Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6233a408cc93152a379651db3cc143d368f78dda https://github.com/galaxyproject/galaxy/commit/6233a408cc93152a379651db3cc14... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst Log Message: ----------- Release notes templated; still needs manual curation Commit: 25fc1617030d392f85abb65ccd95f913561919e2 https://github.com/galaxyproject/galaxy/commit/25fc1617030d392f85abb65ccd95f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Update RN with new merges. Commit: 8c05e2f5f1677950a3279ffa30ccbf8949aa35e4 https://github.com/galaxyproject/galaxy/commit/8c05e2f5f1677950a3279ffa30ccb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add grapdot datatype. Commit: 6ac5966c5e1a95e93c5923a4eddf5fa971518bd6 https://github.com/galaxyproject/galaxy/commit/6ac5966c5e1a95e93c5923a4eddf5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add removal of upgrade logic specific to datatypes from 17.05 Commit: 0698a71861afadb7f16be765223819178d294c30 https://github.com/galaxyproject/galaxy/commit/0698a71861afadb7f16be76522381... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Another few stragglers. Commit: d3db21fa82a834d0d9fa90106b3fa2b4911708dc https://github.com/galaxyproject/galaxy/commit/d3db21fa82a834d0d9fa90106b3fa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6755 Commit: 6cb4c32eb4e613b4d90680450d11804779e5b4a5 https://github.com/galaxyproject/galaxy/commit/6cb4c32eb4e613b4d90680450d118... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6768 Commit: ee47fdb50cef70dd2b940c42594611863e51bde7 https://github.com/galaxyproject/galaxy/commit/ee47fdb50cef70dd2b940c4259461... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6753, 6771 Commit: c51178578dcf67c8dbe16d3d8320f660e0c80027 https://github.com/galaxyproject/galaxy/commit/c51178578dcf67c8dbe16d3d8320f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more PRs Commit: ff65263ab2ee1351bbed11709d8536de694a5776 https://github.com/galaxyproject/galaxy/commit/ff65263ab2ee1351bbed11709d853... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6789 Commit: 96d77b0791592b35fb6e4201d011f5c223060cfe https://github.com/galaxyproject/galaxy/commit/96d77b0791592b35fb6e4201d011f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- More PRs, stub out proposed features. Commit: 3d772dc03bf0ffa1c6d010596488c5cd3a26901d https://github.com/galaxyproject/galaxy/commit/3d772dc03bf0ffa1c6d010596488c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6791 Commit: ce3d43221a8d4e843a25c49c679a4ab75fd3756c https://github.com/galaxyproject/galaxy/commit/ce3d43221a8d4e843a25c49c679a4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- More Prs for the release notes. Commit: b5f7955c5addba2664b6375aa87c9873b2949fad https://github.com/galaxyproject/galaxy/commit/b5f7955c5addba2664b6375aa87c9... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Announce Python 3 Beta Support Commit: 90718843096f115324be8a086d7a6089e0086703 https://github.com/galaxyproject/galaxy/commit/90718843096f115324be8a086d7a6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add deprecation notice for username being null Commit: afffd9bdaa66b4fcadbd790a25387654c23e4aa6 https://github.com/galaxyproject/galaxy/commit/afffd9bdaa66b4fcadbd790a25387... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add final PR. Commit: eacec03d10c00503fdbb4da107254c06082507bb https://github.com/galaxyproject/galaxy/commit/eacec03d10c00503fdbb4da107254... Author: John Chilton <jmchilton@gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Update.... Commit: 4d165a567139abc3b4ad3baac422c9c0ebbaf554 https://github.com/galaxyproject/galaxy/commit/4d165a567139abc3b4ad3baac422c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:jmchilton/galaxy into 18.09_release_notes Commit: 386229d1ce58522be4bece11b8f9473f5dce56b9 https://github.com/galaxyproject/galaxy/commit/386229d1ce58522be4bece11b8f94... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Re-add removed PRs (bad merge I think) Commit: fdaf9ac8641cfa5fa0aad706310aec2b31692ac1 https://github.com/galaxyproject/galaxy/commit/fdaf9ac8641cfa5fa0aad706310ae... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Link up workflow PRs Commit: 381d6ad83183a822baebca44622e506d088f10b1 https://github.com/galaxyproject/galaxy/commit/381d6ad83183a822baebca44622e5... Author: Dannon Baker <dannon.baker@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. Commit: 02410b270d025e5fb8cb4e2036fb627051c7850a https://github.com/galaxyproject/galaxy/commit/02410b270d025e5fb8cb4e2036fb6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Register job monitor as postfork function This should fix https://github.com/galaxyproject/galaxy/issues/6831, and might fix https://github.com/galaxyproject/galaxy/issues/6261. Commit: 6b62a57047f8877ba36e0767aaee04879bbc20c0 https://github.com/galaxyproject/galaxy/commit/6b62a57047f8877ba36e0767aaee0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Should fix bug Jen saw with history panel being masked at bottom Commit: 5844bdc7aa0a90d992c3b36e041abb8d103e3b95 https://github.com/galaxyproject/galaxy/commit/5844bdc7aa0a90d992c3b36e041ab... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Add integration test for remote shell CLI runners This tests both the SecureShell and Paramiko shell plugins and the Slurm and Torque CLI runner. Commit: 57a1f19b069597bde97852b3e0d0a3e1c0068bc4 https://github.com/galaxyproject/galaxy/commit/57a1f19b069597bde97852b3e0d0a... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Fix slurm cli plugin by avoiding `shell=True` in subprocess Fixes the remaining issue in https://github.com/galaxyproject/galaxy/issues/6831#issuecomment-428097520 Commit: fc28e0bd83a2df59f11b80f0119e67da1326887f https://github.com/galaxyproject/galaxy/commit/fc28e0bd83a2df59f11b80f0119e6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use long-form options Commit: 5e12e509bf20d7e4f4464a60f04c7479cb4e232d https://github.com/galaxyproject/galaxy/commit/5e12e509bf20d7e4f4464a60f04c7... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Fix selection of job plugin and image Thanks @nsoranzo. Commit: b08c6219c3fe771e00d0b6d8b9adb1c97e38e9a6 https://github.com/galaxyproject/galaxy/commit/b08c6219c3fe771e00d0b6d8b9adb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Simplify ssh key handling in integration test Commit: ac3e1ca1d0d7bb85cc00e2e113f70e3576f0b048 https://github.com/galaxyproject/galaxy/commit/ac3e1ca1d0d7bb85cc00e2e113f70... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Use Crypto to generate SSH keys Also remove key files in `stop_ssh_docker()`. Commit: cd62461e8486bd4e44aee51907f7d515718ef3d8 https://github.com/galaxyproject/galaxy/commit/cd62461e8486bd4e44aee51907f7d... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6839 from dannon/unified-panel-style-tweaks [18.09] Unified panel style bottom padding fix Commit: a1f7634fd7dca45902a2d3f67d2279db3aa2270d https://github.com/galaxyproject/galaxy/commit/a1f7634fd7dca45902a2d3f67d227... Author: thobalose <lose.thoba@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Updated volume kwds. Commit: fe6c1738c0ea3ee35fa34fec8a2c2e8eb97ec044 https://github.com/galaxyproject/galaxy/commit/fe6c1738c0ea3ee35fa34fec8a2c2... Author: Dannon <dannon.baker@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Merge pull request #6851 from martenson/backport-gie-kwds [18.05] Updated volume kwds for GIEs Commit: fd0b24ecd2bff2f8baa636304e45eb2dbdcaf3a9 https://github.com/galaxyproject/galaxy/commit/fd0b24ecd2bff2f8baa636304e45e... Author: Dannon <dannon.baker@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge pull request #6845 from mvdbeek/fix_slurm_cli_on_secure_shell [18.05] Fix slurm cli on secure shell Commit: c1383bc2d55cb6565fbd63eb4088c734a805700e https://github.com/galaxyproject/galaxy/commit/c1383bc2d55cb6565fbd63eb4088c... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Small fixes Commit: c6193ca4406450cdaa01b9c27bcfb871c916544c https://github.com/galaxyproject/galaxy/commit/c6193ca4406450cdaa01b9c27bcfb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Update DEVTEAM, rebuild, include a few new PRs. Commit: 7cb2eb57aca559c86b3d938912d8f7bde5da9f74 https://github.com/galaxyproject/galaxy/commit/7cb2eb57aca559c86b3d938912d8f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:galaxyproject/galaxy into 18.09_release_notes Commit: baa992d217032b809d321cb800cd2f41af401c63 https://github.com/galaxyproject/galaxy/commit/baa992d217032b809d321cb800cd2... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge pull request #6836 from mvdbeek/fix_job_monitor_thread [18.01] Register job monitor thread as postfork function Commit: d33006cf33f71f4992eebefb7c3065606088aea1 https://github.com/galaxyproject/galaxy/commit/d33006cf33f71f4992eebefb7c306... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Final docs update Commit: d42b899b7805f722a77153c4e33fffcfad846ce0 https://github.com/galaxyproject/galaxy/commit/d42b899b7805f722a77153c4e33ff... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Embellish 18.09 release notes Commit: 9251484e7236cd881cb4df64265a3cee2e654d83 https://github.com/galaxyproject/galaxy/commit/9251484e7236cd881cb4df64265a3... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6731 from galaxyproject/18.09_release_notes [18.09] 18.09 release notes Commit: 20f60a5a44842dda8ffe7b97d1b60b6c5ecfdd9d https://github.com/galaxyproject/galaxy/commit/20f60a5a44842dda8ffe7b97d1b60... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- update paramiko dep Commit: 2c14c2afc4d39626096c3d15828b8c3001aab40f https://github.com/galaxyproject/galaxy/commit/2c14c2afc4d39626096c3d15828b8... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6859 from martenson/paramiko-update [18.09] update paramiko dep Commit: a8fa5a1d4a6c801fc230c037129671978955916c https://github.com/galaxyproject/galaxy/commit/a8fa5a1d4a6c801fc230c03712967... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: d22f652f918f7a49d80ede8652d335d41c478546 https://github.com/galaxyproject/galaxy/commit/d22f652f918f7a49d80ede8652d33... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/util/monitors.py M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 5e71401a7eb502479c7a9b69e60a2351a82258d7 https://github.com/galaxyproject/galaxy/commit/5e71401a7eb502479c7a9b69e60a2... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/util/monitors.py M scripts/bootstrap_history.py M static/style/blue/base.css M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b2477d1223df...5e71401a7eb5 **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.