linkcell 0.3.3

Periodic linked-cell k-nearest neighbour search for molecular simulations
Documentation 
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

name: wheels

on:
  push:
    tags: ["v*"]
  pull_request:
    paths:
      - "python/**"
      - "linkcell/**"
      - "pyproject.toml"
      - "Cargo.toml"
      - "Cargo.lock"
      - "src/**"
      - "third_party/**"
      - "include/**"
      - ".github/workflows/wheels.yml"

concurrency:
  group: wheels-${{ github.ref }}
  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}

jobs:
  # One abi3 wheel per platform (CPython 3.12+ GIL).
  abi3:
    name: abi3 ${{ matrix.name }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        include:
          - name: linux-x86_64
            os: ubuntu-latest
            arch: x86_64
          - name: linux-aarch64
            os: ubuntu-24.04-arm
            arch: aarch64
          - name: macos-arm64
            os: macos-latest
            arch: arm64
    steps:
      - uses: actions/checkout@v4
      - uses: dtolnay/rust-toolchain@stable
      - uses: astral-sh/setup-uv@v5
        with:
          python-version: "3.12"
      - name: Build abi3 wheel
        run: uvx --from 'cibuildwheel>=4,<5' cibuildwheel --output-dir wheelhouse
        env:
          CIBW_BUILD: "cp312-*"
          CIBW_SKIP: "*musllinux* *i686* cp3??t-*"
          CIBW_ARCHS: ${{ matrix.arch }}
          CIBW_ENVIRONMENT: MATURIN_PEP517_ARGS="--features abi3"
          CIBW_TEST_REQUIRES: pytest numpy
          CIBW_TEST_COMMAND: pytest {project}/tests/python -q
      - uses: actions/upload-artifact@v4
        with:
          name: wheels-abi3-${{ matrix.name }}
          path: ./wheelhouse/*.whl

  # One abi3t wheel per platform (CPython 3.15+ GIL and free-threaded).
  # abi3audit --strict still treats PEP 793 PyModExport / PyType_FromSlots
  # as non-abi3, so the audit step is off for this job only.
  abi3t:
    name: abi3t ${{ matrix.name }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        include:
          - name: linux-x86_64
            os: ubuntu-latest
            arch: x86_64
          - name: linux-aarch64
            os: ubuntu-24.04-arm
            arch: aarch64
          - name: macos-arm64
            os: macos-latest
            arch: arm64
    steps:
      - uses: actions/checkout@v4
      - uses: dtolnay/rust-toolchain@stable
      - uses: astral-sh/setup-uv@v5
        with:
          python-version: "3.15"
      - name: Build abi3t wheel
        run: uvx --from 'cibuildwheel>=4,<5' cibuildwheel --output-dir wheelhouse
        env:
          CIBW_BUILD: "cp315-*"
          CIBW_SKIP: "*musllinux* *i686* cp3??t-*"
          CIBW_ARCHS: ${{ matrix.arch }}
          CIBW_ENVIRONMENT: MATURIN_PEP517_ARGS="--features abi3t"
          CIBW_AUDIT_COMMAND: ""
          CIBW_TEST_REQUIRES: pytest numpy
          CIBW_TEST_COMMAND: pytest {project}/tests/python -q
      - uses: actions/upload-artifact@v4
        with:
          name: wheels-abi3t-${{ matrix.name }}
          path: ./wheelhouse/*.whl

  sdist:
    name: Source distribution
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: dtolnay/rust-toolchain@stable
      - uses: astral-sh/setup-uv@v5
        with:
          python-version: "3.12"
      - name: Build sdist
        run: uvx maturin sdist --out dist
      - uses: actions/upload-artifact@v4
        with:
          name: sdist
          path: dist/*.tar.gz

  # Trusted publisher: PyPI project linkcell, repo d-SEAMS/linkcell,
  # workflow wheels.yml, environment (Any). Do not set `environment:`
  # on this job.
  publish:
    name: Publish to PyPI
    needs: [abi3, abi3t, sdist]
    runs-on: ubuntu-latest
    if: >-
      github.repository == 'd-SEAMS/linkcell' &&
      github.event_name == 'push' &&
      startsWith(github.ref, 'refs/tags/v')
    permissions:
      id-token: write
      contents: read
    steps:
      - uses: actions/download-artifact@v4
        with:
          path: dist
          merge-multiple: true
      - name: Publish to PyPI
        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e
        with:
          packages-dir: dist/