msprime/.github/workflows/tests.yml at 42133925391ee262e8da058a27ceef1798da4cfd · tskit-dev/msprime · 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
name: Tests

on:
  pull_request:
  push:
    branches: [main, test]
  merge_group:

jobs:
  pre-commit:
    name: Lint
    uses: tskit-dev/.github/.github/workflows/lint.yml@v2

  test:
    name: Python
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        python: [ 3.9, 3.13 ]
        os:  [ macos-latest, ubuntu-24.04, windows-latest ]
    defaults:
      run:
        shell: bash
    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.12.1
        with:
          access_token: ${{ github.token }}

      - name: Checkout
        uses: actions/checkout@v4.2.2
        with:
          submodules: true

      - name: Install Conda (needed for GSL)
        uses: conda-incubator/setup-miniconda@v3.1.1
        with:
          activate-environment: anaconda-client-env
          python-version: ${{ matrix.python }}
          channels: conda-forge, anaconda
          channel-priority: strict
          auto-update-conda: true

      - name: Fix windows symlinks
        # This is horrible, but the "git config core.symlinks true" didn't work.
        if: matrix.os == 'windows-latest'
        run: |
          rm lwt_interface
          cp -r --dereference git-submodules/tskit/python/lwt_interface ./lwt_interface

      - name: Fix windows .profile
        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
        run: |
          cp ~/.bash_profile ~/.profile

      - name: Install GSL
        if: steps.cache.outputs.cache-hit != 'true'
        shell: bash -l {0} #We need a login shell to get conda
        run: conda install gsl

      - name: Install uv
        uses: astral-sh/setup-uv@v6
        with:
          version: "0.8.15"

      - name: Install pip deps
        shell: bash -l {0}
        run: |
          uv pip install -r pyproject.toml --extra test

      - name: Build module
        env:
          MSP_CONDA_PREFIX: c:\Miniconda\envs\anaconda-client-env
        run: |
          source ~/.profile
          conda activate anaconda-client-env
          python setup.py build_ext --inplace

      - name: Run tests
        run: |
          source ~/.profile
          conda activate anaconda-client-env
          pytest -xvs -n0