March 2019 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 012cf3: ENH: multifile zip testing
by Martin Cech 02 Mar '19

02 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 012cf387d7ce4b9bf1b2278570ab3076b24f0a35 https://github.com/galaxyproject/galaxy/commit/012cf387d7ce4b9bf1b2278570ab… Author: Matthew Dillon <matthewrdillon(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M CONTRIBUTORS.md M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/zip.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_zip.xml Log Message: ----------- ENH: multifile zip testing Commit: 8e82fc71910025ddc77827a9078e25ecfeb0cc30 https://github.com/galaxyproject/galaxy/commit/8e82fc71910025ddc77827a9078e… Author: Matthew Dillon <matthewrdillon(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/zip.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_zip.xml Log Message: ----------- SQUASH ME: rename suggestion from @bgruening Commit: 091fe8121a520673fb9feeeb1884488a613b93f7 https://github.com/galaxyproject/galaxy/commit/091fe8121a520673fb9feeeb1884… Author: Matthew Dillon <matthewrdillon(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/archive.py R lib/galaxy/tools/verify/asserts/zip.py M lib/galaxy/tools/xsd/galaxy.xsd A test-data/testdir1.tar A test-data/testdir1.tar.gz M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_tar.xml A test/functional/tools/validation_tar_gz.xml Log Message: ----------- SQUASH: Adding in other archive containers Per discussion with @bgruening Commit: 10696c2e8482ede9f0e237c98e833b7b19338a2d https://github.com/galaxyproject/galaxy/commit/10696c2e8482ede9f0e237c98e83… Author: Matthew Dillon <matthewrdillon(a)gmail.com> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/archive.py Log Message: ----------- LINT: forgot to lint Commit: cb7566ef02c487df67d10843b5acb55870f5b28d https://github.com/galaxyproject/galaxy/commit/cb7566ef02c487df67d10843b5ac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M CONTRIBUTORS.md M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/archive.py M lib/galaxy/tools/xsd/galaxy.xsd A test-data/testdir1.tar A test-data/testdir1.tar.gz M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_tar.xml A test/functional/tools/validation_tar_gz.xml A test/functional/tools/validation_zip.xml Log Message: ----------- Merge pull request #7400 from thermokarst/zippertest ENH: multifile zip testing Compare: https://github.com/galaxyproject/galaxy/compare/99d4b4090bf5...cb7566ef02c4

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[galaxyproject/galaxy] acde6b: Remove unused code
by Marius van den Beek 02 Mar '19

02 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: acde6b392c10e8d57f03ce917372cd62e2a19166 https://github.com/galaxyproject/galaxy/commit/acde6b392c10e8d57f03ce917372… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M lib/galaxy/tools/cache.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Remove unused code Commit: 99d4b4090bf53e48f0c103ec30212a77ec565107 https://github.com/galaxyproject/galaxy/commit/99d4b4090bf53e48f0c103ec3021… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M lib/galaxy/tools/cache.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Merge pull request #7445 from nsoranzo/remove_unused Remove unused code Compare: https://github.com/galaxyproject/galaxy/compare/ad353c20549d...99d4b4090bf5

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[galaxyproject/galaxy] 84648f: Remove or replace references to Biostars
by Martin Cech 01 Mar '19

01 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84648f49866c26de996674b02a3243b88c1c1958 https://github.com/galaxyproject/galaxy/commit/84648f49866c26de996674b02a32… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M README.rst M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M scripts/bootstrap_history.py Log Message: ----------- Remove or replace references to Biostars Commit: ad353c20549dd73f4790000879f7129418ad6bef https://github.com/galaxyproject/galaxy/commit/ad353c20549dd73f4790000879f7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M README.rst M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #7443 from nsoranzo/remove_biostar_refs Remove or replace references to Biostars Compare: https://github.com/galaxyproject/galaxy/compare/9d5a22f3c584...ad353c20549d

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[galaxyproject/infrastructure-playbook] 80d2b8: More Mailman 3 stuff
by Nate Coraor 01 Mar '19

01 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 80d2b8a0edc7e4f0c5479b58aac2531d623c61f9 https://github.com/galaxyproject/infrastructure-playbook/commit/80d2b8a0edc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M env/mailman/TODO.txt M env/mailman/group_vars/all.yml M env/mailman/group_vars/listservers/vars.yml M env/mailman/group_vars/listservers/vault.yml M env/mailman/group_vars/mailservers-mx/vars.yml M env/mailman/listservers.yml M env/mailman/playbook.yml M env/mailman/templates/nginx/mailman_ssl.j2 M requirements.yml Log Message: ----------- More Mailman 3 stuff

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[galaxyproject/galaxy] e8f5a1: Fix LocalShellRunner
by Marius van den Beek 01 Mar '19

01 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8f5a13f3b4d0f57819db18bb6cde086b92eb6c8 https://github.com/galaxyproject/galaxy/commit/e8f5a13f3b4d0f57819db18bb6cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Fix LocalShellRunner All the `cmd` coming from the plugins are strings, so if cmd is a string we use `shell=True`, brings this on par with the Remote Shell plugins (which consume strings). Should fix https://github.com/galaxyproject/galaxy/issues/7269. Commit: a12d9e367cae5eb19eec905385d6cb9e5ad0826c https://github.com/galaxyproject/galaxy/commit/a12d9e367cae5eb19eec905385d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge pull request #7438 from mvdbeek/fix_shell_runner [18.09] Fix LocalShellRunner Commit: 739bb6310cddceb36d875e4a7f7a145aa00ba85a https://github.com/galaxyproject/galaxy/commit/739bb6310cddceb36d875e4a7f7a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 9d5a22f3c584a36ad783dc548f3c936314c6a44e https://github.com/galaxyproject/galaxy/commit/9d5a22f3c584a36ad783dc548f3c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/480dddac31f4...9d5a22f3c584

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[galaxyproject/galaxy] e8f5a1: Fix LocalShellRunner
by Marius van den Beek 01 Mar '19

01 Mar '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: e8f5a13f3b4d0f57819db18bb6cde086b92eb6c8 https://github.com/galaxyproject/galaxy/commit/e8f5a13f3b4d0f57819db18bb6cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Fix LocalShellRunner All the `cmd` coming from the plugins are strings, so if cmd is a string we use `shell=True`, brings this on par with the Remote Shell plugins (which consume strings). Should fix https://github.com/galaxyproject/galaxy/issues/7269. Commit: a12d9e367cae5eb19eec905385d6cb9e5ad0826c https://github.com/galaxyproject/galaxy/commit/a12d9e367cae5eb19eec905385d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge pull request #7438 from mvdbeek/fix_shell_runner [18.09] Fix LocalShellRunner Commit: 739bb6310cddceb36d875e4a7f7a145aa00ba85a https://github.com/galaxyproject/galaxy/commit/739bb6310cddceb36d875e4a7f7a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/c40689dbd5fe...739bb6310cdd

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[galaxyproject/galaxy] e8f5a1: Fix LocalShellRunner
by John Chilton 01 Mar '19

01 Mar '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: e8f5a13f3b4d0f57819db18bb6cde086b92eb6c8 https://github.com/galaxyproject/galaxy/commit/e8f5a13f3b4d0f57819db18bb6cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Fix LocalShellRunner All the `cmd` coming from the plugins are strings, so if cmd is a string we use `shell=True`, brings this on par with the Remote Shell plugins (which consume strings). Should fix https://github.com/galaxyproject/galaxy/issues/7269. Commit: a12d9e367cae5eb19eec905385d6cb9e5ad0826c https://github.com/galaxyproject/galaxy/commit/a12d9e367cae5eb19eec905385d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge pull request #7438 from mvdbeek/fix_shell_runner [18.09] Fix LocalShellRunner Compare: https://github.com/galaxyproject/galaxy/compare/68e3568bb259...a12d9e367cae

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[galaxyproject/galaxy] 47af06: Add tool hover
by Martin Cech 01 Mar '19

01 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47af069a34d21a034de6250676663884305c371b https://github.com/galaxyproject/galaxy/commit/47af069a34d21a034de625067666… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Add tool hover Commit: 480dddac31f4ef7d583ba2ef50d7e13c6e1c12ce https://github.com/galaxyproject/galaxy/commit/480dddac31f4ef7d583ba2ef50d7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Merge pull request #7437 from erasche/tool-hover Add tool hover Compare: https://github.com/galaxyproject/galaxy/compare/4a63ad753e6e...480dddac31f4

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[galaxyproject/usegalaxy-playbook] 692146: Installed bowtie1 wrapper version 1.2.0 on test.
by Dave B. 01 Mar '19

01 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 69214646d6cee31af02d4aac562d03904e5f17c3 https://github.com/galaxyproject/usegalaxy-playbook/commit/69214646d6cee31a… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed bowtie1 wrapper version 1.2.0 on test.

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[galaxyproject/galaxy] 203937: send post data in payload per @mvdbeek suggestion
by Nicola Soranzo 01 Mar '19

01 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2039376ddf21abb8e56b4ec984ea9d7fed46efb8 https://github.com/galaxyproject/galaxy/commit/2039376ddf21abb8e56b4ec984ea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- send post data in payload per @mvdbeek suggestion Commit: c40689dbd5fe27cace5c11a50d806445aefae97a https://github.com/galaxyproject/galaxy/commit/c40689dbd5fe27cace5c11a50d80… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #7432 from martenson/fix-lib-paths [19.01] send post data in payload Commit: 4a63ad753e6e502ebb89643f675f5d25d260251b https://github.com/galaxyproject/galaxy/commit/4a63ad753e6e502ebb89643f675f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c671b5372789...4a63ad753e6e

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