chore(deps): pre-commit.ci autoupdate (ecmwf#589)

<!--pre-commit.ci start-->
updates:
- [github.com/psf/black-pre-commit-mirror: 25.1.0 →
25.9.0](psf/black-pre-commit-mirror@25.1.0...25.9.0)
- [github.com/pycqa/isort: 6.0.1 →
6.1.0](PyCQA/isort@6.0.1...6.1.0)
- [github.com/astral-sh/ruff-pre-commit: v0.12.11 →
v0.13.3](astral-sh/ruff-pre-commit@v0.12.11...v0.13.3)
- [github.com/tox-dev/pyproject-fmt: v2.6.0 →
v2.7.0](tox-dev/pyproject-fmt@v2.6.0...v2.7.0)
<!--pre-commit.ci end-->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Ana Prieto Nemesio <91897203+anaprietonem@users.noreply.github.com>
Co-authored-by: anaprietonem <ana.prietonemesio@ecmwf.int>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -27,12 +27,12 @@ repos:
     -   id: python-check-blanket-noqa # Check for # noqa: all
     -   id: python-no-log-warn # Check for log.warn
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 25.1.0
+  rev: 25.9.0
   hooks:
   - id: black
     args: [--line-length=120]
 - repo: https://github.com/pycqa/isort
-  rev: 6.0.1
+  rev: 6.1.0
   hooks:
   - id: isort
     args:
@@ -41,7 +41,7 @@ repos:
     - --profile black
     - --project anemoi
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.12.11
+  rev: v0.13.3
   hooks:
   - id: ruff
     args:
@@ -65,7 +65,7 @@ repos:
   - id: docconvert
     args: ["numpy"]
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: "v2.6.0"
+  rev: "v2.7.0"
   hooks:
   - id: pyproject-fmt
 -   repo: https://github.com/jshwi/docsig # Check docstrings against function sig

graphs/pyproject.toml

@@ -52,7 +52,7 @@ dependencies = [
   "typeguard>=4",
 ]
 
-optional-dependencies.all = [ "anemoi-graphs[anemoi,tri,hex,healpix]" ]
+optional-dependencies.all = [ "anemoi-graphs[anemoi,healpix,hex,tri]" ]
 optional-dependencies.anemoi = [ "anemoi-datasets>=0.5.21" ]
 optional-dependencies.dev = [ "anemoi-graphs[docs,tests]" ]
 

training/pyproject.toml

@@ -43,7 +43,7 @@ dependencies = [
   "anemoi-graphs>=0.5.2",
   "anemoi-models[migrations]>=0.9.5",
   "anemoi-transform>=0.1.11",
-  "anemoi-utils[provenance,mlflow]>=0.4.37",
+  "anemoi-utils[mlflow,provenance]>=0.4.37",
   "datashader>=0.16.3,<0.17; python_version<'3.10'",
   "datashader>=0.17; python_version>='3.10'",
   "einops>=0.6.1",
@@ -66,7 +66,7 @@ dependencies = [
 
 optional-dependencies.all = [  ]
 optional-dependencies.dev = [
-  "anemoi-training[docs,tests,all]",
+  "anemoi-training[all,docs,tests]",
   "pre-commit>=3.3.3",
 ]
 optional-dependencies.docs = [

training/src/anemoi/training/schemas/data.py

@@ -13,7 +13,7 @@
 from pydantic import BaseModel as PydanticBaseModel
 from pydantic import Field
 
-from anemoi.models.schemas.data_processor import PreprocessorSchema  # noqa: TC001
+from anemoi.models.schemas.data_processor import PreprocessorSchema  # noqa: TC002
 
 
 class DataSchema(PydanticBaseModel):

training/tests/integration/aicon/test_cicd_aicon_04_icon-dream_medium.py

@@ -137,5 +137,5 @@ def test_aicon_metadata(aicon_config_with_grid: DictConfig) -> None:
 @pytest.mark.slow
 @typechecked
 def test_aicon_training(trained_aicon: tuple) -> None:
-    trainer, initial_sum, final_sum = trained_aicon
+    _, initial_sum, final_sum = trained_aicon
     assert initial_sum != final_sum

training/tests/unit/diagnostics/callbacks/test_variable_order.py

@@ -171,14 +171,14 @@ def test_on_epoch_partial_rename_permute(
     fake_trainer.datamodule.ds_train.name_to_index = name_to_index_partial_rename_permute
     fake_trainer.datamodule.ds_valid.name_to_index = name_to_index_partial_rename_permute
     fake_trainer.datamodule.ds_test.name_to_index = name_to_index_partial_rename_permute
-    with pytest.raises(ValueError, match="The variable order in the model and data is different."):
+    with pytest.raises(ValueError, match=r"The variable order in the model and data is different."):
         callback.on_train_start(fake_trainer, None)
-    with pytest.raises(ValueError, match="The variable order in the model and data is different."):
+    with pytest.raises(ValueError, match=r"The variable order in the model and data is different."):
         callback.on_validation_start(fake_trainer, None)
-    with pytest.raises(ValueError, match="The variable order in the model and data is different."):
+    with pytest.raises(ValueError, match=r"The variable order in the model and data is different."):
         callback.on_test_start(fake_trainer, None)
 
-    with pytest.raises(ValueError, match="The variable order in the model and data is different."):
+    with pytest.raises(ValueError, match=r"The variable order in the model and data is different."):
         fake_trainer.datamodule.data_indices.compare_variables(
             fake_trainer.model.module._ckpt_model_name_to_index,
             name_to_index_partial_rename_permute,