61e6fd1 | Nicola Soranzo | 12 December 2019, 17:43:26 UTC | Merge branch 'release_16.10' into release_17.01 | 12 December 2019, 17:43:26 UTC |
267037f | Nicola Soranzo | 12 December 2019, 17:42:02 UTC | Merge branch 'release_16.07' into release_16.10 | 12 December 2019, 17:42:02 UTC |
6c02000 | Nicola Soranzo | 12 December 2019, 17:30:59 UTC | Merge branch 'release_16.04' into release_16.07 | 12 December 2019, 17:30:59 UTC |
48510a2 | John Chilton | 12 December 2019, 16:37:38 UTC | Merge pull request #9089 from nsoranzo/release_16.04_extra-index-url [16.04] Explicitly include PyPI as an ``--extra-index-url`` to pip | 12 December 2019, 16:37:38 UTC |
aca9490 | Nicola Soranzo | 10 December 2019, 23:21:29 UTC | Explicitly include PyPI as an ``--extra-index-url`` to pip Backport combining commits 244fc834cd4dd3980cc3edb755d22ca5a9372421 and 09fdac513d59ca6dad440616a53daa97751ff905 . This is now needed because wheels.galaxyproject.org is not a full-fledged pypiserver any more but just an S3 bucket served via a CDN. | 10 December 2019, 23:29:06 UTC |
1b30a9a | Nicola Soranzo | 16 December 2018, 22:42:04 UTC | Merge branch 'release_16.10' into release_17.01 | 16 December 2018, 22:42:04 UTC |
a2e70ef | Nicola Soranzo | 16 December 2018, 22:40:26 UTC | Merge branch 'release_16.07' into release_16.10 | 16 December 2018, 22:40:26 UTC |
f3c8181 | Nicola Soranzo | 16 December 2018, 22:36:18 UTC | Merge branch 'release_16.04' into release_16.07 | 16 December 2018, 22:36:18 UTC |
87fa609 | Nicola Soranzo | 16 December 2018, 22:29:19 UTC | Merge branch 'release_16.01' into release_16.04 | 16 December 2018, 22:29:19 UTC |
8f14121 | Nicola Soranzo | 16 December 2018, 22:28:21 UTC | Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 | 16 December 2018, 22:28:21 UTC |
efe8475 | Nicola Soranzo | 26 November 2018, 16:30:00 UTC | Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 | 11 December 2018, 22:22:01 UTC |
b10cfa4 | Nate Coraor | 20 May 2016, 13:44:55 UTC | Remove unused $GXPIP_VERSION | 11 December 2018, 22:01:24 UTC |
0e5c96e | Nate Coraor | 19 May 2016, 18:42:52 UTC | Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). | 11 December 2018, 22:01:13 UTC |
fa7f2a4 | Dannon Baker | 28 September 2018, 16:37:49 UTC | Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 | 28 September 2018, 16:37:49 UTC |
809ae58 | Dannon Baker | 28 September 2018, 16:37:20 UTC | Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 | 28 September 2018, 16:37:20 UTC |
8a1616a | Dannon Baker | 28 September 2018, 16:36:48 UTC | Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 | 28 September 2018, 16:36:48 UTC |
482f1ea | Dannon Baker | 28 September 2018, 16:35:30 UTC | Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 | 28 September 2018, 16:35:30 UTC |
f3ba9e2 | John Chilton | 28 September 2018, 16:09:38 UTC | Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method | 28 September 2018, 16:09:38 UTC |
814c7f9 | Dannon Baker | 28 September 2018, 15:50:18 UTC | Drop unused peek method (this used unencoded ids) | 28 September 2018, 15:50:18 UTC |
54b9b09 | John Chilton | 15 November 2017, 01:25:38 UTC | Merge remote-tracking branch 'upstream/release_16.10' into HEAD | 15 November 2017, 01:25:38 UTC |
4a28142 | John Chilton | 15 November 2017, 01:23:44 UTC | Merge remote-tracking branch 'upstream/release_16.07' into HEAD | 15 November 2017, 01:23:44 UTC |
9a13a4a | John Chilton | 15 November 2017, 01:22:42 UTC | Merge pull request #5008 from martenson/fix-ldda-access-check [16.07] history contents api - remove the default flag override | 15 November 2017, 01:22:42 UTC |
63f039b | Martin Cech | 14 November 2017, 19:15:22 UTC | remove the default override since it is wrong and ignores the access permissions | 14 November 2017, 19:15:22 UTC |
c7b09f8 | Nicola Soranzo | 30 October 2017, 18:49:17 UTC | Merge branch 'release_16.10' into release_17.01 Conflicts: lib/galaxy/dependencies/pinned-requirements.txt | 30 October 2017, 18:49:17 UTC |
7bf2bbf | John Chilton | 27 October 2017, 15:31:49 UTC | Merge pull request #4873 from jmchilton/fix_test_fixtures [16.10] Fix test fixtures dependency. | 27 October 2017, 15:31:49 UTC |
aef5f4f | John Chilton | 26 October 2017, 16:56:46 UTC | [16.10] Fix test fixtures dependency. It should have never been in the pinned requirements and has disappeared from PyPI. | 26 October 2017, 16:56:59 UTC |
a7bf160 | Nicola Soranzo | 25 October 2017, 18:05:24 UTC | Merge branch 'release_16.10' into release_17.01 | 25 October 2017, 18:05:24 UTC |
90289b6 | Nicola Soranzo | 25 October 2017, 18:03:52 UTC | Merge branch 'release_16.07' into release_16.10 | 25 October 2017, 18:03:52 UTC |
e3e28dd | Nicola Soranzo | 25 October 2017, 18:02:00 UTC | Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory [16.07] Fix galaxy.util.in_directory()... | 25 October 2017, 18:02:00 UTC |
7e08ba6 | John Chilton | 25 October 2017, 16:08:03 UTC | Rework in_directory fix to move realpath expansion into galaxy.util. | 25 October 2017, 16:08:03 UTC |
95f8f48 | John Chilton | 25 October 2017, 14:43:54 UTC | Doc fix thanks to @nsoranzo. | 25 October 2017, 14:43:54 UTC |
fcb23eb | John Chilton | 25 October 2017, 14:34:35 UTC | Some documentation to clarify discussion on #4856. | 25 October 2017, 14:34:35 UTC |
4b5dc39 | John Chilton | 25 October 2017, 14:31:07 UTC | Add basic test for in_directory. | 25 October 2017, 14:32:20 UTC |
899b0d8 | John Chilton | 25 October 2017, 02:48:02 UTC | 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. | 25 October 2017, 02:49:24 UTC |
a4a8f15 | John Chilton | 25 October 2017, 01:55:23 UTC | Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions [16.07] Fix regressions in library API | 25 October 2017, 01:55:23 UTC |
9791dd2 | Nicola Soranzo | 24 October 2017, 18:34:40 UTC | Fix regressions in library API Introduced in commit 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 | 24 October 2017, 18:36:19 UTC |
c4855af | Nate Coraor | 23 October 2017, 14:30:33 UTC | Merge branch 'release_16.10' into release_17.01 | 23 October 2017, 14:30:33 UTC |
dda175d | Nate Coraor | 23 October 2017, 14:29:59 UTC | Merge branch 'release_16.07' into release_16.10 | 23 October 2017, 14:29:59 UTC |
658f126 | Nate Coraor | 19 October 2017, 13:29:00 UTC | [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. | 19 October 2017, 14:26:49 UTC |
1bccbef | Nate Coraor | 12 September 2017, 19:06:30 UTC | Security: Fix issues with path handling in libraries and in general. | 19 October 2017, 14:26:44 UTC |
9e672f9 | Nate Coraor | 19 October 2017, 13:29:00 UTC | [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. | 19 October 2017, 14:26:28 UTC |
ed045cd | Nate Coraor | 12 September 2017, 19:06:30 UTC | Security: Fix issues with path handling in libraries and in general. | 19 October 2017, 14:26:23 UTC |
0e69881 | Nate Coraor | 19 October 2017, 13:29:00 UTC | [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. | 19 October 2017, 14:26:14 UTC |
93a8bfc | Nate Coraor | 12 September 2017, 19:06:30 UTC | Security: Fix issues with path handling in libraries and in general. | 19 October 2017, 14:26:08 UTC |
ae14094 | Nate Coraor | 19 October 2017, 13:13:31 UTC | Merge remote-tracking branch 'origin/release_16.10' into release_17.01 | 19 October 2017, 13:13:31 UTC |
34344a7 | Nate Coraor | 19 October 2017, 13:12:07 UTC | Merge remote-tracking branch 'origin/release_16.07' into release_16.10 | 19 October 2017, 13:12:07 UTC |
8e199a3 | Marius van den Beek | 19 October 2017, 13:07:33 UTC | Merge pull request #4812 from natefoo/hardening-extras-16.07 [16.07] Additional hardening for older releases | 19 October 2017, 13:07:33 UTC |
6d89482 | Nate Coraor | 16 October 2017, 19:09:15 UTC | Additional hardening for older releases | 18 October 2017, 16:54:34 UTC |
54d3994 | Nicola Soranzo | 17 October 2017, 00:04:53 UTC | Merge pull request #4807 from natefoo/backport-hardening-17.01 [17.01] Various bits of hardening from #4604 | 17 October 2017, 00:04:53 UTC |
25fc098 | Nate Coraor | 16 October 2017, 12:59:58 UTC | Merge branch 'release_16.10' into backport-hardening-17.01 | 16 October 2017, 12:59:58 UTC |
d8ee1a9 | Nate Coraor | 15 October 2017, 02:29:47 UTC | Revert ignoring I201 from 16.10 in 17.01 | 15 October 2017, 02:29:47 UTC |
950f926 | Nate Coraor | 14 October 2017, 02:45:45 UTC | Add missing backport of hardening to scripts/grt.py | 15 October 2017, 02:28:09 UTC |
9955c4d | Nate Coraor | 13 October 2017, 23:50:42 UTC | Ignore I201 errors in 16.10 | 15 October 2017, 02:27:49 UTC |
24c8a26 | Nate Coraor | 13 October 2017, 16:19:25 UTC | Fix backport issues | 15 October 2017, 02:26:09 UTC |
b13f5d7 | E Rasche | 28 September 2017, 08:07:55 UTC | Rebase script integrity check improvements (#4720) from dev | 15 October 2017, 02:26:07 UTC |
7ad6182 | Nate Coraor | 13 October 2017, 16:10:19 UTC | Fix additional uses of subprocess shell=True | 15 October 2017, 02:25:41 UTC |
f9213b1 | John Chilton | 26 September 2017, 11:57:37 UTC | Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. | 15 October 2017, 02:25:37 UTC |
03087e5 | E Rasche | 13 September 2017, 06:03:55 UTC | Rebase hardening commits from dev | 15 October 2017, 02:24:01 UTC |
139ba7c | John Chilton | 09 October 2017, 19:28:39 UTC | Pin pydocstyle... | 15 October 2017, 02:23:57 UTC |
b04aafa | Nicola Soranzo | 14 October 2017, 13:44:38 UTC | Merge pull request #4804 from natefoo/backport-hardening-16.10 [16.10] Various bits of hardening from #4604 | 14 October 2017, 13:44:38 UTC |
6d8f8ec | Nate Coraor | 14 October 2017, 02:45:45 UTC | Add missing backport of hardening to scripts/grt.py | 14 October 2017, 02:45:45 UTC |
8d573db | Nicola Soranzo | 26 April 2017, 11:46:21 UTC | Use container-based infrastructure (sudo: false) in TravisCI | 13 October 2017, 23:50:55 UTC |
3bb5d82 | Nate Coraor | 13 October 2017, 23:50:42 UTC | Ignore I201 errors in 16.10 | 13 October 2017, 23:50:42 UTC |
36b974c | John Chilton | 09 October 2017, 19:28:39 UTC | Pin pydocstyle... | 13 October 2017, 19:40:53 UTC |
fe9839b | Nicola Soranzo | 11 August 2017, 10:53:48 UTC | Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . | 13 October 2017, 19:40:52 UTC |
d70713d | Nicola Soranzo | 24 January 2017, 17:00:11 UTC | Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. | 13 October 2017, 19:40:52 UTC |
ef26802 | E Rasche | 13 September 2017, 06:03:55 UTC | Hardening backport differences from dev present in 16.10 but not 16.07 | 13 October 2017, 19:40:52 UTC |
e60f324 | Nate Coraor | 13 October 2017, 18:56:55 UTC | Merge remote-tracking branch 'origin/release_16.07' into backport-hardening-16.10 | 13 October 2017, 18:56:55 UTC |
f925ffe | Nicola Soranzo | 13 October 2017, 18:09:39 UTC | Merge pull request #4801 from natefoo/backport-hardening-16.07 [16.07] Various bits of hardening from #4604 | 13 October 2017, 18:09:39 UTC |
9fa9d42 | Nate Coraor | 13 October 2017, 16:19:25 UTC | Fix backport issues | 13 October 2017, 17:19:19 UTC |
2f79351 | E Rasche | 28 September 2017, 08:07:55 UTC | Rebase script integrity check improvements (#4720) from dev | 13 October 2017, 17:19:03 UTC |
545d555 | Nate Coraor | 13 October 2017, 16:10:19 UTC | Fix additional uses of subprocess shell=True | 13 October 2017, 16:10:19 UTC |
b5ded00 | John Chilton | 26 September 2017, 11:57:37 UTC | Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. | 13 October 2017, 15:45:22 UTC |
e4518ff | E Rasche | 13 September 2017, 06:03:55 UTC | Rebase hardening commits from dev | 12 October 2017, 21:04:55 UTC |
f64b7fc | Martin Cech | 10 October 2017, 14:41:25 UTC | Merge pull request #4777 from jmchilton/release_17.01_pydocstyle_ping [17.01] Pin linting functions in tox.ini. | 10 October 2017, 14:41:25 UTC |
012aaf8 | John Chilton | 09 October 2017, 19:28:39 UTC | Pin pydocstyle... | 09 October 2017, 19:28:39 UTC |
706a5b2 | Nate Coraor | 21 September 2017, 19:25:36 UTC | Merge branch 'release_16.10' into release_17.01 | 21 September 2017, 19:25:36 UTC |
e178879 | Nate Coraor | 21 September 2017, 19:25:16 UTC | Merge branch 'release_16.07' into release_16.10 | 21 September 2017, 19:25:16 UTC |
2ffeedf | Nicola Soranzo | 21 September 2017, 16:33:50 UTC | Merge pull request #4663 from natefoo/fix-modules-resolver [16.07] Fix modules resolver | 21 September 2017, 16:33:50 UTC |
69a8700 | Nate Coraor | 21 September 2017, 00:26:21 UTC | Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy). | 21 September 2017, 00:26:21 UTC |
a9facdc | Dannon Baker | 14 September 2017, 18:54:27 UTC | Merge branch 'release_16.10' into release_17.01 | 14 September 2017, 18:54:27 UTC |
14ceb6d | John Chilton | 14 September 2017, 18:10:15 UTC | Merge pull request #4615 from dannon/release_16.10_backport2 [16.10] Allow fetchMore to actually specify a 0 offset when intentional, fixes multiview | 14 September 2017, 18:10:15 UTC |
7fdce2e | Dannon Baker | 13 September 2017, 19:01:31 UTC | Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. | 14 September 2017, 15:53:25 UTC |
759780b | Nicola Soranzo | 06 September 2017, 17:19:50 UTC | Merge branch 'release_16.10' into release_17.01 | 06 September 2017, 17:19:50 UTC |
140c570 | Nicola Soranzo | 06 September 2017, 17:18:51 UTC | Merge branch 'release_16.07' into release_16.10 | 06 September 2017, 17:18:51 UTC |
4345d8e | Nicola Soranzo | 06 September 2017, 17:12:53 UTC | Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/config.py | 06 September 2017, 17:12:53 UTC |
dad5563 | Nicola Soranzo | 06 September 2017, 17:06:07 UTC | Merge branch 'release_16.01' into release_16.04 | 06 September 2017, 17:06:07 UTC |
2207e7f | Dannon Baker | 06 September 2017, 16:35:30 UTC | Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. | 06 September 2017, 16:35:30 UTC |
02c7792 | John Chilton | 06 September 2017, 13:34:11 UTC | [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 | 06 September 2017, 13:34:11 UTC |
5a18464 | E Rasche | 28 August 2017, 08:53:22 UTC | 2017-08 Security Patch | 28 August 2017, 08:53:22 UTC |
47ba644 | E Rasche | 28 August 2017, 08:53:05 UTC | 2017-08 Security Patch | 28 August 2017, 08:53:05 UTC |
748539a | Dannon Baker | 17 August 2017, 18:12:54 UTC | Merge pull request #4450 from mvdbeek/fix_file_lock_error [17.01] Fix file lock error handling | 17 August 2017, 18:12:54 UTC |
a765472 | Matthias Bernt | 11 May 2017, 11:35:03 UTC | Set timeout for aquiring lock to 5min | 17 August 2017, 18:02:47 UTC |
349c9c8 | Matthias Bernt | 10 May 2017, 13:51:44 UTC | version with no repetition at all | 17 August 2017, 18:02:41 UTC |
a1b8a54 | Matthias Bernt | 10 May 2017, 13:40:44 UTC | ensure_installed is now iterative instead of recursive | 17 August 2017, 18:02:36 UTC |
1e1c549 | Matthias Bernt | 10 May 2017, 11:36:51 UTC | added missing parameter to function ensure_installed | 17 August 2017, 18:02:29 UTC |
0f5ad34 | Marius van den Beek | 14 August 2017, 10:27:14 UTC | Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes [17.01] Add missing chemical formats to datatypes_conf.xml.sample | 14 August 2017, 10:27:14 UTC |
a249dc0 | Nicola Soranzo | 26 April 2017, 11:46:21 UTC | Use container-based infrastructure (sudo: false) in TravisCI | 11 August 2017, 11:25:28 UTC |
61d172f | Nicola Soranzo | 11 August 2017, 10:53:48 UTC | Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . | 11 August 2017, 10:53:52 UTC |
ba3249a | Nicola Soranzo | 10 August 2017, 19:36:50 UTC | Add missing chemical formats to datatypes_conf.xml.sample | 10 August 2017, 19:36:50 UTC |