Merge pull request #38 from microbiomedata/37-configure-gha-to-run-bl…

…ack-and-pytest-in-more-scenarios

Use individual GHA workflows to run tests (`pytest`) and check code format (`black`)

.github/workflows/build-and-publish-package-to-pypi.yml

@@ -6,11 +6,24 @@ on:
     types: [ published ]
 
 # Note: Since the building and publishing are done in separate jobs,
-#       we use GitHub's artifact persistent system to give the later
+#       we use GitHub's artifact persistence system to give the later
 #       job access to files generated by the earlier job.
 jobs:
+  # Use existing workflows.
+  # Reference: https://docs.github.com/en/actions/using-workflows/reusing-workflows#calling-a-reusable-workflow
+  check-source-code-format:
+    name: Check source code format
+    uses: ./.github/workflows/check-source-code-format.yml
+  run-tests:
+    name: Run tests
+    uses: ./.github/workflows/run-tests.yml
   build:
     name: Build package
+    # This job depends upon other jobs succeeding.
+    # Reference: https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions#jobsjob_idneeds
+    needs:
+      - check-source-code-format
+      - run-tests
     runs-on: ubuntu-latest
     steps:
       - name: Check out commit  # Docs: https://github.com/actions/checkout
@@ -25,8 +38,6 @@ jobs:
         uses: snok/install-poetry@v1
       - name: Install dependencies  # Docs: https://python-poetry.org/docs/cli/#install
         run: poetry install --no-interaction
-      - name: Run tests  # TODO: Consider extracting this and preceding steps into a separate job and/or workflow
-        run: poetry run pytest -v
       - name: Update package version  # Docs: https://python-poetry.org/docs/cli/#version
         run: poetry version ${{ github.ref_name }}
       - name: Build package  # Docs: https://python-poetry.org/docs/cli/#build

.github/workflows/check-source-code-format.yml

@@ -0,0 +1,28 @@
+# GitHub Actions workflow that checks the format of the source code.
+# Reference: https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions
+name: Check source code format
+
+on:
+  pull_request: { branches: [ main ] }
+  push: { branches: [ main ] }
+  workflow_dispatch: { }
+
+jobs:
+  check-source-code-format:
+    name: Check source code format
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out commit  # Docs: https://github.com/actions/checkout
+        uses: actions/checkout@v4
+      - name: Set up Python  # Docs: https://github.com/actions/setup-python
+        uses: actions/setup-python@v5
+        with:
+          # Specify a Python version that satisfies the `tool.poetry.dependencies.python`
+          # version requirement specified in `pyproject.toml`.
+          python-version: '3.9'
+      - name: Install Poetry  # Docs: https://github.com/snok/install-poetry
+        uses: snok/install-poetry@v1
+      - name: Install dependencies  # Docs: https://python-poetry.org/docs/cli/#install
+        run: poetry install --no-interaction
+      - name: Check source code format
+        run: poetry run black --check .

.github/workflows/run-tests.yml

@@ -0,0 +1,29 @@
+# GitHub Actions workflow that runs tests.
+# Reference: https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions
+name: Run tests
+
+on:
+  pull_request: { branches: [ main ] }
+  push: { branches: [ main ] }
+  workflow_dispatch: { }
+
+jobs:
+  test:
+    name: Run tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out commit  # Docs: https://github.com/actions/checkout
+        uses: actions/checkout@v4
+      - name: Set up Python  # Docs: https://github.com/actions/setup-python
+        uses: actions/setup-python@v5
+        with:
+          # Specify a Python version that satisfies the `tool.poetry.dependencies.python`
+          # version requirement specified in `pyproject.toml`.
+          python-version: '3.9'
+      - name: Install Poetry  # Docs: https://github.com/snok/install-poetry
+        uses: snok/install-poetry@v1
+      - name: Install dependencies  # Docs: https://python-poetry.org/docs/cli/#install
+        run: poetry install --no-interaction
+      - name: Run tests
+        run: |
+          poetry run pytest -vv --color=yes

tests/test_cli.py

@@ -60,7 +60,18 @@ def test_graph_command_with_custom_output_path():
 
 def test_graph_command_help():
     """Test the `graph` command with the --help flag."""
-    runner = CliRunner()
+
+    # Note: For this test, we define an environment variable (in the context of the `CliRunner`) named `TERM` having
+    #       a value `"unknown"`. When Rich "sees" that environment variable, Rich will refrain from coloring its output.
+    #       The reason we influence Rich in this way here is that, when we don't, this test fails when run via GitHub
+    #       Actions. I think it has to do with the fact that GitHub Actions Runners do not allocate a TTY.
+    #
+    # References:
+    # - https://click.palletsprojects.com/en/stable/api/#click.testing.CliRunner (re: the `env` kwarg)
+    # - https://rich.readthedocs.io/en/stable/console.html#environment-variables (re: the `TERM` environment variable)
+    # - https://github.com/actions/runner/issues/241 (re: GHA Runners not allocating a TTY)
+    #
+    runner = CliRunner(env=dict(TERM="unknown"))
     result = runner.invoke(app, ["graph", "--help"])
 
     assert result.exit_code == 0, f"Unexpected exit code: {result.exit_code}"