Merge pull request #713 from theislab/fix/ci_examples_error

Fix: CI examples not throwing error from some commands

.run_notebooks.sh

@@ -0,0 +1,62 @@
+#!/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/plotting/*.ipynb"
+    "$base_dir/examples/problems/*.ipynb"
+    "$base_dir/examples/solvers/*.ipynb"
+)
+
+# 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 $nb"
+    jupytext -k moscot --execute "$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."

pyproject.toml

@@ -306,8 +306,7 @@ extras = docs
 changedir = {tox_root}{/}docs
 commands =
     python -m ipykernel install --user --name=moscot
-    bash -c "for nb in notebooks/examples/plotting/*.ipynb notebooks/examples/problems/*ipynb notebooks/examples/solvers/*ipynb; do echo Running $nb; jupytext -k moscot --execute $nb; done"
-
+    bash {tox_root}/.run_notebooks.sh {tox_root}{/}docs/notebooks
 
 [testenv:clean-docs]
 description = Remove the documentation.