PHANTOM/.github/workflows/latex.yml

name: Build PDF
on:
  push:
    branches: [ main ]
    paths:
      - 'paper/**'
      - '.github/**'
  pull_request:
    paths:
      - 'paper/**'
      - '.github/**'
jobs:
  build:
    runs-on: ubuntu-latest
    env:
      OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
      R2_ACCESS_KEY_ID: ${{ secrets.R2_ACCESS_KEY_ID }}
      R2_SECRET_ACCESS_KEY: ${{ secrets.R2_SECRET_ACCESS_KEY }}
      R2_ENDPOINT: ${{ secrets.R2_ENDPOINT }}
      R2_BUCKET_NAME: ${{ secrets.R2_BUCKET_NAME }}
    steps:
      - uses: actions/checkout@v4

      - name: Prepare appendix code snapshot
        run: bash paper/concat_code.sh

      - name: Generate mirrors with Codex
        if: ${{ env.OPENAI_API_KEY != '' }}
        uses: openai/codex-action@v1
        with:
          openai-api-key: ${{ env.OPENAI_API_KEY }}
          sandbox: workspace-write
          safety-strategy: drop-sudo
          working-directory: .
          prompt: |
            Read and follow the mirror instructions in `paper/src/mirrors/genpop/INSTRUCTIONS.md`.

            Source chapters are in `paper/src/chapters/`:
            - 01-intro.tex
            - 02-literature-review.tex
            - 03-methodology.tex
            - 04-results.tex
            - 05-discussion.tex
            - 06-conclusion.tex

            Update `paper/src/mirrors/genpop/*.tex` so they mirror the thesis for a general audience according to the instruction file.
            Keep LaTeX valid and preserve citation commands and section order.

            Then create or update `paper/src/main-mirror-genpop.tex` by using `paper/src/main.tex` as the base and replacing chapter inputs from `chapters/...` to `mirrors/genpop/...`.
            Do not change any other project files.

      - name: Compute LaTeX roots
        id: roots
        run: |
          {
            echo "root_files<<EOF"
            echo "main.tex"
            for file in paper/src/main-mirror-*.tex; do
              if [ -f "$file" ]; then
                basename "$file"
              fi
            done
            echo "EOF"
          } >> "$GITHUB_OUTPUT"

          echo "Compiling roots:"
          echo "main.tex"
          for file in paper/src/main-mirror-*.tex; do
            if [ -f "$file" ]; then
              basename "$file"
            fi
          done

      - name: Compile LaTeX documents
        uses: xu-cheng/latex-action@v3
        with:
          root_file: ${{ steps.roots.outputs.root_files }}
          working_directory: paper/src
          args: -pdf -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build

      - name: Upload PDF artifacts
        uses: actions/upload-artifact@v4
        with:
          name: thesis-pdf
          path: |
            paper/build/main.pdf
            paper/build/main-mirror-*.pdf

      - name: Get current date
        id: date
        if: ${{ github.event_name == 'push' }}
        run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT

      - name: Upload to Cloudflare R2
        if: ${{ github.event_name == 'push' && env.R2_ACCESS_KEY_ID != '' && env.R2_SECRET_ACCESS_KEY != '' && env.R2_ENDPOINT != '' && env.R2_BUCKET_NAME != '' }}
        env:
          AWS_ACCESS_KEY_ID: ${{ env.R2_ACCESS_KEY_ID }}
          AWS_SECRET_ACCESS_KEY: ${{ env.R2_SECRET_ACCESS_KEY }}
          AWS_ENDPOINT_URL: ${{ env.R2_ENDPOINT }}
          DATE: ${{ steps.date.outputs.date }}
          BUCKET_NAME: ${{ env.R2_BUCKET_NAME }}
        run: |
          pip install boto3
          python3 << 'EOF'
          import boto3
          import os

          s3 = boto3.client('s3',
              endpoint_url=os.environ['AWS_ENDPOINT_URL'],
              aws_access_key_id=os.environ['AWS_ACCESS_KEY_ID'],
              aws_secret_access_key=os.environ['AWS_SECRET_ACCESS_KEY']
          )

          date = os.environ['DATE']
          bucket = os.environ['BUCKET_NAME']

          # upload dated version
          dated_filename = f"thesis-{date}.pdf"
          s3.upload_file(
              'paper/build/main.pdf',
              bucket,
              dated_filename,
              ExtraArgs={'ContentType': 'application/pdf'}
          )
          print(f"Uploaded {dated_filename}")

          # upload latest version
          s3.upload_file(
              'paper/build/main.pdf',
              bucket,
              'thesis-latest.pdf',
              ExtraArgs={'ContentType': 'application/pdf'}
          )
          print(f"Uploaded thesis-latest.pdf")

          # upload mirror versions (if generated)
          build_dir = 'paper/build'
          for filename in os.listdir(build_dir):
              if not filename.startswith('main-mirror-') or not filename.endswith('.pdf'):
                  continue
              mirror_name = filename[len('main-mirror-'):-4]
              source_path = os.path.join(build_dir, filename)

              dated_mirror = f"thesis-{mirror_name}-{date}.pdf"
              latest_mirror = f"thesis-{mirror_name}-latest.pdf"
              namespaced_dated = f"mirrors/{mirror_name}/thesis-{date}.pdf"
              namespaced_latest = f"mirrors/{mirror_name}/thesis-latest.pdf"

              s3.upload_file(
                  source_path,
                  bucket,
                  dated_mirror,
                  ExtraArgs={'ContentType': 'application/pdf'}
              )
              print(f"Uploaded {dated_mirror}")

              s3.upload_file(
                  source_path,
                  bucket,
                  latest_mirror,
                  ExtraArgs={'ContentType': 'application/pdf'}
              )
              print(f"Uploaded {latest_mirror}")

              s3.upload_file(
                  source_path,
                  bucket,
                  namespaced_dated,
                  ExtraArgs={'ContentType': 'application/pdf'}
              )
              print(f"Uploaded {namespaced_dated}")

              s3.upload_file(
                  source_path,
                  bucket,
                  namespaced_latest,
                  ExtraArgs={'ContentType': 'application/pdf'}
              )
              print(f"Uploaded {namespaced_latest}")
          EOF