October 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 381d6a: Add two recently merged PRs.
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 381d6ad83183a822baebca44622e506d088f10b1 https://github.com/galaxyproject/galaxy/commit/381d6ad83183a822baebca44622e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add two recently merged PRs. **NOTE:** This service has 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] adcd73: Fix broken gxformat2 imports.
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: adcd7333325dc34b7edcb5540730b350ff3f4e33 https://github.com/galaxyproject/galaxy/commit/adcd7333325dc34b7edcb5540730… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M test/manual/workflows_scaling.py M test/selenium_tests/framework.py Log Message: ----------- Fix broken gxformat2 imports. Commit: 1f389ae3e77352920566f09c4f1be1a1e40ff862 https://github.com/galaxyproject/galaxy/commit/1f389ae3e77352920566f09c4f1b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M test/manual/workflows_scaling.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #6834 from jmchilton/fix_gxformat2_imports Fix broken gxformat2 imports. Compare: https://github.com/galaxyproject/galaxy/compare/8ed5d8c9414f...1f389ae3e773 **NOTE:** This service has 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] 1d6596: Automatically return roundup nodes to service upon...
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1d659600da46427c171cc9d02495e227484b124d https://github.com/galaxyproject/infrastructure-playbook/commit/1d659600da4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Automatically return roundup nodes to service upon reboot **NOTE:** This service has 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] a5b5bf: Add some additional body filter spam rules
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a5b5bfcb0227884187392f752e3c8a29612cc399 https://github.com/galaxyproject/infrastructure-playbook/commit/a5b5bfcb022… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M roles/postfix/templates/local.cf.j2 Log Message: ----------- Add some additional body filter spam rules **NOTE:** This service has 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] 9044e6: Upgrade concurrently; this fixes a 'null' return f...
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9044e614f03b4d0daa3e67e32be15d7d3f1268f1 https://github.com/galaxyproject/galaxy/commit/9044e614f03b4d0daa3e67e32be1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade concurrently; this fixes a 'null' return from webpack run vi aconcurrently, which can fail the build in some situations. Commit: 5205ed7eebe4b9a2a25d0f19abd5fd732f42e302 https://github.com/galaxyproject/galaxy/commit/5205ed7eebe4b9a2a25d0f19abd5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Merge pull request #6828 from dannon/null_exit_bug_fix [18.09] Upgrade concurrently for 'null' return fix Compare: https://github.com/galaxyproject/galaxy/compare/58ea67eb457c...5205ed7eebe4 **NOTE:** This service has 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] 98a9c8: Allow testing tags in input collections.
by GitHub 07 Oct '18

07 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 98a9c86badd87a4db4a815490c06c717b67fced0 https://github.com/galaxyproject/galaxy/commit/98a9c86badd87a4db4a815490c06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Allow testing tags in input collections. Commit: 58ea67eb457ce154e1d119e94c07a81a1e617ba4 https://github.com/galaxyproject/galaxy/commit/58ea67eb457ce154e1d119e94c07… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6823 from jmchilton/tag_input_tests [18.09] Allow testing tags in input collections. Compare: https://github.com/galaxyproject/galaxy/compare/8ea455303ab7...58ea67eb457c **NOTE:** This service has 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] c61617: Replace trans.sa_session with sa_session in PSACod...
by GitHub 07 Oct '18

07 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c61617fed6ae59f237cb22fa0f6103508484fc3b https://github.com/galaxyproject/galaxy/commit/c61617fed6ae59f237cb22fa0f61… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSACode. Commit: 12a3f7b54531f667885d1187538c9b06f244744b https://github.com/galaxyproject/galaxy/commit/12a3f7b54531f667885d1187538c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSAAssociation. Commit: 49bb3a66668f94bed1534b007237f0b1db3b71d9 https://github.com/galaxyproject/galaxy/commit/49bb3a66668f94bed1534b007237… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSANonce. Commit: a4d03f0de07df762055210f0c3812cbe0c0bccaf https://github.com/galaxyproject/galaxy/commit/a4d03f0de07df762055210f0c381… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in PSAPartial. Commit: 17eac4fe84465706f3b6b8290ae8872d6985afe7 https://github.com/galaxyproject/galaxy/commit/17eac4fe84465706f3b6b8290ae8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Replace trans.sa_session with sa_session in UserAuthnzToken. Commit: ebb37f8ff02f246344d73db7c3751b531c4fd38f https://github.com/galaxyproject/galaxy/commit/ebb37f8ff02f246344d73db7c375… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Replace trans with app & sa_session in on_the_fly_config function. Commit: 69bd26e6046c0dd18eaae4cee433d34d26d87d80 https://github.com/galaxyproject/galaxy/commit/69bd26e6046c0dd18eaae4cee433… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Remove `app` from `on_the_fly_config` signature. Commit: 8ed5d8c9414f8b086852a2a347d79e530c231b0c https://github.com/galaxyproject/galaxy/commit/8ed5d8c9414f8b086852a2a347d7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6826 from VJalili/authnz_trans Remove `trans` from OIDC-related types Compare: https://github.com/galaxyproject/galaxy/compare/7d9093d5ab30...8ed5d8c9414f **NOTE:** This service has 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] 18b427: Import gxformat2 as an external dependency.
by GitHub 07 Oct '18

07 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18b4274e651f85db2019faba0674613ef02921aa https://github.com/galaxyproject/galaxy/commit/18b4274e651f85db2019faba0674… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M test/base/populators.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py Log Message: ----------- Import gxformat2 as an external dependency. Commit: 319c29937e30075d0dab45bca87577fd86bc7492 https://github.com/galaxyproject/galaxy/commit/319c29937e30075d0dab45bca875… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- gxformat2 - allow CWL style 'in' declarations for step connections. Makes gxformat2 look a lot closer to CWL workflows with Galaxy tools and state. Commit: c7fa2860d807229ebb29233d99c545534f3d7079 https://github.com/galaxyproject/galaxy/commit/c7fa2860d807229ebb29233d99c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Toward new format2 syntaxes in test workflows. Commit: d010077830ccdf2c28e978bc65c9871db646f880 https://github.com/galaxyproject/galaxy/commit/d010077830ccdf2c28e978bc65c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Allow workflow import of workflows with connections that don't have matching empty tool state entries. There is a long conversation in the added doc string. Commit: 7d9093d5ab308301e2ec9e464ce8e7cfbeba77ea https://github.com/galaxyproject/galaxy/commit/7d9093d5ab308301e2ec9e464ce8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py Log Message: ----------- Merge pull request #6807 from jmchilton/gxformat2_030 Support for Enhancements to gxformat2. Compare: https://github.com/galaxyproject/galaxy/compare/10e984ce85c2...7d9093d5ab30 **NOTE:** This service has 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] 50019e: Refactor method for running format 2 workflows int...
by GitHub 06 Oct '18

06 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50019e503adf811a54b54011d64ef92b8a610b13 https://github.com/galaxyproject/galaxy/commit/50019e503adf811a54b54011d64e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Refactor method for running format 2 workflows into populators.py for reuse. Commit: 3e774713a902fb59b4164e4deac2688b9678f0ce https://github.com/galaxyproject/galaxy/commit/3e774713a902fb59b4164e4deac2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml Log Message: ----------- Fill in needed state defaults when importing manually curated workflows. Commit: 10e984ce85c2d02d95cb96a11d1738fb1d6ab951 https://github.com/galaxyproject/galaxy/commit/10e984ce85c2d02d95cb96a11d17… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml Log Message: ----------- Merge pull request #6746 from jmchilton/workflow_state_touch_1 Fill in needed state defaults when importing manually crafted workflows. Compare: https://github.com/galaxyproject/galaxy/compare/56ca1cdef4d3...10e984ce85c2 **NOTE:** This service has 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] 0a6de6: Add more detail about container tags
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a6de6b8d7581a2ca27bad3388b936c6b560ea93 https://github.com/galaxyproject/galaxy/commit/0a6de6b8d7581a2ca27bad3388b9… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add more detail about container tags Explain that singularity container tags are now supported and add some detail about how to use them. Commit: 5601d893a3350a3efca0238d672f059d2404be5c https://github.com/galaxyproject/galaxy/commit/5601d893a3350a3efca0238d672f… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fixes to workding as per nsoranzo Commit: 56ca1cdef4d373958426c5a0028542854edfb48a https://github.com/galaxyproject/galaxy/commit/56ca1cdef4d373958426c5a00285… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6818 from pvanheus/patch-7 Add more detail about container tags Compare: https://github.com/galaxyproject/galaxy/compare/973c73ce722a...56ca1cdef4d3 **NOTE:** This service has 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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