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
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
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
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
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
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