SciTools
diff --git a/‎.flake8‎
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diff --git a/‎.github/dependabot.yml‎
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diff --git a/‎.github/workflows/ci-citation.yml‎
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diff --git a/‎.github/workflows/ci-docs.yml‎
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diff --git a/‎.github/workflows/ci-manifest.yml‎
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diff --git a/‎.github/workflows/ci-template-check.yml‎
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diff --git a/‎.github/workflows/ci-tests.yml‎
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diff --git a/‎.github/workflows/stale.yml‎
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diff --git a/‎.gitignore‎
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diff --git a/‎.pre-commit-config.yaml‎
Lines changed: 97 additions & 11 deletions b/‎.pre-commit-config.yaml‎
Lines changed: 97 additions & 11 deletions
@@ -17,3 +17,7 @@ updates:
       timezone: "Europe/London"
     labels:
       - "🤖 Bot"
+    groups:
+      actions:
+        patterns:
+          - "*"
@@ -20,7 +20,7 @@ jobs:
     name: "validate"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
 
@@ -18,9 +18,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       with:
         key: tox-${{ hashFiles('requirements/dev.yml') }}-${{ hashFiles('tox.ini') }}
         path: |
 
@@ -23,4 +23,4 @@ concurrency:
 jobs:
   manifest:
     name: "check-manifest"
-    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2024.09.1
+    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2025.07.3
@@ -0,0 +1,16 @@
+# Checks if a PR makes any changes that ought to be shared via templating.
+# See the called workflow in the scitools/workflows repo for more details.
+
+name: ci-template-check
+
+on:
+  pull_request_target:
+    branches:
+      - main
+
+jobs:
+  prompt-share:
+    uses: scitools/workflows/.github/workflows/ci-template-check.yml@2025.07.3
+    secrets: inherit
+    with:
+      pr_number: ${{ github.event.pull_request.number }}
@@ -13,18 +13,31 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  build:
+  tests:
+    name: "${{ matrix.session }} (${{ matrix.version }})"
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest" ]
+        version: ["py310", "py311"]
+        session: [ "test" ]
+        include:
+          - version: "py311"
+            coverage: "--cov-report= --cov=tephi"
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       with:
         key: tox-${{ hashFiles('requirements/dev.yml') }}-${{ hashFiles('tox.ini') }}
         path: |
           .tox
 
     - name: Run tox
-      run: pipx run 'tox<4'
+      run: |
+        pip install 'tox<4'
+        tox -e ${{ matrix.version }}-${{ matrix.session }}
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/stale@v8
+      - uses: actions/stale@v9
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
 
@@ -59,7 +59,7 @@ coverage.xml
 # Sphinx documentation
 docs/_build/
 # ignore autogen apidoc files
-docs/tephi/source/api
+docs/source/api
 # misc
 *.lock
 
 
@@ -1,28 +1,114 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+# See https://pre-commit.ci/#configuration
+# See https://github.com/scientific-python/cookie#sp-repo-review
+
+ci:
+  autofix_prs: false
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+
+
+# Alphabetised, for lack of a better order.
+files: |
+    (?x)(
+        docs\/.+\.py|
+        docs\/.+\.rst|
+        pyproject\.toml|
+        setup\.py|
+        src\/.+\.py
+    )
+minimum_pre_commit_version: 1.21.0
+
 repos:
+
+# Hook for pre-commit's  built-in checks
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.4.0'
+    rev: v5.0.0
     hooks:
         # Prevent giant files from being committed.
     -   id: check-added-large-files
+        # Check whether files parse as valid Python.
+    -   id: check-ast
+        # Check for file name conflicts on case-insensitive filesystems.
+    -   id: check-case-conflict
         # Check for files that contain merge conflict strings.
     -   id: check-merge-conflict
-        # Check for debugger imports and py37+ `breakpoint()` calls in python source.
+        # Check for debugger imports and py37+ `breakpoint()` calls in Python source.
     -   id: debug-statements
-        # Don't commit to master branch.
+        # Check TOML file syntax.
+    -   id: check-toml
+        # Check YAML file syntax.
+    -   id: check-yaml
+        # Makes sure files end in a newline and only a newline.
+        # Duplicates Ruff W292 but also works on non-Python files.
+    -   id: end-of-file-fixer
+        # Replaces or checks mixed line ending.
+    -   id: mixed-line-ending
+        # Don't commit to main branch.
     -   id: no-commit-to-branch
+        # Trims trailing whitespace.
+        # Duplicates Ruff W291 but also works on non-Python files.
+    -   id: trailing-whitespace
+
+# Hooks from all other repos
+# NOTE : keep these in hook-name (aka 'id') order
 
--   repo: https://github.com/psf/black
-    rev: 23.7.0
+-   repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.19.1
     hooks:
-    -   id: black
+    -   id: blacken-docs
+        types: [file, rst]
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: "v2.4.1"
+    hooks:
+    -   id: codespell
+        types_or: [asciidoc, python, markdown, rst]
+        additional_dependencies: [tomli]
+
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.17.0'
+    hooks:
+    -   id: mypy
+        exclude: 'noxfile\.py|docs/conf\.py'
+
+-   repo: https://github.com/numpy/numpydoc
+    rev: v1.9.0
+    hooks:
+      - id: numpydoc-validation
+        types: [file, python]
+
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.12.5"
+    hooks:
+    -   id: ruff
+        types: [file, python]
+        args: [--fix, --show-fixes]
+    -   id: ruff-format
         types: [file, python]
-        args: [--config=./pyproject.toml]
 
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+-   repo: https://github.com/aio-libs/sort-all
+    rev: v1.3.0
     hooks:
-    -   id: flake8
+    -   id: sort-all
         types: [file, python]
-        args: [--config=./.flake8]
+
+-   repo: https://github.com/scientific-python/cookie
+    rev: 2025.05.02
+    hooks:
+    - id: sp-repo-review
+      additional_dependencies: ["repo-review[cli]"]
+      args: ["--show=errskip"]
+
+-   repo: https://github.com/abravalheri/validate-pyproject
+    # More exhaustive than Ruff RUF200.
+    rev: "v0.24.1"
+    hooks:
+    - id: validate-pyproject
+
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: "v1.10.0"
+  hooks:
+    - id: rst-backticks
+    - id: rst-directive-colons
+    - id: rst-inline-touching-normal