Taskfile.yml

version: "3"

dotenv: [".env"]

tasks:
  install:
    desc: >-
      Install the project using poetry (including dependencies and git hooks).
    cmds:
      - poetry install
      - pre-commit install

  format-check:
    desc: >-
      Check code formatting using ruff.
    cmds:
      - ruff format --diff --check .

  format:
    desc: >-
      Format code using ruff.
    cmds:
      - ruff format .

  lint:
    desc: >-
      Run linting using ruff.

    summary: |
      Run linting using ruff.

      This will check the code using the ruff linter.
      If the `FIX` environment variable is set to "true", the linter will attempt to fix the issues.
      If the `UNSAFE_FIXES` environment variable is set to "true", the linter will attempt to fix the issues using unsafe fixes.
    vars:
      FIX: '{{ .FIX | default "false" }}'
      UNSAFE_FIXES: '{{ .UNSAFE_FIXES | default "false" }}'
    cmds:
      - ruff check src tests
        {{ if eq .FIX "true" }}
        --fix
        {{end}}
        {{ if eq .UNSAFE_FIXES "true" }}
        --unsafe-fixes
        {{end}}

  typecheck:
    desc: >-
      Run type checking using mypy.
    cmds:
      - mypy --ignore-missing-imports --install-types --non-interactive src tests

  test:
    desc: |-
      Run tests using pytest with the default flags defined in pyproject.toml.
    cmds:
      - pytest tests {{ .CLI_ARGS }}

  test-workflow:
    desc: >-
      Run workflow tests using pytest.
    cmds:
      - pytest tests -m "workflow_test and not external_workflow_test" {{ .CLI_ARGS }}

  test-workflow-external:
    desc: >-
      Run external workflow tests using pytest.
    summary: |
      Run external workflow tests using pytest.

      This will run the tests marked with the `external_workflow_test` marker using pytest.
      These tests can take a very long time to run and require input data to be available in a fixed location.
      External workflow test are not included in the `test-all` task.
    cmds:
      - pytest tests -m external_workflow_test

  test-web:
    desc: >-
      Run web tests using pytest.
    cmds:
      - pytest tests -m web_test {{ .CLI_ARGS }}

  test-all:
    desc: >-
      Run all tests using pytest.
    deps:
      - test
      - test-workflow
      - test-web

  test-watch:
    desc: >-
      Run tests using pytest anytime you save a file.
    summary: Run tests using pytest every time a file changes.

      This will run the tests using pytest in a watch loop. The tests will be re-run
      whenever a file changes.

      The `MARKS` environment variable can be used to filter the tests using pytest marks.
      The `TEST_PATH` environment variable can be used to specify the path to the tests.

      The default is to run all unit tests in `tests/`
    vars:
      MARKS: '{{ .MARKS | default "" }}'
      TEST_PATH: '{{ .TEST_PATH | default "tests/" }}'
    cmds:
      - ptw -- {{ .TEST_PATH }} {{ .MARKS }}

  test-benchmark:
    desc: >-
      Run only the benchmark tests using pytest.
    cmds:
      - pytest --benchmark-enable --benchmark-only tests/ {{ .CLI_ARGS }}

  coverage:
    desc: >-
      Run tests using pytest and generate a coverage report.
    summary: |
      Run tests using pytest and generate a coverage report.

      This will run the tests using pytest and generate a coverage report.
      The coverage report will be output to the terminal.

      The `WORKFLOW_TEST` environment variable can be set to "true" to run
      the workflow tests as well. This will include the tests marked with the
      `workflow_test` marker (but not the `external_workflow_test` marker).
      This is disabled by default to reduce the runtime.
    sources:
      - src/**
      - tests/**
      - pyproject.toml
      - poetry.lock
    vars:
      WORKFLOW_TEST: '{{ .WORKFLOW_TEST | default "false" }}'
    cmds:
      - 'coverage run --source src -m pytest
        {{ if eq .WORKFLOW_TEST "true" }}
        -m "not external_workflow_test and not web_test"
        {{else}}
        -m "not workflow_test and not web_test"
        {{end}}'
      - coverage report

  test-nf-core-pixelator:
    desc: >-
      Run the default nf-core/pixelator test profile with this version of pixelator.
    summary: |
      Run the default nf-core/pixelator test profile with this version of pixelator.

      If the pipeline is not found in the directory `PIPELINE_SOURCE_DIR`, it will be cloned
      from the PixelgenTechnologies/nf-core-pixelator repository using the `PIPELINE_BRANCH` branch.
      By default the "pixelator-next" branch of nf-core-pixelator will be used.

      If the `PIPELINE_SOURCE_DIR` exists this task will assume that the pipeline is already present and checked out
      in the right branch.

      Note that the current dev version of pixelator must be installed and available in the PATH.

      If the `RESUME` environment variable is set to "true", the pipeline will be resumed if it was previously run.

    dir: "{{ .USER_WORKING_DIR }}"
    vars:
      RESUME: '{{ .RESUME | default "false" }}'
      PIPELINE_BRANCH: '{{ .PIPELINE_BRANCH | default "pixelator-next" }}'
      PIPELINE_SOURCE_DIR: '{{ .PIPELINE_SOURCE_DIR | default ".nf-core-pixelator-{{ .BRANCH }}" }}'
    cmds:
      - task: tests:pull-nf-core-pixelator
        vars:
          {
            PIPELINE_BRANCH: "{{ .PIPELINE_BRANCH }}",
            PIPELINE_SOURCE_DIR: "{{ .PIPELINE_SOURCE_DIR }}",
          }
      - task: tests:run-nf-core-pixelator-test-profile
        vars: { PIPELINE_SOURCE_DIR: "{{ .PIPELINE_SOURCE_DIR }}" }

includes:
  tests:
    taskfile: ./tests/Taskfile.yml
    dir: ./tests