- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] a47a4f: Remove len(stderr), breaks on recent docker versio...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a47a4f40b47302c43dea33f8b040f41570b0587c https://github.com/galaxyproject/galaxy/commit/a47a4f40b47302c43dea33f8b040… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove len(stderr), breaks on recent docker versions Commit: f2a27acff8fd5d199eda841fd575305c3644c439 https://github.com/galaxyproject/galaxy/commit/f2a27acff8fd5d199eda841fd575… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Drop Python 2.6 with 16.04. xref #1596 Commit: b4020934793829f3735fa696de1fa3237391d945 https://github.com/galaxyproject/galaxy/commit/b4020934793829f3735fa696de1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- format_source in workflow editor is too restrictive. Case made well by @erasche on #1746, fixes #1746. To resolve this more correctly (and many other potential type problems) - the workflow editor should be significantly reworked to track the datatype (or a range of datatypes) on each terminal (the way it does for collection mapping information). The change would be a weeks worth of development effort and inappropriate to apply to a release branch. Commit: 9acbfdf3c3444ca0cb0cf87f80c57d00765673d9 https://github.com/galaxyproject/galaxy/commit/9acbfdf3c3444ca0cb0cf87f80c5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Fix chrome-only intermittent rendering error of font awesome icons that have their sizes changed by overriding 4.2 font-size inheritance rule from core.less Commit: 3621d6f2212566b8a172424177b8eafc92af7fca https://github.com/galaxyproject/galaxy/commit/3621d6f2212566b8a172424177b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1784 from carlfeberhard/fix.fa [16.01] Fix chrome-only intermittent rendering error of font awesome icons th… Commit: 805b5906b2f43947af36814fe67b5914acc35a08 https://github.com/galaxyproject/galaxy/commit/805b5906b2f43947af36814fe67b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1772 from jmchilton/python26_drop [16.01] Deprecation notice - Python 2.6. Commit: a5c30c563e878c3b0171bdc992eaea248e2371cf https://github.com/galaxyproject/galaxy/commit/a5c30c563e878c3b0171bdc992ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1771 from mvdbeek/16.01_fix_ies [16.01] Remove len(stderr), breaks on recent docker versions Commit: 6bb43aa4aff83f832997d01fc5663b9d501bc866 https://github.com/galaxyproject/galaxy/commit/6bb43aa4aff83f832997d01fc566… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- Merge pull request #1786 from jmchilton/format_source_restrictive [16.01] format_source in workflow editor is too restrictive. Commit: 1f530b45b3d6815a4ff876fda98ca57bf7a2ef89 https://github.com/galaxyproject/galaxy/commit/1f530b45b3d6815a4ff876fda98c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M doc/source/releases/16.01_announce.rst M lib/galaxy/workflow/modules.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M test/functional/tools/output_format.xml Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2a64fac0c7bf...1f530b45b3d6

1 0

[galaxyproject/galaxy] b40209: format_source in workflow editor is too restrictiv...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: b4020934793829f3735fa696de1fa3237391d945 https://github.com/galaxyproject/galaxy/commit/b4020934793829f3735fa696de1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- format_source in workflow editor is too restrictive. Case made well by @erasche on #1746, fixes #1746. To resolve this more correctly (and many other potential type problems) - the workflow editor should be significantly reworked to track the datatype (or a range of datatypes) on each terminal (the way it does for collection mapping information). The change would be a weeks worth of development effort and inappropriate to apply to a release branch. Commit: 6bb43aa4aff83f832997d01fc5663b9d501bc866 https://github.com/galaxyproject/galaxy/commit/6bb43aa4aff83f832997d01fc566… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- Merge pull request #1786 from jmchilton/format_source_restrictive [16.01] format_source in workflow editor is too restrictive. Compare: https://github.com/galaxyproject/galaxy/compare/a5c30c563e87...6bb43aa4aff8

1 0

[galaxyproject/galaxy] c8469b: Refactor the Html Datatype Class into text.py inst...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c8469b7d0e788eb0a1b4e80b686eebfd5a3e6d11 https://github.com/galaxyproject/galaxy/commit/c8469b7d0e788eb0a1b4e80b686e… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refactor the Html Datatype Class into text.py instead of images.py Commit: 2a64fac0c7bf098b1c459055b6d145f07b4d178a https://github.com/galaxyproject/galaxy/commit/2a64fac0c7bf098b1c459055b6d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #1760 from remimarenco/html_refactoring Refactor the Html Datatype Class into text.py instead of images.py Compare: https://github.com/galaxyproject/galaxy/compare/a41f4750179c...2a64fac0c7bf

1 0

[galaxyproject/galaxy] a47a4f: Remove len(stderr), breaks on recent docker versio...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: a47a4f40b47302c43dea33f8b040f41570b0587c https://github.com/galaxyproject/galaxy/commit/a47a4f40b47302c43dea33f8b040… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove len(stderr), breaks on recent docker versions Commit: a5c30c563e878c3b0171bdc992eaea248e2371cf https://github.com/galaxyproject/galaxy/commit/a5c30c563e878c3b0171bdc992ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1771 from mvdbeek/16.01_fix_ies [16.01] Remove len(stderr), breaks on recent docker versions Compare: https://github.com/galaxyproject/galaxy/compare/805b5906b2f4...a5c30c563e87

1 0

[galaxyproject/galaxy] f2a27a: Drop Python 2.6 with 16.04.
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f2a27acff8fd5d199eda841fd575305c3644c439 https://github.com/galaxyproject/galaxy/commit/f2a27acff8fd5d199eda841fd575… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Drop Python 2.6 with 16.04. xref #1596 Commit: 805b5906b2f43947af36814fe67b5914acc35a08 https://github.com/galaxyproject/galaxy/commit/805b5906b2f43947af36814fe67b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1772 from jmchilton/python26_drop [16.01] Deprecation notice - Python 2.6. Compare: https://github.com/galaxyproject/galaxy/compare/3621d6f22125...805b5906b2f4

1 0

[galaxyproject/galaxy] 9acbfd: Fix chrome-only intermittent rendering error of fo...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9acbfdf3c3444ca0cb0cf87f80c57d00765673d9 https://github.com/galaxyproject/galaxy/commit/9acbfdf3c3444ca0cb0cf87f80c5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Fix chrome-only intermittent rendering error of font awesome icons that have their sizes changed by overriding 4.2 font-size inheritance rule from core.less Commit: 3621d6f2212566b8a172424177b8eafc92af7fca https://github.com/galaxyproject/galaxy/commit/3621d6f2212566b8a172424177b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1784 from carlfeberhard/fix.fa [16.01] Fix chrome-only intermittent rendering error of font awesome icons th… Compare: https://github.com/galaxyproject/galaxy/compare/4c815a7d0589...3621d6f22125

1 0

[galaxyproject/galaxy] dda851: Fix sections
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dda851def5e30ea0b48bd9535a7b2f075a1af63b https://github.com/galaxyproject/galaxy/commit/dda851def5e30ea0b48bd9535a7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix sections Commit: a41f4750179c7306c176a6149e821e2a32993fcf https://github.com/galaxyproject/galaxy/commit/a41f4750179c7306c176a6149e82… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1783 from guerler/fix_sections_000 Fix tool form rendering of sections Compare: https://github.com/galaxyproject/galaxy/compare/390d3b7eb70b...a41f4750179c

1 0

[galaxyproject/galaxy] dbab6f: Workaround for #1739 - fixing up subworkflow inut ...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dbab6f5b979f19c33c3cd1aeb5c459dcc5612eec https://github.com/galaxyproject/galaxy/commit/dbab6f5b979f19c33c3cd1aeb5c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Workaround for #1739 - fixing up subworkflow inut connections. Do the same relaxed thing we do for inputs of type 'input' as we do for outputs of this type. Someday we should have better tracking, but such a change is probably not wise for a release branch. Commit: 5b720b4a02408a0601e7ecaf4fb2374c8c5753a7 https://github.com/galaxyproject/galaxy/commit/5b720b4a02408a0601e7ecaf4fb2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1774 from jmchilton/wf_fixes [16.01] Workaround for #1739 - fixing up subworkflow input connections. Commit: 4c815a7d0589a00df8c8fffba730a79030ad7791 https://github.com/galaxyproject/galaxy/commit/4c815a7d0589a00df8c8fffba730… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1778 from nsoranzo/release_16.01_fix_download_file [16.01] Strip URL of download_file and download_by_url install actions. Commit: 390d3b7eb70b438d215d66180342aa86c9e1e7f1 https://github.com/galaxyproject/galaxy/commit/390d3b7eb70b438d215d66180342… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge branch 'release_16.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/f06b8205897a...390d3b7eb70b

1 0

[galaxyproject/usegalaxy-playbook] c1f80b: Update Test and Main Tool Shed
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c1f80b83ba1e5edd4b1751b356faf5d8ee93d0a0 https://github.com/galaxyproject/usegalaxy-playbook/commit/c1f80b83ba1e5edd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M production/group_vars/toolshedservers.yml M stage/group_vars/toolshedservers.yml Log Message: ----------- Update Test and Main Tool Shed

1 0

[galaxyproject/usegalaxy-playbook] a63287: Update Test and Main
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a63287b90a825caad36a7caa5c08a9db50304e21 https://github.com/galaxyproject/usegalaxy-playbook/commit/a63287b90a825caa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version A production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample A production/files/interactive_environments/plugins/phinch/config/phinch.xml A production/files/interactive_environments/plugins/phinch/static/js/phinch.js A production/files/interactive_environments/plugins/phinch/templates/phinch.mako M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/group_vars/all.yml M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/all.yml M stage/inventory Log Message: ----------- Update Test and Main Commit: 55a3aea169de339b7dd380e09283613c2eddeed2 https://github.com/galaxyproject/usegalaxy-playbook/commit/55a3aea169de339b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs from Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c9696f8218c4...…

1 0