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28 Commits
Author SHA1 Message Date
Matthias Bernt db7395b423 Create version 24.1.4 2024-12-11 10:47:48 +01:00
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
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
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
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
John Davis fa344f7b4e Upgrade SQLAlchemy to 2.0 
This conflicts with dependency requirements for sqlalchemy-graphene
(used only in toolshed, new WIP client)
 2024-04-02 10:08:52 -04:00
Nicola Soranzo f9384bb0df Disallow pydantic 2.6.0 and 2.6.1 
xref: https://github.com/pydantic/pydantic/issues/8760

Fix the following error when testing with mypy:

```
$ tox -e mypy
Deferral trace:
    cwltool.utils:62
    cwltool.utils:-1
    ...
    galaxy.model:666
    galaxy.model:666
    galaxy.model:666
    galaxy.model:666
lib/galaxy/model/__init__.py: error: INTERNAL ERROR: maximum semantic analysis
iteration count reached
Found 1 error in 1 file (errors prevented further checking)
```
 2024-02-14 00:57:47 +00:00
mvdbeek b278d8a2aa Merge branch 'release_23.2' into dev 2024-02-08 11:35:49 +01:00
John Davis ac15c87379 Update package versions to 23.2.dev0 
Update setup.cfg, HISTORY.rst.
Make all dev package versions consistent.
 2024-02-01 22:50:21 -05:00
Ubuntu 6860c9a0fb Add support for Python 3.12 2024-01-21 11:57:59 +00:00
mvdbeek e63c3ba9d4 Update fastapi and pydantic dependencies 2024-01-08 11:33:34 +01:00
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 65b71cbbd1 Fix requirements of packages 2023-11-21 17:54:31 +00:00
Nate Coraor 2ca678482f Merge remote-tracking branch 'upstream/release_23.0' into release_23.1 2023-06-30 15:56:50 -04:00
Nate Coraor ab1e0485d7 Pin pydantic in packages to <2 2023-06-30 14:51:18 -04:00
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 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 922263089d Modernise build of galaxy-web-framework package 
Also:
- Add missing directory to `MANIFEST.in`
 2022-06-09 23:48:35 +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
John Chilton 9b47a2dfe0 Add galaxy-web-stack and galaxy-web-framework packages. 2019-07-06 14:15:13 +02:00