Update Python dependencies#21043
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mvdbeek merged 7 commits intogalaxyproject:devfrom Oct 16, 2025
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nsoranzo
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by running `make update-dependencies`.
Fix the following error at Galaxy startup:
```
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.9.23/x64/lib/python3.9/logging/config.py", line 543, in configure
formatters[name] = self.configure_formatter(
File "/opt/hostedtoolcache/Python/3.9.23/x64/lib/python3.9/logging/config.py", line 655, in configure_formatter
result = self.configure_custom(config)
File "/opt/hostedtoolcache/Python/3.9.23/x64/lib/python3.9/logging/config.py", line 470, in configure_custom
c = self.resolve(c)
File "/opt/hostedtoolcache/Python/3.9.23/x64/lib/python3.9/logging/config.py", line 391, in resolve
self.importer(used)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/web_stack/__init__.py", line 13, in <module>
from galaxy.model import database_utils
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 144, in <module>
from galaxy.files.templates import (
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/files/__init__.py", line 13, in <module>
from galaxy.files.sources import (
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/files/sources/__init__.py", line 19, in <module>
from galaxy.files.models import (
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/files/models.py", line 135, in <module>
class FilesSourceProperties(StrictModel):
File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.9/site-packages/pydantic/_internal/_model_construction.py", line 242, in __new__
set_model_fields(cls, config_wrapper=config_wrapper, ns_resolver=ns_resolver)
File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.9/site-packages/pydantic/_internal/_model_construction.py", line 566, in set_model_fields
fields, class_vars = collect_model_fields(cls, config_wrapper, ns_resolver, typevars_map=typevars_map)
File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.9/site-packages/pydantic/_internal/_fields.py", line 364, in collect_model_fields
field_info = FieldInfo_.from_annotated_attribute(ann_type, assigned_value, _source=AnnotationSource.CLASS)
File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.9/site-packages/pydantic/fields.py", line 443, in from_annotated_attribute
field_info = FieldInfo._construct(
File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.9/site-packages/pydantic/fields.py", line 519, in _construct
merged_field_info = cls(**merged_kwargs)
File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.9/site-packages/pydantic/fields.py", line 232, in __init__
Error: raise TypeError('cannot specify both default and default_factory')
TypeError: cannot specify both default and default_factory
```
nsoranzo
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mvdbeek
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Oct 15, 2025
| [key: string]: string[]; | ||
| }; | ||
| tags: components["schemas"]["TagCollection"]; | ||
| tags: components["schemas"]["galaxy__schema__schema__TagCollection"]; |
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Can we control the model name ? this seems unfortunate
xref: pydantic/pydantic#12374 . Also: - Update client schema.
nsoranzo
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It's never used as a model. Prevents ugly component names in client schema due to model recursion in the new `partial_model()` implementation.
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|
Package tests failure unrelated (it's due to fastapi/fastapi#14168 , which is in fastapi 0.119.0, so not part of this PR). |
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Should 7608bf6 go into the release, as it causes errors on packages using it? |
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Yes. Unfortunately fastapi 0.119 contains other breaking changes in
This is not necessary since |
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by running
make update-dependencies.