.gitlab-ci.yml

## Disclaimer - This GitLab CI script allow contributors to perform CI on 

# We assume the runner uses Docker as executor
# We assume that the following images are available on the system :
#   - elodiegermani/open_pipeline

default:
  # Run all scripts in a docker container based on this image
  image: elodiegermani/open_pipeline

before_script:
  # Activate conda virtual environment
  - source activate neuro

  # Install the narps_open python package from the source code
  - pip install .

stages:
  - code_quality
  - testing

# Static analysis of the project's code
pylint_job:
  stage: code_quality
  script:
    # Install pylint
    - pip install pylint

    # Run pylint
    - pylint --exit-zero narps_open > pylint_report_narps_open.txt
    - pylint --exit-zero tests > pylint_report_tests.txt

  artifacts:
    when: always
    paths:
      - pylint_report_narps_open.txt
      - pylint_report_tests.txt
      - todos_narps_open.txt
      - todos_tests.txt

# Running tests for narps_open (except pipelines)
unit_tests-job:
  stage: testing
  script:
    # Install pytest & coverage
    - pip install pytest pytest-cov

    # Run tests and produce reports
    - coverage run -m pytest --junit-xml=pytest_report.xml --ignore=tests/pipelines/ tests/
    - coverage report
    - coverage xml

  artifacts:
    when: on_success
    reports:
      junit: pytest_report.xml
      coverage_report:
        coverage_format: cobertura
        path: coverage.xml

  rules:
    # If something changed in narps_open (except in narps_open/pipelines)
    - if: $CI_COMMIT_BRANCH
      changes:
        compare_to: 'refs/heads/main'
        paths:
          - 'narps_open/(?!pipelines)*'

# Running tests for pipelines
pipeline_tests-job:
  stage: testing
  variables:
    PIPELINES_TEST_FILES : ""
    #GIT_STRATEGY: clone # So that we can access the main branch for git diff purpose
  script:
    # Install pytest & coverage
    - pip install pytest pytest-cov

    - git switch main
    - git switch $CI_COMMIT_BRANCH

    # List test files corresponding to modified files
    - |
      for file in $(git diff --name-only origin/main...$CI_COMMIT_BRANCH)
      do
        if [[ "$file" =~ .*"pipeline".* ]]; then
          echo "Modified pipeline = $file"

          tmp=${file#*"team_"} # remove prefix ending in "team_"
          team_id=${tmp%".py"*}   # remove suffix starting with ".py"

          PIPELINES_TEST_FILES="$PIPELINES_TEST_FILES tests/pipelines/test_team_$team_id.py"
        fi
      done

    - echo "$PIPELINES_TEST_FILES"

    # Run tests and produce reports
    - coverage run -m pytest --junit-xml=pytest_report.xml "$PIPELINES_TEST_FILES"
    - coverage report
    - coverage xml

  artifacts:
    when: on_success
    reports:
      junit: pytest_report.xml
      coverage_report:
        coverage_format: cobertura
        path: coverage.xml

  rules:
    # If something changed in narps_open/pipelines
    - if: $CI_COMMIT_BRANCH
      changes:
        compare_to: 'refs/heads/main'
        paths:
          - 'narps_open/pipelines*'

# Running tests that changed
test_changes-job:
  stage: testing
  variables:
    TEST_FILES : ""
    #GIT_STRATEGY: clone # So that we can access the main branch for git diff purpose
  script:
    # Install pytest & coverage
    - pip install pytest pytest-cov

    - git switch main
    - git switch $CI_COMMIT_BRANCH

    # List test files corresponding to modified files
    - TEST_FILES=$(git diff --name-only origin/main...$CI_COMMIT_BRANCH)

    # Run tests and produce reports
    - coverage run -m pytest --junit-xml=pytest_report.xml "$TEST_FILES"
    - coverage report
    - coverage xml

  artifacts:
    when: on_success
    reports:
      junit: pytest_report.xml
      coverage_report:
        coverage_format: cobertura
        path: coverage.xml

  rules:
    # If something changed in narps_open/pipelines
    - if: $CI_COMMIT_BRANCH
      changes:
        compare_to: 'refs/heads/main'
        paths:
          - 'tests/*'