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
Previously, when running pytest from `packages/test.sh`, it was using
our main `pytest.ini` as configfile, therefore setting the wrong
rootdir and using `lib` as `pythonpath`.
This was hiding various packaging issues fixed in the previous commits.
To make them consistent with other package versions:
23.1.0.dev0 >> 23.1.dev0.
The extra "0" was likely added automatically by running the
build_packages.sh script.
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.
Matthias Bernt