Merge branch 'develop' into SYNPY-1794

Author: andrewelamb

.github/workflows/build.yml

@@ -84,7 +84,7 @@ jobs:
           path: |
             ${{ steps.get-dependencies.outputs.site_packages_loc }}
             ${{ steps.get-dependencies.outputs.site_bin_dir }}
-          key: ${{ runner.os }}-${{ matrix.python }}-build-${{ env.cache-name }}-${{ hashFiles('setup.py') }}-v32
+          key: ${{ runner.os }}-${{ matrix.python }}-build-${{ env.cache-name }}-${{ hashFiles('setup.py', 'setup.cfg') }}-v33
 
       - name: Install py-dependencies
         if: steps.cache-dependencies.outputs.cache-hit != 'true'
@@ -209,6 +209,7 @@ jobs:
 
             # Run only the failed tests
             pytest -sv --reruns 3 --cov-append --cov=. --cov-report xml \
+              --html=integration-test-report.html --self-contained-html \
               --junit-xml=test-results.xml \
               -n 8 --dist loadscope \
               $(cat failed_tests.txt | tr '\n' ' ')
@@ -217,12 +218,13 @@ jobs:
 
             # use loadscope to avoid issues running tests concurrently that share scoped fixtures
             pytest -sv --reruns 3 --cov-append --cov=. --cov-report xml \
+              --html=integration-test-report.html --self-contained-html \
               --junit-xml=test-results.xml \
               tests/integration -n 8 $IGNORE_FLAGS --dist loadscope
           fi
 
           # Execute the CLI tests in a non-dist way because they were causing some test instability when being run concurrently
-          pytest -sv --reruns 3 --cov-append --cov=. --cov-report xml tests/integration/synapseclient/test_command_line_client.py
+          pytest -sv --reruns 3 --cov-append --cov=. --cov-report xml --html=cli-test-report.html --self-contained-html tests/integration/synapseclient/test_command_line_client.py
 
       - name: Extract Failed Tests
         if: always() && steps.integration_tests.outcome == 'failure'
@@ -292,6 +294,17 @@ jobs:
           echo "::error::Integration tests failed after ${{ github.run_attempt }} attempt(s)"
           exit 1
 
+      - name: Upload integration test HTML report
+      # make sure report always gets uploaded if the integration tests ran, even if they failed, but skip if the integration tests were skipped
+        if: always() && steps.integration_tests.outcome != 'skipped'
+        uses: actions/upload-artifact@v4
+        with:
+          name: integration-test-report-${{ matrix.os }}-${{ matrix.python }}
+          path: |
+            integration-test-report.html
+            cli-test-report.html
+          retention-days: 14
+
       - name: Upload coverage report
         id: upload_coverage_report
         uses: actions/upload-artifact@v4

setup.cfg

@@ -72,6 +72,7 @@ tests_require =
     pytest-rerunfailures~=12.0
     func-timeout~=4.3
     pytest-cov~=4.1.0
+    pytest-html~=4.1.0
     pandas>=1.5,<3.0
 
 [options.extras_require]
@@ -85,6 +86,7 @@ dev =
     pytest-rerunfailures~=12.0
     func-timeout~=4.3
     pytest-cov~=4.1.0
+    pytest-html~=4.1.0
     black
     pre-commit
     filelock>=3.20.3
@@ -100,6 +102,7 @@ tests =
     pytest-rerunfailures~=12.0
     func-timeout~=4.3
     pytest-cov~=4.1.0
+    pytest-html~=4.1.0
     pandas>=1.5,<3.0
     jsonschema>=4.23.0
 

tests/integration/conftest.py

@@ -238,4 +238,3 @@ def wrap_with_otel(request):
         finally:
             for processor in active_span_processors:
                 processor.force_flush()
-            span.end()

tests/integration/synapseclient/models/async/test_json_schema_async.py

@@ -309,7 +309,7 @@ async def _get_derived_keys():
 
             response = await wait_for_condition(
                 _get_derived_keys,
-                timeout_seconds=30,
+                timeout_seconds=60,
                 poll_interval_seconds=2,
                 description="schema derived keys to be populated",
             )
@@ -373,7 +373,7 @@ async def _validate_invalid():
 
             response = await wait_for_condition(
                 _validate_invalid,
-                timeout_seconds=30,
+                timeout_seconds=60,
                 poll_interval_seconds=2,
                 description="schema validation results (invalid) to be available",
             )

tests/integration/synapseclient/models/async/test_recordset_async.py

@@ -637,9 +637,10 @@ async def test_get_validation_results_with_default_location_async(
             "expected type: String, found: Null"
             in results_df.loc[2, "validation_error_message"]
         ), f"Row 2 should have null type error, got: {results_df.loc[2, 'validation_error_message']}"
-        assert "#/name: expected type: String, found: Null" in str(
-            results_df.loc[2, "all_validation_messages"]
-        ), f"Row 2 all_validation_messages incorrect: {results_df.loc[2, 'all_validation_messages']}"
+        ##TODO: uncomment the test after PLFM-9532 is resolved
+        # assert "#/name: expected type: String, found: Null" in str(
+        #     results_df.loc[2, "all_validation_messages"]
+        # ), f"Row 2 all_validation_messages incorrect: {results_df.loc[2, 'all_validation_messages']}"
 
         # AND row 3 should be invalid (multiple violations: minLength, maximum, enum)
         assert (
@@ -648,18 +649,18 @@ async def test_get_validation_results_with_default_location_async(
         assert (
             "3 schema violations found" in results_df.loc[3, "validation_error_message"]
         ), f"Row 3 should have 3 violations, got: {results_df.loc[3, 'validation_error_message']}"
-        all_msgs_3 = str(results_df.loc[3, "all_validation_messages"])
-        assert (
-            "#/name: expected minLength: 3, actual: 2" in all_msgs_3
-        ), f"Row 3 should have minLength violation: {all_msgs_3}"
-        assert (
-            "#/value: 1500 is not less or equal to 1000" in all_msgs_3
-            or "1500" in all_msgs_3
-        ), f"Row 3 should have maximum violation: {all_msgs_3}"
-        assert (
-            "#/category: X is not a valid enum value" in all_msgs_3
-            or "enum" in all_msgs_3.lower()
-        ), f"Row 3 should have enum violation: {all_msgs_3}"
+        # all_msgs_3 = str(results_df.loc[3, "all_validation_messages"])
+        # assert (
+        #     "#/name: expected minLength: 3, actual: 2" in all_msgs_3
+        # ), f"Row 3 should have minLength violation: {all_msgs_3}"
+        # assert (
+        #     "#/value: 1500 is not less or equal to 1000" in all_msgs_3
+        #     or "1500" in all_msgs_3
+        # ), f"Row 3 should have maximum violation: {all_msgs_3}"
+        # assert (
+        #     "#/category: X is not a valid enum value" in all_msgs_3
+        #     or "enum" in all_msgs_3.lower()
+        # ), f"Row 3 should have enum violation: {all_msgs_3}"
 
         # AND row 4 should be invalid (value below minimum)
         assert (
@@ -669,9 +670,9 @@ async def test_get_validation_results_with_default_location_async(
             "-50.0 is not greater or equal to 0"
             in results_df.loc[4, "validation_error_message"]
         ), f"Row 4 should have minimum violation, got: {results_df.loc[4, 'validation_error_message']}"
-        assert "#/value: -50.0 is not greater or equal to 0" in str(
-            results_df.loc[4, "all_validation_messages"]
-        ), f"Row 4 all_validation_messages incorrect: {results_df.loc[4, 'all_validation_messages']}"
+        # assert "#/value: -50.0 is not greater or equal to 0" in str(
+        #     results_df.loc[4, "all_validation_messages"]
+        # ), f"Row 4 all_validation_messages incorrect: {results_df.loc[4, 'all_validation_messages']}"
 
     async def test_get_validation_results_with_custom_location_async(
         self, record_set_with_validation_fixture: RecordSet
@@ -719,9 +720,9 @@ async def test_get_validation_results_with_custom_location_async(
             assert pd.notna(
                 row["validation_error_message"]
             ), f"Row {idx} is marked invalid but has no validation_error_message"
-            assert pd.notna(
-                row["all_validation_messages"]
-            ), f"Row {idx} is marked invalid but has no all_validation_messages"
+            # assert pd.notna(
+            #     row["all_validation_messages"]
+            # ), f"Row {idx} is marked invalid but has no all_validation_messages"
 
     async def test_get_validation_results_no_file_handle_emits_warning_async(
         self, syn_with_logger: Synapse, caplog: pytest.LogCaptureFixture

tests/integration/synapseclient/models/async/test_virtualtable_async.py

@@ -4,6 +4,7 @@
 
 import pandas as pd
 import pytest
+import pytest_asyncio
 
 from synapseclient import Synapse
 from synapseclient.core.exceptions import SynapseHTTPError
@@ -149,12 +150,12 @@ async def test_virtual_table_lifecycle(self, project_model: Project) -> None:
 
 
 class TestVirtualTableWithDataOperations:
-    @pytest.fixture(autouse=True, scope="function")
+    @pytest_asyncio.fixture(autouse=True, scope="function")
     def init(self, syn: Synapse, schedule_for_cleanup: Callable[..., None]) -> None:
         self.syn = syn
         self.schedule_for_cleanup = schedule_for_cleanup
 
-    @pytest.fixture(scope="class")
+    @pytest_asyncio.fixture(scope="class")
     async def base_table_with_data(
         self,
         project_model: Project,