Convert to myst markdown notebooks

.github/workflows/main.yml

@@ -1,6 +1,6 @@
 name: CI
 env:
-  micromamba_version: 1.5
+  micromamba_version: 2
 
 
 on:
@@ -16,42 +16,59 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install nbqa ruff black jupytext isort
+
+      - name: Lint with Ruff
+        run: nbqa ruff notebooks/**/*.md
+
+      - name: Lint with Isort
+        run: nbqa isort notebooks/**/*.md
+
+      - name: Check formatting with Black
+        run: nbqa black notebooks/**/*.md
+
   build_0:
     name: wradlib notebooks - linux
     runs-on: ubuntu-latest
+    needs: [lint]
     defaults:
       run:
         shell: bash -l {0}
     env:
       WRADLIB_DATA: ./wradlib-data
-      CONDA_ENV_FILE: ci/requirements/notebooks.yml
+      CONDA_ENV_FILE: environment.yml
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
     - name: Install micromamba environment
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: wradlib-notebooks
         environment-file: ${{env.CONDA_ENV_FILE}}
         cache-environment: true
         cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
         create-args: >-
           python=${{matrix.python-version}}
-    - name: Install wradlib
-      run: |
-        git clone https://github.com/wradlib/wradlib.git
-        cd wradlib
-        echo "WRADLIB_TAG=`git name-rev --name-only --tags HEAD`" >> $GITHUB_ENV
-        python -m pip install . --no-deps
-    - name: Install wradlib-data
-      run: |
-        python -m pip install wradlib-data
-        mkdir ./wradlib-data
     - name: Version Info
       run: |
         python -c "import wradlib; print(wradlib.version.version)"
@@ -62,60 +79,34 @@ jobs:
       run: |
         export WRADLIB_DATA=`realpath $WRADLIB_DATA`
         pytest -n auto --verbose --durations=15 --pyargs notebooks
-    - name: Commit files
-      if: github.event_name == 'push' || github.event_name == 'workflow_dispatch'
-      run: |
-        git config --global user.email "wradlib-docs@wradlib.org"
-        git config --global user.name "wradlib-docs-bot"
-        git checkout --orphan render
-        git add --all .
-        git commit -m "Rendering at commit $GITHUB_SHA"
-    - name: Push changes
-      if: github.event_name == 'push' || github.event_name == 'workflow_dispatch'
-      run: |
-        if [ $WRADLIB_TAG == 'undefined' ]; then
-            BRANCH=devel
-        else
-            BRANCH=$WRADLIB_TAG
-        fi
-        git push https://${{ secrets.GITHUB_TOKEN }}@github.com/wradlib/wradlib-notebooks.git render:$BRANCH -fq
 
   build_1:
     name: wradlib notebooks - macosx
     runs-on: macos-latest
+    needs: [lint]
     defaults:
       run:
         shell: bash -l {0}
     env:
       WRADLIB_DATA: ./wradlib-data
-      CONDA_ENV_FILE: ci/requirements/notebooks.yml
+      CONDA_ENV_FILE: environment.yml
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
     - name: Install micromamba environment
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: wradlib-notebooks
         environment-file: ${{env.CONDA_ENV_FILE}}
         cache-environment: true
         cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
         create-args: >-
           python=${{matrix.python-version}}
-    - name: Install wradlib
-      run: |
-        git clone https://github.com/wradlib/wradlib.git
-        cd wradlib
-        echo "WRADLIB_TAG=`git name-rev --name-only --tags HEAD`" >> $GITHUB_ENV
-        python -m pip install . --no-deps
-    - name: Install wradlib-data
-      run: |
-        python -m pip install wradlib-data
-        mkdir ./wradlib-data
     - name: Version Info
       run: |
         python -c "import wradlib; print(wradlib.version.version)"
@@ -130,38 +121,30 @@ jobs:
   build_2:
     name: wradlib notebooks - windows
     runs-on: windows-latest
+    needs: [lint]
     defaults:
       run:
         shell: bash -l {0}
     env:
       WRADLIB_DATA: ./wradlib-data
-      CONDA_ENV_FILE: ci/requirements/notebooks.yml
+      CONDA_ENV_FILE: environment.yml
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
     - name: Install micromamba environment
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: wradlib-notebooks
         environment-file: ${{env.CONDA_ENV_FILE}}
         cache-environment: true
         cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
         create-args: >-
           python=${{matrix.python-version}}
-    - name: Install wradlib
-      run: |
-        git clone https://github.com/wradlib/wradlib.git
-        cd wradlib
-        python -m pip install . --no-deps
-    - name: Install wradlib-data
-      run: |
-        python -m pip install wradlib-data
-        mkdir ./wradlib-data
     - name: Version Info
       run: |
         python -c "import wradlib; print(wradlib.version.version)"
@@ -172,20 +155,3 @@ jobs:
       run: |
         export WRADLIB_DATA=`python -c "import os, sys; print(os.path.realpath(sys.argv[1]))" $WRADLIB_DATA`
         pytest -n auto --verbose --durations=15 --pyargs notebooks
-
-  trigger_rtd:
-    if: github.event_name == 'push' || github.event_name == 'workflow_dispatch'
-    needs: [build_0]
-    name: trigger readthedocs
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-    env:
-      RTD_TOKEN: ${{ secrets.RTD_TOKEN }}
-      RTD_URL: ${{ secrets.RTD_URL }}
-    steps:
-    - name: trigger readthedocs
-      run: |
-        echo "triggering"
-        curl -X POST -H "Authorization: Token $RTD_TOKEN" "$RTD_URL"

.gitignore

@@ -13,6 +13,8 @@
 # whitelist notebooks
 !notebooks/
 #!/notebooks/**
+# ignore .py (paired notebooks)
+notebooks/**/*.py
 
 # whitelist .dask
 !.dask/

.pre-commit-config.yaml

@@ -1,32 +1,47 @@
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+  # --- Jupytext: create temporary .py mirrors from MyST notebooks ---
+  - repo: https://github.com/mwouts/jupytext
+    rev: v1.19.0.dev0
     hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-      - id: check-docstring-first
-      - id: check-json
-      - id: check-yaml
-      - id: debug-statements
-      - id: mixed-line-ending
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-      - id: pyupgrade
-        args:
-          - '--py38-plus'
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
-    hooks:
-      - id: nbstripout
-        args: ['--extra-keys', 'metadata.kernelspec cell.metadata.pycharm cell.metadata.tags']
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.0.254'
+      - id: jupytext
+        name: jupytext (md → py)
+        files: "^notebooks/.*\\.md$"
+        args: ["--to", "py:percent"]
+        pass_filenames: false
+        always_run: true
+
+  # --- Ruff ---
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.6
     hooks:
       - id: ruff
-        args: [ "--fix" ]
+        name: ruff (lint + fix)
+        files: "^notebooks/.*\\.py$"
+        args: ["--fix"]
+
+  # --- Black ---
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 25.11.0
     hooks:
       - id: black
-      - id: black-jupyter
+        files: "^notebooks/.*\\.py$"
+
+  # --- Jupytext: sync py → md (only paired mirrors) ---
+  - repo: https://github.com/mwouts/jupytext
+    rev: v1.19.0.dev0
+    hooks:
+      - id: jupytext
+        name: jupytext (sync py → md)
+        files: '^notebooks/(?!__init__\\.py$)(?!conftest\\.py$).*\\.py$'
+        args: ["--sync"]
+        # DO NOT set pass_filenames: false
+        always_run: false
+
+  # --- Cleanup temporary .py files ---
+  - repo: local
+    hooks:
+      - id: cleanup-jupytext
+        name: Remove temporary Jupytext Python mirrors
+        entry: bash -c "find notebooks -type f -name '*.py' ! -name '__init__.py' ! -name 'conftest.py' -exec rm -f {} +"
+        language: system
+        always_run: true

.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: mambaforge-latest
+
+conda:
+  environment: environment.yml
+
+sphinx:
+  builder: html
+  configuration: conf.py