/59060783a9e169496548ae38766f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- replace the administration header in admin menu with version closes #1201 Commit: 9b2101e948942f6b239a2c45892c4535a13ec9f9 https://github.com/galaxyproject/galaxy/commit/9b2101e948942f6b239a2c45892c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Merge remote-tracking branch 'martenson/show-version-admin' into dev Commit: a51ad0fc5204ae138d024c19358be720359f09ab https://github.com/galaxyproject/galaxy/commit/a51ad0fc5204ae138d024c19358b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Client format and build from several upstream changes Compare: https://github.com/galaxyproject/galaxy/compare/ee267e956116...a51ad0fc5204 **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] 1e9e38: Add zoom support to workflow editor.
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e9e38703a53767d22ef4ce21e9dcf73ebe03a99 https://github.com/galaxyproject/galaxy/commit/1e9e38703a53767d22ef4ce21e9d… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add zoom support to workflow editor. Zoom levels are discrete from a pre-defined set. Uses css transforms and... math. Commit: 8be94009680ef9efaa081d56cedb78eff270d098 https://github.com/galaxyproject/galaxy/commit/8be94009680ef9efaa081d56cedb… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Fix incorrect variable reference Commit: ee267e95611652ed0a6068144f88320c9b602ae2 https://github.com/galaxyproject/galaxy/commit/ee267e95611652ed0a6068144f88… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6441 from jxtx/workflow-zoom Add zoom support to workflow editor. Compare: https://github.com/galaxyproject/galaxy/compare/b062a8c4f312...ee267e956116 **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] 258fff: py3 compat: fixes test_vcf, test_sniff_compressed*
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 258fff927633bcafe844dec09c1d8e40979b9f73 https://github.com/galaxyproject/galaxy/commit/258fff927633bcafe844dec09c1d… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- py3 compat: fixes test_vcf, test_sniff_compressed* Commit: b062a8c4f312952441696da9cca825ca35549523 https://github.com/galaxyproject/galaxy/commit/b062a8c4f312952441696da9cca8… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- Merge pull request #6442 from caleb-easterly/is_gzip_bz2 py3 compat: fixes test_vcf, test_sniff_compressed* Compare: https://github.com/galaxyproject/galaxy/compare/073d04474913...b062a8c4f312 **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 02 Jul '18

02 Jul '18

Branch: refs/heads/dev 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 Commit: 073d04474913913e6e8fc20346297fc3a9ef2a3e https://github.com/galaxyproject/galaxy/commit/073d04474913913e6e8fc2034629… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1f9894069c74...073d04474913 **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] 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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[galaxyproject/galaxy] 98c72f: Fix positioning for tool search box.
by GitHub 30 Jun '18

30 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 98c72fea520724a393106ac7dedd329fec7ef51e https://github.com/galaxyproject/galaxy/commit/98c72fea520724a393106ac7dedd… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/scss/base.scss Log Message: ----------- Fix positioning for tool search box. Modifies the .unified-panel styles to layout using flex, and moves the tool-search box to a controls area that does not scroll. Commit: 302805922837be711bd4a97ceee494b6421813b0 https://github.com/galaxyproject/galaxy/commit/302805922837be711bd4a97ceee4… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix missing '}' Commit: 617b196d9748042d5d0c92c200e0c6ea43e0f910 https://github.com/galaxyproject/galaxy/commit/617b196d9748042d5d0c92c200e0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Drop extra padding we don't need w/ tool search position fixes. Commit: 29e5bd3aebafc712f104689a9e42f444ab981eb8 https://github.com/galaxyproject/galaxy/commit/29e5bd3aebafc712f104689a9e42… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Standardize workflow toolbox to match analysis view. Commit: 60470c05f825e49c5fda02284a9edf8768531fe9 https://github.com/galaxyproject/galaxy/commit/60470c05f825e49c5fda02284a9e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6416 from jxtx/tool-search-position-fix Fix positioning for tool search box. Compare: https://github.com/galaxyproject/galaxy/compare/5dbae1ddcf49...60470c05f825 **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/infrastructure-playbook] fc958d: Wheels access for travis/starforge
by GitHub 30 Jun '18

30 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fc958d297f5a2541c06a494b0906bd83be38ce84 https://github.com/galaxyproject/infrastructure-playbook/commit/fc958d297f5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M env/galaxy/host_vars/delirium.galaxyproject.org/vault.yml Log Message: ----------- Wheels access for travis/starforge **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] 29f8e2: Fix empty datatypes.
by GitHub 30 Jun '18

30 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29f8e29b0bf5d50c0b735aa707d2a61623cc805b https://github.com/galaxyproject/galaxy/commit/29f8e29b0bf5d50c0b735aa707d2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt Log Message: ----------- Fix empty datatypes. Commit: 9b232c87ad056e8e53498fdf7f899d0bbb5a92d8 https://github.com/galaxyproject/galaxy/commit/9b232c87ad056e8e53498fdf7f89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Allow empty files to be uploaded if check content is off. Commit: 5dbae1ddcf494fb816eed5dfd904830bf369c1ca https://github.com/galaxyproject/galaxy/commit/5dbae1ddcf494fb816eed5dfd904… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt M tools/data_source/upload.py Log Message: ----------- Merge pull request #6418 from jmchilton/empty_file_behavior_fixes Fixes for uploading empty files to Galaxy. Compare: https://github.com/galaxyproject/galaxy/compare/5dbcf516aaf6...5dbae1ddcf49 **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] d7bbf7: py3 port: testfile as text, add built-in as exampl...
by GitHub 30 Jun '18

30 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d7bbf7938bdd68259b05d816708ddb4487990ce4 https://github.com/galaxyproject/galaxy/commit/d7bbf7938bdd68259b05d816708d… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/unittest_utils/tempfilecache.py Log Message: ----------- py3 port: testfile as text, add built-in as example w/o __iter__ Commit: 1e52f066cddbb7bcdbd561b97f617196a428c574 https://github.com/galaxyproject/galaxy/commit/1e52f066cddbb7bcdbd561b97f61… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M test/unit/datatypes/test_bam.py Log Message: ----------- replace e.message with str(e) Commit: d70c42a9acad01b597bda1cc8ce616fada43095f https://github.com/galaxyproject/galaxy/commit/d70c42a9acad01b597bda1cc8ce6… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- py3 support: fixes /test/unit/datatypes/test_cram.py Commit: 8fa64b33ec00f28408a070643ef013e4899ca7d3 https://github.com/galaxyproject/galaxy/commit/8fa64b33ec00f28408a070643ef0… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- py3 port: fixes test/unit/workflows/test_modules.py Commit: bc5a4521ef4a4efed1ede7748506e81f534a9f53 https://github.com/galaxyproject/galaxy/commit/bc5a4521ef4a4efed1ede7748506… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M lib/galaxy/model/custom_types.py M test/unit/unittest_utils/tempfilecache.py Log Message: ----------- Small code simplifications Commit: 5dbcf516aaf6268bdc0c529ba6a6f769497e6420 https://github.com/galaxyproject/galaxy/commit/5dbcf516aaf6268bdc0c529ba6a6… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/model/custom_types.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py M test/unit/unittest_utils/tempfilecache.py Log Message: ----------- Merge pull request #6420 from caleb-easterly/dev python 3 porting Compare: https://github.com/galaxyproject/galaxy/compare/93ad468be7ae...5dbcf516aaf6 **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] d17603: removing binary as input
by GitHub 30 Jun '18

30 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d17603b384b3390470a3357dbad2f3a4e00169d7 https://github.com/galaxyproject/galaxy/commit/d17603b384b3390470a3357dbad2… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- removing binary as input Commit: 93ad468be7aefb5e588ba4bf109c0713d7fc4f07 https://github.com/galaxyproject/galaxy/commit/93ad468be7aefb5e588ba4bf109c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Merge pull request #6417 from eslerm/python3-eslerm removing binary as input for python compatibility Compare: https://github.com/galaxyproject/galaxy/compare/33944260378a...93ad468be7ae **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] 97b34a: Drop the test, doesn't make sense in python3
by GitHub 30 Jun '18

30 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97b34a175d7641144636c670f1350e39d5ddcae2 https://github.com/galaxyproject/galaxy/commit/97b34a175d7641144636c670f135… Author: Yunchen Gong <yunchen.gong(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Drop the test, doesn't make sense in python3 Commit: 77a8ad3e042a065ebf6af5f8370188f949ed29e0 https://github.com/galaxyproject/galaxy/commit/77a8ad3e042a065ebf6af5f83701… Author: Yunchen Gong <yunchen.gong(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M test/unit/test_security_helper.py Log Message: ----------- Fixed test_security_helper.py, remove encode("utf-8") Commit: 33944260378af743c482377eceae8666890eed4e https://github.com/galaxyproject/galaxy/commit/33944260378af743c482377eceae… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M test/unit/test_galaxy_mapping.py M test/unit/test_security_helper.py Log Message: ----------- Merge pull request #6419 from ycgong/dev GCC2018 python3 unit-test fixes Compare: https://github.com/galaxyproject/galaxy/compare/0ea09e4dd6fc...33944260378a **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] 2083dd: Upgrade vue-loader to v15 (not backwards compatibl...
by GitHub 29 Jun '18

29 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2083ddeae2cd4ccec87c959008b7f8548110c794 https://github.com/galaxyproject/galaxy/commit/2083ddeae2cd4ccec87c959008b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock Log Message: ----------- Upgrade vue-loader to v15 (not backwards compatible, needed minor changes -- this silences the scary warnings on client build) Commit: 1e7c5b312f1ee345d4317110656488b19a5329dd https://github.com/galaxyproject/galaxy/commit/1e7c5b312f1ee345d43171106564… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/layout/data.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Client-format catchup, and commit style changes from upstream, since we're still keeping that in the repo for right now Commit: 7aa83f33aaae89c4eaca8198abda2a403432acea https://github.com/galaxyproject/galaxy/commit/7aa83f33aaae89c4eaca8198abda… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade underscore // supports existing API, just performance improvements and a few new methods Commit: 3420e88542ff5dcf31bbf53231feddf719cff798 https://github.com/galaxyproject/galaxy/commit/3420e88542ff5dcf31bbf53231fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade babel and related components. Commit: 8b84c77929d93af1862733e3cdf26ce7f2014908 https://github.com/galaxyproject/galaxy/commit/8b84c77929d93af1862733e3cdf2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M client/package.json M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Upgrade gulp and related components. Commit: 7e3095aa9f6bb068c3f64713a4cf0808e7915d53 https://github.com/galaxyproject/galaxy/commit/7e3095aa9f6bb068c3f64713a4cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/package.json M client/yarn.lock Log Message: ----------- Upgrade Prettier, reformat (looks like it fixed some formatting issues) Commit: 8964523a6e3cac39597907bcdafda3990306cd62 https://github.com/galaxyproject/galaxy/commit/8964523a6e3cac39597907bcdafd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-26 (Tue, 26 Jun 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade more misc compatible client libraries. Commit: 0ea09e4dd6fc470fa19658255ec6ba563c398857 https://github.com/galaxyproject/galaxy/commit/0ea09e4dd6fc470fa19658255ec6… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/package.json M client/webpack.config.js M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Merge pull request #6400 from dannon/vue-loader-v15 Client library upgrades. Compare: https://github.com/galaxyproject/galaxy/compare/fb4895d91ea1...0ea09e4dd6fc **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] c07ac6: Create client build hash on toplevel concurrent wa...
by GitHub 29 Jun '18

29 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c07ac639fe49aa80b952708c6668bd33c4a575cf https://github.com/galaxyproject/galaxy/commit/c07ac639fe49aa80b952708c6668… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M client/package.json Log Message: ----------- Create client build hash on toplevel concurrent watch, in addition to individual builds. Commit: 455b2deb6ec82c26126af89b40d7451ce020e539 https://github.com/galaxyproject/galaxy/commit/455b2deb6ec82c26126af89b40d7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M client/package.json Log Message: ----------- Swap hash save outside the concurrent builds, just do it before kicking off after staging. Commit: fb4895d91ea1000ab5029ad50df75ee1f9730111 https://github.com/galaxyproject/galaxy/commit/fb4895d91ea1000ab5029ad50df7… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M client/package.json Log Message: ----------- Merge pull request #6381 from dannon/hash_on_watch Create client build hash on toplevel concurrent watch in addition to individual builds. Compare: https://github.com/galaxyproject/galaxy/compare/02e7734868df...fb4895d91ea1 **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] 6ddcc9: Add py34-unit (allowed to fail) job to Travis
by GitHub 29 Jun '18

29 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6ddcc9340d5a36497642339c52c2e3e4cb0fca67 https://github.com/galaxyproject/galaxy/commit/6ddcc9340d5a36497642339c52c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-27 (Wed, 27 Jun 2018) Changed paths: M .travis.yml Log Message: ----------- Add py34-unit (allowed to fail) job to Travis Commit: e49ee433e82a31f4d0560bb4727cd5b80aefd8e9 https://github.com/galaxyproject/galaxy/commit/e49ee433e82a31f4d0560bb4727c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-27 (Wed, 27 Jun 2018) Changed paths: M .travis.yml Log Message: ----------- Speedup the py34-first_startup TravisCI job By skipping most database migrations, as for py27-first_startup. Commit: 02e7734868df8e9a7d3e8583e163ba13694764d0 https://github.com/galaxyproject/galaxy/commit/02e7734868df8e9a7d3e8583e163… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #6406 from nsoranzo/py34-unit_on_travis Add py34-unit (allowed to fail) job to Travis Compare: https://github.com/galaxyproject/galaxy/compare/2b55e3a09962...02e7734868df **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/usegalaxy-playbook] bd52ea: Install Seqtk 1.2
by GitHub 29 Jun '18

29 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bd52ea967973d6deb8de057ba918d6fcb8889f53 https://github.com/galaxyproject/usegalaxy-playbook/commit/bd52ea967973d6de… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Install Seqtk 1.2 **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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