Run notebooks in CI

.github/workflows/test-notebooks.yml

@@ -0,0 +1,41 @@
+name: Test notebooks
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: recursive
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install pip dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+      - name: Test notebooks
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          tox -e examples-docs

.run_notebooks.sh

@@ -0,0 +1,64 @@
+#!/bin/bash
+
+# Check if the base directory is provided as an argument
+if [ "$#" -ne 1 ]; then
+    echo "Usage: $0 <base_notebook_directory>"
+    exit 1
+fi
+
+# Base directory for notebooks
+base_dir=$1
+
+# Define notebook directories or patterns
+declare -a notebooks=(
+    "$base_dir/examples/tools/*.ipynb"
+    "$base_dir/examples/plotting/*.ipynb"
+    "$base_dir/examples/image/*.ipynb"
+    "$base_dir/examples/graph/*.ipynb"
+    # "$base_dir/tutorials/*.ipynb" don't include because it contains many external modules
+)
+
+# Initialize an array to hold valid notebook paths
+declare -a valid_notebooks
+
+# Gather all valid notebook files from the patterns
+echo "Gathering notebooks..."
+for pattern in "${notebooks[@]}"; do
+    for nb in $pattern; do
+        if [[ -f "$nb" ]]; then  # Check if the file exists
+            valid_notebooks+=("$nb")  # Add to the list of valid notebooks
+        fi
+    done
+done
+
+# Check if we have any notebooks to run
+if [ ${#valid_notebooks[@]} -eq 0 ]; then
+    echo "No notebooks found to run."
+    exit 1
+fi
+
+# Echo the notebooks that will be run for clarity
+echo "Preparing to run the following notebooks:"
+for nb in "${valid_notebooks[@]}"; do
+    echo "$nb"
+done
+
+# Initialize a flag to track the success of all commands
+all_success=true
+
+# Execute all valid notebooks
+for nb in "${valid_notebooks[@]}"; do
+    echo "Running $nb"
+    jupytext -k squidpy --execute "$nb" || {
+        echo "Failed to run $nb"
+        all_success=false
+    }
+done
+
+# Check if any executions failed
+if [ "$all_success" = false ]; then
+    echo "One or more notebooks failed to execute."
+    exit 1
+fi
+
+echo "All notebooks executed successfully."

tox.ini

@@ -140,3 +140,22 @@ description = Download and cache data.
 skip_install = false
 deps =
 commands = python ./.scripts/ci/download_data.py {posargs}
+
+
+
+[testenv:examples-docs]
+allowlist_externals = bash
+description = Run the notebooks.
+use_develop = true
+deps =
+    ipykernel
+    jupytext
+    nbconvert
+    leidenalg
+    watermark
+    napari-spatialdata
+extras = docs,neural
+changedir = {tox_root}{/}docs
+commands =
+    python -m ipykernel install --user --name=squidpy
+    bash {tox_root}/.run_notebooks.sh {tox_root}{/}docs/notebooks