Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4dcba21d838bd2bad806687d7c212d7da0b8e85e https://github.com/galaxyproject/galaxy/commit/4dcba21d838bd2bad806687d7c212... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst Log Message: ----------- initial release notes for 17.09 Commit: 272ed6217d4662f7bdc6b385206a7f301295a033 https://github.com/galaxyproject/galaxy/commit/272ed6217d4662f7bdc6b385206a7... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- add deprecations Commit: 06d3f4051543e7c319e775884ea3aab8abef9a2c https://github.com/galaxyproject/galaxy/commit/06d3f4051543e7c319e775884ea3a... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- amend add missing line Commit: eab76b9ae014c4fa2dd3a1ba09199f3351536924 https://github.com/galaxyproject/galaxy/commit/eab76b9ae014c4fa2dd3a1ba09199... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- add listing of 17.09 release to index Commit: 812b04d14eb1c3d3ec016efb6aa8f1024811c560 https://github.com/galaxyproject/galaxy/commit/812b04d14eb1c3d3ec016efb6aa8f... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst Log Message: ----------- more work on RN Commit: 5bde1d1c3a0239ef37369f59e90ceca863d6821f https://github.com/galaxyproject/galaxy/commit/5bde1d1c3a0239ef37369f59e90ce... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst Log Message: ----------- Small progress on 17.09 release notes. Commit: ee27188b59d174f4db16d2ce4b7cd2181ea93517 https://github.com/galaxyproject/galaxy/commit/ee27188b59d174f4db16d2ce4b7cd... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: A client/galaxy/scripts/libs/jquery/jquery.complexify.js A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/releases/17.09_announce.rst Log Message: ----------- add security release notes Commit: 180472a3d8ceb40f6d015c0bfe5ef1dd08da5513 https://github.com/galaxyproject/galaxy/commit/180472a3d8ceb40f6d015c0bfe5ef... Author: Dave Clements <clements@galaxyproject.org> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Small edits to 17.09 release notes. Commit: c8efbb3327cb4e2805c0099975c5a2be70b95a21 https://github.com/galaxyproject/galaxy/commit/c8efbb3327cb4e2805c0099975c5a... Author: Dave Clements <clements@galaxyproject.org> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Fixed indenting in release notes. Commit: 4252f4f813c3d5a390ead3d86c4eec78273163cb https://github.com/galaxyproject/galaxy/commit/4252f4f813c3d5a390ead3d86c4ee... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- Small 17.09 release note improvements. Commit: 199ec6dd4c70c733edd200e61d6470dedcf0da85 https://github.com/galaxyproject/galaxy/commit/199ec6dd4c70c733edd200e61d647... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- Condense several 17.09 release notes items. Commit: 3e8bf27fca44f5b70ac9e7e1f66acbdb11c98162 https://github.com/galaxyproject/galaxy/commit/3e8bf27fca44f5b70ac9e7e1f66ac... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- More release notes improvements. Move a couple things higher, merge a couple more things, improved language (toward sentences). Commit: 1b5421c1df5392ce83a66de22dceb6ef404134bf https://github.com/galaxyproject/galaxy/commit/1b5421c1df5392ce83a66de22dceb... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Merge pull request #24 from tnabtaf/17.09_release_notes 17.09 release notes edits Commit: 00bc7a51f9c780e15041b465e0245848f7b26244 https://github.com/galaxyproject/galaxy/commit/00bc7a51f9c780e15041b465e0245... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- More 17.09 release note fixes. Merge more items, fix more sentences, etc... Commit: d1190bb067146d76bc16ec403562d4ba2d905710 https://github.com/galaxyproject/galaxy/commit/d1190bb067146d76bc16ec403562d... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- deprecate undocumented refresh_on_change functionality Commit: fe440d27367ef00b663057bf8ebe30b7b9ab0344 https://github.com/galaxyproject/galaxy/commit/fe440d27367ef00b663057bf8ebe3... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- Merge branch '17.09_release_notes' of github.com:martenson/galaxy into 17.09_release_notes Commit: 6bbf345c282782efac6a026d36f60296571deabe https://github.com/galaxyproject/galaxy/commit/6bbf345c282782efac6a026d36f60... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: R client/galaxy/scripts/libs/jquery/jquery.complexify.js R doc/source/api/api.rst R doc/source/api/ts_api.rst Log Message: ----------- remove wrongly added files Commit: 73b31ce3199ac73a0208dd784420800064278454 https://github.com/galaxyproject/galaxy/commit/73b31ce3199ac73a0208dd7844208... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #4772 from martenson/17.09_release_notes [17.09] release notes Commit: f5981e6ef381d5c4be33e0725cdb697a5515ca7b https://github.com/galaxyproject/galaxy/commit/f5981e6ef381d5c4be33e0725cdb6... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- add tldr for security Commit: add3a97bb014392d773c7a5bb8243f7341c1219c https://github.com/galaxyproject/galaxy/commit/add3a97bb014392d773c7a5bb8243... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- this is not markdown Commit: cfb61e069659fa43b4ad290b4cc4a93ebd71e3e0 https://github.com/galaxyproject/galaxy/commit/cfb61e069659fa43b4ad290b4cc4a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Rework security wording a bit. I waffle on adding security notes for the 17.09-only issues... Commit: 01b244a810434a1184d3e72ff9476af2a1243dcc https://github.com/galaxyproject/galaxy/commit/01b244a810434a1184d3e72ff9476... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Merge pull request #4853 from martenson/improve-RN [17.09] release notes - add tldr for security Commit: 9791dd22d4d9084989cafa3498ae313dd4cd13f0 https://github.com/galaxyproject/galaxy/commit/9791dd22d4d9084989cafa3498ae3... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix regressions in library API Introduced in commit 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 Commit: a4a8f155376119277df2cfebd13376e919873c4f https://github.com/galaxyproject/galaxy/commit/a4a8f155376119277df2cfebd1337... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions [16.07] Fix regressions in library API Commit: 899b0d806808d29291bf132a8c9e45df31fc28e1 https://github.com/galaxyproject/galaxy/commit/899b0d806808d29291bf132a8c9e4... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix galaxy.util.in_directory() - broken because it takes realpath of just one argument. Easy to see on Mac OS X since /tmp isn't really /tmp for instance: ``` % touch /tmp/moo % python
import galaxy.util galaxy.util.in_directory("/tmp/moo", "/tmp/moo") False
... and this is why the Travis tests are failing under Mac OS X. Broken with 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4.
Commit: 4b5dc399b934542092bfe66c3c4e03acc3980d49
https://github.com/galaxyproject/galaxy/commit/4b5dc399b934542092bfe66c3c4e03acc3980d49
Author: John Chilton <jmchilton@gmail.com>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Add basic test for in_directory.
Commit: fcb23eb8f878700bfd77384ef679a569c59f7a62
https://github.com/galaxyproject/galaxy/commit/fcb23eb8f878700bfd77384ef679a569c59f7a62
Author: John Chilton <jmchilton@gmail.com>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Some documentation to clarify discussion on #4856.
Commit: 95f8f48416c5a4d2590120e965cf9714c752ed61
https://github.com/galaxyproject/galaxy/commit/95f8f48416c5a4d2590120e965cf9714c752ed61
Author: John Chilton <jmchilton@gmail.com>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/util/path/__init__.py
Log Message:
-----------
Doc fix thanks to @nsoranzo.
Commit: 7e08ba6f19346668350d358ee4eb01ef722e74e7
https://github.com/galaxyproject/galaxy/commit/7e08ba6f19346668350d358ee4eb01ef722e74e7
Author: John Chilton <jmchilton@gmail.com>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/path/__init__.py
Log Message:
-----------
Rework in_directory fix to move realpath expansion into galaxy.util.
Commit: e3e28ddc2dac1c4faaa45a9764abc7970129beb3
https://github.com/galaxyproject/galaxy/commit/e3e28ddc2dac1c4faaa45a9764abc7970129beb3
Author: Nicola Soranzo <nsoranzo@tiscali.it>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/path/__init__.py
Log Message:
-----------
Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory
[16.07] Fix galaxy.util.in_directory()...
Commit: 90289b6116c6a6ba1f6f0b4cbdee059003f916a3
https://github.com/galaxyproject/galaxy/commit/90289b6116c6a6ba1f6f0b4cbdee059003f916a3
Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/util/path/ntpath.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Merge branch 'release_16.07' into release_16.10
Commit: a7bf1601a1ad34e5896978e1bce9c8081aafbb05
https://github.com/galaxyproject/galaxy/commit/a7bf1601a1ad34e5896978e1bce9c8081aafbb05
Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/util/path/ntpath.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Merge branch 'release_16.10' into release_17.01
Commit: 20621b7d09443fc80c8326d91bdd204decb80b81
https://github.com/galaxyproject/galaxy/commit/20621b7d09443fc80c8326d91bdd204decb80b81
Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/util/path/ntpath.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Merge branch 'release_17.01' into release_17.05
Commit: 986031bf190b82317cf687ed7e82ebd6b2646957
https://github.com/galaxyproject/galaxy/commit/986031bf190b82317cf687ed7e82ebd6b2646957
Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/util/path/ntpath.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Merge branch 'release_17.05' into release_17.09
Conflicts:
lib/galaxy/webapps/galaxy/controllers/library_common.py
Commit: 1baed58e1e7c813e6a87b5a83883c5940a78035d
https://github.com/galaxyproject/galaxy/commit/1baed58e1e7c813e6a87b5a83883c5940a78035d
Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/library_datasets.py
Log Message:
-----------
Backport fix for E201 and E202 errors
>From commit 9b4de72ca68afc2353beff333775422039baae25
Commit: 9b3d217a2e5d9ccaa37b345cdd9487599fc5b699
https://github.com/galaxyproject/galaxy/commit/9b3d217a2e5d9ccaa37b345cdd9487599fc5b699
Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: 2017-10-25 (Wed, 25 Oct 2017)
Changed paths:
A doc/source/releases/17.09.rst
M doc/source/releases/17.09_announce.rst
A doc/source/releases/18.01_announce.rst
M doc/source/releases/index.rst
M lib/galaxy/util/__init__.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Merge branch 'release_17.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/0f5927b628ea...9b3d217a2e5d