Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 649d8bad5280174c2f9a74bd847a44ba7158ec3f
https://github.com/galaxyproject/galaxy/commit/649d8bad5280174c2f9a74bd847a…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2018-11-07 (Wed, 07 Nov 2018)
Changed paths:
M lib/galaxy/jobs/mapper.py
Log Message:
-----------
Added support for overriding the rules module per destination
Commit: 65979e473c5623a5116819bd93c182744117e6f0
https://github.com/galaxyproject/galaxy/commit/65979e473c5623a5116819bd93c1…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M test/unit/jobs/test_mapper.py
A test/unit/jobs/test_rules_override/10_rule.py
A test/unit/jobs/test_rules_override/__init__.py
Log Message:
-----------
Added test for rules module overriding
Commit: 33b7f0f9d1e105dfbcbdab0a92081a9302cfe7eb
https://github.com/galaxyproject/galaxy/commit/33b7f0f9d1e105dfbcbdab0a9208…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M lib/galaxy/jobs/mapper.py
Log Message:
-----------
Refactor to use importlib
Commit: 4b5312fe80fe4d8bc0a429229d84366b630d8eac
https://github.com/galaxyproject/galaxy/commit/4b5312fe80fe4d8bc0a429229d84…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/config_watchers.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Updated watchers to reload rule module overrides
Commit: bf1f2fe0ab5248acd86d646f1c80314561c0cdc2
https://github.com/galaxyproject/galaxy/commit/bf1f2fe0ab5248acd86d646f1c80…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2018-11-09 (Fri, 09 Nov 2018)
Changed paths:
M lib/galaxy/containers/__init__.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/tools/lint.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/submodules.py
M lib/galaxy/webapps/galaxy/config_watchers.py
M test/unit/jobs/test_mapper.py
Log Message:
-----------
Refactor submodule imports
Commit: 265a43507ebda1bac9bc5dbe2ac601912bef66d8
https://github.com/galaxyproject/galaxy/commit/265a43507ebda1bac9bc5dbe2ac6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-15 (Thu, 15 Nov 2018)
Changed paths:
M lib/galaxy/containers/__init__.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/lint.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/submodules.py
M lib/galaxy/webapps/galaxy/config_watchers.py
M test/unit/jobs/test_mapper.py
A test/unit/jobs/test_rules_override/10_rule.py
A test/unit/jobs/test_rules_override/__init__.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge pull request #6993 from nuwang/allow_rules_module_override
Allow rules module override and refactor submodule imports
Compare: https://github.com/galaxyproject/galaxy/compare/17299356f011...265a43507ebd
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ab75fe8a37c4aaef2724bb1746f0fb7bb32c6fab
https://github.com/galaxyproject/galaxy/commit/ab75fe8a37c4aaef2724bb1746f0…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-11-12 (Mon, 12 Nov 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
Log Message:
-----------
Update pysam to v0.15.1
For Python 3.7 compatibility.
Reported by @wm75.
Commit: a53629ebae992e685020676f72cbcb55c954b677
https://github.com/galaxyproject/galaxy/commit/a53629ebae992e685020676f72cb…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-11-13 (Tue, 13 Nov 2018)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Update virtualenv installation to v16.1.0
which bundles `wheel` 0.32.2.
The old virtualenv 13.1.2 included wheel 0.24.0, where tagging is broken
for Python >=3.5, producing tracebacks like:
```
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-c53eutpg/uwsgi/setup.py", line 138, in <module>
'Programming Language :: Python :: 3.6',
File "/tmp/wheel_venv/lib/python3.7/site-packages/setuptools/__init__.py", line 143, in setup
return distutils.core.setup(**attrs)
File "/usr/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 213, in run
archive_basename = self.get_archive_basename()
File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 161, in get_archive_basename
impl_tag, abi_tag, plat_tag = self.get_tag()
File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 155, in get_tag
assert tag == supported_tags[0]
AssertionError
```
This was fixed in wheel 0.25.0. Reported by @wm75.
Also update `urlretrieve` import for Python 3.
Commit: d88f2b63daa91f1fce1ca161f9a9192ce20a5cd5
https://github.com/galaxyproject/galaxy/commit/d88f2b63daa91f1fce1ca161f9a9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-11-13 (Tue, 13 Nov 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #7008 from nsoranzo/python3.7
Fixes for Python 3.7
Compare: https://github.com/galaxyproject/galaxy/compare/0395fcabf083...d88f2b63daa9
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.