apbs/.github/workflows/python-package.yml at main · Electrostatics/apbs · 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
name: Python package

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  workflow_dispatch:

permissions:
  contents: read

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

jobs:
  test:
    name: Python ${{ matrix.python-version }}
    runs-on: ubuntu-latest
    timeout-minutes: 15
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.14"]

    steps:
      - name: Check out repository
        uses: actions/checkout@v7

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v7
        with:
          python-version: ${{ matrix.python-version }}
          cache: pip

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install --editable .
          python -m pip install coverage flake8 pytest

      - name: Check for Python errors
        run: flake8 apbs --count --select=E9,F63,F7,F82 --show-source --statistics

      - name: Run tests with coverage
        run: |
          python -m coverage run --source=apbs -m pytest test
          python -m coverage report --show-missing | tee coverage.txt
          python -m coverage xml

      - name: Store coverage results
        uses: actions/upload-artifact@v7
        with:
          name: python-${{ matrix.python-version }}-coverage
          path: |
            coverage.txt
            coverage.xml

  bindings:
    name: Python bindings
    runs-on: ubuntu-22.04
    timeout-minutes: 30
    env:
      CMAKE_POLICY_VERSION_MINIMUM: "3.5"

    steps:
      - name: Check out repository
        uses: actions/checkout@v7
        with:
          submodules: recursive

      - name: Set up Python 3.14
        uses: actions/setup-python@v7
        with:
          python-version: "3.14"

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            bison \
            build-essential \
            flex \
            libboost-dev \
            libeigen3-dev \
            liblapack-dev \
            libopenblas-serial-dev \
            libreadline-dev \
            libsuitesparse-dev \
            swig
          git clone --depth 1 https://github.com/Electrostatics/metis-fork.git /tmp/metis
          cd /tmp/metis
          make config prefix=/usr/local
          sudo make install

      - name: Configure Python bindings
        run: |
          cmake -S . -B build-bindings \
            -DAPBS_STATIC_BUILD=OFF \
            -DBLA_VENDOR=OpenBLAS \
            -DBUILD_DOC=OFF \
            -DBUILD_SHARED_LIBS=ON \
            -DBUILD_TOOLS=ON \
            -DCMAKE_BUILD_TYPE=Release \
            -DCMAKE_INSTALL_PREFIX="$PWD/build-bindings/install" \
            -DENABLE_BEM=OFF \
            -DENABLE_GEOFLOW=OFF \
            -DENABLE_iAPBS=OFF \
            -DENABLE_PBAM=OFF \
            -DENABLE_PBSAM=OFF \
            -DENABLE_PYGBE=OFF \
            -DENABLE_PYTHON=ON \
            -DENABLE_TESTS=OFF \
            -DGET_NanoShaper=OFF \
            -DPYTHON_VERSION=3.14

      - name: Build and install Python bindings
        run: cmake --build build-bindings --parallel 2 --target install

      - name: Test Python bindings
        run: |
          cd /tmp
          PYTHONPATH="$GITHUB_WORKSPACE/build-bindings/install/lib" \
            python "$GITHUB_WORKSPACE/tools/python/test_bindings.py"