feat(API): Setup the library for development

.github/workflows/push-tests.yml

@@ -48,6 +48,33 @@ jobs:
         run: |
           pip install -r tools/ontology-builder/requirements.txt
           pip install -r tools/ontology-builder/requirements-dev.txt
-      - name: Ontology Dry Run Unit Tests
+      - name: Ontology builder unit tests
         run: |
           cd tools/ontology-builder && make unit-tests
+
+  unit-test-python-api:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.11
+      - name: Python cache
+        uses: actions/cache@v1
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/api/python/pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Install dependencies
+        run: |
+          cd api/python
+          make install-dev
+      - name: Python API unit tests
+        run: |
+          cd api/python
+          make unit-tests

.gitignore

@@ -0,0 +1 @@
+/api/python/src/cellxgene_ontology_guide/_version.py

.pre-commit-config.yaml

@@ -34,4 +34,4 @@ repos:
       - id: mypy
         args: [--strict, --ignore-missing-imports]
         additional_dependencies: [types-PyYAML]
-        files: ^(api/python|tools/ontology-builder/src)/
+        files: ^(api/python/src|tools/ontology-builder/src)/

api/python/Makefile

@@ -0,0 +1,11 @@
+install:
+	pip install -e .
+
+install-dev:
+	pip install -e .[test]
+
+clean:
+	rm -rf ./build ./src/cellxgene_ontology_guide.egg-info
+
+unit-tests:
+	python -m pytest tests

api/python/README.md

@@ -0,0 +1,14 @@
+# Python API
+
+# Install
+
+```bash
+make install
+```
+
+# Run Unit Tests
+
+```bash
+make install-dev
+make unit-tests
+```

api/python/pyproject.toml

@@ -0,0 +1,35 @@
+[build-system]
+requires = ["setuptools>=69", "setuptools-scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cellxgene_ontology_guide"
+dynamic = ["version"]
+description = "Access ontology data used by CZ cellxgene"
+authors = [
+    { name = "Chan Zuckerberg Initiative Foundation", email = "[email protected]" }
+]
+license = { text = "MIT" }
+readme = "README.md"
+requires-python = "~= 3.11"
+dependencies = [
+    "owlready2"
+]
+
+[project.optional-dependencies]
+test = ["pytest"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["cellxgene_ontology_guide"]
+
+[tool.pytest.ini_options]
+pythonpath = ["src/cellxgene_ontology_guide"]
+
+[tool.setuptools_scm]
+version_file = "src/cellxgene_ontology_guide/_version.py"
+version_scheme = "python-simplified-semver"
+root = "../.."
+relative_to = "__file__"
+#TODO: setup the github tag for the pypi releases so setuptools-SCM can identify it using a python regex
+#tag_regex="^python-api-(?P<version>[vV]?\d+(?:\.\d+){0,2}[^\+]*)(?:\+.*)?$')"

api/python/src/cellxgene_ontology_guide/__init__.py

@@ -0,0 +1,3 @@
+import _version
+
+__version__ = _version.__version__

api/python/tests/test_version.py

@@ -0,0 +1,5 @@
+import cellxgene_ontology_guide
+
+
+def test_version():
+    assert cellxgene_ontology_guide.__version__