From 6a52501a3a171de4d27d618ae6708e01b543623e Mon Sep 17 00:00:00 2001
From: alexPatrie <alexanderpatrie@gmail.com>
Date: Mon, 4 Mar 2024 12:06:14 -0500
Subject: [PATCH] added notebook formatter in workflow

---
 .github/workflows/fixNotebooks.yaml | 31 +++++++++++++++++++++++++++++
 biosimulator_processes/utils.py     |  8 ++++++++
 2 files changed, 39 insertions(+)
 create mode 100644 .github/workflows/fixNotebooks.yaml

diff --git a/.github/workflows/fixNotebooks.yaml b/.github/workflows/fixNotebooks.yaml
new file mode 100644
index 000000000..5899e9363
--- /dev/null
+++ b/.github/workflows/fixNotebooks.yaml
@@ -0,0 +1,31 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  fix-notebooks:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@main
+      with:
+        ref: main
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@main
+      with:
+        python-version: '3.10'
+
+    - id: fixNotebooks
+      name: Fix notebook output
+      uses: GabrielBB/xvfb-action@v1
+      with:
+        working-directory: ${{ github.workspace }}
+        run: |
+          python -c "from biosimulator_processes.utils import fix_notebooks_execution_count; fix_notebooks_execution_count(); exit();"
diff --git a/biosimulator_processes/utils.py b/biosimulator_processes/utils.py
index 14266928d..51f2abcff 100644
--- a/biosimulator_processes/utils.py
+++ b/biosimulator_processes/utils.py
@@ -1,4 +1,5 @@
 from typing import Dict
+import os
 from basico import biomodels, load_model_from_string
 from process_bigraph import Composite, pf
 import nbformat
@@ -241,3 +242,10 @@ def fix_execution_count(notebook_path):
 
     with open(notebook_path, 'w', encoding='utf-8') as f:
         nbformat.write(nb, f)
+
+
+def fix_notebooks_execution_count():
+    for root, _, files in os.walk('../notebooks'):
+        for _file in files:
+            notebook_path = os.path.join(root, _file)
+            fix_execution_count(notebook_path)