Commit Graph
98 Commits
Author SHA1 Message Date
Nate Coraor 751b52f1ec Start work on 25.0.2.dev0 2025-06-20 16:37:11 -04:00
Nate Coraor 5915a88342 Create version 25.0.1 2025-06-20 16:37:07 -04:00
Nicola Soranzo 8b8d9794fa Fix one more package extra name containing underscores 2025-06-20 12:12:59 +01:00
Nate Coraor 713a1b57a0 Pin isa-rwval minimum in data package 2025-06-19 14:40:50 -04:00
Ahmed Awan 0d223a99b2 Start work on 25.0.1.dev0 2025-06-18 11:59:57 -05:00
Ahmed Awan b15565d03e Create version 25.0.0 2025-06-18 11:59:32 -05:00
John Davis 9b63eaf76c Add script to delete old job metrics records 2025-05-09 12:19:14 +02:00
John Davis f236237d81 Add script to delete old galaxy session records 2025-04-28 12:49:10 -04:00
mvdbeek 3c6b6c5971 Merge branch 'release_24.2' into dev 2025-03-26 09:51:08 +01:00
mvdbeek 648239a31f Merge branch 'release_24.1' into release_24.2 2025-03-26 09:48:18 +01:00
mvdbeek 953a972349 Merge branch 'release_24.0' into release_24.1 2025-03-26 09:44:07 +01:00
Nicola Soranzo fb6139449c Drop unused alembic-utils from galaxy-data package requirements
Last use removed in https://github.com/galaxyproject/galaxy/pull/15876 .
2025-03-25 13:59:13 +00:00
Leonid Kostrykin 8a7191982e Fix package tests 2025-03-25 14:36:47 +01:00
mvdbeek 6a610a1b4b Start work on 24.2.4.dev0 2025-03-16 11:38:12 +01:00
mvdbeek f82f1fc5e8 Create version 24.2.3 2025-03-16 11:37:42 +01:00
mvdbeek 7ad18a9d78 Start work on 24.2.3.dev0 2025-03-08 11:44:06 +01:00
mvdbeek c80d7d92a1 Create version 24.2.2 2025-03-08 11:44:03 +01:00
Matthias Bernt 5547ad5db9 Start work on 24.2.2.dev0 2025-02-28 12:39:06 +01:00
Matthias Bernt 8ff7c9b1b8 Create version 24.2.1 2025-02-28 12:39:03 +01:00
Nicola Soranzo edd8bccf4f Drop support for Python 3.8 2025-02-25 19:20:46 +00:00
John Davis b56638b9d6 Start work on 24.2.1.dev0 2025-02-11 20:41:00 -05:00
John Davis 490257d237 Create version 24.2.0
This is the final version 24.2.0.
It contains the content generated by the release script, minus the
duplicate content (which resulted from the existing 24.2.0 changelogs
that had been pushed upstream on 2/6/25).
2025-02-11 20:36:31 -05:00
John Davis 898fcfc981 Merge branch 'release_24.2' into dev 2025-02-11 09:48:43 -05:00
John Davis a6f3d74f9b Remove isa-rwval dependency from data package 2025-02-10 16:53:01 -05:00
Nicola Soranzo 829c7459f9 Merge branch 'release_24.2' into dev 2025-02-08 21:14:23 +00:00
Nicola Soranzo 1bc76f0c40 Add Python 3.13 classifier to packages
Follow-up on https://github.com/galaxyproject/galaxy/pull/18449 .
2025-02-08 18:58:58 +00:00
John Davis 54f918d09c Fix package versions 2025-02-07 00:53:54 -05:00
John Davis e3b1795275 Start work on 24.2.1.dev0 2025-02-06 22:46:15 -05:00
John Davis 2bff8f5a9a Create version 24.2.0 2025-02-06 22:46:04 -05:00
Matthias Bernt 0f83529907 Start work on 24.1.5.dev0 2024-12-11 10:47:56 +01:00
Matthias Bernt db7395b423 Create version 24.1.4 2024-12-11 10:47:48 +01:00
Nicola Soranzo ac480e7df5 Drop use of deprecated imghdr standard library module
which has been removed in the upcoming Python 3.13 .
2024-10-31 12:09:21 +00:00
Nicola Soranzo f0420d70a3 Pin minimum package versions for Python 3.13 support
Also:
- Cheetah3 package on PyPI has been renamed to CT3 since 3.3.0, see
  https://cheetahtemplate.org/news.html
2024-10-31 12:09:20 +00:00
Nicola Soranzo b2c9f192e3 Merge branch 'release_24.1' into dev 2024-10-27 12:41:02 +00:00
Nate Coraor ccf4353f09 Merge pull request #19052 from natefoo/unpin-data-pkg-social-auth-core
[24.1] Unpin social-auth-core in galaxy-data package
2024-10-25 09:37:38 -04:00
Matthias Bernt 17056521bd Start work on 24.1.4.dev0 2024-10-25 12:51:08 +02:00
Matthias Bernt 71f5048e52 Create version 24.1.3 2024-10-25 12:51:02 +02:00
Nate CoraorandNicola Soranzo fb4e1d0e61 Update packages/data/setup.cfg
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
2024-10-24 08:36:46 -04:00
Nate Coraor 7e4e62eac9 Unpin social-auth-core in galaxy-data package 2024-10-23 17:48:14 -04:00
Nicola Soranzo 3f9cdb40be Disallow SQLAlchemy 2.0.36
due to https://github.com/sqlalchemy/sqlalchemy/issues/12019 .
2024-10-21 18:11:21 +01:00
Matthias Bernt c80ce1d431 Start work on 24.1.3.dev0 2024-09-25 15:02:09 +02:00
Matthias Bernt b34611f422 Create version 24.1.2 2024-09-25 15:01:59 +02:00
Nicola Soranzo 6948206ba7 Install isa-rwval from my fork to relax pin on networkx
xref. https://github.com/ISA-tools/isa-rwval/pull/17
2024-07-03 13:56:47 +01:00
John Davis 329aa9360d Update package dev versions 2024-07-02 17:07:31 -04:00
John Davis 922e2c8f4e Start work on 24.1.2.dev0 2024-07-02 16:02:13 -04:00
John Davis 940a87c8bf Create version 24.1.1 2024-07-02 16:02:06 -04:00
Matthias Bernt ba5e53be70 Start work on 24.0.4.dev0 2024-06-28 11:08:05 +02:00
Matthias Bernt d94748193f Create version 24.0.3 2024-06-28 11:08:00 +02:00
Nicola Soranzo 88d3849960 Pin pydantic to >=2.7.4
Pydantic <2.7.4 is broken on Python>=3.12.4 , see
https://github.com/pydantic/pydantic/issues/9609 .
Fixed upstream in https://github.com/pydantic/pydantic/pull/9639 .

Fix the following traceback in startup test on Python 3.12:

```
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/bin/galaxyctl", line 10, in <module>
    sys.exit(galaxyctl())
             ^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1682, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1729, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/cli.py", line 59, in get_command
    return name_to_command(name)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/cli.py", line 45, in name_to_command
    mod = __import__(mod_name, None, None, ["cli"])
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/commands/cmd_stop.py", line 4, in <module>
    from gravity import process_manager
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/process_manager/__init__.py", line 14, in <module>
    from gravity.config_manager import ConfigManager
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/config_manager.py", line 18, in <module>
    from gravity.state import ConfigFile, service_for_service_type
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/state.py", line 42, in <module>
    class ConfigFile(BaseModel):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/main.py", line 286, in __new__
    cls.__try_update_forward_refs__()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/main.py", line 807, in __try_update_forward_refs__
    update_model_forward_refs(cls, cls.__fields__.values(), cls.__config__.json_encoders, localns, (NameError,))
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/typing.py", line 554, in update_model_forward_refs
    update_field_forward_refs(f, globalns=globalns, localns=localns)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/typing.py", line 520, in update_field_forward_refs
    field.type_ = evaluate_forwardref(field.type_, globalns, localns or None)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/typing.py", line 66, in evaluate_forwardref
    return cast(Any, type_)._evaluate(globalns, localns, set())
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: ForwardRef._evaluate() missing 1 required keyword-only argument: 'recursive_guard'
```

Example: https://github.com/galaxyproject/galaxy/actions/runs/9581802216/job/26419972297
2024-06-19 19:30:46 +01:00
mvdbeek b9808b3e8e Start work on 24.0.3.dev0 2024-05-07 15:55:40 +02:00