starting point

.github/workflows/merge.yml

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+name: Run Merge Script
+
+on:
+  workflow_dispatch:
+  # run after layout verification
+  workflow_run:
+    workflows: ["Run Layout Verification"]
+    types:
+      - completed
+
+jobs:
+  merge:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo content
+        uses: actions/checkout@v2
+
+        # can also specify python version if needed
+      - name: setup python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11' 
+          cache: 'pip'
+
+      - name: install python packages
+        run: |
+          #python -m pip install --upgrade pip
+          pip install klayout SiEPIC siepic_ebeam_pdk pandas
+          python -m pip install --upgrade SiEPIC
+
+      - name: run merge script
+        run: |
+
+          python merge/EBeam_merge.py
+
+      - name: move merge output files to new folder
+        run: |
+          #output_files="EBeam.gds EBeam.oas EBeam.txt EBeam.coords"
+          output_files="EBeam.oas EBeam.txt"
+
+          IFS=' '
+
+          mkdir -p merge_output
+
+          for file in $output_files; do
+            cp "merge/$file" merge_output/
+          done
+
+      - name: upload artifact
+        uses: actions/upload-artifact@v4
+        id: artifact-upload
+        with:
+          name: merge-files
+          path: merge_output/
+
+      - name: get artifact url
+        run: |
+          IFS='/' read -ra REPO <<< "$GITHUB_REPOSITORY"
+          OWNER="${REPO[0]}"
+          REPO_NAME="${REPO[1]}"
+          echo "Owner: $OWNER"
+          echo "Repository: $REPO_NAME"
+          
+          RUN_ID=${{ github.run_id }}
+          ARTIFACT_ID=${{ steps.artifact-upload.outputs.artifact-id }}
+          ARTIFACT_URL="https://github.com/$OWNER/$REPO_NAME/actions/runs/$RUN_ID/artifacts/$ARTIFACT_ID"
+          echo "Artifact URL: $ARTIFACT_URL"
+          
+          echo "ARTIFACT_URL=$ARTIFACT_URL" >> $GITHUB_ENV
+          echo "OWNER=$OWNER" >> $GITHUB_ENV
+          
+      - name: update url in runner README 
+        run: |
+          start_delim="<!-- start-link -->"
+          end_delim="<!-- end-link -->"
+          
+          # remove current URL
+          sed -i "/$start_delim/,/$end_delim/d" README.md
+          
+          # add new URL
+          printf "$start_delim\n$ARTIFACT_URL\n$end_delim\n" >> README.md
+          
+      # merge script always runs on any PR, this ensures link is only updated after a PR is merged into SiEPIC
+      - name: commit and push changes to README if we are in SiEPIC repo
+        run: |
+          git diff
+          git config --local user.email "${{ github.actor }}@users.noreply.github.com"
+          git config --local user.name "${{ github.actor }}"
+          git add README.md
+          git commit -m "update README with new artifact url $ARTIFACT_URL"
+          git push 
+        if: ${{ env.OWNER == 'SiEPIC'}}

.github/workflows/python-to-oas_gds.yml

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+name: Run Python Files
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - "submissions/KLayout Python/**.py"
+    branches:
+      - '**'
+
+jobs:
+  run-python:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo content
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+        # can also specify python version if needed
+      - name: setup python
+        uses: actions/setup-python@v4
+
+      - name: install python packages
+        run: |
+          python -m pip install --upgrade pip
+          pip install klayout SiEPIC siepic_ebeam_pdk
+          python -m pip install --upgrade SiEPIC
+
+      - name: run python scripts and get output gds / oas file
+        run: |
+
+          # get added/modified py files
+          export FILES=$(git diff --name-only --diff-filter=ACM ${{ github.event.before }} ${{ github.sha }} -- "submissions/KLayout Python" | grep -E '\.py$')
+          echo "FILES=$FILES" >> $GITHUB_ENV
+
+          echo "Added / modified Python files; $FILES"
+
+          # delete .oas and .gds files in the runner's submissions folder
+          # this is needed in the case where someone already has file_name.gds and is now trying to generate file_name.oas (or vice versa)
+          rm -f submissions/*.gds submissions/*.oas
+
+          IFS=$'\n'
+        
+          OUTPUT_FILES=""
+          
+          for file in $FILES; do
+
+            echo "Getting oas/gds output for $file"
+
+            # run file and generate a gds / oas output
+            python "$file" 
+
+            # get output and save to OUTPUT_FILES
+            gds_files=$(find submissions -type f -name "*.gds" -exec basename {} .gds \;)
+            oas_files=$(find submissions -type f -name "*.gds" -exec basename {} .oas \;)
+
+            file_name=$(basename "$file")
+            file_name_no_py=$(basename "$file_name" .py)
+
+            output_files=""
+            if echo "$gds_files" | grep -q "$file_name_no_py"; then
+              output_file="${file_name_no_py}.gds"
+            else
+              output_file="${file_name_no_py}.oas"
+            fi
+
+            OUTPUT_FILES+="$output_file "
+
+            echo "Done for $file"
+
+          done
+
+          echo "output files; $OUTPUT_FILES"
+
+          echo "OUTPUT_FILES=$OUTPUT_FILES" >> $GITHUB_ENV
+
+      - name: write added oas and gds files to txt file
+        run: |
+          echo "$OUTPUT_FILES" > python-to-gds_oas.txt
+
+      - name: commit outputted oas and gds files into repository
+        run: |
+          git config --local user.email "${{ github.actor }}@users.noreply.github.com"
+          git config --local user.name "${{ github.actor }}"
+
+          git add python-to-gds_oas.txt
+
+          echo "git add python-to-gds_oas.txt"
+
+          # git add all produced oas files
+          for file in $OUTPUT_FILES; do
+            git add "submissions/$file"
+            echo "git add $file"
+          done
+
+          git commit -m "Add oas and gds files produced from .py files" 
+          git push
+

.github/workflows/run-verification.yml

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+name: Run Layout Verification
+
+on:
+  workflow_dispatch:
+  workflow_run:
+    workflows: ["Run Python Files"]
+    types:
+      - completed
+  push:
+    paths:
+      - 'submissions/**.gds'
+      - 'submissions/**.oas'
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+
+jobs:
+  verification:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo content
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+        # can also specify python version if needed
+      - name: setup python
+        uses: actions/setup-python@v4
+
+      - name: install python packages
+        run: |
+          python -m pip install --upgrade pip
+          pip install klayout SiEPIC siepic_ebeam_pdk
+          python -m pip install --upgrade SiEPIC
+          
+      - name: get .gds and .oas files, run example layout verification
+        id: run-script
+        run: |
+        
+          # if the action is being triggered after running python files, get resulting oas files from txt file
+          # github actions is not configured to detect files pushed from another action, thus we cannot use the method below
+          if [ -s "python-to-gds_oas.txt" ] && [ -n "$(cat python-to-gds_oas.txt)" ]; then
+            export FILES=$(cat python-to-gds_oas.txt)
+            IFS=' '
+            echo "" > python-to-gds_oas.txt
+             
+            # push empty text file to repo
+            git config --local user.email "${{ github.actor }}@users.noreply.github.com"
+            git config --local user.name "${{ github.actor }}"
+            git add python-to-gds_oas.txt
+            git commit -m "Emptying text file" 
+            git push
+
+          else
+            if [ "${{ github.event_name }}" = "pull_request" ]; then
+              # triggered on pull request, get all changed / added files from forked repo
+              export FILES=$(git diff --name-only --diff-filter=ACM FETCH_HEAD | grep -E '\.(gds|oas)$' | sed 's|^submissions/||')
+            else
+              # triggered push, locate the changed / added .gds and .oas files in the submission folder
+              export FILES=$(git diff --name-status --diff-filter=ACM --relative=submissions ${{ github.event.before }} ${{ github.sha }} submissions | grep -E '\.(gds|oas)$' | awk '{print $2}')
+            fi
+            IFS=$'\n'
+          fi
+
+          # print the names of the files
+          echo "Files for verification; $FILES"
+
+          files_with_errors=""
+        
+          # run verification on all files
+          for file in $FILES; do
+
+            echo "Running verification on $file"
+
+            output=$(python run_verification.py "submissions/$file")
+
+            # get number of errors
+            errors_from_output=$(echo "$output" | tail -n 1)
+
+            echo "$errors_from_output errors detected for $file"
+
+            # if file results in verification errors add to string files_with_errors
+            if [[ "$errors_from_output" -ge 1 ]]; then
+              files_with_errors+="$file, $errors_from_output errors. "
+            fi
+
+            echo "Done verification on $file"
+          done
+
+          echo "files_with_errors=$files_with_errors" >> $GITHUB_ENV
+
+      - name: move output files to new folder
+        run: |
+          export OUTPUT_FILES=$(find /home/runner/work/openEBL-2024-02/openEBL-2024-02/submissions -name "*.lyrdb")
+          echo "Output files: $OUTPUT_FILES"
+
+          mkdir -p verification_output
+
+          for file in $OUTPUT_FILES; do
+            cp "$file" verification_output/
+          done
+
+      - name: upload artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: layout-errors
+          path: verification_output/
+
+      - name: fail if there are errors from layout verification
+        run: |
+          if [ -z "$files_with_errors" ]; then
+            echo "No errors detected."
+          else
+            echo "Errors detected: $files_with_errors"
+            exit 1
+          fi
+