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67 Commits
Author SHA1 Message Date
Nicola Soranzo 23185e7039 Add GitHub CI workflow to test on Python 3.7 the packages needed by Pulsar 
so we will be able to drop Python 3.7 support for the rest of the code base.

Add a new `test_galaxy_packages_for_pulsar` tox environment and modify the
`test.sh` script so that when the `--for-pulsar` argument is passed:
- only the 4 packages used by Pulsar are tested
- mypy checks are skipped
- unit tests don't skip the tests marked with
  `external_dependency_management` (i.e. those conda/container-related).

Also:
- Add missing pydantic requirement to the galaxy-objectstore package
 2023-09-06 11:07:56 +01:00
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 b8c465939c Modernise build of galaxy-objectstore package 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 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
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
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
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
John Chilton 336cf7b918 Package objectstore's unittest helpers and drop hacks for running test_model_copy.py in galaxy-data. 2021-09-24 12:16:54 -04:00
mvdbeek 5332eb246a Update version to 22.01.dev0 2021-09-20 19:53:11 +02:00
mvdbeek 07fb59937e Update version to 21.09.dev0 2021-05-05 21:48:01 +02:00
Nate Coraor 7ed0f5337f Merge remote-tracking branch 'upstream/release_20.09' into release_21.01 2021-03-01 16:47:23 -05:00
Nate Coraor 373489e8f4 Starting work on objectstore 20.9.2 2021-03-01 16:37:33 -05:00
Nate Coraor 0fbbf734f5 Version 20.9.1 of objectstore (tag galaxy-objectstore-20.9.1). 2021-03-01 15:29:38 -05:00
Nicola Soranzo 2bab40a7bd Remove already unsupported Python 2 from packages 2021-01-15 18:34:37 +00:00
John Chilton b9c9eb0d33 mypy checks for galaxy-objectstore 2020-12-25 19:29:43 -05:00
Nicola Soranzo e40e5aef7e Upgrade syntax using pyupgrade --py36-plus 2020-11-18 16:16:46 +00:00
Nicola Soranzo e96c96eb79 Merge branch 'release_20.09' into dev 2020-10-19 17:48:30 +01:00
Nicola Soranzo a3b954126d Add *requirements.txt files to source packages 2020-10-19 10:32:05 +01:00
mvdbeek 6ac956b57c Merge branch 'release_20.09' into dev 2020-10-17 10:43:51 +02:00
John Chilton c31a2745f6 Starting work on objectstore 20.9.1 2020-10-15 11:56:04 -04:00
John Chilton f5b0d2b109 Version 20.9.0 of objectstore (tag galaxy-objectstore-20.9.0). 2020-10-15 11:55:51 -04:00
John Chilton 7c9b123a6f Prep release of galaxy-objectstore 20.9.0. 2020-10-15 11:55:31 -04:00
Nicola Soranzo 9d74bba7fb Drop support for retired Python 3.5 
Upgrade syntax using `pyupgrade --py36-plus` .

Manually drop several `six` imports.

Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
 2020-10-07 11:52:13 +01:00