hsp2-pip-install-test.yml

name: Python application

on:
  push:
    branches: [ "master" ]
  pull_request:
    branches: [ "master", "develop", "develop-specact" ]

permissions:
  contents: read

jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.11"
          cache: "pip"
      - name: Install dependencies
        run: |
          pip install flake8
      - name: Lint with flake8
        run: |
          # stop the build if there are Python syntax errors or undefined names
          flake8 . --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics --exclude=build/*
          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
  
  test-pytest:
    runs-on: ubuntu-latest
    continue-on-error: true
    strategy:
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12"]
        include:
          - python-version: "3.11"
            pandas-version: "pandas>2.0"
          - python-version: "3.11"
            pandas-version: "pandas>1.5,<2.0"
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
          cache: "pip"
      - name: Install hsp2
        run: |
          # install the hsp2 executable
          pip install .[dev]
      - if: ${{ matrix.pandas-version }}
        run: pip install ${{ matrix.pandas-version }}
      - name: Test with pytest
        run: |
          # python coverage
          NUMBA_DISABLE_JIT=1 pytest --cov --cov-branch --cov-report term-missing
  
  test-cmd:
    runs-on: ubuntu-latest
    continue-on-error: true
    strategy:
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12"]
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
          cache: "pip"
      - name: Install hsp2
        run: |
          # install the hsp2 executable
          pip install .
      - name: Run hsp2
        run: |
          # TODO: find much shorter test case.
          hsp2 import_uci ./tests/test10/HSP2results/test10.uci _temp_test10.h5
          hsp2 run _temp_test10.h5