Merge pull request #4 from geneontology/issue-2-cleanup-and-publish

Clean up Python code and GitHub Actions

.github/workflows/deploy-docs.yaml

@@ -15,23 +15,22 @@ jobs:
       id-token: write  # to verify the deployment originates from an appropriate source
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
         with:
-          fetch-depth: 0  # otherwise, you will failed to push refs to dest repo
+          fetch-depth: 0  # otherwise, it will fail to push refs to dest repo
 
-      - name: Set up Python.
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.9
-
-      - name: Install Poetry.
+      - name: Install Poetry
         run: pipx install poetry
 
-      - name: Install dependencies.
-        run: poetry install -E docs
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'poetry'
+
+      - name: Install dependencies
+        run: poetry install
 
-      - name: Build documentation.
+      - name: Build documentation
         run: |
           mkdir -p docs
           touch docs/.nojekyll

.github/workflows/main.yaml

@@ -11,26 +11,21 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.12"]
 
     steps:
+      - uses: actions/checkout@v4
 
-      - name: Check out repository
-        uses: actions/checkout@v3
+      - name: Install Poetry
+        run: pipx install poetry
 
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Install Poetry
-        run: pipx install poetry
+          cache: 'poetry'
 
       - name: Install dependencies
-        run: poetry install --no-interaction --no-root
-
-      - name: Install project
-        run: poetry install --no-interaction
+        run: poetry install
 
       - name: Run test suite
         run: make test

.github/workflows/pypi-publish.yaml

@@ -9,28 +9,37 @@ jobs:
   build-n-publish:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/gocam
+    permissions:
+      # this permission is mandatory for trusted publishing
+      id-token: write
 
     steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.9
+      - uses: actions/checkout@v4
 
       - name: Install Poetry
         run: |
           pipx install poetry
-          poetry self add "poetry-dynamic-versioning[plugin]"
+          pipx inject poetry "poetry-dynamic-versioning[plugin]"
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'poetry'
 
-      # - name: Install dependencies
-      #   run: poetry install --no-interaction
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Generate project files
+        run: make clean all
+
+      - name: Test project
+        run: make test
 
       - name: Build source and wheel archives
         run: poetry build
 
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/[email protected]
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_PASSWORD }}
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test_pages_build.yaml

@@ -13,21 +13,20 @@ jobs:
   run:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - name: Set up Python 3
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.9
-
       - name: Install Poetry
         run: pipx install poetry
 
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'poetry'
+
       - name: Install dependencies
-        run: poetry install -E docs
+        run: poetry install
 
       - name: Build documentation
         run: |

Makefile

@@ -105,7 +105,7 @@ create-data-harmonizer:
 	npm init data-harmonizer $(SOURCE_SCHEMA_PATH)
 
 all: site
-site: gen-project gendoc
+site: gen-project gendoc $(PYDANTIC)
 %.yaml: gen-project
 deploy: all mkd-gh-deploy
 
@@ -143,7 +143,7 @@ test-schema:
 	$(RUN) gen-project ${CONFIG_YAML} -d tmp $(SOURCE_SCHEMA_PATH)
 
 test-python:
-	$(RUN) python -m unittest discover
+	$(RUN) pytest tests
 
 lint:
 	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH)
@@ -219,6 +219,6 @@ clean:
 	rm -rf $(DEST)
 	rm -rf tmp
 	rm -fr docs/*
-	rm -fr $(PYMODEL)/*
+	rm -fr $(PYDANTIC)
 
 include project.Makefile