Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 90e4bc5aa3ec6fc6471d42603205ae8af3c0490c
https://github.com/galaxyproject/galaxy/commit/90e4bc5aa3ec6fc6471d42603205…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-09-19 (Wed, 19 Sep 2018)
Changed paths:
M .gitignore
Log Message:
-----------
Ignore run_selenium_tests.html
Commit: ff19438039360bf46bc0642655b6a6d5daac4b42
https://github.com/galaxyproject/galaxy/commit/ff19438039360bf46bc0642655b6…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-09-19 (Wed, 19 Sep 2018)
Changed paths:
M .ci/jenkins/api-py3/run_tests.sh
M .ci/jenkins/api/run_tests.sh
M .ci/jenkins/framework-py3/run_tests.sh
M .ci/jenkins/framework/run_tests.sh
M .ci/jenkins/main-tools-py3/run_tests.sh
M .ci/jenkins/main-tools/run_tests.sh
M .ci/jenkins/selenium-py3/run_tests.sh
M .ci/jenkins/selenium/run_tests.sh
M .ci/jenkins/toolshed/run_tests.sh
Log Message:
-----------
Make run_tests.sh scripts in .ci/jenkins/ executable
Commit: c9f2361e8e1f6244893f43bb361a0e3b5242518d
https://github.com/galaxyproject/galaxy/commit/c9f2361e8e1f6244893f43bb361a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-19 (Wed, 19 Sep 2018)
Changed paths:
M .ci/jenkins/api-py3/run_tests.sh
M .ci/jenkins/api/run_tests.sh
M .ci/jenkins/framework-py3/run_tests.sh
M .ci/jenkins/framework/run_tests.sh
M .ci/jenkins/main-tools-py3/run_tests.sh
M .ci/jenkins/main-tools/run_tests.sh
M .ci/jenkins/selenium-py3/run_tests.sh
M .ci/jenkins/selenium/run_tests.sh
M .ci/jenkins/toolshed/run_tests.sh
M .gitignore
Log Message:
-----------
Merge pull request #6738 from nsoranzo/local_testing_improvs
Small local testing improvements
Compare: https://github.com/galaxyproject/galaxy/compare/da421294f80d...c9f2361e8e1f
**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: c8cb164ab8ad4fe5d7ea9768e3f7e58051200525
https://github.com/galaxyproject/galaxy/commit/c8cb164ab8ad4fe5d7ea9768e3f7…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-09-10 (Mon, 10 Sep 2018)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Merge pull request #6687 from dannon/version-18.09
Update version to 18.09.rc1
Commit: 471162eadb4408318db534c6d24f7685bedb29eb
https://github.com/galaxyproject/galaxy/commit/471162eadb4408318db534c6d24f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-11 (Tue, 11 Sep 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/extract_dataset.xml
Log Message:
-----------
[18.09] Fix new extract dataset to perserve collection element identifier.
Commit: ba4e7d199b4bc080dcd741710d2241147bdbe745
https://github.com/galaxyproject/galaxy/commit/ba4e7d199b4bc080dcd741710d22…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-12 (Wed, 12 Sep 2018)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Make gro and top datatypes tabular subclasses
I think that was the intention in https://github.com/galaxyproject/galaxy/commit/56d55399ebe2ecd614a7ba5a1467…
Commit: 80266129fe3d3d4b9657da0a3c5e8232bfa2a46b
https://github.com/galaxyproject/galaxy/commit/80266129fe3d3d4b9657da0a3c5e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-09-12 (Wed, 12 Sep 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/extract_dataset.xml
Log Message:
-----------
Merge pull request #6692 from jmchilton/1809_fix_extract_name
[18.09] Fix new extract dataset tool to preserve collection element identifier.
Commit: 1f8c234c2be8baac9db94e17f4727e6c3c6c55ef
https://github.com/galaxyproject/galaxy/commit/1f8c234c2be8baac9db94e17f472…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2018-09-12 (Wed, 12 Sep 2018)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Make top datatype inherit from Text.
Commit: 17157dd0633b4deb91a39bbc76288dd2968423f5
https://github.com/galaxyproject/galaxy/commit/17157dd0633b4deb91a39bbc7628…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-09-12 (Wed, 12 Sep 2018)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #9 from blankenberg/gro2
Make top datatype inherit from Text.
Commit: 9657cd6b32ed0768d2c73dd9d63c38432afb4b71
https://github.com/galaxyproject/galaxy/commit/9657cd6b32ed0768d2c73dd9d63c…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-09-12 (Wed, 12 Sep 2018)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #6695 from mvdbeek/fix_gro_top_datatypes
[18.09] Make gro and top datatypes tabular subclasses
Commit: b4b49dc2028da2064fd34d7345b23b47150a1039
https://github.com/galaxyproject/galaxy/commit/b4b49dc2028da2064fd34d7345b2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-13 (Thu, 13 Sep 2018)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
Add self help to error reporting interface.
Commit: 88bf3435775e94217bccfc46a5215311dea321aa
https://github.com/galaxyproject/galaxy/commit/88bf3435775e94217bccfc46a521…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-13 (Thu, 13 Sep 2018)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
Import Backbone consistently across the app
Commit: 84d66bea6008dc534aa6a2331e824005b204da19
https://github.com/galaxyproject/galaxy/commit/84d66bea6008dc534aa6a2331e82…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-14 (Fri, 14 Sep 2018)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
h2!=h3
Commit: 32223161c7ca735647d53ebfe4b90f1cd4051051
https://github.com/galaxyproject/galaxy/commit/32223161c7ca735647d53ebfe4b9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-09-14 (Fri, 14 Sep 2018)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
Log Message:
-----------
Merge pull request #6711 from dannon/error_help
[18.09] Add self help to error reporting interface
Commit: df4fbe6b92457fa910f014bbd3a8dd84c25d3969
https://github.com/galaxyproject/galaxy/commit/df4fbe6b92457fa910f014bbd3a8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-17 (Mon, 17 Sep 2018)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
Log Message:
-----------
Swap badge-default to badge-primary
Commit: b2193bddc2aea250a189171ae61ed992b0449c84
https://github.com/galaxyproject/galaxy/commit/b2193bddc2aea250a189171ae61e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-17 (Mon, 17 Sep 2018)
Changed paths:
M client/galaxy/docs/bootstrap.md
Log Message:
-----------
Drop badge-default from docs, correctly refer to secondary.
Commit: a9273218424c1687bedf112591f2bbf735d32aa8
https://github.com/galaxyproject/galaxy/commit/a9273218424c1687bedf112591f2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-17 (Mon, 17 Sep 2018)
Changed paths:
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Client format.
Commit: 0040c36d4561155af3f32262d186e186349d989d
https://github.com/galaxyproject/galaxy/commit/0040c36d4561155af3f32262d186…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-17 (Mon, 17 Sep 2018)
Changed paths:
M client/galaxy/docs/bootstrap.md
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Merge pull request #6726 from dannon/badge-default-fix
[18.09] Badge default fix
Commit: 072d40f3e9a9050f034f440b76c8b84536bc0ead
https://github.com/galaxyproject/galaxy/commit/072d40f3e9a9050f034f440b76c8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-09-17 (Mon, 17 Sep 2018)
Changed paths:
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
remove html tags and newlines from the help text
this should improve the toolsearch for certain keywords
and also make the search index smaller
Commit: b7f16228575215c9be134d1bbc1cf9e37b700488
https://github.com/galaxyproject/galaxy/commit/b7f16228575215c9be134d1bbc1c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-09-17 (Mon, 17 Sep 2018)
Changed paths:
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
replace the replacement for newline
from empty string to space, that should avoid unwanted word merges
Commit: 17d67e24c072c8953e482aff41e9b1faed78b4d3
https://github.com/galaxyproject/galaxy/commit/17d67e24c072c8953e482aff41e9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-09-17 (Mon, 17 Sep 2018)
Changed paths:
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
use bleach isntead of custom regex
thanks @nsoranzo
Commit: 54d137edab3fb33beac87c23cd35fb19dd7f44fa
https://github.com/galaxyproject/galaxy/commit/54d137edab3fb33beac87c23cd35…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Remove deprecated `decode_param_names` parameter
It has been deprecated since WebOb 1.1 and ignored since WebOb 1.2 .
Commit: 8ed19a3a09df9b66266f66bc53e504c781ae524d
https://github.com/galaxyproject/galaxy/commit/8ed19a3a09df9b66266f66bc53e5…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/verify/interactor.py
Log Message:
-----------
`async` is a reserved keyword in Python 3.7
- Remove unused `async` parameter of `stage_data_async()` method.
- Rename `async` parameter of `quick_load()` method.
Fix https://github.com/galaxyproject/galaxy/issues/6717 .
xref. https://github.com/galaxyproject/galaxy/issues/1715
Commit: 8982212d396c1ab216c5c9ea0656e5231e05d745
https://github.com/galaxyproject/galaxy/commit/8982212d396c1ab216c5c9ea0656…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M lib/galaxy/util/xml_macros.py
M scripts/loc_files/create_all_fasta_loc.py
Log Message:
-----------
Replace deprecated `xml.etree.ElementTree.Element.getiterator()` with `iter()`
Commit: f0708488aa08393cfdf3ab3e0e45e37982d050d0
https://github.com/galaxyproject/galaxy/commit/f0708488aa08393cfdf3ab3e0e45…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M pytest.ini
Log Message:
-----------
pytest: disable test collection of classes starting with `Test`
Fix warnings like:
```
/home/travis/build/galaxyproject/galaxy/lib/galaxy/tools/verify/test_data.py:29: PytestWarning: cannot collect test class 'TestDataResolver' because it has a __init__ constructor
class TestDataResolver(object):
```
appearing e.g. in https://travis-ci.org/galaxyproject/galaxy/jobs/428114139 .
See pytest documentation:
https://docs.pytest.org/en/latest/reference.html#confval-python_classes
Commit: 2874e87debcc1940e1f1143a7af4dacb38c95585
https://github.com/galaxyproject/galaxy/commit/2874e87debcc1940e1f1143a7af4…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
Merge pull request #6728 from martenson/fix-toolhelp-parsing
[18.09] remove html tags and newlines from the help text
Commit: 0974b130ef922e3177de27f6365ccd624bf194a7
https://github.com/galaxyproject/galaxy/commit/0974b130ef922e3177de27f6365c…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/web/framework/base.py
M pytest.ini
M scripts/loc_files/create_all_fasta_loc.py
Log Message:
-----------
Merge pull request #6730 from nsoranzo/release_18.09_backport_6722
[18.09] Partial backport of #6722
Commit: 376516610ef6ac28cef7a9558adab1a88d8c0c12
https://github.com/galaxyproject/galaxy/commit/376516610ef6ac28cef7a9558ada…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Bugfix - missing tests for data source sniffing.
Ensure #6334 is fixed I think.
Commit: aca30f0b158a9ab0647747b957f55ea6716a4d18
https://github.com/galaxyproject/galaxy/commit/aca30f0b158a9ab0647747b957f5…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Merge pull request #6733 from jmchilton/1809_sniff_test
[18.09] Fix missing tests for data source sniffing.
Commit: ed147ee052a1628aa07e33b3849f1d4fb2778d2b
https://github.com/galaxyproject/galaxy/commit/ed147ee052a1628aa07e33b3849f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M client/galaxy/docs/bootstrap.md
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M config/datatypes_conf.xml.sample
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/extract_dataset.xml
M lib/galaxy/tools/search/__init__.py
M test/api/test_tools.py
Log Message:
-----------
Merge branch 'release_18.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/e049786c4c75...ed147ee052a1
**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.