- galaxy-commits - lists.galaxyproject.org

[galaxyproject/ansible-galaxy]
by Helena Rasche 09 Apr '19

09 Apr '19

Branch: refs/heads/fix Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] d787e0: do not run in check mode
by Helena Rasche 09 Apr '19

09 Apr '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: d787e0774345d34a6ea24410d737afb90625a9ad https://github.com/galaxyproject/ansible-galaxy/commit/d787e0774345d34a6ea2… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-04-09 (Tue, 09 Apr 2019) Changed paths: M tasks/dependencies.yml Log Message: ----------- do not run in check mode Commit: 4e763911859058df529f1473810a4fd3060e147b https://github.com/galaxyproject/ansible-galaxy/commit/4e763911859058df529f… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-04-09 (Tue, 09 Apr 2019) Changed paths: M tasks/dependencies.yml Log Message: ----------- Merge pull request #65 from galaxyproject/asdf Do not attempt to install conditional deps in check mode Compare: https://github.com/galaxyproject/ansible-galaxy/compare/badffb979b9a...4e76…

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[galaxyproject/ansible-galaxy] d787e0: do not run in check mode
by Helena Rasche 09 Apr '19

09 Apr '19

Branch: refs/heads/asdf Home: https://github.com/galaxyproject/ansible-galaxy Commit: d787e0774345d34a6ea24410d737afb90625a9ad https://github.com/galaxyproject/ansible-galaxy/commit/d787e0774345d34a6ea2… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-04-09 (Tue, 09 Apr 2019) Changed paths: M tasks/dependencies.yml Log Message: ----------- do not run in check mode

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[galaxyproject/ansible-galaxy] 526e7d: option
by Helena Rasche 05 Apr '19

05 Apr '19

Branch: refs/heads/fix Home: https://github.com/galaxyproject/ansible-galaxy Commit: 526e7d55bd86c5cbd1d0d4989bbb40e9cf40865f https://github.com/galaxyproject/ansible-galaxy/commit/526e7d55bd86c5cbd1d0… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-04-05 (Fri, 05 Apr 2019) Changed paths: M defaults/main.yml M tasks/paths.yml Log Message: ----------- option

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The Galaxy-Commits List is going away
by Dave Clements 11 Mar '19

11 Mar '19

Hello all, This will be one of the last message posted to the Galaxy-Commits mailing list. This list was created almost 9 years ago as a way for the community to easily find out what was happening with the Galaxy code base. A lot has happened in 9 years, including 1) moving to GitHub <https://github.com/galaxyproject>, and 2) a proliferation of related repositories. A single "commits" list no longer makes sense and is no longer necessary, as it's easy to set up email alerts for commits in GitHub. To continue receiving email alerts about commits: 1) Log in to GitHub. 2) Navigate to the home page for the repo you are interested in, say https://github.com/galaxyproject/galaxy 3) Select "Watching" from the "Watch" pulldown menu at the top of the page. 4) Go to your account's settings -> Notifications page and tell GitHub how you want to get your notifications. Thanks and see you in GitHub, Dave C -- https://galaxyproject.org/ https://usegalaxy.org/

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[galaxyproject/galaxy] 88fd52: Test PJA actions
by Dannon 11 Mar '19

11 Mar '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 88fd52a4bb55641fe44a630ae5702adcc630f3a5 https://github.com/galaxyproject/galaxy/commit/88fd52a4bb55641fe44a630ae570… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test PJA actions The rename action works, the hide action fails. Building this to fix https://github.com/galaxyproject/galaxy/issues/7473. Commit: f26a1177b871c65dd14258024cc1ef65d4e7a8c9 https://github.com/galaxyproject/galaxy/commit/f26a1177b871c65dd14258024cc1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix delayed post jobs actions for DatabaseOperationTools Commit: dc232273781bc96a3cda8b4f83245ae7e603fa01 https://github.com/galaxyproject/galaxy/commit/dc232273781bc96a3cda8b4f8324… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Add tests for delete_intermediate and change_datatype PJAs `change_datatype` wasn't part of gxformat2, so this also requires a new release of gxformat2 with https://github.com/jmchilton/gxformat2/pull/7 Commit: 4cceb67d62dbae06dd6726b0db32e1d757505c3c https://github.com/galaxyproject/galaxy/commit/4cceb67d62dbae06dd6726b0db32… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Fix ChangeDatatype action for collection output Commit: 34725f61ac61dcf1366ec20de857fe7d67e9f0b3 https://github.com/galaxyproject/galaxy/commit/34725f61ac61dcf1366ec20de857… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Consolidate hiding HDAs in DatabaseOperation tools This fixes dataset being added to histories when the source HDA is visible. Commit: df8a4dcf16c60f323aa11001a31079345c4803f5 https://github.com/galaxyproject/galaxy/commit/df8a4dcf16c60f323aa11001a310… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py Log Message: ----------- Fix ChangeDatatypeAction for collections Commit: 5522360953f8d578792cf2fd681db007a97a8de5 https://github.com/galaxyproject/galaxy/commit/5522360953f8d578792cf2fd681d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update to gxformat2 with change_datatype action Commit: de7732f2777b63f02ac4cc31213831813421cc8b https://github.com/galaxyproject/galaxy/commit/de7732f2777b63f02ac4cc312138… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Merge pull request #7511 from mvdbeek/backport_pja_fixes [19.01] Backport Fix post job actions for Database Operation tools, implement change_datatype for collection output Compare: https://github.com/galaxyproject/galaxy/compare/aef53f6cde6f...de7732f2777b

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[galaxyproject/galaxy] 75ae68: remove biostar integrations
by Dannon 11 Mar '19

11 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 75ae68693fb1c0669de8a48df4ae64f9c45e0124 https://github.com/galaxyproject/galaxy/commit/75ae68693fb1c0669de8a48df4ae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M config/error_report.yml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py R lib/galaxy/tools/error_reports/plugins/biostars.py R lib/galaxy/util/biostar.py M lib/galaxy/webapps/galaxy/config_schema.yml R lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/config.py R templates/webapps/galaxy/biostar/post_redirect.mako M templates/webapps/galaxy/galaxy.masthead.mako M test/functional/webhooks/masthead_test/config.yml Log Message: ----------- remove biostar integrations we stopped using it and this will lower our maintenance burden Commit: 5d90d78d2c2a57a62dd692849c4fc1847d4ac981 https://github.com/galaxyproject/galaxy/commit/5d90d78d2c2a57a62dd692849c4f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M config/error_report.yml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py R lib/galaxy/tools/error_reports/plugins/biostars.py R lib/galaxy/util/biostar.py M lib/galaxy/webapps/galaxy/config_schema.yml R lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/config.py R templates/webapps/galaxy/biostar/post_redirect.mako M templates/webapps/galaxy/galaxy.masthead.mako M test/functional/webhooks/masthead_test/config.yml Log Message: ----------- Merge pull request #7510 from martenson/rip-biostar remove biostar integrations Compare: https://github.com/galaxyproject/galaxy/compare/cc62d06899b1...5d90d78d2c2a

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[galaxyproject/galaxy] 34dcc2: Test PJA actions
by John Chilton 11 Mar '19

11 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 34dcc2458ef5f1b6f51aae899d47b3708d5c5811 https://github.com/galaxyproject/galaxy/commit/34dcc2458ef5f1b6f51aae899d47… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test PJA actions The rename action works, the hide action fails. Building this to fix https://github.com/galaxyproject/galaxy/issues/7473. Commit: 0951324aef6935104e17a14f9e0fe21f3d29262b https://github.com/galaxyproject/galaxy/commit/0951324aef6935104e17a14f9e0f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix delayed post jobs actions for DatabaseOperationTools Commit: 62d8f2d5dfbee3b3092039902cced90b8d08ed40 https://github.com/galaxyproject/galaxy/commit/62d8f2d5dfbee3b3092039902cce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Add tests for delete_intermediate and change_datatype PJAs `change_datatype` wasn't part of gxformat2, so this also requires a new release of gxformat2 with https://github.com/jmchilton/gxformat2/pull/7 Commit: 54adb6e73a193291dc27c9ed9a0dc24012c305ff https://github.com/galaxyproject/galaxy/commit/54adb6e73a193291dc27c9ed9a0d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Fix ChangeDatatype action for collection output Commit: 199468e920a409cb6a7dbb5ae40c3d7c3dd27028 https://github.com/galaxyproject/galaxy/commit/199468e920a409cb6a7dbb5ae40c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Consolidate hiding HDAs in DatabaseOperation tools This fixes dataset being added to histories when the source HDA is visible. Commit: 377bffd3aedd2a98c40a16b9ebbff95902cb19dc https://github.com/galaxyproject/galaxy/commit/377bffd3aedd2a98c40a16b9ebbf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py Log Message: ----------- Fix ChangeDatatypeAction for collections Commit: 48c303365c5d214cff823138a3ef510afe38350f https://github.com/galaxyproject/galaxy/commit/48c303365c5d214cff823138a3ef… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update to gxformat2 with change_datatype action Commit: cc62d06899b161645e7bf59a3ea3762ec6c2dfbb https://github.com/galaxyproject/galaxy/commit/cc62d06899b161645e7bf59a3ea3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Merge pull request #7480 from mvdbeek/fix_build_list_pjas Fix post job actions for Database Operation tools, implement change_datatype for collection output Compare: https://github.com/galaxyproject/galaxy/compare/8ae44cd8cb87...cc62d06899b1

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[galaxyproject/galaxy] c491b5: Add Globus config to PSA authnz backend.
by Martin Cech 11 Mar '19

11 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c491b5ea4e0d31ed19eed6f208c72bf1a7dc75f3 https://github.com/galaxyproject/galaxy/commit/c491b5ea4e0d31ed19eed6f208c7… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add Globus config to PSA authnz backend. Commit: 157c14088c28ac6ed0634de2a1355e6a983537b2 https://github.com/galaxyproject/galaxy/commit/157c14088c28ac6ed0634de2a135… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Make idp name matching generic, read from a dict of supported backends. Commit: c148606a4243d231bc1d0d69b7479f04122d8b72 https://github.com/galaxyproject/galaxy/commit/c148606a4243d231bc1d0d69b747… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Make idp setup generic. Commit: 686aa18a303c80b862331071c7824c7eb22e2acb https://github.com/galaxyproject/galaxy/commit/686aa18a303c80b862331071c782… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Add Globus to OIDC backends config file. Commit: c6afb31f2247d9f8cb188ccb241d3c900031d80f https://github.com/galaxyproject/galaxy/commit/c6afb31f2247d9f8cb188ccb241d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Add a link to Globus documentaiton page on backend config example. Commit: 6a98f96b9018a99450f3692f92ccb5f47090e092 https://github.com/galaxyproject/galaxy/commit/6a98f96b9018a99450f3692f92cc… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add Elixir backend. Commit: 38a0733b799dd60689ad3071b251196607cc0f2a https://github.com/galaxyproject/galaxy/commit/38a0733b799dd60689ad3071b251… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add PixelPin backend. Commit: 61efb8c838c6c14535b73457e7e951b3a77ebf3f https://github.com/galaxyproject/galaxy/commit/61efb8c838c6c14535b73457e7e9… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt Log Message: ----------- Update PSA version to 3.1.0 and run `make update-dependencies`. Commit: e101d14230df11ae3acedc92c1a27775ae9cac8f https://github.com/galaxyproject/galaxy/commit/e101d14230df11ae3acedc92c1a2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- More dep updates Commit: 06dd2f8bae88230bddacff4318ff83a405352be8 https://github.com/galaxyproject/galaxy/commit/06dd2f8bae88230bddacff4318ff… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Revert sqlalchemy version increment, since it breaks all the tests. Commit: 8e56a53a7bfe5f93618c9d8e388de41f0640fb8a https://github.com/galaxyproject/galaxy/commit/8e56a53a7bfe5f93618c9d8e388d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Drop support to Elixir IdP per missing ID token in authn response. Commit: 81fbfdac4aba04a37c439eb373b0b62e38ca38e4 https://github.com/galaxyproject/galaxy/commit/81fbfdac4aba04a37c439eb373b0… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Drop support for PixelPin IdP. Commit: 8ae44cd8cb87aa0b3d68c149472e76f7d07e750b https://github.com/galaxyproject/galaxy/commit/8ae44cd8cb87aa0b3d68c149472e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M config/oidc_backends_config.xml.sample M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt Log Message: ----------- Merge pull request #7463 from VJalili/upgrade_psa_2 Update to PSA 3.1 and support login with Globus identity Compare: https://github.com/galaxyproject/galaxy/compare/1ca256aaba84...8ae44cd8cb87

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[galaxyproject/usegalaxy-playbook] 0982f6: Standardize galaxy-bugs address format.
by Nate Coraor 11 Mar '19

11 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0982f6ceafdae5db7bbdf734e3ecf25e06f6f707 https://github.com/galaxyproject/usegalaxy-playbook/commit/0982f6ceafdae5db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M env/common/files/galaxy/error/413/index.html M env/common/files/galaxy/error/502/index.shtml M env/main/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxywebservers.yml Log Message: ----------- Standardize galaxy-bugs address format.

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