Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4eefd885eccd0c42c7a74c8415add3a948a91135
https://github.com/galaxyproject/galaxy/commit/4eefd885eccd0c42c7a74c8415ad…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-22 (Tue, 22 Dec 2015)
Changed paths:
A lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M run.sh
M run_tests.sh
M scripts/common_startup.sh
Log Message:
-----------
Improve startup options related to wheel/dependency/virtualenv
management. Drop hard requirement on lzo (doubt anyone other than
usegalaxy.org is using it, but it will be added as a extras option for
bxlab/bx-python for anyone who is).
Fixes #1150
Commit: 9934a45134283d307814058fa09e4b26d3d8452f
https://github.com/galaxyproject/galaxy/commit/9934a45134283d307814058fa09e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-22 (Tue, 22 Dec 2015)
Changed paths:
M tox.ini
Log Message:
-----------
Run tox/Travis with --no-create-venv instead of --skip-venv
Commit: 26d7e97ed7b4eaa845bf86fd4991b1fbf4a3ead0
https://github.com/galaxyproject/galaxy/commit/26d7e97ed7b4eaa845bf86fd4991…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-23 (Wed, 23 Dec 2015)
Changed paths:
A lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M run.sh
M run_tests.sh
M scripts/common_startup.sh
M tox.ini
Log Message:
-----------
Merge pull request #1389 from natefoo/wheel-startup-option-improvements
Improve startup options related to wheel/dependency/virtualenv management.
Compare: https://github.com/galaxyproject/galaxy/compare/ded904cb1258...26d7e97ed7b4
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 630ac3658f3c64bd9a9abe5757cce0ed01cad229
https://github.com/galaxyproject/galaxy/commit/630ac3658f3c64bd9a9abe5757cc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-22 (Tue, 22 Dec 2015)
Changed paths:
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/json.py
M lib/galaxy/util/xml_macros.py
Log Message:
-----------
Python 3 fixes and galaxy-lib updates from planemo.
(Minus changes for conda which - should be merged as their own PR obviously.)
Commit: ded904cb12580723b192fe571cf2a4f20ec16619
https://github.com/galaxyproject/galaxy/commit/ded904cb12580723b192fe571cf2…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-23 (Wed, 23 Dec 2015)
Changed paths:
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/json.py
M lib/galaxy/util/xml_macros.py
Log Message:
-----------
Merge pull request #1388 from jmchilton/py3_2
Python 3 fixes and galaxy-lib updates from planemo.
Compare: https://github.com/galaxyproject/galaxy/compare/61cba6c9429f...ded904cb1258
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b5ad20401b28e29b727c1212be5443d7dd9c2dad
https://github.com/galaxyproject/galaxy/commit/b5ad20401b28e29b727c1212be54…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Refactor UI component out of AbstractToolBox.
If it belongs in the base class ToolBox which is more concerned with Galaxy-spcifics like UI, AbstractToolBox is suppose to be an abstract description of a toolbox - it is about data management.
Commit: 536b4e2a2038d889486bbf0836341e03d737f53c
https://github.com/galaxyproject/galaxy/commit/536b4e2a2038d889486bbf083634…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/tool_shed/util/common_util.py
Log Message:
-----------
Improve some random tool shed code.
Commit: 75e7276e5e9c43ec6f09f68adea2870b3a6917dc
https://github.com/galaxyproject/galaxy/commit/75e7276e5e9c43ec6f09f68adea2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
Log Message:
-----------
Eliminate sqlalchemy and tool shed dependencies from AbstractToolBox.
Provide an extension point instead that allows Galaxy's ToolBox class to provide the functionality that required these dependencies. And optionally load ToolVersion class required for reasoning about tool shed logic.
Commit: 61cba6c9429fe790da19f843d8e2b0d415459b4c
https://github.com/galaxyproject/galaxy/commit/61cba6c9429fe790da19f843d8e2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-22 (Tue, 22 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/util/__init__.py
M lib/tool_shed/util/common_util.py
Log Message:
-----------
Merge pull request #1367 from jmchilton/toolbox_refactor_0
Refactor AbstractToolbox toward reuse outside Galaxy
Compare: https://github.com/galaxyproject/galaxy/compare/f874d559b7db...61cba6c9429f
Branch: refs/heads/release_15.10
Home: https://github.com/galaxyproject/galaxy
Commit: f042fe8548ec4a0f2f29b72d0c34736e2ff524f9
https://github.com/galaxyproject/galaxy/commit/f042fe8548ec4a0f2f29b72d0c34…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M test/api/test_jobs.py
Log Message:
-----------
Attempt to fix transiently failing API tests.
- Fix default timeout of wait_on_state api helper. Had the wrong default specified and might fix this failure: https://jenkins.galaxyproject.org/job/docker-api/229/testReport/junit/api.t…
- Modify job search test case to allow a little more time between the history being "ok" and the job, in case there is a timing condition if the HDA is committed first and then job. Also improve the test output in case this isn't the problem.
Commit: 93c6d0542124c220e36c1e90d62e3e2aef607e9a
https://github.com/galaxyproject/galaxy/commit/93c6d0542124c220e36c1e90d62e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/test.py
M test/base/twilltestcase.py
A test/functional/tools/maxseconds.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Revise and fix waiting for tool tests.
- maxseconds on test tag stopped being respected at some point, fix that.
- maxseconds on test tag stopped being parsed at some later point, fix that.
- Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT.
- Add test case to ensure there is no future regression of these behaviors.
Commit: ffb973477b02c4bc1cbfa95c7a6247f1d7949fdd
https://github.com/galaxyproject/galaxy/commit/ffb973477b02c4bc1cbfa95c7a62…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M scripts/functional_tests.py
Log Message:
-----------
Do not check for tool migrations when running tests.
This is an inappropriate time for the check and causes slow down when running tests.
Commit: 641b275aa424421591833f6a3bce3ebd8b358017
https://github.com/galaxyproject/galaxy/commit/641b275aa424421591833f6a3bce…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M test/api/helpers.py
M test/api/test_jobs.py
Log Message:
-----------
Wait on jobs and history in certain API test cases.
This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases.
Commit: 57a76065a54f63a47874158c121f002308648025
https://github.com/galaxyproject/galaxy/commit/57a76065a54f63a47874158c121f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M test/api/helpers.py
Log Message:
-----------
Fix missing assertion pointed out @nsoranzo.
Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing.
Commit: 2817eabf95a980a250e272c3917e5dcfc24743b2
https://github.com/galaxyproject/galaxy/commit/2817eabf95a980a250e272c3917e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-18 (Fri, 18 Dec 2015)
Changed paths:
M test/functional/tools/maxseconds.xml
Log Message:
-----------
Fail maxseconds test tool if sleep is interrupted.
Commit: 5d26f589cc475ff95b97ef2dcb34d5a290079e8b
https://github.com/galaxyproject/galaxy/commit/5d26f589cc475ff95b97ef2dcb34…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-22 (Tue, 22 Dec 2015)
Changed paths:
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/test.py
M scripts/functional_tests.py
M test/api/helpers.py
M test/api/test_jobs.py
M test/base/twilltestcase.py
A test/functional/tools/maxseconds.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #1295 from jmchilton/test_fixes_backport_15_10
[15.10] Backport various testing fixes.
Compare: https://github.com/galaxyproject/galaxy/compare/52b66d0dee8c...5d26f589cc47