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794 Commits
Author SHA1 Message Date
Ubuntu 6860c9a0fb Add support for Python 3.12 2024-01-21 11:57:59 +00:00
Nicola Soranzo 4eb94cde5f Install future from my fork with Python 3.12 patches 2024-01-21 11:57:58 +00:00
Nicola Soranzo bbf02a0fdb Use venv module instead of virtualenv 2024-01-15 17:31:57 +00:00
mvdbeek 5cd6254e69 Fix merge conflicts in packages/web_apps/setup.cfg 2024-01-10 17:30:02 +01:00
mvdbeek b70680c5f8 Import IdEncodingHelper for type-checking only 2024-01-10 17:27:58 +01:00
mvdbeek 6863ac4c5f Add pycryptodome dependency to galaxy-schema 2024-01-08 11:33:45 +01:00
mvdbeek 46dc767a4c Update pydantic package dependencies 2024-01-08 11:33:45 +01:00
mvdbeek 9dfdd7dcba Update dependencies 2024-01-08 11:33:41 +01:00
mvdbeek e63c3ba9d4 Update fastapi and pydantic dependencies 2024-01-08 11:33:34 +01:00
mvdbeek 5afce686b0 Merge branch 'release_23.2' into dev 2024-01-04 16:15:31 +01:00
mvdbeek 7fc0b15be7 Merge branch 'release_23.1' into release_23.2 
# 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
 2024-01-04 16:15:26 +01:00
mvdbeek 20e560c2e2 Start work on 23.1.5.dev0 2024-01-04 16:15:18 +01:00
mvdbeek 5dccc48db7 Create version 23.1.4 2024-01-04 16:15:11 +01:00
John Chilton 4bb1c4b4ce Merge pull request #17205 from jdavcs/dev_cbv 
Vendorize fastapi-utls.cbv
 2023-12-22 10:28:32 -05:00
John Davis 52d7fa704f Bump graphene-sqlalchemy to 3.0.0rc1 2023-12-19 12:37:49 -05:00
John Davis 377d7d134f Remove fastapi-utils from pyproject.toml, packages 2023-12-18 14:52:01 -05:00
Nicola Soranzo ddbcb39fb3 Merge pull request #17058 from davelopez/remove_web_dependency_from_tools 
Remove web framework dependency from tools
 2023-12-01 12:29:26 +00:00
mvdbeek ca6f9b3586 Merge branch 'release_23.2' into dev 2023-12-01 11:54:53 +01:00
mvdbeek 87c98787a4 Merge branch 'release_23.1' into release_23.2 
# 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
 2023-12-01 11:54:51 +01:00
mvdbeek 316f8c1a2c Start work on 23.1.4.dev0 2023-12-01 11:54:46 +01:00
mvdbeek d7cc988979 Create version 23.1.3 2023-12-01 11:54:43 +01:00
davelopez aedfa820f5 Add symlink to short_term_storage in app package 
Temporarily include it in app until the STS goes into its own package.
 2023-11-30 17:01:29 +01:00
mvdbeek dbe1e7464f Merge branch 'release_23.2' into dev 2023-11-29 19:20:17 +01:00
mvdbeek 64a813e763 Merge branch 'release_23.1' into release_23.2 
# 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
 2023-11-29 19:20:15 +01:00
mvdbeek cb1bb4a6ab Start work on 23.1.3.dev0 2023-11-29 19:20:10 +01:00
mvdbeek 3642185621 Create version 23.1.2 2023-11-29 19:20:07 +01:00
mvdbeek 5d48e33339 Merge branch 'release_23.2' into dev 2023-11-29 18:47:44 +01:00
mvdbeek 59d48ff194 Merge branch 'release_23.1' into release_23.2 2023-11-29 18:44:51 +01:00
mvdbeek cb99976e7c Fix web_apps dependencies 2023-11-29 13:32:21 +01:00
Michael R. Crusoe 8611d3ccb8 pin kombu to >= 5.3 for importlib-metadata fix (poetry had already picked up 5.3.x) 2023-11-27 00:01:55 +00:00
Michael R. Crusoe 14fb5acc69 importlib_resources is only needed in Python 3.8 
Add type hints + fixes
 2023-11-27 00:01:54 +00:00
Michael R. Crusoe 8bb13b39a8 packages: synchronize pins with pyproject.toml 2023-11-26 18:34:12 +00:00
Michael R. Crusoe df807e6d17 Use the walrus := operator! 
Fixed by running:

```
ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^tools/\|^.venv/\|^.tox/' | grep -v '^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/' | xargs auto-walrus
make format
```

Note that the directories for the packages listed in
`packages/packages_for_pulsar_by_dep_dag.txt`
were explictly excluded.
 2023-11-26 18:34:10 +00:00
Michael R. Crusoe c00967cca4 Python 3.8 as new minimum version 
Fixes: https://github.com/galaxyproject/galaxy/issues/16394

Also upgrade code to Python 3.8 syntax with:

```
ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|lib/tool_shed_client/schema/trs.*.py\|^tools/\|^.venv/\|^.tox/' | grep -v '^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/' | xargs pyupgrade --py38-plus
```
 2023-11-26 18:34:09 +00:00
Nicola Soranzo 3af812ce6c Fix testing of the galaxy-tool-shed package 
It was not tested before because of the missing newline at the end of
`packages/packages_by_dep_dag.txt` and of how `read` works in bash.

Also:
- Allow empty lines in packages_by_dep_dag.txt and divide it into layers, so
  that packages in each layer depend only on packages in the layers above.
- Fix type annotations and use of re-exported imports
 2023-11-21 18:08:28 +00:00
Nicola Soranzo 65b71cbbd1 Fix requirements of packages 2023-11-21 17:54:31 +00:00
mvdbeek 0d74680762 Merge branch 'release_23.1' into dev 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/auth/HISTORY.rst
#	packages/config/HISTORY.rst
#	packages/data/HISTORY.rst
#	packages/files/HISTORY.rst
#	packages/job_execution/HISTORY.rst
#	packages/job_metrics/HISTORY.rst
#	packages/navigation/HISTORY.rst
#	packages/objectstore/HISTORY.rst
#	packages/selenium/HISTORY.rst
#	packages/test_api/HISTORY.rst
#	packages/test_base/HISTORY.rst
#	packages/test_driver/HISTORY.rst
#	packages/tool_util/HISTORY.rst
#	packages/tours/HISTORY.rst
#	packages/util/HISTORY.rst
#	packages/web_apps/HISTORY.rst
#	packages/web_framework/HISTORY.rst
#	packages/web_stack/HISTORY.rst
 2023-10-23 21:35:31 +02:00
mvdbeek 3dd88a4357 Start work on 23.1.2.dev0 2023-10-23 21:35:28 +02:00
mvdbeek e77b17df06 Create version 23.1.1 2023-10-23 21:35:24 +02:00
mvdbeek 5e2d094f62 Merge branch 'release_23.1' into dev 
# Conflicts:
#	packages/app/HISTORY.rst
#	packages/auth/HISTORY.rst
#	packages/config/HISTORY.rst
#	packages/data/HISTORY.rst
#	packages/files/HISTORY.rst
#	packages/job_execution/HISTORY.rst
#	packages/job_metrics/HISTORY.rst
#	packages/navigation/HISTORY.rst
#	packages/objectstore/HISTORY.rst
#	packages/selenium/HISTORY.rst
#	packages/test_api/HISTORY.rst
#	packages/test_base/HISTORY.rst
#	packages/test_driver/HISTORY.rst
#	packages/tool_util/HISTORY.rst
#	packages/tours/HISTORY.rst
#	packages/util/HISTORY.rst
#	packages/web_apps/HISTORY.rst
#	packages/web_framework/HISTORY.rst
#	packages/web_stack/HISTORY.rst
 2023-10-23 18:01:54 +02:00
mvdbeek 5aeff97113 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
 2023-10-23 18:01:52 +02:00
mvdbeek e88541e645 Start work on 23.0.7.dev0 2023-10-23 18:01:40 +02:00
mvdbeek bce8be24fe Create version 23.0.6 2023-10-23 18:01:36 +02:00
Martin Cech a33ea00eaf Merge pull request #16743 from dannon/package-version-handling 
Fix package version handling for initial minor releases
 2023-10-09 16:24:32 +02:00
John Chilton 7dc0b1378b WIP: modern tool shed frontend 2023-09-27 14:30:42 -04:00
John Chilton 59cff45fb1 Decompose tool shed + schema package. 
This commit creates two new packages - below a description of these packages and why they are being created.

galaxy-schema: This package contains the pydantic models that power the API. The purpose of packaging them is to ensure they can be reused by clients with minimal external dependencies. Reusing the schema in client code would very quickly provide rapid documentation and validation and static checking for Python clients using the Galaxy API.

galaxy-tool-shed: This package contains the tool shed server code. This has been a long term project to allow the tool shed to be spun out but maintain real galaxy dependencies and maintain testing. More discussions around this project can be found as part of https://github.com/galaxyproject/galaxy/pull/8830.
 2023-09-26 13:46:55 -04:00
Dannon Baker d1c1af7b48 Fix package version handling for initial release 2023-09-26 09:15:49 -04:00
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