Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5dea33a86a79334b831776529956105c173673b https://github.com/galaxyproject/galaxy/commit/d5dea33a86a79334b831776529956... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2019-01-14 (Mon, 14 Jan 2019)

Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

Log Message: ----------- Pin pysam to 0.15.2 . Update all dependencies

with `make update-dependencies` using pipenv 2018.11.26 .

Commit: ce5895f585878a8952e8cda7df952027b2c48c11 https://github.com/galaxyproject/galaxy/commit/ce5895f585878a8952e8cda7df952... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2019-01-14 (Mon, 14 Jan 2019)

Changed paths: M doc/source/conf.py

Log Message: ----------- Update recommonmark configuration in Sphinx

See https://github.com/rtfd/recommonmark/pull/113

Commit: 4bb6f18b30d850019230cd4e347b574ac0593052 https://github.com/galaxyproject/galaxy/commit/4bb6f18b30d850019230cd4e347b5... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-14 (Mon, 14 Jan 2019)

Changed paths: M doc/source/conf.py

Log Message: ----------- Do not build rst files starting with '_'

Commit: 46b3539a35c09fc3d8d2d9b2a7ec7fefbc53c95e https://github.com/galaxyproject/galaxy/commit/46b3539a35c09fc3d8d2d9b2a7ec7... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-14 (Mon, 14 Jan 2019)

Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/dev/index.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/18.01.rst

Log Message: ----------- Fix doc bugs

Use proper cross-referencing with `:doc:`.

Commit: 891576627515febaa749981fbb7e0aa850df495a https://github.com/galaxyproject/galaxy/commit/891576627515febaa749981fbb7e0... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-14 (Mon, 14 Jan 2019)

Changed paths: M doc/source/conf.py

Log Message: ----------- Do not exclude releases docs when using ``GALAXY_DOCS_SKIP_SOURCE``

They are quite fast to build.

Commit: 1f3eec2879e356a671a2280b3589e938c391c668 https://github.com/galaxyproject/galaxy/commit/1f3eec2879e356a671a2280b3589e... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M test/api/test_galaxy_interactor.py

Log Message: ----------- Fix ``GalaxyInteractorBackwardCompatTestCase.test_local_test_data_download`` API test

Broken in commit bf851269c30996876c0614e7a5b57da495c44ac9 .

Commit: b23a2a44d99c9d68def546bda3bbf0d7059c8f95 https://github.com/galaxyproject/galaxy/commit/b23a2a44d99c9d68def546bda3bbf... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webhooks/__init__.py

Log Message: ----------- Fix ``UnicodeDecodeError`` exception under Python3

Fix the following exception reported in the startup logs: ``` galaxy.webhooks ERROR 2019-01-15 11:31:18,095 'ascii' codec can't decode byte 0xef in position 8291: ordinal not in range(128) Traceback (most recent call last): File "/galaxy/lib/galaxy/webhooks/__init__.py", line 62, in load_webhooks self.load_webhook_from_config(directory, config_file_path) File "/galaxy/lib/galaxy/webhooks/__init__.py", line 96, in load_webhook_from_config webhook.script = file.read() File "/galaxy_venv3/lib/python3.5/encodings/ascii.py", line 26, in decode return codecs.ascii_decode(input, self.errors)[0] UnicodeDecodeError: 'ascii' codec can't decode byte 0xef in position 8291: ordinal not in range(128) ```

Also rename variables from `file` (Python2 standard library function and class) to `fh`.

Commit: f70d24afb5ed151237d7c7e0491b5db9337fdefc https://github.com/galaxyproject/galaxy/commit/f70d24afb5ed151237d7c7e0491b5... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M test/api/test_histories.py

Log Message: ----------- Python3: open 2 files in binary mode

Fix `HistoriesApiTestCase.test_import_metadata_regeneration()` API test introduced in commit 38f7aded0b11f4c75f2265ba95ed674e8d655e7d .

See:

https://jenkins.galaxyproject.org/job/docker-api-py3/193/testReport/junit/te...

Commit: e42dcfab2a930e8d736b021ff69cb3428a77663e https://github.com/galaxyproject/galaxy/commit/e42dcfab2a930e8d736b021ff69cb... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/conf.py M doc/source/dev/index.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/18.01.rst M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webhooks/__init__.py M test/api/test_galaxy_interactor.py M test/api/test_histories.py

Log Message: ----------- Merge pull request #7215 from nsoranzo/recommonmark_0.5.0

Dependency update and doc fixes

Compare: https://github.com/galaxyproject/galaxy/compare/c6a681fa8bb2...e42dcfab2a93 **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.