healthcare-ai-foundations/weekly_literature_update.yml at main · sanjaybasu/healthcare-ai-foundations · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
name: Weekly Literature Update

on:
  schedule:
    # Run every Monday at 6 AM UTC
    - cron: '0 6 * * 1'
  workflow_dispatch: # Allow manual triggering

jobs:
  update_chapters:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.11'
          cache: 'pip'

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -r requirements.txt

      - name: Run PubMed literature search
        run: |
          python scripts/search_pubmed.py --output-dir data/papers --days-back 7
        env:
          PUBMED_API_KEY: ${{ secrets.PUBMED_API_KEY }}

      - name: Search arXiv for preprints
        run: |
          python scripts/search_arxiv.py --output-dir data/papers --days-back 7

      - name: Monitor AI lab announcements
        run: |
          python scripts/monitor_ai_labs.py --output-dir data/announcements

      - name: Analyze papers with Claude
        run: |
          python scripts/analyze_papers.py --papers-dir data/papers --output-dir data/analysis
        env:
          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}

      - name: Update chapters with new findings
        run: |
          python scripts/update_chapters.py --analysis-dir data/analysis --chapters-dir chapters
        env:
          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}

      - name: Generate update summary
        run: |
          python scripts/generate_summary.py --analysis-dir data/analysis --output-file UPDATE_SUMMARY.md

      - name: Update timestamp
        run: |
          python scripts/update_timestamp.py

      - name: Create Pull Request
        uses: peter-evans/create-pull-request@v6
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          commit-message: "Weekly automated literature update"
          title: "Weekly Literature Update - ${{ github.run_id }}"
          body-path: UPDATE_SUMMARY.md
          branch: literature-update-${{ github.run_id }}
          delete-branch: true
          labels: |
            automated
            literature-update
          reviewers: yourusername

      - name: Notify on failure
        if: failure()
        uses: actions/github-script@v7
        with:
          script: |
            github.rest.issues.create({
              owner: context.repo.owner,
              repo: context.repo.repo,
              title: 'Literature Update Workflow Failed',
              body: `The weekly literature update workflow failed. Please check the logs: ${context.payload.repository.html_url}/actions/runs/${context.runId}`,
              labels: ['bug', 'automated']
            })