Merge pull request #17 from monarch-initiative/issue_13

Add GH action for pytest

.github/workflows/qc.yml

@@ -0,0 +1,63 @@
+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://github.com/snok/install-poetry#workflows-and-tips
+
+name: Build and test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+#  lint:
+#    runs-on: ubuntu-latest
+#    continue-on-error: true  # This line allows the job to continue even if errors occur
+#    strategy:
+#      matrix:
+#        python-version: [ '3.9', '3.10' ]
+#    steps:
+#      - uses: actions/checkout@v3
+#      - name: Set up Python ${{ matrix.python-version }}
+#        uses: actions/setup-python@v4.3.0
+#        with:
+#          python-version: ${{ matrix.python-version }}
+#      - name: Install dependencies
+#        run: |
+#          pip install tox
+#      - name: Check code quality with flake8
+#        run: tox -e flake8
+
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, windows-latest ]
+        python-version: [ "3.10" ]
+        exclude:
+          - os: windows-latest
+            python-version: "3.10"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.3.1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+      - name: Install dependencies
+        run: poetry install --no-interaction --no-root
+      - name: Run Doctests
+        run: poetry run tox -e doctest
+      - name: Generate coverage results
+        run: |
+          poetry run pip install -U pytest
+          poetry run coverage run -p -m pytest tests/
+          poetry run coverage combine
+          poetry run coverage xml
+          poetry run coverage report -m

.gitignore

@@ -5,3 +5,4 @@ data/*
 prompts/*
 inputdir
 outputdir
+.openai_cache.db

pyproject.toml

@@ -20,8 +20,10 @@ pytest = "^7.1.2"
 pylint = "^2.15.6"
 pycodestyle = "^2.10.0"
 coverage = "^6.5.0"
-# https://github.com/monarch-initiative/ontogpt.git branch multilanguage_gpt
-ontogpt = {git = "https://github.com/monarch-initiative/ontogpt.git", branch = "multilanguage_gpt"}
+ontogpt = {git = "https://github.com/monarch-initiative/ontogpt.git", branch = "main"}
+
+[tool.poetry.group.dev.dependencies]
+tox = "^4.15.0"
 
 [tool.pytest.ini_options]
 pythonpath = [

tox.ini

@@ -44,6 +44,17 @@ commands =
     flake8 src/ tests/
 description = Run the flake8 tool with several plugins (bandit, docstrings, import order, pep8 naming).
 
+[testenv:doctest]
+deps =
+    pytest
+    pytest-cov
+isolated_build = true
+allowlist_externals = poetry
+commands_pre =
+    poetry install
+commands =
+    pytest --doctest-modules src/
+
 #########################
 # Flake8 Configuration  #
 # (.flake8)             #
@@ -66,7 +77,7 @@ ignore =
     #S603 # subprocess call - check for execution of untrusted input.
     S607 # Starting a process with a partial executable path ["open" in both cases]
     #S608 # Possible SQL injection vector through string-based query construction.
-    #B024 # StreamingWriter is an abstract base class, but it has no abstract methods. 
+    #B024 # StreamingWriter is an abstract base class, but it has no abstract methods.
          # Remember to use @abstractmethod, @abstractclassmethod and/or @abstractproperty decorators.
     #B027 # empty method in an abstract base class, but has no abstract decorator. Consider adding @abstractmethod
     #N803 # math-oriented classes can ignore this (e.g. hypergeometric.py)
@@ -80,4 +91,4 @@ application-import-names =
     pheval_template
     tests
 # exclude =
-#    datamodels   ## datamodels are auto-generated
+#    datamodels   ## datamodels are auto-generated