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1492 Commits
Author SHA1 Message Date
Dannon Baker 0538f3bcf1 Update static-safe mappings to match new layout, rebuild client. 2020-08-11 10:26:06 -04:00
Dannon Baker 3de5d7ac5d Merge remote-tracking branch 'upstream/dev' into py3-compat-drop 2020-07-20 11:40:25 -04:00
John Chilton 2c2ed3f288 Decouple API and Selenium tests from galaxy-test-driver (and the whole app!) 
I've been refactoring toward this for at least half a decade. Being able to pip install the API and Selenium tests without bringing in the whole app is important to make them usable outside the context of the app - for testing remote, running servers for instance.

If galaxy-test-driver is available the test cases will still spawn a Galaxy instance if needed, but this is not longer required for import or use.
 2020-07-06 13:57:48 -04:00
Dannon Baker 8d17fafa4e Missed one new style class here. 2020-06-26 08:20:49 -04:00
Nicola Soranzo 7ded4170ce Merge branch 'release_20.05' into dev 2020-06-23 10:25:25 +01:00
Nicola Soranzo e8466d002a Python 2.7 is officially unsupported on 20.05 2020-06-20 19:04:57 +01:00
Dannon Baker 0c3a81b0d2 Merge remote-tracking branch 'upstream/release_20.05' into dev 2020-06-17 12:05:55 -04:00
Martin Cech 3bed89490e Merge pull request #9838 from galaxyproject/20.05_release_notes 
Release notes for 20.05
 2020-06-16 18:21:33 +02:00
Nicola Soranzo a3c423873d Merge branch 'release_20.05' into dev 2020-06-05 10:22:05 +01:00
Nicola Soranzo 089e11ce65 Small refactor to `validate_password()`. Add back deleted line 
Follow-up on https://github.com/galaxyproject/galaxy/pull/9587
 2020-06-04 18:52:59 +01:00
Helena Rasche bb903c60cf shorten url 2020-06-03 13:54:48 +02:00
Helena Rasche 039a3d0233 And ensure not forgotten in future 2020-06-03 12:10:00 +02:00
mvdbeek 81abd93658 Merge branch 'release_20.05' into dev 2020-06-02 12:30:41 +02:00
Marius van den Beek 0fe6be60ea Merge pull request #9587 from nuwang/set_password_if_null 
[20.05] Assign random password in user manager if none specified
 2020-06-02 12:04:50 +02:00
Matthias Bernt d22fe1f3b4 release process: merge IUC/devteam CI and PR update 2020-05-26 11:31:57 +02:00
Nuwan Goonasekera c9f29aa888 Refactor toolshed password validation 2020-05-25 23:39:52 +05:30
Matthias Bernt 2b0e419a59 switch branch of IUC CI earlier in release process 2020-05-22 11:33:30 +02:00
Nate Coraor 8cf33be81f Merge remote-tracking branch 'upstream/release_20.05' into dev 2020-05-13 10:56:53 -04:00
mvdbeek f219fa6d82 Switch to lxml for xml parsing 2020-05-12 15:00:27 +02:00
mvdbeek 6a0653affc Skip check for branch protection 2020-05-05 22:45:39 +02:00
John Chilton 705669a783 Merge pull request #9610 from mvdbeek/store_tool_source 
Startup speedups (XML doc cache, delay non-essential tool param parsing & indexing)
 2020-04-27 14:54:32 -04:00
Nicola Soranzo 7118b4fa11 Hide "python: not found" error when Python 2 is not installed 2020-04-27 02:32:06 +01:00
mvdbeek 51549d0391 Only build toolbox index for webapps, delay until after startup 2020-04-25 20:40:26 +02:00
Nicola Soranzo b481e0c2c8 Merge pull request #9637 from mvdbeek/fix_issue_creation 2020-04-21 13:01:25 +01:00
mvdbeek 3c0f22d451 Use pygithub for issue creation 2020-04-21 12:55:39 +02:00
mvdbeek a36b4486bf Merge branch 'release_20.01' into dev 2020-03-26 10:51:46 +01:00
mvdbeek 7105de2fb0 Fix import order 2020-03-21 13:27:53 +01:00
mvdbeek 159a94b95d Move index logic to lib.tool_shed.util.shed_index 
Since we need the index for browsing repos in the new client
we should incrementally build the index with every repo update.
Having this in tool_shed will make re-use easier.
 2020-03-21 13:27:53 +01:00
mvdbeek afce65249f Implement incremental indexing 2020-03-21 13:27:53 +01:00
mvdbeek 2bb2f0989f Make build_ts_whoosh_index.py py3 compatible 2020-03-21 13:27:53 +01:00
Nicola Soranzo 56450de8a9 Print help if no action is selected 2020-03-05 13:26:28 +01:00
Dannon Baker e183cc1f7b Merge remote-tracking branch 'upstream/release_20.01' into dev 2020-02-29 09:55:46 -05:00
Nicola Soranzo 088653e2cb Add missing pygithub dev-requirement 
Follow-up to https://github.com/galaxyproject/galaxy/pull/9271

Also move GitHub client initialisation and check for `requests` closer to where they
are used to prevent error messages when running `make`.
 2020-02-29 01:55:05 +00:00
mvdbeek a02480f35b Merge branch 'release_20.01' into dev 2020-02-27 17:51:34 +01:00
Nicola Soranzo 4e96e3edce Use with statement to open file 2020-02-27 11:49:49 +00:00
Nicola Soranzo 765f59175c Create Python3 virtualenv by default 
- Allow specifying Python to use to create virtualenv using GALAXY_PYTHON
  environment variable.
- Integrate Python support docs from https://galaxyproject.org/admin/python/
- Update virtualenv installation to use v16.7.9
 2020-02-26 10:53:43 +01:00
mvdbeek 6b304586c4 Fix missing newline after section 2020-02-26 10:15:33 +01:00
mvdbeek 2dc072609f Update scripts/bootstrap_history.py for python 3 / pygithub 2020-02-26 10:15:33 +01:00
Nicola Soranzo 2c3f63751a Fix py27-first_startup Travis job to actually use Python 2 
`scripts/common_startup.sh` now prefers python3 when creating Galaxy's
virtual environment, so it needs to be run when inside the tox virtualenv,
where `GALAXY_PYTHON` is defined.
 2020-02-25 11:54:27 +00:00
Nicola Soranzo f9b99fcf97 Merge branch 'release_20.01' into dev 2020-02-24 11:48:30 +00:00
Nicola Soranzo da256571e6 Source the full path of conda activate script 
Otherwise, if a virtualenv is active on top of conda base env (e.g. when
running py37-first_startup tox test in TravisCI), the wrong `activate`
script is sourced.

Also fix `CONDA_PREFIX` environment variable definition when using a shell
not supported by conda.
 2020-02-23 23:06:01 +00:00
Nicola Soranzo f61ae2c42a Don't check if python is from conda when CONDA_EXE env var is set 
Since at least version 3.7.4 of the `python` package from the `defaults`
conda channel, `python -V` doesn't reveal its origin any more.

Also some fixes suggested by `shellcheck`.
 2020-02-23 23:05:52 +00:00
Nicola Soranzo d4662fd952 Merge branch 'release_20.01' into dev 2020-02-19 12:43:07 +00:00
Nicola Soranzo 437f51c2a6 Create Python3 virtualenv by default 
- Allow specifying Python to use to create virtualenv using GALAXY_PYTHON
  environment variable.
- Integrate Python support docs from https://galaxyproject.org/admin/python/
- Update virtualenv installation to use v16.7.9
 2020-02-09 02:54:24 +00:00
Dannon Baker 4834b7535f Drop static-safe from DEFAULT_ARGS, relying on an explicit add now. 2020-02-06 13:27:33 -05:00
Dannon Baker e7a2e9a440 With it configured to always set static-safe, this is no longer necessary 2020-02-06 13:23:42 -05:00
Dannon Baker 127be4842a Automatically resolve and add static-safe mappings for client-based images. This is safe, and we might as well just automate/force it here. People can always add additional ones, of course, but this ensures galaxy internal static files are resolvable. 2020-02-06 13:21:04 -05:00
Nate Coraor acb9bc1ea1 Merge pull request #9306 from dannon/blue-elimination 
Clean up old 'blue' style path, update documentation and samples
 2020-02-05 09:31:34 -05:00
Dannon Baker f935c6206b Clean up old 'blue' style path, update documentation and samples to refer to plain old 'static' now. 2020-02-03 22:41:29 -05:00
Nicola Soranzo 3525cf7a8e Remove broken script 
None of the 3 other scripts called by this one exists anymore.
 2020-02-03 18:48:57 +00:00