lint_and_test.yml

name: Lint And Test

on:
  workflow_dispatch:
    # Have to declare parameters here for those that will be sent through 'workflow-dispatch'
    # event in branch_dispatch.yml. Otherwise, there'll be github API errors:
    # '"message": "Unexpected inputs provided: ...",'
    inputs:
      event_type:
        description: An arbitrary string used to dispatch steps
        required: true
        type: string
      commit_message:
        description: The commit message
        required: true
        type: string
      sender_repo:
        description: The repository which initiated the workflow dispatch
        required: true
        type: string
      sender_repo_owner:
        description: The account name of the repository initiated the workflow dispatch
        required: true
        type: string
      wic_owner:
        description: The account name of the wic repository
        required: true
        type: string
      wic_ref:
        description: The branch name within the wic repository
        required: true
        type: string
      mm-workflows_owner:
        description: The account name of the mm-workflows repository
        required: true
        type: string
      mm-workflows_ref:
        description: The branch name within the mm-workflows repository
        required: true
        type: string
      biobb_adapters_owner:
        description: The account name of the biobb_adapters repository
        required: true
        type: string
      biobb_adapters_ref:
        description: The branch name within the biobb_adapters repository
        required: true
        type: string

# See https://github.com/orgs/community/discussions/15690
# For workflow_dispatch, the commit message, repo, and branch name are not displayed by default.
run-name: "${{ inputs.commit_message}} - ${{ inputs.sender_repo }} - ${{ inputs.wic_ref }}"

defaults:
  run:
    shell: bash -l {0} # Invoke bash in login mode, NOT interactive mode.
    # This will cause bash to look for the startup file ~/.bash_profile, NOT ~/.bashrc
    # This is important since conda init writes to ~/.bashrc

# https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions#jobs
# Rather than use a single job with a linear pipeline of steps, you may be
# tempted to make each step into a separate job and specify the dependencies
# using the `needs` syntax for more parallelism.
# However, data cannot be shared between jobs because each job will be run on a
# different runner. Even on a self-hosted runner, the `needs` syntax does not
# guarantee that the data can be shared!

# Using if: always() allows all steps to run, while still properly reporting failure.
# See https://stackoverflow.com/questions/62045967/github-actions-is-there-a-way-to-continue-on-error-while-still-getting-correct

permissions:
  actions: read
  contents: read
  pull-requests: read

jobs:
  lint_and_test:
    # See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#concurrency
    # This will prevent DOS attacks from people blasting the CI with rapid fire commits.
    concurrency:
      group: ${{ github.workflow }}-${{ matrix.os }}-${{ github.ref }}-${{ inputs.sender_repo }}-${{ inputs.mm-workflows_ref}}
      cancel-in-progress: true
    strategy:
      fail-fast: false
      matrix:
        # NOTE: Due to 10X minute multiplier, do NOT run on macos-latest on every push!
        # https://docs.github.com/en/billing/managing-billing-for-github-actions/about-billing-for-github-actions#minute-multipliers
        # Run on macos on a separate weekly schedule.
        os: [ubuntu-latest, windows-latest]
    runs-on: ${{ matrix.os }}

    steps:
      - name: Checkout workflow-inference-compiler
        if: always()
        uses: actions/checkout@v3
        with:
          repository: ${{ inputs.wic_owner }}/workflow-inference-compiler
          ref: ${{ inputs.wic_ref }}
          path: workflow-inference-compiler

      - name: Checkout biobb_adapters
        if: always()
        uses: actions/checkout@v3
        with:
          repository: ${{ inputs.biobb_adapters_owner }}/biobb_adapters
          ref: ${{ inputs.biobb_adapters_ref }}
          path: biobb_adapters

      - name: Checkout mm-workflows
        if: always()
        uses: actions/checkout@v3
        with:
          repository: ${{ inputs.mm-workflows_owner }}/mm-workflows
          ref: ${{ inputs.mm-workflows_ref }}
          path: mm-workflows

      # NOTE: pypy actually decreases performance for lint_and_test.yml (by a factor of ~2)
      # - name: Append pypy to conda environment files
      #   if: runner.os != 'Windows'
      #   run: cd workflow-inference-compiler/install/ && echo "  - pypy" >> system_deps.yml

      # - name: Append pypy to conda environment files
      #   if: runner.os == 'Windows'
      #   run: cd workflow-inference-compiler/install/ && echo "  - pypy" >> system_deps_windows.yml

      - name: Setup mamba (linux, macos)
        if: runner.os != 'Windows'
        uses: conda-incubator/setup-miniconda@v3.0.1
        with:
          miniforge-variant: Mambaforge-pypy3
          miniforge-version: latest
          environment-file: workflow-inference-compiler/install/system_deps.yml
          activate-environment: wic
          channels: conda-forge
          python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11

      - name: Setup mamba (windows)
        if: runner.os == 'Windows'
        uses: conda-incubator/setup-miniconda@v3.0.1
        with:
          miniforge-variant: Mambaforge-pypy3
          miniforge-version: latest
          environment-file: workflow-inference-compiler/install/system_deps_windows.yml
          activate-environment: wic
          channels: conda-forge
          python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11

      - name: ShellCheck Script Quality
        if: always()
        # "SC1017 (error): Literal carriage return. Run script through tr -d '\r' ."
        run: shellcheck -e SC1017 $(find workflow-inference-compiler/ -name "*.sh" -and -not -path "./3/*")

      - name: Install Workflow Inference Compiler
        if: always()
        run: cd workflow-inference-compiler/ && pip install ".[all]"

      - name: Generate WIC Validation Jsonschema
        if: always()
        run: cd workflow-inference-compiler/ && wic --generate_schemas_only

      - name: Install Molecular Modeling Workflows
        if: always()
        # Also run mm-workflows command to generate
        # mm-workflows/autogenerated/schemas/config_schemas.json
        # NOTE: Use ".[test]" instead of ".[all]"
        # We do not want or need to install the workflow_deps extra.
        # (Many of the packages conflict with pypy.)
        run: cd mm-workflows/ && pip install ".[test]" && mm-workflows

      - name: Build Documentation
        if: always()
        run: cd workflow-inference-compiler/docs && make html

      - name: MyPy Check Type Annotations
        if: always()
        run: cd workflow-inference-compiler/ && mypy src/ examples/ tests/
        # NOTE: Do not use `mypy .` because then mypy will check both src/ and build/ causing:
        # src/workflow-inference-compiler/__init__.py: error: Duplicate module named "wic"
        # (also at "./build/lib/workflow-inference-compiler/__init__.py")

      - name: PyLint Check Code Quality
        if: always()
        run: cd workflow-inference-compiler/ && pylint src/ examples/**/*.py tests/
        # NOTE: See fail-under threshold in .pylintrc

      - name: PEP8 Code Formatting
        if: always()
        id: autopep8
        run: cd workflow-inference-compiler/ && autopep8 --exit-code --recursive --diff --max-line-length 120 examples/ src/ tests/
      - name: Fail if autopep8 made changes
        if: steps.autopep8.outputs.exit-code == 2
        run: exit 1

  # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252

      - name: PyTest CWL Embedding Independence
        if: always()
        run: cd workflow-inference-compiler/ && pytest -k test_cwl_embedding_independence # --cov --cov-config=.coveragerc_serial
        # NOTE: This test MUST be run in serial! See is_isomorphic_with_timeout()
        timeout-minutes: 5 # backup timeout for windows

      - name: PyTest Inline Subworkflows
        if: always()
        run: cd workflow-inference-compiler/ && pytest -k test_inline_subworkflows # --cov --cov-config=.coveragerc_serial
        # NOTE: This test MUST be run in serial! See is_isomorphic_with_timeout()
        timeout-minutes: 5 # backup timeout for windows

      - name: PyTest Scattering Scaling
        if: runner.os == 'Linux'
        # Avoid Windows and macOS due to 2X and 10X minute multipliers.
        # https://docs.github.com/en/billing/managing-billing-for-github-actions/about-billing-for-github-actions#minute-multipliers
        # Also, cannot run on Windows (natively) yet
        run: cd workflow-inference-compiler/ && pytest -k test_scattering_scaling

      # NOTE: The steps below are for repository_dispatch only. For all other steps, please insert above
      # this comment.

      # Need to store success value in environment variable, rather than using 'success()' in-line inside a run tag.
      # Otherwise: "The workflow is not valid. ... Unrecognized function: 'success'."
      # https://github.com/actions/runner/issues/834#issuecomment-889484016
      - name: The workflow has succeeded
        if: success()
        run: |
          echo 'workflow_success=true' >> "$GITHUB_ENV"

      # It is not clear from the documentation, but the 'success()' and 'failure()' functions
      # do not consider skipped steps. Specifically, the above 'success()' function will not
      # affect the 'failure()' function here.
      # https://docs.github.com/en/actions/learn-github-actions/expressions#status-check-function
      - name: The workflow has failed
        if: failure()
        run: |
          echo 'workflow_success=false' >> "$GITHUB_ENV"

      # See token.md
      - name: Generate a token
        if: always()
        id: generate_token
        uses: tibdex/github-app-token@b62528385c34dbc9f38e5f4225ac829252d1ea92
        with:
          app_id: ${{ secrets.APP_ID }}
          private_key: ${{ secrets.APP_PRIVATE_KEY }}

      - name: Reply CI results to sender
        # In case of failure, we still need to return the failure status to the original repository.
        # Use 'always()' so this step runs even if there's a failure and use an internal if-statement
        # to only run this step only if the repository_dispatch sends the signal.
        # https://github.com/actions/runner/issues/834#issuecomment-907096707
        # Use inputs.sender_repo to reply the original sender.
        if: always()
        uses: ./workflow-inference-compiler/.github/my_actions/reply_sender/ # Must start with ./
        with:
          github_repository: ${{ github.repository }}
          event_type: ${{ inputs.event_type }}
          sender_repo: ${{ inputs.sender_repo }}
          operating_system: ${{ matrix.os }}
          commit_message: ${{ inputs.commit_message }}
          mm_workflows_ref: ${{ inputs.mm-workflows_ref }}
          workflow_success: ${{ env.workflow_success }}
          access_token: ${{ steps.generate_token.outputs.token }}