Update tests

.gitignore

@@ -148,5 +148,8 @@ tags
 # prefect artifacts
 .prefectignore
 
+# test assets
+test/input_files/*/Assets/*
+
 # Dask
 dask-worker-space/

helper_scripts/hedwig_reg_listen.sh

@@ -41,7 +41,7 @@ fi
 
 # start worker specific to THAT venv
 WFLOWS="$HEDWIG_HOME/image_portal_workflows/em_workflows"
-WORKPOOL=default-pool
+WORKPOOL=workpool
 
 if [[ $ACTION == "listen" ]]; then
 	printf "\nStarting $HEDWIG_ENV Worker\n"

test/conftest.py

@@ -83,8 +83,8 @@ def _mock_bioformats_gen_zarr(file_path: FilePath, *a, **kw):
     monkeypatch.setattr(ng, "bioformats_gen_zarr", _mock_bioformats_gen_zarr)
 
 
-@pytest.fixture
-def prefect_test():
+@pytest.fixture(autouse=True, scope="session")
+def prefect_test_fixture():
     """
     Reference: https://docs.prefect.io/2.13.5/guides/testing/
     """

test/input_files/.gitattributes

@@ -5,3 +5,4 @@
 *jpeg filter=lfs diff=lfs merge=lfs -text
 *jpg filter=lfs diff=lfs merge=lfs -text
 *.mrc filter=lfs diff=lfs merge=lfs -text
+*.czi filter=lfs diff=lfs merge=lfs -text

test/test_czi.py

@@ -48,12 +48,12 @@ def test_no_mount_point_flow_fails(mock_binaries, monkeypatch, caplog):
 
     monkeypatch.setattr(config, "NFS_MOUNT", _mock_NFS_MOUNT)
 
-    state = czi_flow(
-        file_share=share_name,
-        input_dir="test/input_files/IF_czi/Projects/smaller",
-        no_api=True,
-    )
-    assert not state.is_successful()
+    with pytest.raises(RuntimeError):
+        czi_flow(
+            file_share=share_name,
+            input_dir="test/input_files/IF_czi/Projects/smaller",
+            no_api=True,
+        )
     assert f"{share_name} doesn't exist. Failing!" in caplog.text, caplog.text
 
 
@@ -66,7 +66,7 @@ def test_czi_workflow_callback_structure(
     """
     from em_workflows.czi.flow import czi_flow
 
-    input_dir = "test/input_files/IF_czi/Projects/smaller"
+    input_dir = "test/input_files/IF_czi/Projects/Cropped_Image"
     if not Path(input_dir).exists():
         pytest.skip("Missing input files")
 

test/test_dm.py

@@ -14,6 +14,7 @@ def test_dm4_conv(mock_nfs_mount):
         file_share="test",
         input_dir="/test/input_files/dm_inputs/Projects/Lab/PI",
         no_api=True,
+        return_state=True,
     )
     assert state.is_completed()
 
@@ -29,6 +30,7 @@ def test_dm4_conv_clean_workdir(mock_nfs_mount):
             file_name="20210525_1416_A000_G000.dm4",
             no_api=True,
             keep_workdir=False,
+            return_state=True,
         )
         assert state.is_completed()
     # keep_workdir = False removes the workdir
@@ -41,6 +43,7 @@ def test_dm4_conv_clean_workdir(mock_nfs_mount):
             file_name="20210525_1416_A000_G000.dm4",
             no_api=True,
             keep_workdir=True,
+            return_state=True,
         )
         assert state.is_completed()
     # keep_workdir keeps the workdir