sync thicket tutorial notebooks onto thicket docs

.github/workflows/notebook-sync.yaml

@@ -3,14 +3,21 @@ name: Sync thicket docs with executed notebook from thicket-tutorial
 on:
   push:
     branches: [ develop ]
+  # TODO: remove before merge
+  pull_request:
+    branches: [ develop ]
+  ######
+
+env:
+  GH_TOKEN: ${{ secrets.THICKET_GITHUB_TOKEN }}
 
 jobs:
-  parse_file_tracker:
+  sync_notebooks:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Parse config file
-        id: parse
+      - name: Detect Changes
+        id: detect
         run: |
           jq_out=$(cat .github/workflows/tutorials_sync.json | jq -r 'to_entries|map("\(.key) \(.value.thicket_fname) \(.value.tutorial_fname)")|.[]')
           IFS=$'\n' rows=( $( echo "$jq_out" | while read -r; do echo "$REPLY"; done ) )
@@ -23,24 +30,81 @@ jobs:
           done
           out_list=${out_list%?}
           out_list="$out_list]"
-          echo "tracked_files=$out_list" >> "$GITHUB_OUTPUT"
-          echo "change_track_filter=$change_track_filter" >> "$GITHUB_OUTPUT"
-
-  detect_changes:
-    needs: parse_file_tracker
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
+          echo "change_track_filter=$change_track_filter" >> $GITHUB_ENV
+          echo "tracked_files=$out_list" >> $GITHUB_ENV
       - name: Get changed files
         uses: dorny/paths-filter@v2
         id: changes
         with:
+          list-files: json
           filters: |
-            ${{ needs.outputs.change_track_filter }}
+            changed:
+              - $change_track_filter
       - name: Get number of changed files
         id: calc_num
-        env:
-          changes: ${{ toJSON(changes.changes) }}
         run: |
+          changes=${{ steps.changes.outputs.changed_files }}
           num_changes=$(echo $changes | jq '. | length')
-          echo "num_changes=$num_changes" >> "$GITHUB_OUTPUT"
+          echo "num_changes=$num_changes" >> $GITHUB_ENV
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Install Jupyter + dependencies
+        run: |
+          python3 -m pip install jupyter "nbconvert>=6.0.0"
+          python3 -m pip install papermill 
+          python3 -m pip install -r requirements.txt
+      - name: Prints GitHub CLI Info
+        env:
+          GH_TOKEN: ${{ secrets.THICKET_GITHUB_TOKEN }}
+        run: |
+          echo "GitHub CLI Version: $(gh --version)"
+          #echo "GitHub CLI Username: $(gh api user | jq -r '.login')"
+          gh api user
+      - name: Sync Files
+        run: |
+          git config user.name 'Thicket Tutorial Sync Bot'
+          git config user.email '<>'
+          sha=$(git rev-parse --short HEAD)
+          gh repo clone LLNL/thicket thicket_src
+          cd thicket_src
+          branch_name="autosync-$(date +%s)"
+          git checkout -b $branch_name
+          #username=$(gh api user | jq -r '.login')
+          #num_prs=$(gh pr list -A "$username" | wc -l)
+          #if test $num_prs -gt 1; then
+              #echo "ERROR: multiple PRs from user $username exist!"
+              #exit 1
+          #elif test $num_prs -eq 1; then
+              #pr_num=$(gh pr list --json number -A "$username" | jq -r '.[0].number')
+              #gh pr close $pr_num -c "Closing for new sync PR" -d
+          #fi
+          thicket_dir=$(pwd)
+          cd ..
+          for elem in $(echo ${{ needs.parse_file_tracker.outputs.tracked_files }} | jq -r '.[]'); do
+              th_file=$(echo $elem | jq -r '.thicket_file')
+              tut_file=$(echo $elem | jq -r '.tutorials_file')
+              tut_abs_file=$(realpath "./${tut_file}")
+              if test ! -f $tut_abs_file; then
+                  echo "ERROR: tutorial file $tut_abs_file does not exist!"
+                  exit 1
+              fi
+              th_abs_file=$(realpath "${thicket_dir}/${th_file}")
+              if test -f $th_abs_file; then
+                  rm $th_abs_file
+              fi
+              # change to running notebook with papermil, creates a new notebook, 
+              # add that to docs
+              papermill $tut_abs_file $th_abs_file
+          done
+          cd $thicket_dir
+          git add --all
+          commit_time="$(date +"%m/%d/%Y - %H:%M:%S")"
+          git commit -m "Auto sync notebooks from thicket-tutorial"
+          git push -u origin $branch_name
+          gh pr create -B develop -b \
+              "This is an autogenerated PR for syncing the tutorial notebooks onto Thicket docs\nthicket-tutorial commit: LLNL/thicket-tutorial@$sha" \ 
+              -t "Autosync Notebooks from thicket-tutorial"
+        env:
+          GH_TOKEN: ${{ secrets.THICKET_GITHUB_TOKEN }}