Enhance notebook build process by adding error handling and logging; update environment.yml with specific package versions and dependencies; improve dataset import script to check for existing directories and files.

Author: Han Lin Mai

.github/ci_support/build_notebooks.sh

@@ -1,27 +1,45 @@
 #!/bin/bash
+set -e  # Exit on any error
+
+echo "Starting notebook build process..."
+
 # pyiron config 
+echo "Setting up pyiron configuration..."
 python .github/ci_support/pyironconfig.py
 
 # import dataset
+echo "Importing datasets..."
 bash .github/ci_support/import_dataset.sh
 
-# install papermill (already in environment.yml)
-# conda install -c conda-forge papermill
-
 # register jupyter kernel
+echo "Registering Jupyter kernel..."
 python -m ipykernel install --user --name python3 --display-name "Python 3"
 
+# verify papermill is available
+echo "Verifying papermill installation..."
+python -c "import papermill; print('papermill version:', papermill.__version__)"
+
 # execute notebooks
+echo "Executing notebooks..."
 current_dir=$(pwd)
 i=0;
 for f in $(find . -name "*.ipynb" | sort -n); do
+    echo "Processing notebook: $f"
     cd $(dirname $f);
     notebook=$(basename $f);
-    papermill ${notebook} ${notebook%.*}-out.${notebook##*.} -k "python3" || i=$((i+1));
+    if papermill ${notebook} ${notebook%.*}-out.${notebook##*.} -k "python3"; then
+        echo "Successfully executed: $notebook"
+    else
+        echo "Failed to execute: $notebook"
+        i=$((i+1));
+    fi
     cd $current_dir;
 done;
 
 # push error to next level
 if [ $i -gt 0 ]; then
+    echo "Failed to execute $i notebook(s)"
     exit 1;
 fi;
+
+echo "All notebooks executed successfully!"

.github/ci_support/environment.yml

@@ -1,8 +1,21 @@
 channels:
   - conda-forge
 dependencies:
+  - python>=3.11,<3.13
+  - pip
+  - numpy =1.26.4
+  - ase =3.26.0
+  - pymatgen =2025.6.14
+  - pyiron_workflow =0.15.2
+  - pyiron_lammps =0.4.6
+  - pandas =2.3.1
+  - lammps =2024.08.29=*_mpi*
+  - pysqa =0.3.0
   - jupyter-book
   - ipykernel
   - jupyter
   - papermill
-  
+  - pip:
+      - pyiron-workflow-atomistics==0.0.2
+      - pyiron-workflow-lammps==0.0.2
+      - pyiron-snippets==0.2.0

.github/ci_support/import_dataset.sh

@@ -1,5 +1,18 @@
 #!/bin/bash
+# Check if pyiron directory exists, if not create it
+if [ ! -d "pyiron" ]; then
+    echo "Creating pyiron directory..."
+    mkdir -p pyiron/calculation
+fi
+
 cd pyiron
+
+# Check if calculation directory and tar.gz files exist
+if [ ! -d "calculation" ] || [ ! "$(ls -A calculation/*.tar.gz 2>/dev/null)" ]; then
+    echo "No calculation/*.tar.gz files found. Skipping dataset import."
+    exit 0
+fi
+
 for ds in $(ls calculation/*.tar.gz); do 
     cp ${ds} .
     cp calculation/export.csv .

.github/workflows/notebooks.yml

@@ -17,7 +17,7 @@ jobs:
       with:
         auto-update-conda: true
         python-version: 3.12
-        environment-file: environment.yml
+        environment-file: .github/ci_support/environment.yml
         auto-activate-base: false
     - name: Tests
       shell: bash -l {0}