From b562360c5350de9cfd83049cc2e60474e6ec1e7b Mon Sep 17 00:00:00 2001
From: James Kent <jamesdkent21@gmail.com>
Date: Tue, 22 Apr 2025 14:59:12 -0500
Subject: [PATCH 1/4] add testing workflow

---
 .github/workflows/run_notebook.yml | 80 ++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100644 .github/workflows/run_notebook.yml

diff --git a/.github/workflows/run_notebook.yml b/.github/workflows/run_notebook.yml
new file mode 100644
index 0000000..3752f8c
--- /dev/null
+++ b/.github/workflows/run_notebook.yml
@@ -0,0 +1,80 @@
+name: Run Notebook
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  run-notebook:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          
+      - name: Extract dependencies from colabtools
+        run: |
+          # Download setup.py
+          curl -s https://raw.githubusercontent.com/googlecolab/colabtools/refs/heads/main/setup.py > setup.py
+          # Extract DEPENDENCIES using Python
+          python3 - <<EOF
+          with open('setup.py', 'r') as f:
+              content = f.read()
+          
+          # Find DEPENDENCIES tuple
+          start = content.find('DEPENDENCIES = (')
+          end = content.find(')', start)
+          deps = content[start:end+1]
+          
+          # Execute the tuple to get the values
+          exec(deps)
+          
+          # Write dependencies to requirements file
+          with open('colab_requirements.txt', 'w') as f:
+              for dep in DEPENDENCIES:
+                  f.write(f"{dep}\n")
+          EOF
+          
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # Install colabtools dependencies
+          pip install -r colab_requirements.txt
+          # Install additional required packages
+          pip install -r requirements.txt
+
+      - name: Modify notebook
+        run: |
+          # Convert notebook to Python script for easier text processing
+          jupyter nbconvert --to script run_and_explore.ipynb
+          
+          # Replace META_ID
+          sed -i 's/META_ID = ""/META_ID = "36Dm86NVjoTJ"/' run_and_explore.py
+          
+          # Add no_upload parameter to run function
+          sed -i 's/url, meta_result = run(META_ID)/url, meta_result = run(META_ID, no_upload=True)/' run_and_explore.py
+          
+          # Remove View the Report section (everything after the line containing "## View the Report")
+          sed -i '/^## View the Report/,$d' run_and_explore.py
+          
+          # Convert back to notebook
+          jupyter nbconvert --to notebook run_and_explore.py
+          
+          # Move converted notebook back to original name
+          mv run_and_explore.nbconvert.ipynb run_and_explore.ipynb
+          
+      - name: Execute notebook
+        run: |
+          jupyter nbconvert --to notebook --execute run_and_explore.ipynb --output executed_notebook.ipynb
+          
+      - name: Upload notebook
+        uses: actions/upload-artifact@v3
+        with:
+          name: executed-notebook
+          path: executed_notebook.ipynb

From 6b419b09351c8aa9edfaedf7dfe1f1086327ed9e Mon Sep 17 00:00:00 2001
From: James Kent <jamesdkent21@gmail.com>
Date: Tue, 22 Apr 2025 15:02:03 -0500
Subject: [PATCH 2/4] run it on a cron job

---
 .github/workflows/run_notebook.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/run_notebook.yml b/.github/workflows/run_notebook.yml
index 3752f8c..224167f 100644
--- a/.github/workflows/run_notebook.yml
+++ b/.github/workflows/run_notebook.yml
@@ -2,6 +2,9 @@ name: Run Notebook
 
 on:
   workflow_dispatch:
+  schedule:
+    # Runs at 9:00 AM Central (14:00 UTC)
+    - cron: '0 14 * * *'
   push:
     branches: [ main ]
   pull_request:

From 4468360948b0a0fda93cf6f1455e4c8d92eb6c17 Mon Sep 17 00:00:00 2001
From: James Kent <jamesdkent21@gmail.com>
Date: Tue, 22 Apr 2025 15:06:05 -0500
Subject: [PATCH 3/4] use v4 for upload artifact

---
 .github/workflows/run_notebook.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run_notebook.yml b/.github/workflows/run_notebook.yml
index 224167f..a84a112 100644
--- a/.github/workflows/run_notebook.yml
+++ b/.github/workflows/run_notebook.yml
@@ -77,7 +77,7 @@ jobs:
           jupyter nbconvert --to notebook --execute run_and_explore.ipynb --output executed_notebook.ipynb
           
       - name: Upload notebook
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: executed-notebook
           path: executed_notebook.ipynb

From 370037ab5fd31997c86b90c4c1d36ba2f4ac8efa Mon Sep 17 00:00:00 2001
From: James Kent <jamesdkent21@gmail.com>
Date: Mon, 28 Apr 2025 13:42:23 -0500
Subject: [PATCH 4/4] process notebook file to test run

---
 .github/workflows/run_notebook.yml | 27 +++++++++++++--------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/run_notebook.yml b/.github/workflows/run_notebook.yml
index a84a112..a19a336 100644
--- a/.github/workflows/run_notebook.yml
+++ b/.github/workflows/run_notebook.yml
@@ -57,27 +57,26 @@ jobs:
           # Convert notebook to Python script for easier text processing
           jupyter nbconvert --to script run_and_explore.ipynb
           
+          # Remove Setup environment section
+          sed -i '/#@title Setup environment/,/# In\[ \]:/d' run_and_explore.py
+          
           # Replace META_ID
           sed -i 's/META_ID = ""/META_ID = "36Dm86NVjoTJ"/' run_and_explore.py
           
           # Add no_upload parameter to run function
           sed -i 's/url, meta_result = run(META_ID)/url, meta_result = run(META_ID, no_upload=True)/' run_and_explore.py
           
-          # Remove View the Report section (everything after the line containing "## View the Report")
-          sed -i '/^## View the Report/,$d' run_and_explore.py
-          
-          # Convert back to notebook
-          jupyter nbconvert --to notebook run_and_explore.py
-          
-          # Move converted notebook back to original name
-          mv run_and_explore.nbconvert.ipynb run_and_explore.ipynb
-          
-      - name: Execute notebook
+          # Remove View the Report section (everything after the line containing "# View")
+          sed -i '/^#@title View/,$d' run_and_explore.py
+
+      - name: Execute Python script
         run: |
-          jupyter nbconvert --to notebook --execute run_and_explore.ipynb --output executed_notebook.ipynb
+          python run_and_explore.py
           
-      - name: Upload notebook
+      - name: Upload results
         uses: actions/upload-artifact@v4
         with:
-          name: executed-notebook
-          path: executed_notebook.ipynb
+          name: analysis-results
+          path: |
+            results/
+            report/