[pre-commit.ci] pre-commit autoupdate (#932)

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

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.7](astral-sh/ruff-pre-commit@v0.4.3...v0.4.7)
- [github.com/tox-dev/pyproject-fmt: 1.8.0 → 2.1.3](tox-dev/pyproject-fmt@1.8.0...2.1.3)
- [github.com/abravalheri/validate-pyproject: v0.16 → v0.18](abravalheri/validate-pyproject@v0.16...v0.18)
- https://github.com/codespell-project/codespell/: v2.2.6 → v2.3.0

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update pytest.yml

* Update pytest.yml

* cleanup and move to .ruff.toml

* pyproject.toml

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Çağtay Fabry <[email protected]>

.github/workflows/pytest.yml

@@ -39,12 +39,12 @@ jobs:
         with:
           fetch-depth: '0' # Fetch all history for all tags and branches
 
-      - uses: CagtayFabry/pydeps2env@main
+      - uses: CagtayFabry/pydeps2env@v1.1.0
         with:
-          file: 'pyproject.toml'
+          files: 'pyproject.toml'
           channels: 'conda-forge defaults'
           extras: 'test vis media'
-          setup_requires: 'include'
+          build_system: 'include'
 
       - name: Setup Conda Environment
         uses: mamba-org/[email protected]
@@ -139,12 +139,12 @@ jobs:
         with:
           fetch-depth: '0' # Fetch all history for all tags and branches
 
-      - uses: CagtayFabry/pydeps2env@main
+      - uses: CagtayFabry/pydeps2env@v1.1.0
         with:
-          file: 'pyproject.toml'
+          files: 'pyproject.toml'
           channels: 'conda-forge defaults'
           extras: 'test vis media'
-          setup_requires: 'include'
+          build_system: 'include'
 
       - name: Setup Conda Environment
         uses: mamba-org/[email protected]

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
           - mdformat-config
   # ----- Python formatting -----
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.4.7
     hooks:
     # Run ruff linter.
     - id: ruff
@@ -39,11 +39,11 @@ repos:
     # Run ruff formatter.
     - id: ruff-format
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: 1.8.0
+    rev: 2.1.3
     hooks:
     - id: pyproject-fmt
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.16
+    rev: v0.18
     hooks:
       - id: validate-pyproject
   # ----- Jupyter Notebooks -----
@@ -63,7 +63,7 @@ repos:
           - --remove-kernel-metadata
   # ----- spellchecking -----
   - repo: https://github.com/codespell-project/codespell/
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         exclude: doc/src/legal-notice.md

.ruff.toml

@@ -0,0 +1,81 @@
+# Exclude a variety of commonly ignored directories.
+extend-exclude = [
+    "__init__.py",
+    "doc/src/conf.py",
+]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+# Assume Python 3.9
+target-version = "py39"
+
+
+[lint]
+# TODO: should be the following list, but Ruff does not yet impl all of them.
+#    W503,W504
+#    E203
+#    C408
+ignore = [
+    "C408",
+    #"E203",
+    "E402",
+    #"W503",
+    #"W504",
+    "D203",
+    "D211",
+    "D213",
+    "UP006",
+    "UP007", # see ruff GH#4427
+]
+select = [
+    "B", # flake8-bugbear
+    "C", # flake8-comprehensions
+    #"D", # note: all relevant D's will be set by setting pydocstyle.convention=numpy!
+    "E",    # pycodestyles
+    "F",    # pyflakes
+    "W",    # pycodestyle warnings
+    "UP",   # pyupgrade
+    "T2",   # flake8-print
+    "I001", # isort
+    "ICN",  # import conventions, e.g. import numpy as np
+    #"B950",  # not yet implemented by Ruff.
+    "RUF100", # ensure 'noqa' declarations are still valid.
+]
+
+[lint.extend-per-file-ignores]
+# Allow pydocstyle violations in certain areas.
+"**/{tests,tags,asdf,devtools}/**" = [
+    "D",
+]
+"conftest.py" = [
+    "D",
+]
+"doc/src/tutorials/*" = [
+    "D",
+]
+"doc/src/conf.py" = [
+    "E501",   # ignore long lines.
+    "RUF100", # do no check if 'noqa' is needed (circular import workaround)
+]
+"**/{cli,tests,tutorials,devtools}/**/*{.py,ipynb}" = [
+    "T2",
+] # Allow prints in certain areas.
+
+[lint.pydocstyle]
+convention = "numpy"
+
+[lint.mccabe]
+max-complexity = 15 # max branches inside a function.
+
+[lint.isort]
+known-first-party = [
+    "weldx",
+]
+required-imports = [
+    "from __future__ import annotations",
+]
+
+[flake8-import-conventions]
+extend-aliases = { xarray = "xr" }

doc/json_mime_render_plugin/pyproject.toml

@@ -1,5 +1,12 @@
 [project]
 name = "myst-nb-json-renderer"
 version = "1"
-[project.entry-points."myst_nb.mime_renderers"]
-json_mime = "myst_nb_json_render_plugin:MimeRenderPlugin"
+classifiers = [
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+]
+entry-points."myst_nb.mime_renderers".json_mime = "myst_nb_json_render_plugin:MimeRenderPlugin"

doc/src/tutorials/timeseries_01.ipynb

@@ -283,7 +283,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can also use `Quantites` with the appropriate dimension as Inputs for our interpolation:"
+    "We can also use `Quantities` with the appropriate dimension as Inputs for our interpolation:"
    ]
   },
   {

doc/src/tutorials/transformations_02_coordinate_system_manager.ipynb

@@ -529,7 +529,7 @@
    "metadata": {},
    "source": [
     "The `SpatialData` class we used above is mostly a container class for 3d data.\n",
-    "Additionally to pure point data, it can also store connectivety data in form of triangles.\n",
+    "Additionally to pure point data, it can also store connectivity data in form of triangles.\n",
     "Consult the [class documentation](https://weldx.readthedocs.io/en/latest/_autosummary/weldx.SpatialData.html#weldx.SpatialData) for further information.\n",
     "Now we add the data to the CSM:"
    ]