- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 42a461: Fix linting of 16.07 broken with security patches.
by GitHub 23 Dec '16

23 Dec '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 42a461353bc2dd07f60daf33a42e6d45ec7c86a8 https://github.com/galaxyproject/galaxy/commit/42a461353bc2dd07f60daf33a42e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of 16.07 broken with security patches. Commit: 69fe5ae83ae53cb84a2d0bdd9ea53389b8af5a3a https://github.com/galaxyproject/galaxy/commit/69fe5ae83ae53cb84a2d0bdd9ea5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tox.ini Log Message: ----------- Fix 16.07 linting of imports broken with release of flake8-import-order 0.11. This is pinned to 0.11 in release_16.10 and unpinned in dev, when merging forward keep these "forward" branches the same (i.e. do not revert to flake8-import-order 0.10). Commit: b400a15c78faba3b873ecf1ce2237c36bc24f440 https://github.com/galaxyproject/galaxy/commit/b400a15c78faba3b873ecf1ce223… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge pull request #3352 from jmchilton/1607_lintfixes [16.07] Attempt to fix TravisCI for release 16.07. Compare: https://github.com/galaxyproject/galaxy/compare/8b75305c49c3...b400a15c78fa

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[galaxyproject/galaxy] a7818e: Remove workflow testing stuff in test/functional a...
by GitHub 23 Dec '16

23 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a7818e306598e5aa800123578cdad7936c88f34f https://github.com/galaxyproject/galaxy/commit/a7818e306598e5aa800123578cda… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py R test/functional/workflow.py Log Message: ----------- Remove workflow testing stuff in test/functional and references. There are more fully developed approaches including Planemo and wft4galaxy (https://github.com/phnmnl/wft4galaxy) Commit: 58c1828c4c268aa80f1fe62888227d64d63b65d2 https://github.com/galaxyproject/galaxy/commit/58c1828c4c268aa80f1fe6288822… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py R test/functional/workflow.py Log Message: ----------- Merge pull request #3342 from jmchilton/remove_workflow_testing Remove workflow testing stuff in test/functional and references. Compare: https://github.com/galaxyproject/galaxy/compare/8463c8a2024e...58c1828c4c26

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[galaxyproject/infrastructure-playbook] 02bc15: Add n6 as Jenkins slave
by GitHub 22 Dec '16

22 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 02bc15217958781958e7e4771e99047af53a508d https://github.com/galaxyproject/infrastructure-playbook/commit/02bc1521795… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: A galaxyenv/files/jenkins/jenkins_server_user_ssh_config A galaxyenv/files/jenkins/jenkins_slave_user_ssh_config M galaxyenv/group_vars/jenkinsservers.yml M galaxyenv/group_vars/jenkinsslaves.yml A galaxyenv/host_vars/n6.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/playbook.yml A galaxyenv/secret_group_vars/jenkinsslaves.yml R galaxyenv/secret_host_vars/n4.galaxyproject.org.yml Log Message: ----------- Add n6 as Jenkins slave

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[galaxyproject/galaxy] 05cd16: Fix explicit Docker container resolution.
by GitHub 22 Dec '16

22 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05cd16f11cb523345894816ab6cc8165ebe71559 https://github.com/galaxyproject/galaxy/commit/05cd16f11cb523345894816ab6cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Fix explicit Docker container resolution. Fix thanks to @stevecassidy. Fixes #3207. Broken with introduction of container resolution stradegies in #2986. Commit: fe2a1d8ade4fbda158ae035c78133258d7fec099 https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Do not replace Galaxy's Python environment for select tools. This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly. Fixes #3238. Fixes #3224. Fixes https://biostar.usegalaxy.org/p/20865/. Rebased to add a comment as suggested by @nsoranzo. Commit: 4969c4a308fd5bfc8bc52739b024765147af49e8 https://github.com/galaxyproject/galaxy/commit/4969c4a308fd5bfc8bc52739b024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge 16.07 conda fix from #3351 into 16.10. Tricky merge - please review. Conflicts: lib/galaxy/tools/deps/resolvers/conda.py Commit: 14549d0f1b202a720dfc2dbb1f6501fc2cd8fd49 https://github.com/galaxyproject/galaxy/commit/14549d0f1b202a720dfc2dbb1f65… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3354 from jmchilton/1610_conda_fixes [16.10] Merge forward #3351. Commit: 17a752d1f2fbc19fdccbd9dd24ca1bdfd26aae5e https://github.com/galaxyproject/galaxy/commit/17a752d1f2fbc19fdccbd9dd24ca… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Merge pull request #3346 from jmchilton/docker_tools_fix [16.10] Fix explicit Docker container resolution. Commit: 2783212c754ee9449688ce89893ada18afc0b8af https://github.com/galaxyproject/galaxy/commit/2783212c754ee9449688ce89893a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge branch 'release_16.10' into dev Commit: 8463c8a2024eef59d4faded15fd40f7850d7de7e https://github.com/galaxyproject/galaxy/commit/8463c8a2024eef59d4faded15fd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3358 from jmchilton/dev_merge Merge latest release 16.10 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/cac828ee8e91...8463c8a2024e

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[galaxyproject/galaxy] 83d9dd: Expose job metrics
by GitHub 22 Dec '16

22 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83d9ddd0b3e090829e70b95ac6bd26b63179e40f https://github.com/galaxyproject/galaxy/commit/83d9ddd0b3e090829e70b95ac6bd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/show_params.mako Log Message: ----------- Expose job metrics Commit: ae87eb94131e2a0da8ebae4ca6137ba111072852 https://github.com/galaxyproject/galaxy/commit/ae87eb94131e2a0da8ebae4ca613… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/show_params.mako Log Message: ----------- Address the review comments Commit: cac828ee8e91a8e0f4671042702e6898157bfd4e https://github.com/galaxyproject/galaxy/commit/cac828ee8e91a8e0f4671042702e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/show_params.mako Log Message: ----------- Merge pull request #3344 from erasche/expose-metrics Expose metrics to non-admins Compare: https://github.com/galaxyproject/galaxy/compare/c000e68baae4...cac828ee8e91

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[galaxyproject/galaxy] 38d316: Fix history list selector
by GitHub 22 Dec '16

22 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38d3163b2c7d0e9c4e428f4884cbed971a2f5bae https://github.com/galaxyproject/galaxy/commit/38d3163b2c7d0e9c4e428f4884cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix history list selector Commit: 10720fa4f9e26b3feec1a90468f4ecc726a99c05 https://github.com/galaxyproject/galaxy/commit/10720fa4f9e26b3feec1a90468f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Fixup and test core.history.yaml tour. Commit: c000e68baae47dc7624465dacc3c6aa0217ece0a https://github.com/galaxyproject/galaxy/commit/c000e68baae47dc7624465dacc3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Merge pull request #3185 from dannon/tour_history_fixes History Introduction tour fixes for structural changes Compare: https://github.com/galaxyproject/galaxy/compare/7ae30948be60...c000e68baae4

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[galaxyproject/galaxy] 318e5a: Update UCSC_SERVERS list to include new SOE prefix...
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 318e5a23ad0ef2d50debfe72a0366ec5fd8513c3 https://github.com/galaxyproject/galaxy/commit/318e5a23ad0ef2d50debfe72a036… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Update UCSC_SERVERS list to include new SOE prefix. Commit: 7ae30948be60e34bc7b54cbf74f23da45414bad1 https://github.com/galaxyproject/galaxy/commit/7ae30948be60e34bc7b54cbf74f2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #3345 from dannon/ucsc_redirect_fix Update UCSC_SERVERS list to include new(ish?) soe subdomain Compare: https://github.com/galaxyproject/galaxy/compare/306c64d1bc3c...7ae30948be60

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[galaxyproject/galaxy] 05cd16: Fix explicit Docker container resolution.
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 05cd16f11cb523345894816ab6cc8165ebe71559 https://github.com/galaxyproject/galaxy/commit/05cd16f11cb523345894816ab6cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Fix explicit Docker container resolution. Fix thanks to @stevecassidy. Fixes #3207. Broken with introduction of container resolution stradegies in #2986. Commit: 17a752d1f2fbc19fdccbd9dd24ca1bdfd26aae5e https://github.com/galaxyproject/galaxy/commit/17a752d1f2fbc19fdccbd9dd24ca… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Merge pull request #3346 from jmchilton/docker_tools_fix [16.10] Fix explicit Docker container resolution. Compare: https://github.com/galaxyproject/galaxy/compare/14549d0f1b20...17a752d1f2fb

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[galaxyproject/galaxy] fe2a1d: Do not replace Galaxy's Python environment for sel...
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: fe2a1d8ade4fbda158ae035c78133258d7fec099 https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Do not replace Galaxy's Python environment for select tools. This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly. Fixes #3238. Fixes #3224. Fixes https://biostar.usegalaxy.org/p/20865/. Rebased to add a comment as suggested by @nsoranzo. Commit: 4969c4a308fd5bfc8bc52739b024765147af49e8 https://github.com/galaxyproject/galaxy/commit/4969c4a308fd5bfc8bc52739b024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge 16.07 conda fix from #3351 into 16.10. Tricky merge - please review. Conflicts: lib/galaxy/tools/deps/resolvers/conda.py Commit: 14549d0f1b202a720dfc2dbb1f6501fc2cd8fd49 https://github.com/galaxyproject/galaxy/commit/14549d0f1b202a720dfc2dbb1f65… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3354 from jmchilton/1610_conda_fixes [16.10] Merge forward #3351. Compare: https://github.com/galaxyproject/galaxy/compare/5eafa8bae312...14549d0f1b20

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[galaxyproject/galaxy] fe2a1d: Do not replace Galaxy's Python environment for sel...
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: fe2a1d8ade4fbda158ae035c78133258d7fec099 https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Do not replace Galaxy's Python environment for select tools. This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly. Fixes #3238. Fixes #3224. Fixes https://biostar.usegalaxy.org/p/20865/. Rebased to add a comment as suggested by @nsoranzo. Commit: 8b75305c49c3e9fe3fb4665177af977cdfc9a582 https://github.com/galaxyproject/galaxy/commit/8b75305c49c3e9fe3fb4665177af… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3351 from jmchilton/galaxy_environment_fixes [16.07] Do not allow Conda to replace Galaxy's Python environment for select tools. Compare: https://github.com/galaxyproject/galaxy/compare/22fda449f9d4...8b75305c49c3

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