Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2be7eb8cfa0640dbec5954de006bab3c10f700f2
https://github.com/galaxyproject/galaxy/commit/2be7eb8cfa0640dbec5954de006b…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M .travis.yml
M tox.ini
Log Message:
-----------
Add py34-first_startup and py34-unit tox environments
Also:
- rename `first_startup` to `py27-first_startup`
- rename other tox environments to use hyphens only to delimit factors
- use the more specific
```
setenv =
GALAXY_VIRTUAL_ENV={envdir}
```
instead of passing `--no-create-venv` to run unit tests inside the tox
virtualenv (xref. commit 744835bbfe8bb07041600326af2f2f5d203365f5).
Previously, `.venv` would be used if present.
Commit: 6346b9e30949cd72a57eb683abd9bbaf431dd732
https://github.com/galaxyproject/galaxy/commit/6346b9e30949cd72a57eb683abd9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M .ci/check_py3_compatibility.sh
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M .ci/flake8_wrapper_docstrings.sh
M .gitignore
Log Message:
-----------
Ignore the future default Python3 virtualenv
Commit: f2c6e083a15eab453ea7c94565464575b0356ae1
https://github.com/galaxyproject/galaxy/commit/f2c6e083a15eab453ea7c9456546…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/develop/Pipfile
M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
Log Message:
-----------
twill and pygithub3 are not Python3-compatible
Commit: 0a44e77a89f6533c7ceaad99ffb9942517989ea4
https://github.com/galaxyproject/galaxy/commit/0a44e77a89f6533c7ceaad99ffb9…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Fix missing space
Commit: 0b60de76b93edbfeae5560a3a531d27e31e027f6
https://github.com/galaxyproject/galaxy/commit/0b60de76b93edbfeae5560a3a531…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-04 (Sun, 04 Feb 2018)
Changed paths:
M .ci/check_py3_compatibility.sh
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M .ci/flake8_wrapper_docstrings.sh
M .gitignore
M .travis.yml
M lib/galaxy/dependencies/pipfiles/develop/Pipfile
M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
M lib/tool_shed/util/repository_util.py
M tox.ini
Log Message:
-----------
Merge pull request #5453 from nsoranzo/python3
Preparations for testing under Python3
Compare: https://github.com/galaxyproject/galaxy/compare/245394acb694...0b60de76b93e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6d8edce33157e81112889ae7f241903747da3c92
https://github.com/galaxyproject/galaxy/commit/6d8edce33157e81112889ae7f241…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/scaling.md
Log Message:
-----------
Admin doc corrections
Commit: f24043e8a74e3cb2070b06652d9a72be46e6a278
https://github.com/galaxyproject/galaxy/commit/f24043e8a74e3cb2070b06652d9a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/scaling.md
Log Message:
-----------
Merge pull request #5441 from natefoo/framework-dependencies-doc-update-18.01
[18.01] Admin doc corrections
Commit: 7490fd452046b4a4578f6401501439773cbf2f28
https://github.com/galaxyproject/galaxy/commit/7490fd452046b4a4578f64015014…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
Log Message:
-----------
More robust nametag discovery and propagation.
- Nametags weren't being picked up on collection inputs - so for instance tools that take in a single collection and produce a dataset or file weren't propagating nametags (unless the collection contents had tags). To see this create two unnamed datasets without tags, create a pair from them, add a tag to the pair, and run the pair through the "paired_test" test tool.
- Nametags weren't being propagated to the outputs of collection operations.
Commit: 6f40f7098d507895c6c6608aff6a698289f2eeb6
https://github.com/galaxyproject/galaxy/commit/6f40f7098d507895c6c6608aff6a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Cleanup collection operation tagging implementation thanks to @mvdbeek comments.
Commit: 6022fe7d7e90b0da0cad83589d5d630f6dd1d386
https://github.com/galaxyproject/galaxy/commit/6022fe7d7e90b0da0cad83589d5d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Handle optional inputs when collecting preserved tags.
https://github.com/galaxyproject/galaxy/pull/5403/files#r165283450
Commit: 60561c20307cf0585e553d0fa5cd612716ab7975
https://github.com/galaxyproject/galaxy/commit/60561c20307cf0585e553d0fa5cd…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
Log Message:
-----------
Merge pull request #5403 from jmchilton/collection_operation_tags
[18.01] More robust nametag discovery and propagation.
Commit: a392b5750aa776fbc8ba27736d78901ddf0db29d
https://github.com/galaxyproject/galaxy/commit/a392b5750aa776fbc8ba27736d78…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
Log Message:
-----------
Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail
Commit: 2b8df110d0fad7c874c35c3176bf18d65cbcdbe3
https://github.com/galaxyproject/galaxy/commit/2b8df110d0fad7c874c35c3176bf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
Log Message:
-----------
Apply rename PJA to collection outputs including $ replacements.
Update PJA collection test to test HDCA is renamed also.
Commit: f6f9f9a8914845c995d665dc5396ac5e43187324
https://github.com/galaxyproject/galaxy/commit/f6f9f9a8914845c995d665dc5396…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
Log Message:
-----------
Extend mapped collection output rename PJAs to include # replacements.
Also make sure output collections in non-mapping scenarios are also properly renamed as well.
Commit: 0529153ac090de0601f38af2fbf4f9a4fcccb615
https://github.com/galaxyproject/galaxy/commit/0529153ac090de0601f38af2fbf4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix bug in PJAs for collection mapping.
Reported by @mvdbeek here (https://github.com/galaxyproject/galaxy/pull/5416#issuecomment-362194157).
Commit: 6c013d0cb3eebffdb69c865a4cbe4019bd8ab95e
https://github.com/galaxyproject/galaxy/commit/6c013d0cb3eebffdb69c865a4cbe…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
Log Message:
-----------
Merge pull request #5444 from dannon/multidelete_fix
[18.01] Ensure jobStateSummariesCollection exists;
Commit: fbfbdd51bb3e06754efc1ae9e0cec4c1c1db9ce4
https://github.com/galaxyproject/galaxy/commit/fbfbdd51bb3e06754efc1ae9e0ce…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #5416 from jmchilton/rename_collections_pja
[18.01] Fix rename post job actions to be more intuitive when mapping over collections.
Commit: 245394acb694020c0f9f78185749fbccf45ec587
https://github.com/galaxyproject/galaxy/commit/245394acb694020c0f9f78185749…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/scaling.md
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
Log Message:
-----------
Merge branch 'release_18.01' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/988cab4db7ef...245394acb694
Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: 2b8df110d0fad7c874c35c3176bf18d65cbcdbe3
https://github.com/galaxyproject/galaxy/commit/2b8df110d0fad7c874c35c3176bf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
Log Message:
-----------
Apply rename PJA to collection outputs including $ replacements.
Update PJA collection test to test HDCA is renamed also.
Commit: f6f9f9a8914845c995d665dc5396ac5e43187324
https://github.com/galaxyproject/galaxy/commit/f6f9f9a8914845c995d665dc5396…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
Log Message:
-----------
Extend mapped collection output rename PJAs to include # replacements.
Also make sure output collections in non-mapping scenarios are also properly renamed as well.
Commit: 0529153ac090de0601f38af2fbf4f9a4fcccb615
https://github.com/galaxyproject/galaxy/commit/0529153ac090de0601f38af2fbf4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix bug in PJAs for collection mapping.
Reported by @mvdbeek here (https://github.com/galaxyproject/galaxy/pull/5416#issuecomment-362194157).
Commit: fbfbdd51bb3e06754efc1ae9e0cec4c1c1db9ce4
https://github.com/galaxyproject/galaxy/commit/fbfbdd51bb3e06754efc1ae9e0ce…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #5416 from jmchilton/rename_collections_pja
[18.01] Fix rename post job actions to be more intuitive when mapping over collections.
Compare: https://github.com/galaxyproject/galaxy/compare/6c013d0cb3ee...fbfbdd51bb3e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bc50c14490e4f81144e5bc59f76e6abe2d93a8fa
https://github.com/galaxyproject/galaxy/commit/bc50c14490e4f81144e5bc59f76e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Drop py26 XML parsing variant
Commit: 49872e7612070df9aee607897fb4cf5cb9cb2242
https://github.com/galaxyproject/galaxy/commit/49872e7612070df9aee607897fb4…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/util/logging/__init__.py
M lib/galaxy/web/stack/message.py
Log Message:
-----------
Use six.create_bound_method() instead of types.MethodType()
On Python2 the MethodType constructor requires the object's class to be
passed.
Commit: f43a3268b11841f65d3de195611bc6b0a940544c
https://github.com/galaxyproject/galaxy/commit/f43a3268b11841f65d3de195611b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
M templates/webapps/galaxy/dataset/security_common.mako
Log Message:
-----------
Use builtin set
Commit: 39104af3b42e6d253391a9b73f6912cf4423e783
https://github.com/galaxyproject/galaxy/commit/39104af3b42e6d253391a9b73f69…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Define file_types instead of types.FileType and pull up TarFile
Commit: 046f3265dd50ec6ff53470a96a4dfdb0193d7c17
https://github.com/galaxyproject/galaxy/commit/046f3265dd50ec6ff53470a96a4d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/model/custom_types.py
Log Message:
-----------
Fix loading custom JSONType
Commit: 0be36ef4fce3b50bec37d199af2a404f3372ed65
https://github.com/galaxyproject/galaxy/commit/0be36ef4fce3b50bec37d199af2a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Use string.ascii_letters instead of string.letters for Py2/3 compat
Update <sanitizer> documentation.
Commit: 553d165087335528892232b17706b398bb3bf941
https://github.com/galaxyproject/galaxy/commit/553d165087335528892232b17706…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M templates/galaxy_client_app.mako
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Python3 exception syntax fixes in templates/
Commit: 52586fcca2ef6ef6926fcd25b6c6f1b9ed598a6e
https://github.com/galaxyproject/galaxy/commit/52586fcca2ef6ef6926fcd25b6c6…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/datatypes/phylip.py
Log Message:
-----------
Fix relative import to be Python3-compatible
Commit: 386526d928be1de57268163db1814640baa13459
https://github.com/galaxyproject/galaxy/commit/386526d928be1de57268163db181…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/visualization/data_providers/genome.py
Log Message:
-----------
Replace distutils.version with packaging.version
distutils under Python3 has this bug:
https://bugs.python.org/issue14894
which causes this traceback:
```
Traceback (most recent call last):
File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory
app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
File "lib/galaxy/app.py", line 125, in __init__
self._configure_toolbox()
File "lib/galaxy/config.py", line 930, in _configure_toolbox
self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self)
File "lib/galaxy/tools/__init__.py", line 232, in __init__
app=app,
File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__
super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app)
File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__
self._load_tool_panel()
File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel
self.__add_tool_to_tool_panel(section_val, section, section=True)
File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel
related_tool = self._lineage_in_panel(panel_dict, tool=tool)
File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel
lineage_tool_versions = reversed(tool_lineage.get_versions())
File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions
return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)]
File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids
return ["%s/%s" % (tool_id, version) for version in self.tool_versions]
File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions
return sorted(self._tool_versions, key=LooseVersion)
File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__
c = self._cmp(other)
File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp
if self.version < other.version:
TypeError: unorderable types: str() < int()
```
when a tool version contains a letter in the "wrong" place (e.g. in the first position).
Fix https://github.com/galaxyproject/galaxy/issues/5408 .
Commit: 988cab4db7ef83714cf6f0c57f73f4255e3f075d
https://github.com/galaxyproject/galaxy/commit/988cab4db7ef83714cf6f0c57f73…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/phylip.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/logging/__init__.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/stack/message.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/tool_shed/util/xml_util.py
M templates/galaxy_client_app.mako
M templates/webapps/galaxy/dataset/security_common.mako
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Merge pull request #5422 from nsoranzo/python3
Mixed Python3 fixes
Compare: https://github.com/galaxyproject/galaxy/compare/5a31ac84ce12...988cab4db7ef