python.yaml

name: python
on:
  push:
  pull_request:
    branches:
      - main
  workflow_call:
  workflow_dispatch:
    inputs:
      debug_enabled:
        type: boolean
        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
        required: false
        default: false

jobs:
  Python-Collect-Data-and-Test:
    runs-on: ${{ matrix.os }}

    env:
      ECAT_TEST_FOLDER: "cimbi36"
      REAL_TEST_ECAT_PATH: cimbi36/Gris_102_19_2skan-2019.04.30.13.04.41_em_3d.v
      SMALLER_ECAT_PATH: ${{ github.workspace }}/ecat_validation/ECAT7_multiframe.v.gz
      TEST_ECAT_PATH: ${{ github.workspace }}/ecat_validation/ECAT7_multiframe.v
      OUTPUT_NIFTI_PATH: ${{ github.workspace}}/pypet2bids/tests/ECAT7_multiframe.nii
      READ_ECAT_SAVE_AS_MATLAB: ${{ github.workspace }}/pypet2bids/tests/ECAT7_multiframe.mat
      NIBABEL_READ_ECAT_SAVE_AS_MATLAB: ${{ github.workspace }}/pypet2bids/tests/ECAT7_multiframe.nibabel.mat
      MATLAB_CODE_PATH: ${{ github.workspace }}/matlab/

    strategy:
      matrix:
        os: [macOS-latest, ubuntu-latest]
        python: ['3.8', '3.9', '3.10']

    steps:
      - name: Checkout Repo
        uses: actions/checkout@v2

      - name: Cache ECAT
        id: cache-ecat
        uses: actions/cache@v2
        with:
          path: cimbi36
          key: ${{ runner.os }}-ecats

      - name: Set up python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python }}

      - name: Install dependencies
        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
        run: |
          cd pypet2bids
          pip3 install .

      - name: Install gdown and collect Ecat from Google Drive
        if: steps.cache-ecat.outputs.cache-hit != 'true'
        run: "python3 -m pip install gdown && gdown ${{ secrets.CIMBI_ECAT_ON_GOOGLE_DRIVE }} -O ecat_test"

      - name: Decompress dataset
        if: steps.cache-ecat.outputs.cache-hit != 'true'
        run: "tar xvzf ecat_test && rm ecat_test"

      - name: Test CLI --help
        run: |
          cd pypet2bids/
          python3 -m pypet2bids.ecat_cli --help

      - name: Test CLI Ecat Dump
        run: |
          cd pypet2bids/
          python3 -m pypet2bids.ecat_cli ../${{ env.REAL_TEST_ECAT_PATH }} --dump

      # the larger real data file uses too much ram for the github runner, we use the small file for
      # heavy io operations instead
      - name: Unzip Test File(s)
        run: |
          gzip -d ${{ env.SMALLER_ECAT_PATH }}
      
      - name: Test ecatread
        run: "cd pypet2bids/ && python3 -m tests.test_ecatread"

      - name: Run All Other Python Tests w/ Pytest
        run: |
          cd pypet2bids
          pytest -k 'not write_pixel_data' -k 'not test_convert_pmod_to_blood' tests/