- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 5142d0: Fix loading workflows with steps without default l...
by Nicola Soranzo 03 Mar '19

03 Mar '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 5142d0df0732faaf5983d4bb2c025a89e93f5964 https://github.com/galaxyproject/galaxy/commit/5142d0df0732faaf5983d4bb2c02… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix loading workflows with steps without default label Prior to https://github.com/galaxyproject/galaxy/pull/7422 we'd call str(default_label), so if `default_label` was None we'd get 'None'. Fixes part of https://github.com/galaxyproject/galaxy/issues/7447 Commit: bc8cf37d09b66efaa994735e994d69998ee34695 https://github.com/galaxyproject/galaxy/commit/bc8cf37d09b66efaa994735e994d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Remove broken tool_submission_burst Commit: d96034062af9fc358b1c4f3964f0492d4000b3b8 https://github.com/galaxyproject/galaxy/commit/d96034062af9fc358b1c4f3964f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- fix lint Commit: 6c80ca50a44d75a675a08c466cbd78726cc64b90 https://github.com/galaxyproject/galaxy/commit/6c80ca50a44d75a675a08c466cbd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7449 from mvdbeek/remove_broken_tool_submission_burst [18.09] Remove broken tool_submission_burst Commit: 996d7c9a60f037ca1e0120c201e74d2072c29d8d https://github.com/galaxyproject/galaxy/commit/996d7c9a60f037ca1e0120c201e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #7448 from mvdbeek/fix_when_default_label_is_none [18.09] Fix loading workflows with steps without default label Commit: 91e49acf374fe60b5c8a4dae2fbb448cc626019d https://github.com/galaxyproject/galaxy/commit/91e49acf374fe60b5c8a4dae2fbb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/739bb6310cdd...91e49acf374f

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[galaxyproject/galaxy] 5142d0: Fix loading workflows with steps without default l...
by Martin Cech 03 Mar '19

03 Mar '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 5142d0df0732faaf5983d4bb2c025a89e93f5964 https://github.com/galaxyproject/galaxy/commit/5142d0df0732faaf5983d4bb2c02… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix loading workflows with steps without default label Prior to https://github.com/galaxyproject/galaxy/pull/7422 we'd call str(default_label), so if `default_label` was None we'd get 'None'. Fixes part of https://github.com/galaxyproject/galaxy/issues/7447 Commit: 996d7c9a60f037ca1e0120c201e74d2072c29d8d https://github.com/galaxyproject/galaxy/commit/996d7c9a60f037ca1e0120c201e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #7448 from mvdbeek/fix_when_default_label_is_none [18.09] Fix loading workflows with steps without default label Compare: https://github.com/galaxyproject/galaxy/compare/6c80ca50a44d...996d7c9a60f0

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[galaxyproject/galaxy] bc8cf3: Remove broken tool_submission_burst
by Martin Cech 03 Mar '19

03 Mar '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: bc8cf37d09b66efaa994735e994d69998ee34695 https://github.com/galaxyproject/galaxy/commit/bc8cf37d09b66efaa994735e994d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Remove broken tool_submission_burst Commit: d96034062af9fc358b1c4f3964f0492d4000b3b8 https://github.com/galaxyproject/galaxy/commit/d96034062af9fc358b1c4f3964f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-02 (Sat, 02 Mar 2019) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- fix lint Commit: 6c80ca50a44d75a675a08c466cbd78726cc64b90 https://github.com/galaxyproject/galaxy/commit/6c80ca50a44d75a675a08c466cbd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7449 from mvdbeek/remove_broken_tool_submission_burst [18.09] Remove broken tool_submission_burst Compare: https://github.com/galaxyproject/galaxy/compare/a12d9e367cae...6c80ca50a44d

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[galaxyproject/galaxy] f3afac: init circleci config
by Martin Cech 03 Mar '19

03 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3afacc3cf2bf3633f855807708d7093145de6b4 https://github.com/galaxyproject/galaxy/commit/f3afacc3cf2bf3633f855807708d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: A .circleci/config.yml Log Message: ----------- init circleci config limit builds to just one branch add sudo try shallow cloning indent yml clone to workdir add unit tests use workflow instead of parallel invocations maybe ym likes this? maybe like this really yaml? well that did not work yeye maybe like this? not like this like this for suuuure yep add unit tests run first startup add startup to workflow add more jobs add even more sudo all the things ALL THE THINGS I said add moar add js unit test things try like this sur elike this add cache for yarn usage add jslint to workflow use more aliases add python 35 first startup fix path to yarn lock more aliases Commit: fdfe30651e09f8d02211f986e0e0e6d84877801c https://github.com/galaxyproject/galaxy/commit/fdfe30651e09f8d02211f986e0e0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M .circleci/config.yml Log Message: ----------- move run command ti proper section Commit: b66bf6a1046ca4b25ea56d73c8d76f7f5c7acda7 https://github.com/galaxyproject/galaxy/commit/b66bf6a1046ca4b25ea56d73c8d7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M .circleci/config.yml Log Message: ----------- rmeov ethe restriction to single branch Commit: aa2142200ba0161ddea5640d3b2c2449da29de25 https://github.com/galaxyproject/galaxy/commit/aa2142200ba0161ddea5640d3b2c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M .circleci/config.yml Log Message: ----------- just a commit Commit: 137cedd7e1392a6bbab83f5c3fe03ca1f89226b1 https://github.com/galaxyproject/galaxy/commit/137cedd7e1392a6bbab83f5c3fe0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M .circleci/config.yml Log Message: ----------- Rename some keys Commit: e3a41af9e1d7d57208ac57a8908aa48b0c7f1991 https://github.com/galaxyproject/galaxy/commit/e3a41af9e1d7d57208ac57a8908a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M .circleci/config.yml Log Message: ----------- Add restore_yarn_cache alias Commit: e6620cd4d9f9c0f356239c67c0d24d9914a8a4b7 https://github.com/galaxyproject/galaxy/commit/e6620cd4d9f9c0f356239c67c0d2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: M .circleci/config.yml Log Message: ----------- Add comment Commit: d04b32d0ac58b72f7a2db11c7b0689243eaf100c https://github.com/galaxyproject/galaxy/commit/d04b32d0ac58b72f7a2db11c7b06… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-03 (Sun, 03 Mar 2019) Changed paths: A .circleci/config.yml Log Message: ----------- Merge pull request #7424 from martenson/circle-ci experiment - run all travis tests on circleci Compare: https://github.com/galaxyproject/galaxy/compare/cb7566ef02c4...d04b32d0ac58

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[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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