May 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 0f984d: Unicodify pretty datetimes which can contain non-A...
by GitHub 09 May '16

09 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 0f984d3bfda9efaa6869286b13ff6842a6df67fb https://github.com/galaxyproject/galaxy/commit/0f984d3bfda9efaa6869286b13ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Unicodify pretty datetimes which can contain non-ASCII chars Commit: 79dd8c82f034de51531fb843796249e2b21d9d62 https://github.com/galaxyproject/galaxy/commit/79dd8c82f034de51531fb8437962… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-07 (Sat, 07 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #2312 from nsoranzo/release_16.01_fix_makos [16.01] Unicodify pretty datetimes which can contain non-ASCII chars Commit: 5710506229e16a64a6fe35279fb49df5c73bc0ce https://github.com/galaxyproject/galaxy/commit/5710506229e16a64a6fe35279fb4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: templates/show_params.mako Compare: https://github.com/galaxyproject/galaxy/compare/5bb7c1d44815...5710506229e1

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[galaxyproject/galaxy] 0f984d: Unicodify pretty datetimes which can contain non-A...
by GitHub 07 May '16

07 May '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 0f984d3bfda9efaa6869286b13ff6842a6df67fb https://github.com/galaxyproject/galaxy/commit/0f984d3bfda9efaa6869286b13ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Unicodify pretty datetimes which can contain non-ASCII chars Commit: 79dd8c82f034de51531fb843796249e2b21d9d62 https://github.com/galaxyproject/galaxy/commit/79dd8c82f034de51531fb8437962… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-07 (Sat, 07 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #2312 from nsoranzo/release_16.01_fix_makos [16.01] Unicodify pretty datetimes which can contain non-ASCII chars Compare: https://github.com/galaxyproject/galaxy/compare/41e6f22f338a...79dd8c82f034

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[galaxyproject/galaxy] 427804: Do not sniff one-line files as CSV/TSV
by GitHub 07 May '16

07 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 427804ff823e4b4277e768e1822bd1642c549a1f https://github.com/galaxyproject/galaxy/commit/427804ff823e4b4277e768e1822b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Do not sniff one-line files as CSV/TSV Commit: 5bb7c1d448156c1d20f52eaac3fcab4b1a79e0e5 https://github.com/galaxyproject/galaxy/commit/5bb7c1d448156c1d20f52eaac3fc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-07 (Sat, 07 May 2016) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #2317 from nsoranzo/release_16.04_tsv_fix [16.04] Do not sniff one-line files as CSV/TSV Compare: https://github.com/galaxyproject/galaxy/compare/ff903ac684d7...5bb7c1d44815

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[galaxyproject/galaxy] bd2245: Revise selectors, add test cases
by GitHub 06 May '16

06 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd22456c417427c3e39e2dcb9a81ecaf7f173d82 https://github.com/galaxyproject/galaxy/commit/bd22456c417427c3e39e2dcb9a81… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M test/qunit/tests/ui_tests.js Log Message: ----------- Revise selectors, add test cases Commit: cfb0ddb2ddd170875d2ea19cea941a266894095c https://github.com/galaxyproject/galaxy/commit/cfb0ddb2ddd170875d2ea19cea94… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/views/group.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js Log Message: ----------- Revise options, add test cases Commit: 995509776ef002c6c7be30caabcfd3dfcab3811c https://github.com/galaxyproject/galaxy/commit/995509776ef002c6c7be30caabcf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-06 (Fri, 06 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/views/group.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #2305 from guerler/revise_select_000 Revise selection, options and drilldown wrappers, add tests Compare: https://github.com/galaxyproject/galaxy/compare/1809a22e9fe3...995509776ef0

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[galaxyproject/galaxy] 75735a: A pass adding new contributors from 15.10->16.04(i...
by GitHub 05 May '16

05 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 75735a498a183b86fa704fdff830b82cb33c2479 https://github.com/galaxyproject/galaxy/commit/75735a498a183b86fa704fdff830… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- A pass adding new contributors from 15.10->16.04(ish). Needs a few blanks filled in. Commit: 7a7e3b46d19033e082a38297464d2e205a292759 https://github.com/galaxyproject/galaxy/commit/7a7e3b46d19033e082a38297464d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Add Sourav's email, add Jay Commit: a2e8d5db6569b8f7f171b930c127b08c22162230 https://github.com/galaxyproject/galaxy/commit/a2e8d5db6569b8f7f171b930c127… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge w/ dave's sortnig. Commit: 9bb80950e3951d0676ef9bf0d3f5d82667588dbe https://github.com/galaxyproject/galaxy/commit/9bb80950e3951d0676ef9bf0d3f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Add Ryan's last name. Commit: e3c09ac1dece3a1dd8ff7b11c8e516545e543597 https://github.com/galaxyproject/galaxy/commit/e3c09ac1dece3a1dd8ff7b11c8e5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Update spelling. Commit: 1809a22e9fe3a105f592a7c3fb38b4cda7e2c42f https://github.com/galaxyproject/galaxy/commit/1809a22e9fe3a105f592a7c3fb38… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #2257 from dannon/contrib_update_000 A pass adding new contributors from 15.10->16.04(ish). Compare: https://github.com/galaxyproject/galaxy/compare/d7465a47fbea...1809a22e9fe3

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[galaxyproject/galaxy] 3005bb: Remove SLURM memory limit warning from stderr if t...
by GitHub 05 May '16

05 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3005bba5e389c86fccabe129326a1f3a675c6911 https://github.com/galaxyproject/galaxy/commit/3005bba5e389c86fccabe129326a… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Remove SLURM memory limit warning from stderr if the job was successful Commit: d40c237102115c1a4e664b8463ef1949a3741387 https://github.com/galaxyproject/galaxy/commit/d40c237102115c1a4e664b8463ef… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- If a Slurm post-mortem determines that a job is in a non-terminal state, return the job to the monitor queue. Commit: 338d25403109244f0b228f9a0df23e02e1de7578 https://github.com/galaxyproject/galaxy/commit/338d25403109244f0b228f9a0df2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Use partial messages to match SLURM memory warnings Commit: ad0647d677cb1979b9841cf0c56ba26d7ec5ca34 https://github.com/galaxyproject/galaxy/commit/ad0647d677cb1979b9841cf0c56b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Change elif to if because drmaa_state can be changed inside the if Commit: ce8fa33d547855c2f9dee914936db73fe5d47705 https://github.com/galaxyproject/galaxy/commit/ce8fa33d547855c2f9dee914936d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2311 from natefoo/drmaa-failed [16.04] If a Slurm post-mortem determines that a job is in a non-terminal state, return the job to the monitor queue Commit: 41e6f22f338a6323cb48a23454ca95e798385045 https://github.com/galaxyproject/galaxy/commit/41e6f22f338a6323cb48a23454ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2309 from nsoranzo/release_16.01_slurm_mem_limit [16.01] Remove SLURM memory limit warning from stderr if the job was successful Commit: ff903ac684d7c59a6bfbde108fe439096505877d https://github.com/galaxyproject/galaxy/commit/ff903ac684d7c59a6bfbde108fe4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: d7465a47fbea34e69ad8fce46a8a6702cf52d97d https://github.com/galaxyproject/galaxy/commit/d7465a47fbea34e69ad8fce46a8a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/432ec84f9206...d7465a47fbea

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[galaxyproject/galaxy] 3005bb: Remove SLURM memory limit warning from stderr if t...
by GitHub 05 May '16

05 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 3005bba5e389c86fccabe129326a1f3a675c6911 https://github.com/galaxyproject/galaxy/commit/3005bba5e389c86fccabe129326a… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Remove SLURM memory limit warning from stderr if the job was successful Commit: 338d25403109244f0b228f9a0df23e02e1de7578 https://github.com/galaxyproject/galaxy/commit/338d25403109244f0b228f9a0df2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Use partial messages to match SLURM memory warnings Commit: ad0647d677cb1979b9841cf0c56ba26d7ec5ca34 https://github.com/galaxyproject/galaxy/commit/ad0647d677cb1979b9841cf0c56b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Change elif to if because drmaa_state can be changed inside the if Commit: 41e6f22f338a6323cb48a23454ca95e798385045 https://github.com/galaxyproject/galaxy/commit/41e6f22f338a6323cb48a23454ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2309 from nsoranzo/release_16.01_slurm_mem_limit [16.01] Remove SLURM memory limit warning from stderr if the job was successful Commit: ff903ac684d7c59a6bfbde108fe439096505877d https://github.com/galaxyproject/galaxy/commit/ff903ac684d7c59a6bfbde108fe4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/ce8fa33d5478...ff903ac684d7

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[galaxyproject/galaxy] 3005bb: Remove SLURM memory limit warning from stderr if t...
by GitHub 05 May '16

05 May '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 3005bba5e389c86fccabe129326a1f3a675c6911 https://github.com/galaxyproject/galaxy/commit/3005bba5e389c86fccabe129326a… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Remove SLURM memory limit warning from stderr if the job was successful Commit: 338d25403109244f0b228f9a0df23e02e1de7578 https://github.com/galaxyproject/galaxy/commit/338d25403109244f0b228f9a0df2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Use partial messages to match SLURM memory warnings Commit: ad0647d677cb1979b9841cf0c56ba26d7ec5ca34 https://github.com/galaxyproject/galaxy/commit/ad0647d677cb1979b9841cf0c56b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Change elif to if because drmaa_state can be changed inside the if Commit: 41e6f22f338a6323cb48a23454ca95e798385045 https://github.com/galaxyproject/galaxy/commit/41e6f22f338a6323cb48a23454ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2309 from nsoranzo/release_16.01_slurm_mem_limit [16.01] Remove SLURM memory limit warning from stderr if the job was successful Compare: https://github.com/galaxyproject/galaxy/compare/063b25f660b6...41e6f22f338a

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[galaxyproject/galaxy] d40c23: If a Slurm post-mortem determines that a job is in...
by GitHub 05 May '16

05 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: d40c237102115c1a4e664b8463ef1949a3741387 https://github.com/galaxyproject/galaxy/commit/d40c237102115c1a4e664b8463ef… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- If a Slurm post-mortem determines that a job is in a non-terminal state, return the job to the monitor queue. Commit: ce8fa33d547855c2f9dee914936db73fe5d47705 https://github.com/galaxyproject/galaxy/commit/ce8fa33d547855c2f9dee914936d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2311 from natefoo/drmaa-failed [16.04] If a Slurm post-mortem determines that a job is in a non-terminal state, return the job to the monitor queue Compare: https://github.com/galaxyproject/galaxy/compare/a54a61897084...ce8fa33d5478

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[galaxyproject/galaxy] eda978: Monkeypatch Whoosh to use mkdtemp rather than a fi...
by GitHub 05 May '16

05 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eda9789ba7af56510af09a1d2f15e2afd44b4b12 https://github.com/galaxyproject/galaxy/commit/eda9789ba7af56510af09a1d2f15… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Monkeypatch Whoosh to use mkdtemp rather than a fixed temporary directory. Commit: 432ec84f920686ca624031b5246d71bab7d7b9a0 https://github.com/galaxyproject/galaxy/commit/432ec84f920686ca624031b5246d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Merge pull request #2310 from natefoo/monkeypatch-whoosh Monkeypatch Whoosh to use mkdtemp rather than a fixed temporary directory Compare: https://github.com/galaxyproject/galaxy/compare/7a7de38b4ac5...432ec84f9206

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