openclatura/.github/workflows/ci.yml at e80e6829c72db055f3c0f47774a5abf51a153e4f · lamalab-org/openclatura · 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
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
name: CI

on:
  push:
    branches: [main, refactor_namer, tests]
  pull_request:
    branches: ["**"]

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
      - name: Install ruff
        run: pip install "ruff==0.15.15"
      - name: Ruff check
        run: ruff check src/openclatura
      - name: Ruff format check
        run: ruff format --check src/openclatura

  test:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.11", "3.12"]
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: pip

      - name: Set up JDK (for OPSIN)
        uses: actions/setup-java@v4
        with:
          distribution: temurin
          java-version: "17"

      - name: Install package
        run: |
          python -m pip install --upgrade pip
          pip install -e ".[dev]"

      - name: Run fast tests
        run: |
          pytest -m "not slow and not dataset and not golden" \
                 --maxfail=20 \
                 --durations=20

  rdkit-compat:
    # Strict golden-output regression across RDKit versions. Detects
    # naming output that drifts with the RDKit upgrade cycle (aromaticity,
    # kekulisation, H-count perception). Each matrix row pins a specific
    # rdkit and runs only the `golden` test.
    runs-on: ubuntu-latest
    needs: [lint]
    strategy:
      fail-fast: false
      matrix:
        rdkit-version:
          - "2024.03.6"
          - "2024.09.6"
          - "2025.03.6"
          - "2025.09.5"
          - "2026.3.2"
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: pip

      - name: Install package + pinned rdkit
        run: |
          python -m pip install --upgrade pip
          pip install -e ".[dev]"
          pip install --force-reinstall --no-deps "rdkit==${{ matrix.rdkit-version }}"

      - name: Show installed versions
        run: |
          python -c "import rdkit, sys; print('python', sys.version); print('rdkit', rdkit.__version__)"

      - name: Run golden corpus test
        run: pytest -m golden -v --no-header -rA

  docker:
    needs: [lint, test, rdkit-compat]
    permissions:
      contents: read
      packages: write
    uses: ./.github/workflows/docker-image.yml
    secrets: inherit
  paper-evaluations:
    if: github.event_name == 'pull_request' && github.base_ref == 'tests'
    needs: [lint, test, rdkit-compat]
    runs-on: ubuntu-latest
    timeout-minutes: 60
    strategy:
      fail-fast: false
      max-parallel: 3
      matrix:
        shard:
          - qm9/qm9_all
          - pubchem/pubchem_seed5_100000
          - pubchem/pubchem_seed17_100000
          - pubchem/pubchem_seed42_100000
          - pubchem/pubchem_seed63_100000
          - pubchem/pubchem_seed87_100000
          - zinc22/zinc22_seed5_100000
          - zinc22/zinc22_seed17_100000
          - zinc22/zinc22_seed42_100000
          - zinc22/zinc22_seed63_100000
          - zinc22/zinc22_seed87_100000

    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: pip

      - name: Set up JDK for changed-name OPSIN checks
        uses: actions/setup-java@v4
        with:
          distribution: temurin
          java-version: "17"

      - name: Install OpenClatura and regression dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e ".[dev]"

      - name: Compare against the paper evaluation
        run: |
          python evaluations/check_regression.py \
            "evaluations/results/${{ matrix.shard }}_openclatura.jsonl" \
            --processes auto \
            --report "regression-reports/${{ strategy.job-index }}.json"

      - name: Upload discrepancy report
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: evaluation-regression-${{ strategy.job-index }}
          path: regression-reports/*.json
          if-no-files-found: error