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43 Commits
Author SHA1 Message Date
mvdbeek 09ff121dd9 Merge branch 'release_23.1' into dev 2023-09-25 10:23:14 +02:00
mvdbeek bb2daafcc9 Move config parsing to util package 2023-09-22 21:18:02 +02:00
mvdbeek cac5495b5d Fix allowlist deserialization in file sources 2023-09-22 19:37:41 +02:00
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 a5f75e7ead Merge branch 'release_23.0' into dev 2023-06-08 15:54:42 +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
mvdbeek ff7908f6be Merge branch 'release_23.0' into dev 2023-05-17 12:15:05 +02:00
mvdbeek 49b0663328 Add missing dates for versions that contain changelog entries 2023-05-15 13:17:12 +02:00
nuwang 11ccfff186 Add s3fs to test requirements 2023-02-09 18:13:32 +05:30
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 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 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
Nuwan Goonasekera d1f804921c Add support for anonymous gcs file source access 2021-12-20 11:08:42 +05:30
Nicola Soranzo 0bdc93a7cc Drop support for Python 3.6, add Python 3.10 2021-12-08 08:14:10 +00:00
Nicola Soranzo a65d8fade9 Add missing typing-extensions requirement 
to `pyproject.toml` and packages' `requirements.txt` .

We have been importing it explicitly since commit
fc2ce45767 (December 2020).

Also:
- Remove now unnecessary minimum version for pygithub
 2021-11-24 01:09:49 +00:00
Michael R. Crusoe 7819fdc7a6 tighten type ignores 2021-11-23 13:12:07 +01:00
John Chilton c791fea0cf Formalize dependency of galaxy-data on galaxy.files package. 
- Create a new project galaxy-files that does not depend on anything but galaxy-util.
- Add a dependency in galaxy-data on galaxy-files, use typing in galaxy.data.sniff to make this clear.
- Cleanup the galaxy-files unit tests to not depend on galaxy.datatypes.sniff code - this wasn't ideal to start with.
- Add a small integration-ish unit test test_sniff_file_sources.py to test that piece of sniff.py that depends on galaxy-files.
 2021-10-11 13:16:30 -04:00