python-test.yml

# This workflow will setup and test the python code using miniconda

name: Setup test publish reports

on: [push, pull_request]
  # Allows you to run this workflow manually from the Actions tab


# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
  contents: read
  pages: write
  id-token: write

# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
concurrency:
  group: "pages"
  cancel-in-progress: false
  
jobs:
  build:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@v2
      - uses: conda-incubator/setup-miniconda@v2
        with:
          auto-update-conda: true
          activate-environment: nrcat
          python-version: "3.10"
          channels: main, conda-forge
          allow-softlinks: true
          channel-priority: flexible
          show-channel-urls: true
      - run: |
            # Conda diagnostic
            echo "Echoing conda diagnostic information"
            conda --version
            conda info
            conda list
            conda config --show-sources
            conda config --show
            conda info --envs
            python --version
            pip --version
            pwd
            ls -l
            ######################
            # Setup linters
            # conda install black isort -y
            # ##################
            # Setup nrcattools
            echo "Setting up nrcatalogtools"
            pip install -r requirements.txt
            export NRC_DIR=${PWD}
            echo $NRC_DIR
            cd ./test
            pwd
            ls
            echo "Downloading lalsuite-extras"
            # ##################
            # LAL extras
            export LAL_DATA_PATH="${PWD}/lalsuite-extra/data/lalsimulation"
            echo "Using LAL_DATA_PATH"
            echo $LAL_DATA_PATH
            mkdir -p $LAL_DATA_PATH
            cd $LAL_DATA_PATH
            ls
            ## lal extras fetch method
            # git lfs pull
            wget -q https://git.ligo.org/lscsoft/lalsuite-extra/-/raw/master/data/lalsimulation/SEOBNRv4ROM_v2.0.hdf5 -O SEOBNRv4ROM_v2.0.hdf5
            cd $NRC_DIR
            pwd
            ls
            pip install -r requirements.txt
            ls
            export WTOOLS_DIR=$PWD
            echo $WTOOLS_DIR
            export PYTHONPATH="$WTOOLS_DIR":$PYTHONPATH
            echo $PYTHONPATH
            ####################
            # Begin linting
            # cd $NRC_DIR
            # isort .
            # black .
            # flake8 .
            # #################
            # Begin testing
            pip install coverage
            echo "Begin testing"
            cd $NRC_DIR/test
            # python -m unittest -v
            coverage run --source=../nrcatalogtools -m unittest discover -v
            coverage html
            python .generate_badge.py
      - name: Upload logs
        uses: actions/upload-artifact@v3
        with:
          name: logs_n_coverage
          path: |
            ./test/logs/*
            ./test/cov_badge.svg
            ./test/htmlcov
            
  cov_reports:
    name: Publish coverage reports
    needs: build
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: Download artefacts from build
        uses: actions/download-artifact@v3
        with:
          name: logs_n_coverage
      - name: Diagnostics
        run: |
          ls
          ls ../
          mv cov_badge.svg htmlcov/
          cd htmlcov
          ls
          pwd
      - name: Setup Pages
        uses: actions/configure-pages@v3
      - name: Upload artifact
        uses: actions/upload-pages-artifact@v1
        with:
          # Upload entire repository
          path: '/home/runner/work/nr-catalog-tools/nr-catalog-tools/htmlcov'
        
      - name: Deploy to GitHub Pages
        id: deployment
        uses: actions/deploy-pages@v2