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586 Commits
Author SHA1 Message Date
Nicola Soranzo b8c465939c Modernise build of galaxy-objectstore package 2022-06-09 22:55:07 +01:00
Nicola Soranzo c4aeb69683 Modernise build of galaxy-util package 
- Move package metadata from `setup.py` and `project_galaxy_util.py`
  to `setup.cfg` (scripts need to be updated).
- Use `build` package to build sdist and wheel packages (Makefile
  needs to be updated).
 2022-06-09 22:55:07 +01:00
Nicola Soranzo 73bf57e9a0 Remove unused and unnecessary code 
- `PROJECT_OWNER`, `PROJECT_USERAME`, `RAW_CONTENT_URL` and `_version_re` are unused.
- `:changelog:` hyperlink target is unnecessary.
- `test_suite` and `tests_require` are deprecated since setuptools v41.5.0
 2022-06-09 22:55:07 +01:00
Nicola Soranzo 7b3b40f1a9 Merge pull request #14012 from jmchilton/test_api_under_ci 2022-06-09 17:57:23 +02:00
John Chilton 1cb4135018 Remove test_selenium from CI - doesn't yet pass mypy... 
Also why is mypy so much more aggressive with packages, it is like it just gives up on the big code base.
 2022-06-09 09:25:41 -04:00
John ChiltonandNicola Soranzo db845f353a Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-06-08 20:00:07 -04:00
John ChiltonandNicola Soranzo e5bc14a544 Update packages/test_api/requirements.txt 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-06-08 10:10:31 -04:00
Nicola Soranzo e9b2262dd3 Move mypy configuration to `mypy.ini` 
So packages can use `setup.cfg` to replace `setup.py` .
 2022-06-08 10:35:18 +01:00
Nicola Soranzo 7902601d21 Replace 2 doctests with unit tests 2022-06-08 10:17:50 +01:00
John Chilton fa3819ccda Bring galaxy-test-api and galaxy-test-selenium under CI also. 2022-06-08 09:24:02 +01:00
John Chilton b63b3735c0 Merge pull request #14022 from nsoranzo/package_fixes 
Use setuptools custom package discovery instead of explicit listing
 2022-06-07 12:24:33 -04:00
Dannon 4644922783 Merge pull request #13655 from mvdbeek/metadata_embed 
Create data_fetch and set_metadata celery tasks
 2022-06-07 10:27:06 -04:00
Nicola Soranzo aeef3318a2 Use setuptools custom package discovery instead of explicit listing 2022-06-06 23:48:37 +01:00
Nicola Soranzo 057b0fbfdf galaxy-app should depend on galaxy-files 2022-06-06 19:24:06 +01:00
Nicola Soranzo 27b2ee0e9e Merge branch 'release_22.01' into dev 2022-06-06 19:18:55 +01:00
Nicola Soranzo 6a00e75410 Merge branch 'release_21.09' into release_22.01 2022-06-06 11:25:14 +01:00
Nuwan Goonasekera 16d9981c45 Fix missing biotools package 2022-06-06 11:45:55 +05:30
Nuwan GoonasekeraandNicola Soranzo 6e43464979 Update packages/app/requirements.txt 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-06-05 23:38:05 +05:30
Nuwan Goonasekera c61e3918d2 Add missing whoosh package to galaxy-app package requirements 2022-06-05 13:21:38 +05:30
Nuwan Goonasekera 635944aa5b Also add missing error_reports.plugins 2022-06-05 12:17:47 +05:30
Nuwan Goonasekera dd0702e89b Add root webapp to webapp package 2022-06-05 02:41:58 +05:30
Nicola Soranzo 283e70601d Fix mypy issues 2022-06-03 18:17:31 +01:00
John Chilton 9b3dd7413e Add galaxy-test-driver to CI package tests. 2022-06-03 09:35:22 -04:00
John Chilton 6bde989e16 Merge pull request #13983 from jmchilton/package_tests_203 
Run CI on test_base so we can catch issues with packaging
 2022-06-03 09:16:57 -04:00
Nicola Soranzo 9300e37fe4 Drop pins on pytest to support Python 3.10 2022-06-02 17:25:07 +01:00
Nicola Soranzo b1262fcbf7 Run pytest on all packages' files 
recovering missed doctests.
 2022-06-02 16:17:55 +01:00
Nicola Soranzo 97e7dceb73 Fix packages' requirements 2022-05-30 22:40:28 +01:00
Nicola Soranzo f2a42ba67e Run mypy on all packages' files 
Also:
- mypy fixes.
- Use `with` statement to open/close files.
 2022-05-30 22:38:55 +01:00
John Chilton d3719517e7 attempt to run CI on test_base so we can catch issues with packaging... 2022-05-30 12:19:29 -04:00
mvdbeek 83d3f551a9 Make only url uploads cancelable 2022-05-27 17:33:53 +02:00
John Chilton 5c807f6b6b Remove tool shed tool_dependencies.xml handling on the client side. 2022-05-27 10:57:44 -04:00
John Chilton c5bf63bc91 Add DEFERRED datasets to Galaxy 
- Improves options and display around discarded datasets.
- Adds new APIs for importing model stores.
- Adds support to model store layer for importing/exporting workflow invocations and APIs and tests to support this.
- Add new DEFERRED dataset state - with APIs for materializing them or the option to defer them on the worker node if using tool_evaluation_strategy=remote on the job destination.
- UI and API options for uploading deferred datasets individually or into collections.
 2022-05-23 19:48:47 -04:00
Nicola Soranzo 47d35a8cc5 Add missing pytest-asyncio test requirement to `webapps` package 
Otherwise all unit tests in `test_request_scoped_sqlalchemy_sessions.py`
are skipped.
 2022-05-12 16:38:14 +01:00
Michael R. Crusoe dd77026527 galaxy-tool-util: better link in the README 2022-05-04 15:25:42 +02:00
Marius van den Beek 2b3486bb25 Merge pull request #13793 from mvdbeek/fetch_data_almost_everywhere 
Port api/tools/fetch to FastAPI, add schema, and use `__FETCH_DATA__` in most tests
 2022-04-26 13:36:51 +02:00
mvdbeek 02ac5b3c9e Add FastAPI route for tools/fetch 2022-04-23 12:01:32 +02:00
Nicola Soranzo 6da2f0e98c Merge branch 'release_22.01' into dev 2022-04-22 18:23:33 +01:00
mvdbeek da61e77068 Fix persistent mulled cache unused for repo_has_name 2022-04-14 12:10:42 +02:00
John Chilton 800d49c467 Short term storage infrastructure. 2022-04-13 09:52:51 -04:00
Björn Grüning b81ea28df1 Merge pull request #13654 from mvdbeek/memoize_ffprobe 
Speed up sniffers by using lru_cache on ffprobe, skip binary sniffers on text files
 2022-04-09 14:13:00 +02:00
Nicola Soranzo 528f847d13 Remove file added by mistake 
in commit 9690680ec7 .
 2022-04-05 18:16:53 +01:00
mvdbeek 37b47e0304 Better binary detection with FilePrefix & libmagic 
FilePrefix reads the first Megabytes of a file, which is much more
than the previously used `check_binary` which read only 1KB.

Since we're re-using FilePrefix instance this shouldn't have any impact
on performace. In addition we're now using `python-magic` to detect
the encoding and mime-type. We're using the mime-type detection
for PDF only at this point, but we're also using the detected encoding
if we encounter non-utf8 content.
 2022-04-05 15:06:04 +02:00
Björn Grüning e5dd7b111e Merge pull request #13634 from jmchilton/job_metrics_revision 
Overhaul job metrics.
 2022-04-04 22:27:21 +02:00
Nicola Soranzo 7cf3ce97ec Unpin alembic in galaxy-data package 2022-03-31 18:50:07 +01:00
Nicola Soranzo d11bbf219d Update mypy to 0.942 . Fix new mypy errors. 
Remove unused `optional()` decorator function that had an annotation issue.
 2022-03-31 18:47:52 +01:00
John Chilton 2613512327 Remove job metrics CollectL plugin. 
The project seems to be a deadend and it was never adopted in production as far as I am aware. The cgroup plugin seems to provide similar information with much less overhead and with easier to manage dependencies.
 2022-03-31 09:25:52 -04:00
John Chilton f9940e35d1 Pin pysam since 0.19.0 seems to have incomplete type definitions. 2022-03-30 16:44:58 -04:00
mvdbeek 443119ccc9 Drop containers package, move to tool_util 2022-03-24 19:51:59 +01:00
mvdbeek 5ce08cc63f Add an alibi test for the containers package, drop another unused method 2022-03-23 19:06:57 +01:00
mvdbeek 08d3078382 Drop docker swarn gie support 2022-03-23 18:38:53 +01:00