healthcare-ai-foundations/literature_monitor.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
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
name: Healthcare AI Literature Monitor

on:
  schedule:
    # Run every Sunday at 00:00 UTC
    - cron: '0 0 * * 0'
  workflow_dispatch:  # Allow manual triggering

permissions:
  contents: write
  pull-requests: write

jobs:
  literature-monitor:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@v4
      with:
        token: ${{ secrets.GITHUB_TOKEN }}

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

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install requests biopython scholarly arxiv feedparser beautifulsoup4
        pip install openai anthropic  # For AI-powered analysis

    - name: Monitor PubMed
      env:
        NCBI_EMAIL: ${{ secrets.NCBI_EMAIL }}
      run: |
        python scripts/monitor_pubmed.py

    - name: Monitor arXiv
      run: |
        python scripts/monitor_arxiv.py

    - name: Monitor Conference Proceedings
      run: |
        python scripts/monitor_conferences.py

    - name: Analyze and Update Chapters
      env:
        ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
      run: |
        python scripts/update_chapters.py

    - name: Generate Update Report
      run: |
        python scripts/generate_report.py

    - name: Commit changes
      run: |
        git config --local user.email "github-actions[bot]@users.noreply.github.com"
        git config --local user.name "github-actions[bot]"
        git add -A
        git diff --quiet && git diff --staged --quiet || (git commit -m "📚 Automated literature update - $(date +'%Y-%m-%d')" && git push)

    - name: Create Pull Request for Major Updates
      if: ${{ env.MAJOR_UPDATES == 'true' }}
      uses: peter-evans/create-pull-request@v5
      with:
        token: ${{ secrets.GITHUB_TOKEN }}
        commit-message: "📚 Major literature updates - $(date +'%Y-%m-%d')"
        title: "Literature Update: New SOTA Methods Detected"
        body: |
          ## Automated Literature Update

          This PR contains updates from the weekly literature monitoring system.

          **Major Changes Detected:**
          - New state-of-the-art methods
          - Highly-cited papers (>100 citations)
          - Breakthrough discoveries

          Please review before merging.
        branch: literature-updates-${{ github.run_number }}
        delete-branch: true

  quality-check:
    needs: literature-monitor
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@v4

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

    - name: Install quality tools
      run: |
        pip install pylint mypy black isort
        pip install markdown-link-check

    - name: Check code quality
      run: |
        python scripts/check_code_quality.py

    - name: Validate citations
      run: |
        python scripts/validate_citations.py

    - name: Check broken links
      run: |
        find _chapters -name "*.md" -exec markdown-link-check {} \;

  deploy:
    needs: quality-check
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@v4

    - name: Setup Ruby
      uses: ruby/setup-ruby@v1
      with:
        ruby-version: '3.1'
        bundler-cache: true

    - name: Build Jekyll site
      run: |
        bundle exec jekyll build

    - name: Deploy to GitHub Pages
      uses: peaceiris/actions-gh-pages@v3
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}
        publish_dir: ./_site
        publish_branch: gh-pages
        user_name: 'github-actions[bot]'
        user_email: 'github-actions[bot]@users.noreply.github.com'