opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-11-03 21:34:30 +08:00
Code Issues Packages Projects Releases Wiki Activity
61,966 Commits 63 Branches 246 Tags
bd56131ebd8eeb043bbc3858f5a4445b779594e7
Commit Graph
615 Commits
Author SHA1 Message Date
Nicola Soranzo 463779b1b5 Merge branch 'release_22.01' into release_22.05 2022-09-13 12:28:05 +01:00
Nicola Soranzo 77553d1711 Pin CacheControl to prevent missing dependency 
schema-salad currently requires:
- "CacheControl >= 0.11.7, < 0.13"
- "lockfile >= 0.9", which is needed for CacheControl's FileCache until 0.12.11

but CacheControl 0.12.12 replaced lockfile with filelock.

Prevent the following traceback:

```
self = <cachecontrol.caches.file_cache.FileCache object at 0x7fe36ac5d190>
directory = PosixPath('/tmp/.cache/salad'), forever = False, filemode = 384
dirmode = 448, lock_class = None

    def __init__(
        self,
        directory,
        forever=False,
        filemode=0o0600,
        dirmode=0o0700,
        lock_class=None,
    ):

        try:
            if lock_class is None:
>               from filelock import FileLock
E               ModuleNotFoundError: No module named 'filelock'

/tmp/gxpkgtestenvcy0lxY/lib/python3.7/site-packages/cachecontrol/caches/file_cache.py:74: ModuleNotFoundError
```
 2022-09-12 21:57:43 +01:00
mvdbeek d1b4f05345 Merge branch 'release_22.01' into release_22.05 2022-08-30 20:32:39 +02:00
Marius van den Beek 609c90fa25 Update packages/tool_util/HISTORY.rst 2022-08-30 17:25:10 +02:00
mvdbeek c07fd27806 Touch up tool util packaging fixes 2022-08-29 13:12:01 +02:00
mvdbeek 0a69d3d882 Update version to 22.1.2.dev0 2022-08-22 21:57:17 +02:00
mvdbeek dc56fc4e61 Update version to 22.01.1 2022-08-22 21:47:47 +02:00
Michael R. Crusoe e955f87c19 pin schema-salad version 2022-07-23 13:59:20 -05:00
John Chilton 7aa9ac539a Allow static components in tours. 2022-06-20 12:20:00 -04:00
Nicola Soranzo 9528dc634d Replace deprecated distutils.version with packaging.version 
Fix https://github.com/galaxyproject/galaxy/issues/12654 .
 2022-06-13 18:47:49 +01:00
Nicola Soranzo 6713818165 Update scripts for modernised package build 2022-06-10 16:34:09 +01:00
Nicola Soranzo 6b643dcf5c Revert "Pin an older version of setuptools for package testing to work around use_2to3 required by rdflib." 
This reverts commit 74e96d3a04.
 2022-06-10 10:48:36 +01:00
Nicola Soranzo 42dcc940f1 Modernise build of galaxy meta-package 2022-06-10 10:32:01 +01:00
Nicola Soranzo 681ed09bb2 Modernise build of galaxy-test-selenium package 
Also:
- Add missing files to `MANIFEST.in`
 2022-06-10 10:32:00 +01:00
Nicola Soranzo 5b9ab20a85 Modernise build of galaxy-selenium package 2022-06-10 10:32:00 +01:00
Nicola Soranzo 701e0112d3 Modernise build of galaxy-test-api package 
Also:
- Add missing files to `MANIFEST.in`
 2022-06-10 02:18:12 +01:00
Nicola Soranzo 1304e44fe0 Modernise build of galaxy-test-driver package 2022-06-10 02:04:24 +01:00
Nicola Soranzo 5de7dbfe99 Modernise build of galaxy-test-base package 
Also:
- Add missing files to `MANIFEST.in`
 2022-06-10 01:54:55 +01:00
Nicola Soranzo 231fda2d22 Modernise build of galaxy-webapps package 
Also:
- Add missing files to `MANIFEST.in`
 2022-06-10 01:41:51 +01:00
Nicola Soranzo c5f3d2d04c Modernise build of galaxy-app package 
Also:
- Add missing files to `MANIFEST.in`
- Add missing requirements
 2022-06-10 00:51:05 +01:00
Nicola Soranzo 922263089d Modernise build of galaxy-web-framework package 
Also:
- Add missing directory to `MANIFEST.in`
 2022-06-09 23:48:35 +01:00
Nicola Soranzo 26caab07d3 Modernise build of galaxy-web-stack package 2022-06-09 23:48:35 +01:00
Nicola Soranzo 1e8514d55e Modernise build of galaxy-auth package 2022-06-09 23:48:34 +01:00
Nicola Soranzo 35909e9efa Modernise build of galaxy-job-execution package 
Also:
- Update package requirements
 2022-06-09 23:48:34 +01:00
Nicola Soranzo 073a8d7956 Modernise build of galaxy-data package 
Also:
- Update MANIFEST.in
 2022-06-09 23:48:33 +01:00
Nicola Soranzo 933f9d4e88 Modernise build of galaxy-tool-util package 
Also:
- Add missing file to `MANIFEST.in`
 2022-06-09 23:48:22 +01:00
Nicola Soranzo 076f1b5170 Modernise build of galaxy-files package 
Also:
- Renamed build_scripts symlink to scripts for consistency
 2022-06-09 22:55:09 +01:00
Nicola Soranzo c2298402b5 Modernise build of galaxy-config package 
Also:
- Add galaxy-util and remove requests requirements
- Update version to 22.5.0.dev0
 2022-06-09 22:55:08 +01:00
Nicola Soranzo f3562c1c65 Modernise build of galaxy-job-metrics package 2022-06-09 22:55:08 +01:00
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