[pre-commit.ci] pre-commit autoupdate (#1350)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)
- [github.com/asottile/pyupgrade: v3.10.1 → v3.15.0](asottile/pyupgrade@v3.10.1...v3.15.0)
- [github.com/psf/black: 23.7.0 → 23.11.0](psf/black@23.7.0...23.11.0)
- [github.com/asottile/setup-cfg-fmt: v2.4.0 → v2.5.0](asottile/setup-cfg-fmt@v2.4.0...v2.5.0)
- [github.com/nbQA-dev/nbQA: 1.7.0 → 1.7.1](nbQA-dev/nbQA@1.7.0...1.7.1)
- [github.com/pre-commit/mirrors-mypy: v1.5.1 → v1.7.1](pre-commit/mirrors-mypy@v1.5.1...v1.7.1)
- [github.com/rstcheck/rstcheck: v6.1.2 → v6.2.0](rstcheck/rstcheck@v6.1.2...v6.2.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](codespell-project/codespell@v2.2.5...v2.2.6)

* 🩹⌨️ Fix typing issue

* 🩹🧹 Fix typos

* 🚇🩹 Fix wrong github action reference

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: s-weigand <s.weigand.phy@gmail.com>

.github/workflows/integration-tests.yml

@@ -96,6 +96,6 @@ jobs:
           python-version: "3.10"
 
       - name: Run result validator
-        uses: s-weigand/pyglotaran-validation@fix-sting-column-detection
+        uses: glotaran/pyglotaran-validation@main
         with:
           validation_name: pyglotaran-examples

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_language_version:
 repos:
   # Formatters
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-ast
       - id: check-builtin-literals
@@ -19,7 +19,7 @@ repos:
         args: [--remove]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.15.0
     hooks:
       - id: pyupgrade
         types: [file]
@@ -36,7 +36,7 @@ repos:
         types_or: [python, pyi]
 
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.11.0
     hooks:
       - id: black
         types: [file]
@@ -52,7 +52,7 @@ repos:
         minimum_pre_commit_version: 2.9.0
 
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.4.0
+    rev: v2.5.0
     hooks:
       - id: setup-cfg-fmt
         args: [--include-version-classifiers]
@@ -68,7 +68,7 @@ repos:
           - "metadata.vscode metadata.language_info.version"
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.7.1
     hooks:
       - id: nbqa-black
         additional_dependencies: [black==22.6.0]
@@ -116,7 +116,7 @@ repos:
         additional_dependencies: [flake8-docstrings, darglint==1.8.0]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.7.1
     hooks:
       - id: mypy
         exclude: "docs|benchmark/|.*/tests?/.*"
@@ -131,7 +131,7 @@ repos:
         additional_dependencies: [click<8]
 
   - repo: https://github.com/rstcheck/rstcheck
-    rev: "v6.1.2"
+    rev: "v6.2.0"
     hooks:
       - id: rstcheck
         additional_dependencies: [sphinx]
@@ -150,9 +150,9 @@ repos:
       - id: rst-inline-touching-normal
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         types: [file]
         types_or: [python, pyi, markdown, rst, jupyter]
-        args: [-L doas]
+        additional_dependencies: [tomli]

glotaran/cli/commands/explore.py

@@ -86,7 +86,7 @@ def export(filename: str, select, out: str, name: str):
                 else:
                     dim = choice
                     choice = prompt(
-                        "Please select a value. Type 2 values sperated by ',' to select a range.",
+                        "Please select a value. Type 2 values separated by ',' to select a range.",
                         default="back",
                         type=util.VALORRANGEORLIST,
                     )

glotaran/deprecation/deprecation_utils.py

@@ -75,7 +75,7 @@ def glotaran_version() -> str:
     This is basically the same as ``glotaran.__version__`` but independent from glotaran.
     This way all of the deprecation functionality can be used even in
     ``glotaran.__init__.py`` without moving the import below the definition of
-    ``__version__`` or causeing a circular import issue.
+    ``__version__`` or causing a circular import issue.
 
     Returns
     -------

glotaran/model/model.py

@@ -59,7 +59,7 @@ def __init__(self, error: str):
 
 
 def _load_item_from_dict(
-    item_type: type[Item], value: Item | Mapping, extra: dict[str, Any] | None = None
+    item_type: type[Item], value: Item | dict[str, Any], extra: dict[str, Any] | None = None
 ) -> Item:
     """Load an item from a dictionary.
 
@@ -94,7 +94,7 @@ def _load_item_from_dict(
 
 
 def _load_model_items_from_dict(
-    item_type: type[Item], item_dict: Mapping[str, ModelItem | dict]
+    item_type: type[Item], item_dict: Mapping[str, ModelItem | dict[str, Any]]
 ) -> dict[str, ModelItem]:
     """Load a model items from a dictionary.
 
@@ -116,7 +116,7 @@ def _load_model_items_from_dict(
 
 
 def _load_global_items_from_dict(
-    item_type: type[Item], item_list: list[Item | dict]
+    item_type: type[Item], item_list: list[Item | dict[str, Any]]
 ) -> list[Item]:
     """Load an item from a dictionary.
 

glotaran/optimization/estimation_provider.py

@@ -28,7 +28,7 @@
 
 
 class UnsupportedResidualFunctionError(ValueError):
-    """Inidcates that the residual function is unsupported."""
+    """Indicates that the residual function is unsupported."""
 
     def __init__(self, residual_function: str):
         """Initialize an UnsupportedMethodError.

pyproject.toml

@@ -112,3 +112,6 @@ ignore_errors = true
 [[tool.mypy.overrides]]
 module = "benchmark.*"
 ignore_errors = true
+
+[tool.codespell]
+ignore-words-list = "projectio"