Merge pull request #12 from monarch-initiative/test-refactor-redux

refactor tests
monarch-initiative · Mar 22, 2023 · 9a3e13e · 9a3e13e
2 parents d1b813c + d2d7d56
commit 9a3e13e
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Showing 33 changed files with 354 additions and 716 deletions.
diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.8", "3.9", "3.10" ]
+        python-version: [ "3.9", "3.10" ]
 
     steps:
       - uses: actions/checkout@v3.0.2
@@ -26,12 +26,12 @@ jobs:
       - name: Install dependencies
         run: poetry install --no-interaction
 
-      - name: Check code quality with flake8
-        run: poetry run tox -e flake8
+#      - name: Check code quality with flake8
+#        run: poetry run tox -e flake8
 #       - name: Check package metadata with Pyroma
 #         run: poetry run tox -e pyroma
-      - name: Check static typing with MyPy
-        run: poetry run tox -e mypy
+#      - name: Check static typing with MyPy
+#        run: poetry run tox -e mypy
 
-      - name: Test with pytest and generate coverage file
-        run: poetry run tox -e py
+      - name: Unit tests only
+        run: poetry run python -m unittest discover tests.unit
diff --git a/src/ontogpt/clients/openai_client.py b/src/ontogpt/clients/openai_client.py
@@ -20,7 +20,8 @@ class OpenAIClient:
     api_key: str = None
 
     def __post_init__(self):
-        self.api_key = get_apikey_value("openai")
+        if not self.api_key:
+            self.api_key = get_apikey_value("openai")
         openai.api_key = self.api_key
 
     def complete(self, prompt, **kwargs) -> str:

diff --git a/src/ontogpt/templates/__init__.py b/src/ontogpt/templates/__init__.py
@@ -0,0 +1,3 @@
+from pathlib import Path
+
+PATH_TO_TEMPLATES = Path(__file__).parent
diff --git a/tests/input/eds-output.pickle b/tests/input/eds-output.pickle
diff --git a/tests/input/recipe-spaghetti.pickle b/tests/input/recipe-spaghetti.pickle
diff --git a/tests/test_clients/__init__.py → tests/integration/__init__.py b/tests/test_clients/__init__.py → tests/integration/__init__.py
diff --git a/tests/test_converters/__init__.py → tests/integration/test_clients/__init__.py b/tests/test_converters/__init__.py → tests/integration/test_clients/__init__.py
diff --git a/tests/test_clients/test_openai_client.py → ...ration/test_clients/test_openai_client.py b/tests/test_clients/test_openai_client.py → ...ration/test_clients/test_openai_client.py
diff --git a/tests/test_clients/test_pubmed_client.py → ...ration/test_clients/test_pubmed_client.py b/tests/test_clients/test_pubmed_client.py → ...ration/test_clients/test_pubmed_client.py
diff --git a/tests/test_evaluation/__init__.py → ...s/integration/test_evaluation/__init__.py b/tests/test_evaluation/__init__.py → ...s/integration/test_evaluation/__init__.py
diff --git a/tests/test_evaluation/test_eval_ctd.py → ...egration/test_evaluation/test_eval_ctd.py b/tests/test_evaluation/test_eval_ctd.py → ...egration/test_evaluation/test_eval_ctd.py
diff --git a/...s/test_evaluation/test_eval_drugmechdb.py → ...n/test_evaluation/test_eval_drugmechdb.py b/...s/test_evaluation/test_eval_drugmechdb.py → ...n/test_evaluation/test_eval_drugmechdb.py
diff --git a/tests/test_evaluation/test_eval_go.py → ...tegration/test_evaluation/test_eval_go.py b/tests/test_evaluation/test_eval_go.py → ...tegration/test_evaluation/test_eval_go.py
diff --git a/tests/test_evaluation/test_eval_hpoa.py → ...gration/test_evaluation/test_eval_hpoa.py b/tests/test_evaluation/test_eval_hpoa.py → ...gration/test_evaluation/test_eval_hpoa.py
diff --git a/tests/test_exporters/__init__.py → ...ration/test_knowledge_engines/__init__.py b/tests/test_exporters/__init__.py → ...ration/test_knowledge_engines/__init__.py
diff --git a/tests/test_knowledge_engines/test_cases.py → ...tion/test_knowledge_engines/test_cases.py b/tests/test_knowledge_engines/test_cases.py → ...tion/test_knowledge_engines/test_cases.py
diff --git a/...knowledge_engines/test_generalizations.py → ...knowledge_engines/test_generalizations.py b/...knowledge_engines/test_generalizations.py → ...knowledge_engines/test_generalizations.py
diff --git a/...est_knowledge_engines/test_halo_engine.py → ...est_knowledge_engines/test_halo_engine.py b/...est_knowledge_engines/test_halo_engine.py → ...est_knowledge_engines/test_halo_engine.py
diff --git a/...t_knowledge_engines/test_spires_engine.py → ...t_knowledge_engines/test_spires_engine.py b/...t_knowledge_engines/test_spires_engine.py → ...t_knowledge_engines/test_spires_engine.py