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Commit Graph
1619 Commits
Author SHA1 Message Date
Martin Cech c9d9009299 refactor and modernize toolshed search indexes build script 
mainly so it can read yml config
 2019-11-14 18:07:06 -05:00
John Chilton 72bae33923 Migrate selenium tests into lib/galaxy_test for packaging. 2019-11-12 09:05:08 -05:00
John Chilton 45019c3fbd Move galaxy testing utilities into more sane package structure. 
Split test/base into lib/galaxy_test/base and lib/galaxy_test/driver. Dividing things on whether they import galaxy-app code or not - with the goal of a galaxy-test-base package that doesn't depend on galaxy-app and a galaxy-test-driver package that does.

I've been refactoring around this division for a long time. Certain tests (namely the integration tests) always need to bootstrap Galaxy - but the API tests and the Selenium tests should be installable and runnable without Galaxy in the Python environment. So future galaxy-test-api and galaxy-test-selenium packages should have only an optional dependency on galaxy-test-driver.

Properly sturcturing these namespaces is a precursor for real packages on PyPI, clean separation of the tool shed testing code, and cleans up all the flake8 noqa hacks in test/.
 2019-11-12 09:03:06 -05:00
John Chilton 559b664b07 Refactor tool_shed webapp out of Galaxy. 2019-11-11 12:32:19 -05:00
Martin Cech a48c7420d7 Merge pull request #8956 from jmchilton/remove_ts_api 
Remove tool shed API examples.
 2019-11-11 10:41:22 -05:00
Nicola Soranzo 6b1bacc2b8 Merge pull request #8957 from jmchilton/remove_legacy_shed 
Remove script for migrating tools to the tool shed...
 2019-11-11 10:54:27 +00:00
John Chilton d4196b61a4 Remove tool shed API examples. 
These aren't tested, bioblend likely has better documentation (https://bioblend.readthedocs.io/en/latest/api_docs/toolshed/all.html), and we should be encouraging TS interactions to be done through Planemo and not raw API calls.

Excluding scripts used by bootstrap.
 2019-11-11 02:55:26 -05:00
John Chilton a27beb0fd8 Remove script for migrating tools to the tool shed... 
from an older tool shed? I completely forgot there even was an older tool shed.
 2019-11-11 02:50:12 -05:00
John Chilton fbe21f94bf Remove tool dependency scripts. 2019-11-11 02:35:31 -05:00
Nicola Soranzo 303f9ec871 Merge pull request #8908 from bernt-matthias/topic/pgcleanup-also-delete 
make pgcleanup also delete HDAs
 2019-11-04 10:21:04 +00:00
Nicola Soranzo 3e64bbb460 Merge branch 'release_19.09' into dev 2019-11-04 09:50:29 +00:00
Sergey Golitsynskiy a855e2ca64 Fix TypeError in logging commands 
Fix the following exception:

```
TypeError: not all arguments converted during string formatting
```

Also, make other log format strings more consistent: %d for numeric object IDs.
 2019-11-03 21:35:07 +00:00
M Bernt 6f010bd49c make pgcleanup also delete HDAs 
follow up to https://github.com/galaxyproject/galaxy/pull/3572
 2019-10-30 13:42:31 +01:00
Nicola Soranzo 85f7f91206 Fix script shebangs 
Improve tools.
 2019-10-26 20:20:01 +01:00
Martin Cech fd6142f6ce Merge branch 'release_19.09' into merge-1909 2019-10-07 10:24:12 -04:00
John Chilton 7620880a9b Release notes for 19.09. 2019-10-01 13:42:46 -04:00
Nicola Soranzo f659c2f86c Merge pull request #8712 from erasche/grt-fixes-n 
GRT: Ensure correct encoding, no partial lines
 2019-09-27 12:19:39 +01:00
Helena RascheandNicola Soranzo 584dbb28df Apply suggestions from code review 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-09-26 14:36:43 +02:00
Helena Rasche f56cc13699 two spaces 2019-09-26 14:35:49 +02:00
Helena Rasche e75a9f67b0 swap to io.open 2019-09-26 13:42:41 +02:00
Helena Rasche f200835445 Ensure correct encoding, no partial lines 2019-09-26 12:12:22 +02:00
will 009611cf04 add .gitattributes file and normalize line endings to use LF instead of CLRF 2019-09-18 22:03:37 -04:00
John Chilton 4287bb787f Merge pull request #8621 from martenson/ux-ts-installer 
[19.09] allow the TS search API to bypass wildcard search
 2019-09-12 13:35:01 -04:00
Martin Cech 99ec4ecf75 adjust indexing and searching of special keywords to be case-insensitive 2019-09-11 16:39:14 -04:00
Martin Cech 02a3342bd6 regenerate ts search indexes in tmp directory 2019-09-10 16:06:21 -04:00
Dannon Baker 9d1e784868 Alternate approach to plugin building; this should be useful as a stepping stone towards moving these out of the repo completely, and it'll work *right now*. 2019-09-06 14:56:10 -04:00
Daniel BlankenbergandNicola Soranzo a2199ee575 Update scripts/interactivetools/key_type_token_mapping.py 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-23 11:29:36 -04:00
Daniel Blankenberg 995fce6b9b Little more RealTimeTools cleanup. 2019-08-23 09:24:55 -04:00
mvdbeek a820e52f2a Fix missed control_worker->queue_worker rename 
Missed that one in 6b52f62fe4
 2019-08-22 10:58:01 +02:00
Daniel Blankenberg 55c929768c more realtime to interactivetools name changes 2019-08-20 16:58:55 -04:00
Daniel Blankenberg c3c4aefcbd Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-08-20 13:44:44 -04:00
Dannon 053510678f Merge pull request #8474 from bgruening/node-conda 
Node is called nodejs in conda land.
 2019-08-20 11:36:38 -04:00
Marius van den Beek ce61509122 Merge pull request #8473 from nsoranzo/restore_mysql 
Fix MySQL database creation and migrations
 2019-08-19 16:52:59 +02:00
Nicola Soranzo ca226282f1 Fix startup checks when using a Conda env 
Unless `--skip-venv` is specified, Galaxy creates/activates a virtualenv
also when using a Conda environment.
 2019-08-19 01:28:35 +01:00
Nicola Soranzo d5633f6285 Enable on-screen logging for create_db.py and manage_db.py 2019-08-18 11:17:34 +01:00
Björn Grüning 4a2c316cfe node is called nodejs in conda-land 2019-08-17 15:42:38 +02:00
John Chilton e611797a77 Merge pull request #8470 from erasche/fix-975 
Fix #975
 2019-08-16 14:42:24 -04:00
Helena Rasche 5f615168bc Fix #975 2019-08-16 15:11:15 +02:00
Helena Rasche b316bab722 Remove scripts deprecated since 1 year 2019-08-15 14:30:53 +02:00
John Chilton 47d46c626e Merge pull request #8452 from erasche/faster-quota 
Replace in-python quota calc with a SQL query
 2019-08-14 14:40:12 -04:00
Helena Rasche 887aae2ab3 Refactor into model 2019-08-14 16:15:49 +02:00
Helena Rasche 58f4f65a4a new method 2019-08-14 16:08:04 +02:00
Dannon Baker 877bd322d6 Add pointer to client/README.md to address 'https://github.com/galaxyproject/galaxy/commit/8bb2b6bfbcac89910ec6b5cc58e23243571ab879#commitcomment-34259049' 2019-08-14 09:59:55 -04:00
Daniel Blankenberg 5ed5ff6d49 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-08-13 14:47:53 -04:00
Nate Coraor 395d98857b Fix config file finding for the manage_db script 2019-08-07 16:33:40 -04:00
M Bernt f6ff679d63 cleanup: use logging instead of print 2019-08-01 09:25:13 +02:00
Daniel Blankenberg 8aebb64ae4 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-07-25 14:59:53 -04:00
Martin Cech 00600e4006 Merge pull request #8298 from jmchilton/selenium_package 
Create galaxy-selenium package.
 2019-07-18 15:17:42 -04:00
Nicola Soranzo e7165c37e3 Fix issues reported by shellcheck 2019-07-17 12:46:46 +01:00
Nicola Soranzo 8e8c64308a Fix use of `PIP_PROGRESS_BAR` env variable 
`PIP_PROGRESS_BAR` environment variable is used by `pip` to set the value
for the `--progress-bar` option. It seems that specifying it also only the
command line does not override it in some configurations, e.g. on TravisCI
Linux builds of BioBlend, see e.g.

https://travis-ci.org/galaxyproject/bioblend/jobs/558857557
 2019-07-16 17:17:32 +01:00