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61 Commits
Author SHA1 Message Date
mvdbeek 521405136a Merge branch 'release_23.1' into dev 2023-07-29 12:28:41 +02:00
mvdbeek c314336705 Merge branch 'release_23.0' into release_23.1 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2023-07-29 12:28:39 +02:00
mvdbeek 2fbbfd8417 Start work on 23.0.6.dev0 2023-07-29 12:28:35 +02:00
mvdbeek af730bc6b5 Create version 23.0.5 2023-07-29 12:28:32 +02:00
Nate Coraor 8fee25f084 Merge branch 'release_23.1' into dev 2023-06-30 17:14:03 -04:00
Nate Coraor ea07ddba98 Merge branch 'release_23.0' into release_23.1 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2023-06-30 17:14:03 -04:00
Nate Coraor 25b52a97f7 Start work on 23.0.5.dev0 2023-06-30 17:14:00 -04:00
Nate Coraor 03d9eb63b8 Create version 23.0.4 2023-06-30 17:13:57 -04:00
mvdbeek bb65b07584 Merge branch 'release_23.1' into dev 2023-06-26 09:32:44 +02:00
mvdbeek 0b1a41bd86 Merge branch 'release_23.0' into release_23.1 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2023-06-26 09:32:42 +02:00
mvdbeek 1ef440e92c Start work on 23.0.4.dev0 2023-06-26 09:32:37 +02:00
mvdbeek b4adbb4ec5 Create version 23.0.3 2023-06-26 09:32:32 +02:00
mvdbeek 5413333aac Merge branch 'release_23.0' into dev 
# Conflicts:
#	lib/galaxy/version.py
 2023-06-13 17:58:26 +02:00
mvdbeek 414abff510 Start work on 23.0.3.dev0 2023-06-13 17:58:19 +02:00
mvdbeek a7f0a365be Create version 23.0.2 2023-06-13 17:58:13 +02:00
Matthias Bernt aa9cc5b9e8 Start work on 23.1.dev0 2023-06-08 15:54:32 +02:00
Matthias Bernt f722e122f7 Create version 23.0.1 2023-06-08 15:54:28 +02:00
Nicola Soranzo 4ca163b9ca Add support for Python 3.11 
- Update Python dependencies that didn't have a cp311 wheel: h5py and
  psycopg2-binary.
- For packages for which there is no recent version that works on all
  Python versions supported by Galaxy (numpy and scipy), replace old
  requirement with multiple Python-version-specific requirements.
 2023-02-02 01:18:25 +00:00
Nicola Soranzo ee7d51f2f5 Merge branch 'release_22.05' into dev 2022-12-09 11:36:00 +00:00
mvdbeek 9c92c55a31 Reset all package HISTORY.rst file to 22.5.0.dev0 2022-12-08 13:24:06 +01:00
Nicola Soranzo dda6feb391 Remove redundant license info from package READMEs 
The license is already specified in `setup.cfg` , which is the
canonical place.
This will simplify the transition to the MIT license.
 2022-09-09 17:20:24 +01:00
Michael R. Crusoe 59ac92c1c8 mark galaxy packages as containing typing information 2022-07-26 23:27:36 +01:00
Nicola Soranzo 26caab07d3 Modernise build of galaxy-web-stack package 2022-06-09 23:48:35 +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 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 aeef3318a2 Use setuptools custom package discovery instead of explicit listing 2022-06-06 23:48:37 +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 800d49c467 Short term storage infrastructure. 2022-04-13 09:52:51 -04:00
Marius van den Beek 550f47db9e Merge pull request #13540 from mvdbeek/dev 
Merge release_22.01 into dev
 2022-03-15 11:30:18 +01:00
mvdbeek faea1c8211 Merge branch 'release_22.01' into dev 2022-03-14 17:06:49 +01:00
Nicola Soranzo 0c80836c34 Upgrade syntax to Python 3.7 
using `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py37-plus`

Also more refactoring of Python files in `packages/` .
 2022-03-14 14:57:43 +00:00
mvdbeek 3fa572d612 First pass at supporting --preload and worker_id 
We do need to include some kind of worker id in the server_name. If we
don't do this and we start with multiple workers the internal
QueueWorker won't work and multiple processes can pick up the same job
if the web process is also a job handler.
 2022-03-10 17:15:37 +01:00
Nicola Soranzo 6057338cbd Format files in packages/ with black 
with:

```
find packages/ -name '*.py' | xargs black
```

The `packages/` directory is currently excluded in the `[tool.black]`
section of `pyproject.toml` because black follows symlinks.
 2022-02-03 14:07:52 +00:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
mvdbeek 0af72e56b2 Update version to 22.05.dev0 2022-02-01 11:10:56 +01:00
mvdbeek 917dbe718c Update version to 22.01.rc1 2022-02-01 11:07:22 +01:00
Nicola Soranzo 0bdc93a7cc Drop support for Python 3.6, add Python 3.10 2021-12-08 08:14:10 +00:00
Michael R. Crusoe 7819fdc7a6 tighten type ignores 2021-11-23 13:12:07 +01:00
Sergey Golitsynskiy e691ab866b Update SQLAlchemy to 1.4.25 2021-09-23 11:29:38 -04:00
mvdbeek 5332eb246a Update version to 22.01.dev0 2021-09-20 19:53:11 +02:00
Sergey Golitsynskiy 003dfc48ae Update SQLAlchmey to 1.4.20 2021-07-04 13:18:13 -04:00
Sergey Golitsynskiy 314e00e643 Update SQLAlchemy to 1.4.19 2021-06-23 11:19:58 -04:00
Sergey Golitsynskiy b3551fec8c Update SQLAlchemy to 1.4.18 2021-06-11 18:53:07 -04:00
Sergey Golitsynskiy 94ce70aa8b Update SQLAlchemy to 1.4.17 2021-06-03 12:22:54 -04:00
Sergey Golitsynskiy 9cb78f7c3d Update SA pin to 1.4.15; update requirements files 2021-05-18 19:02:40 -04:00
Sergey GolitsynskiyandNicola Soranzo 3850f49506 Update SQLAlchemy pin <2 in packages/web_stack/requirements.txt 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-05-18 19:02:40 -04:00
Sergey Golitsynskiy 490655ae97 Update SA pin to 4.7; update requirements files 
Also unpin requirement in packages
 2021-05-18 19:00:55 -04:00
Sergey Golitsynskiy a9868971a8 Update SQLAlchemy pin for packages to >=1.4.5 2021-05-18 19:00:55 -04:00
mvdbeek 07fb59937e Update version to 21.09.dev0 2021-05-05 21:48:01 +02:00
Sergey Golitsynskiy 2f0a024915 Pin sqlalchemy in package requirements files 2021-03-16 13:55:21 -04:00