RF: large packaging update

.flake8

@@ -0,0 +1,11 @@
+[flake8]
+max-line-length = 88
+max-complexity = 10
+exclude =
+    .git,
+    __pycache__,
+    .tox,
+    .eggs,
+    *.egg,
+    build,
+    dist

.github/workflows/codeformat.yml

@@ -0,0 +1,27 @@
+name: Code Format
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  pre-commit:
+    name: Pre-commit checks
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install and run pre-commit hooks
+        uses: pre-commit/action@v3.0.1

.github/workflows/coverage.yml

@@ -0,0 +1,48 @@
+name: Coverage
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  coverage:
+    name: Code Coverage
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[test]
+
+      - name: Run tests with coverage
+        run: |
+          pytest trx/tests --cov=trx --cov-report=xml --cov-report=term-missing
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          flags: unittests
+          name: codecov-trx
+          fail_ci_if_error: false
+          verbose: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docbuild.yml

@@ -17,12 +17,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.13"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Fetch all history and tags for setuptools_scm
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install
@@ -35,13 +37,86 @@ jobs:
         cd docs
         make html
     - name: Upload docs
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v4
+      with:
+        name: docs
+        path: docs/_build/html
+
+  deploy-dev:
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && github.ref == 'refs/heads/master' && github.repository == 'tee-ar-ex/trx-python'
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4
+      with:
+        name: docs
+        path: docs/_build/html
+    - name: Publish dev docs to Github Pages
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: docs/_build/html
+        target-folder: dev
+
+  deploy-release:
+    needs: build
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/') && github.repository == 'tee-ar-ex/trx-python'
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4
       with:
         name: docs
         path: docs/_build/html
-    - name: Publish docs to Github Pages
-      if: startsWith(github.event.ref, 'refs/tags')
+    - name: Get version from tag
+      id: get_version
+      run: echo "VERSION=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+    - name: Fetch existing switcher.json from gh-pages
+      run: |
+        curl -sSL https://tee-ar-ex.github.io/trx-python/switcher.json -o switcher.json || echo '[]' > switcher.json
+    - name: Update switcher.json with new version
+      run: python tools/update_switcher.py switcher.json --version ${{ steps.get_version.outputs.VERSION }}
+    - name: Create root files (redirect + switcher.json)
+      run: |
+        mkdir -p root_files
+        cp switcher.json root_files/
+        cat > root_files/index.html << 'EOF'
+        <!DOCTYPE html>
+        <html lang="en">
+        <head>
+            <meta charset="utf-8">
+            <meta name="viewport" content="width=device-width, initial-scale=1">
+            <title>trx-python - TRX File Format for Tractography</title>
+            <meta name="description" content="trx-python is a Python implementation of the TRX file format for tractography data, designed for efficient handling of brain fiber tract streamlines.">
+            <meta name="robots" content="index, follow">
+            <link rel="canonical" href="https://tee-ar-ex.github.io/trx-python/stable/">
+            <meta http-equiv="refresh" content="0; URL=https://tee-ar-ex.github.io/trx-python/stable/">
+            <script>window.location.replace("https://tee-ar-ex.github.io/trx-python/stable/");</script>
+        </head>
+        <body>
+            <h1>trx-python Documentation</h1>
+            <p>Python implementation of the TRX file format for tractography data.</p>
+            <p>If you are not redirected automatically, visit the <a href="https://tee-ar-ex.github.io/trx-python/stable/">stable documentation</a>.</p>
+        </body>
+        </html>
+        EOF
+    - name: Publish root files (redirect + switcher.json)
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: root_files
+        target-folder: .
+        clean: false
+    - name: Publish release docs to Github Pages
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: docs/_build/html
+        target-folder: ${{ steps.get_version.outputs.VERSION }}
+    - name: Publish stable docs to Github Pages
       uses: JamesIves/github-pages-deploy-action@v4
       with:
         branch: gh-pages
         folder: docs/_build/html
+        target-folder: stable

.github/workflows/publish-to-test-pypi.yml

@@ -1,39 +1,95 @@
 name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
 
-on: push
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - '*'
+
 jobs:
-  build-n-publish:
-    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+  build:
+    name: Build distribution 📦
     runs-on: ubuntu-latest
+    if: github.repository == 'tee-ar-ex/trx-python'
     steps:
-    - uses: actions/checkout@master
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Fetch all history and tags for setuptools_scm
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.11"
     - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
+      run: python -m pip install build --user
     - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        .
+      run: python -m build --sdist --wheel --outdir dist/ .
+    - name: Upload distribution artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/trx-python
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distribution artifacts
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
     - name: Publish distribution 📦 to Test PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
-        password: ${{ secrets.test_pypi_password }}
-        repository_url: https://test.pypi.org/legacy/
+        repository-url: https://test.pypi.org/legacy/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/trx-python
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distribution artifacts
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
     - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.event.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Create GitHub Release
+    needs: publish-to-pypi
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Download distribution artifacts
+      uses: actions/download-artifact@v4
       with:
-        user: __token__
-        password: ${{ secrets.pypi_password }}
+        name: python-package-distributions
+        path: dist/
+    - name: Get version from tag
+      id: get_version
+      run: echo "VERSION=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+    - name: Create GitHub Release
+      env:
+        GH_TOKEN: ${{ github.token }}
+      run: |
+        gh release create "${{ steps.get_version.outputs.VERSION }}" \
+          --title "Release ${{ steps.get_version.outputs.VERSION }}" \
+          --generate-notes \
+          dist/*

.github/workflows/test.yml

@@ -0,0 +1,39 @@
+name: Tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: Python ${{ matrix.python-version }} • ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # needed for setuptools_scm version detection
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[dev,test]
+
+      - name: Test
+        run: spin test