November 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] a16cb0: Fix for re-installing an uninstalled TS repository...
by GitHub 22 Nov '15

22 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a16cb06705676aa49e725c8ab58521c239dfea4d https://github.com/galaxyproject/galaxy/commit/a16cb06705676aa49e725c8ab585… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-22 (Sun, 22 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix for re-installing an uninstalled TS repository with a dependency where both the repository and the dependency were updated in the TS after the repository was uninstalled. Commit: 11f9fed4acb3fb912bc0e0e5c0232fb85c974f2f https://github.com/galaxyproject/galaxy/commit/11f9fed4acb3fb912bc0e0e5c023… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-22 (Sun, 22 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1154 from gregvonkuster/dev Fix for re-installing an uninstalled TS repository with a dependency Compare: https://github.com/galaxyproject/galaxy/compare/2e510bd5e12a...11f9fed4acb3

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[galaxyproject/galaxy] 312746: Allow accessing collection elements in format_sour...
by GitHub 21 Nov '15

21 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 312746d1698e99e13b9a60db881d0093da6cc4c0 https://github.com/galaxyproject/galaxy/commit/312746d1698e99e13b9a60db881d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_actions.py Log Message: ----------- Allow accessing collection elements in format_source. Can do it by numeric index or element name, e.g. input[0] or input["forward"]. Only works for 1-D collections. Implements #699. Run new and most relevant existing tests with the following commands: ``` nosetests test/unit/tools/test_actions.py ./run_tests.sh -framework -id output_format_collection ./run_tests.sh -framework -id output_format ``` Commit: 2e510bd5e12ab5e2c401e835e0f84f29376766db https://github.com/galaxyproject/galaxy/commit/2e510bd5e12ab5e2c401e835e0f8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-21 (Sat, 21 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_actions.py Log Message: ----------- Merge pull request #1113 from jmchilton/format_source_collection Allow accessing collection elements in format_source. Compare: https://github.com/galaxyproject/galaxy/compare/ab0829f2e8df...2e510bd5e12a

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[galaxyproject/galaxy] b4c77b: Introduce "Format 2" workflow definitions.
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4c77b761799b3a8752a6fec500717b1a6f3818b https://github.com/galaxyproject/galaxy/commit/b4c77b761799b3a8752a6fec5007… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py Log Message: ----------- Introduce "Format 2" workflow definitions. This is a slight tightening up of the ad-hoc, experimental workflow YAML definition used by the test framework (and by Kyle, but lets just admit Kyle is part of Galaxy's test framework). This format is still defined entirely client side by transcoding the YAML or python object description into real (or format 1) Galaxy workflows - so these cannot realisticaly be declared part of Galaxy's public interface and can remain experimental and subject to change. In addition to refactoring the code implementing these workflows for upstream modifications to explore new features, the format itself has been made slightly more stringent in two ways: - 'steps' must now be explicit (previously converted auto-convert list to dict). - Ensure the workflow declared a 'class' is defined and the class is 'GalaxyWorkflow'. This will help with discovery of workflow objects with downstream tooling (planemo for workflows?) and brings the Galaxy definition slightly more inline with the CWL definition for workflows (very slightly). Commit: ab0829f2e8df480d467f3b575c18a1ace38543cd https://github.com/galaxyproject/galaxy/commit/ab0829f2e8df480d467f3b575c18… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #1096 from jmchilton/format_2 Outline "Format 2" workflow definitions. Compare: https://github.com/galaxyproject/galaxy/compare/a664deeee76b...ab0829f2e8df

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[galaxyproject/galaxy] 40e3e7: Rebuild style with lessc > 2.5 (which everyone nee...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 40e3e7926aec154fa5f761cf5a7e84fad98b785c https://github.com/galaxyproject/galaxy/commit/40e3e7926aec154fa5f761cf5a7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Rebuild style with lessc > 2.5 (which everyone needs to update to now, or we'll have battling commits of packed css Commit: 5c285eaee751a9257e01b6ae4fcff70305e34d56 https://github.com/galaxyproject/galaxy/commit/5c285eaee751a9257e01b6ae4fcf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/GruntFile.js M client/grunt-tasks/style.js M client/package.json M static/maps/galaxy-app-base.js.map Log Message: ----------- Add grunt check task to verify npm modules are up to date Commit: d4a380b49d0c84fd1765aa5f6e6ad0f85f1b5585 https://github.com/galaxyproject/galaxy/commit/d4a380b49d0c84fd1765aa5f6e6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/package.json Log Message: ----------- Swap devDependencies for flat dependencies -- this allows npm ls (and thereby grunt-check-modules) to enforce dep versions. Commit: a664deeee76bcde33c725f37d61d8b41ea220b3d https://github.com/galaxyproject/galaxy/commit/a664deeee76bcde33c725f37d61d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/GruntFile.js M client/grunt-tasks/style.js M client/package.json M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Merge pull request #1130 from dannon/repack_dev Enforce client build deps are up-to-date. Rebuild style with lessc > 2.5 Compare: https://github.com/galaxyproject/galaxy/compare/119e26f4e5f9...a664deeee76b

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[galaxyproject/galaxy] b8b0e4: Strip whitespace
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b8b0e4412247bd0f7611710ce69e0b4e9a76b4d7 https://github.com/galaxyproject/galaxy/commit/b8b0e4412247bd0f7611710ce69e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js Log Message: ----------- Strip whitespace Commit: f0e28555af8129eae424c3e677b6bb22a4c68154 https://github.com/galaxyproject/galaxy/commit/f0e28555af8129eae424c3e677b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Support onclick for menu items. Commit: 81f1b7f8e0ce0febe18460e67a97651aa1fd72a3 https://github.com/galaxyproject/galaxy/commit/81f1b7f8e0ce0febe18460e67a97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Remove debugging logic and shortcut. Commit: 119e26f4e5f91a2091ff1cacffb3f2f99c4c79f4 https://github.com/galaxyproject/galaxy/commit/119e26f4e5f91a2091ff1cacffb3… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Merge pull request #1142 from dannon/menu_onclick_addition Menu onclick addition Compare: https://github.com/galaxyproject/galaxy/compare/303af68c3369...119e26f4e5f9

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[galaxyproject/galaxy] 844fac: UI, Lists: throttle selector animation when number...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 844facd1f1ea3d669cf7e61463c8ca8966c69006 https://github.com/galaxyproject/galaxy/commit/844facd1f1ea3d669cf7e61463c8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- UI, Lists: throttle selector animation when number of list items > 20 Commit: 303af68c33699bada56ddbc95a5f8272401b2f0e https://github.com/galaxyproject/galaxy/commit/303af68c33699bada56ddbc95a5f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- Merge pull request #1149 from carlfeberhard/history.selector-anim UI, Lists: throttle selector animation when number of list items > 20 Compare: https://github.com/galaxyproject/galaxy/compare/7bb88b3f44a5...303af68c3369

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[galaxyproject/galaxy] 8e8b5d: Remove inbound flag
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 8e8b5d445d28d459dc75cbe3ed35d6c9dd8bbd40 https://github.com/galaxyproject/galaxy/commit/8e8b5d445d28d459dc75cbe3ed35… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove inbound flag Commit: 286f7142871db5cb7b5ec8873cae8cb41fa335e3 https://github.com/galaxyproject/galaxy/commit/286f7142871db5cb7b5ec8873cae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #1085 from guerler/fix_grids_000 [15.10] Fix dataset grid history change Compare: https://github.com/galaxyproject/galaxy/compare/09db120ad84d...286f7142871d

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[galaxyproject/galaxy] f629cb: Refactor tool parsing, parse id first.
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f629cbdb6aa34a349e088382a51054a946e0185e https://github.com/galaxyproject/galaxy/commit/f629cbdb6aa34a349e088382a510… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Refactor tool parsing, parse id first. Small refactoring cleans up downstream diff for dynamic tool branch. Commit: 8189fb450bdb90f3ff7af220c573c128ed776085 https://github.com/galaxyproject/galaxy/commit/8189fb450bdb90f3ff7af220c573… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py Log Message: ----------- Add tool version to workflow extract. Commit: 0b070f406c650e664c413dc60897fafd6e3611a8 https://github.com/galaxyproject/galaxy/commit/0b070f406c650e664c413dc60897… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add app property to workflow contents manager. Most other managers already have this. Commit: 0030f4c5499b0121e2c7e25388ac402272728ba7 https://github.com/galaxyproject/galaxy/commit/0030f4c5499b0121e2c7e25388ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- API test fix from @nsoranzo. Commit: 7bb88b3f44a53fcd881d69f01d84d88624157ff5 https://github.com/galaxyproject/galaxy/commit/7bb88b3f44a53fcd881d69f01d84… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1097 from jmchilton/cwl_refactoring Small Tool and Workflow Cleanups from CWL Work. Compare: https://github.com/galaxyproject/galaxy/compare/05ed24535333...7bb88b3f44a5

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[galaxyproject/galaxy] e9ed5b: clarify the bitbucket support
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: e9ed5bfa626765754629af20f1567d7102bac231 https://github.com/galaxyproject/galaxy/commit/e9ed5bfa626765754629af20f156… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- clarify the bitbucket support Commit: a5aeea0685d5e7d1f4406f9abf69ca3da3add160 https://github.com/galaxyproject/galaxy/commit/a5aeea0685d5e7d1f4406f9abf69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Slight wording tweak Commit: ceb8ee127af9390a2cbd3b6046dc360d98992060 https://github.com/galaxyproject/galaxy/commit/ceb8ee127af9390a2cbd3b6046dc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #11 from dannon/tweak-notes Slight wording tweak Commit: 09db120ad84dcaa851a6ae3dbc351a7a958ce736 https://github.com/galaxyproject/galaxy/commit/09db120ad84dcaa851a6ae3dbc35… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #1141 from martenson/tweak-notes [15.10] release notes tweaks Compare: https://github.com/galaxyproject/galaxy/compare/a98e56c9ee53...09db120ad84d

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[galaxyproject/galaxy] bbef5e: Improvements to release notes generation.
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: bbef5ed7373b33eaa30f2e493311413e0cea018b https://github.com/galaxyproject/galaxy/commit/bbef5ed7373b33eaa30f2e493311… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Improvements to release notes generation. - Add last commit for 15.10 (need to automate finding that). - Generate next release annoucement. - Generate annoucement for this release. - Respect the minor tag. Commit: b7bf42e1b4fae9e4c2e3b246868518992dbcce10 https://github.com/galaxyproject/galaxy/commit/b7bf42e1b4fae9e4c2e3b2468685… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst Log Message: ----------- Fill in release notes for 15.10. Commit: 4f4526bc303eeb40dae9d71d5dc161bb8b398ae6 https://github.com/galaxyproject/galaxy/commit/4f4526bc303eeb40dae9d71d5dc1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- deprecate old Data Libraries Commit: cf16e2c7d39657a13d48615841c192a667428b93 https://github.com/galaxyproject/galaxy/commit/cf16e2c7d39657a13d48615841c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- add bitbucker deprecation notice Commit: 76fc6becd65f829db924e3726ade11dc0735e2ca https://github.com/galaxyproject/galaxy/commit/76fc6becd65f829db924e3726ade… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- add text highlights Commit: a98e56c9ee53a29f89db9740ad418bad12f32259 https://github.com/galaxyproject/galaxy/commit/a98e56c9ee53a29f89db9740ad41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #868 from jmchilton/release_notes [15.10] Release notes Compare: https://github.com/galaxyproject/galaxy/compare/743603b4b720...a98e56c9ee53

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