chore: Update pre-commit (#1454)

.pre-commit-config.yaml

@@ -1,48 +1,41 @@
-# This is the configuration for pre-commit, a local framework for managing pre-commit hooks
-#   Check out the docs at: https://pre-commit.com/
-
-default_stages: [commit]
+default_stages: [pre-commit]
 repos:
--   repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.5
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-    -   id: nbqa-ruff
-        additional_dependencies: [ruff==0.3.7]
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
-    hooks:
-    -   id: check-builtin-literals
-    -   id: check-case-conflict
-    -   id: check-docstring-first
-    -   id: check-executables-have-shebangs
-    -   id: check-toml
-    -   id: detect-private-key
-    -   id: end-of-file-fixer
+      - id: check-builtin-literals
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-toml
+      - id: detect-private-key
+      - id: end-of-file-fixer
         exclude: (\.min\.js$|\.svg$)
-    -   id: trailing-whitespace
--   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.7
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.2
     hooks:
-    - id: ruff
-    - id: ruff-format
--   repo: https://github.com/hoxbro/clean_notebook
-    rev: v0.1.14
+      - id: ruff
+      - id: ruff-format
+        exclude: \.ipynb$
+  - repo: https://github.com/hoxbro/clean_notebook
+    rev: v0.1.15
     hooks:
-    - id: clean-notebook
-      args: [-i, tags]
--   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+      - id: clean-notebook
+        args: [-i, tags]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
     hooks:
-    - id: codespell
-      exclude: (\.min\.js$|\.svg$|\.html$)
-      additional_dependencies:
-      - tomli
--   repo: local
+      - id: codespell
+        exclude: (\.min\.js$|\.svg$|\.html$)
+        additional_dependencies:
+          - tomli
+  - repo: local
     hooks:
-    - id: update_conda_envs
-      name: Update conda envs
-      entry: python scripts/update_conda_envs.py
-      language: python
-      additional_dependencies: [pyproject2conda]
-      files: '(pyproject.toml|update_conda_envs)'
-      pass_filenames: false
+      - id: update_conda_envs
+        name: Update conda envs
+        entry: python scripts/update_conda_envs.py
+        language: python
+        additional_dependencies: [pyproject2conda]
+        files: "(pyproject.toml|update_conda_envs)"
+        pass_filenames: false

doc/user_guide/NetworkX.ipynb

@@ -270,10 +270,10 @@
     "\n",
     "print(\"radius: %d\" % nx.radius(G))\n",
     "print(\"diameter: %d\" % nx.diameter(G))\n",
-    "print(\"eccentricity: %s\" % nx.eccentricity(G))\n",
-    "print(\"center: %s\" % nx.center(G))\n",
-    "print(\"periphery: %s\" % nx.periphery(G))\n",
-    "print(\"density: %s\" % nx.density(G))\n",
+    "print(f\"eccentricity: {nx.eccentricity(G)}\")\n",
+    "print(f\"center: {nx.center(G)}\")\n",
+    "print(f\"periphery: {nx.periphery(G)}\")\n",
+    "print(f\"density: {nx.density(G)}\")\n",
     "\n",
     "hvnx.draw(G, with_labels=True)"
    ]
@@ -757,7 +757,7 @@
     "                                   edge_width=5.0\n",
     "                                  )\n",
     "            other_edges.append(edge)\n",
-    "    plots.append((g*edges*hv.Overlay(other_edges)).relabel(\"p = %6.3f\" % (p)))\n",
+    "    plots.append((g*edges*hv.Overlay(other_edges)).relabel(f\"p = {p:6.3f}\"))\n",
     "\n",
     "hv.Layout(plots).cols(2)"
    ]

pyproject.toml

@@ -196,7 +196,7 @@ filterwarnings = [
 ]
 
 [tool.codespell]
-ignore-words-list = "ser"
+ignore-words-list = "ser,assertIn"
 skip = "doc/generate_modules.py"
 write-changes = true
 
@@ -211,12 +211,6 @@ extend-select = [
 [tool.ruff.format]
 quote-style = "single"
 
-[tool.nbqa.addopts]
-# E402 Module level import not at top of file
-ruff = [
-    "--extend-ignore=E402"
-]
-
 [tool.pyproject2conda.dependencies]
 geoviews = { skip = true, packages = "geoviews-core >=1.9.0" }
 # It should be ibis-framework[duckdb], but it works anyway.