version: 2

variables:

  update_conda: &update_conda

    run:

      name: Update conda

      command: conda update --yes conda

  export_shortcuts: &export_shortcuts

    run:

      name: Export shortcuts 

      command: |

        # for no good reason the wrong version of pytest is choosen by default...

        echo 'export PYTEST=$(conda info --base)/envs/bpnet/bin/pytest' >> $BASH_ENV

        echo 'export HDF5_USE_FILE_LOCKING=FALSE' >> $BASH_ENV

  install_bpnet_env: &install_bpnet_env

    run:

      name: Install bpnet enviroment

      command: |

        conda env create -f conda-env.yml

  run_tests: &run_tests

    run:

      name: Run tests

      command: |

        source activate bpnet

        mkdir test-reports

        $PYTEST --cov=bpnet/ tests/ --disable-warnings --no-cov-on-fail --junitxml=test-reports/junit.xml

      no_output_timeout: 15m

  run_coveralls: &run_coveralls

    run:

      name: run coveralls

      command: |

        source activate bpnet

        coveralls || true

  store_test_results: &store_test_results

    store_test_results:

      path: test-reports

  store_test_artifacts: &store_test_artifacts

    store_artifacts:

      path: test-reports

      destination: test-reports

jobs:

  test-py36:

    docker:

      - image: continuumio/anaconda3:5.0.1

    working_directory: ~/repo

    steps:

      - checkout

      - *update_conda

      - *install_bpnet_env

      - *export_shortcuts

      - *run_tests

      # - *run_coveralls

      - *store_test_results

      - *store_test_artifacts

  build-deploy-docs:

    docker:

      - image: continuumio/anaconda3:5.0.1

    working_directory: ~/repo

    steps:

      # - add_ssh_keys:

      #     fingerprints:

      #       - e3:44:16:ec:72:df:ae:59:82:c2:ee:57:4a:52:71:aa

      - checkout

      - run:

          name: Install pip bpnet

          command: pip install -e .

      - run:

          name: Install build deps

          # use custom pydoc-markdown

          command: pip install nbconvert mkdocs git+https://github.com/kipoi/pydoc-markdown@master

      - run:

          name: Build docs

          command: |

            cd docs/

            mkdir -p theme_dir/img/ipynb/

            ./render_ipynb.bash

            pydocmd build

      - run:

          name: Deploy docs

          command: .circleci/deploy_docs.bash

workflows:

  version: 2

  test:

    jobs:

      - test-py36

      # - build-deploy-docs:

      #     requires:

      #       - test-py36

      #     filters:

      #       branches:

      #         only:

      #           - master

      #           - test_deployment_script