Drop all zarr_urls=[] for converter tasks from tests

Author: tcompa

examples/01_cardio_tiny_dataset/run_workflow.py

@@ -62,7 +62,6 @@
 
 # Create zarr structure
 parallelization_list = cellvoyager_to_ome_zarr_init(
-    zarr_urls=[],
     zarr_dir=zarr_dir,
     image_dirs=[img_path],
     allowed_channels=allowed_channels,

examples/02_cardio_tiny_mip/run_workflow.py

@@ -67,7 +67,6 @@
 
 # Create zarr structure
 parallelization_list = cellvoyager_to_ome_zarr_init(
-    zarr_urls=[],
     zarr_dir=zarr_dir,
     image_dirs=[img_path],
     allowed_channels=allowed_channels,

tests/tasks/test_executable_workflow.py

@@ -58,7 +58,6 @@ def test_workflow_yokogawa_to_ome_zarr(tmp_path: Path, zenodo_images: str):
 
     # Create zarr structure
     args_create_zarr = dict(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         image_dirs=[img_path],
         allowed_channels=allowed_channels,

tests/tasks/test_import_ome_zarr.py

@@ -32,7 +32,6 @@ def test_import_ome_zarr_plate(tmp_path, zenodo_zarr):
 
     # Run import_ome_zarr
     image_list_changes = import_ome_zarr(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         zarr_name=zarr_name,
         grid_y_shape=3,
@@ -86,7 +85,6 @@ def test_import_ome_zarr_well(tmp_path, zenodo_zarr):
 
     # Run import_ome_zarr
     image_list_changes = import_ome_zarr(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         zarr_name=zarr_name,
         grid_y_shape=3,
@@ -131,7 +129,6 @@ def test_import_ome_zarr_image(tmp_path, zenodo_zarr, reset_omero):
 
     # Run import_ome_zarr
     image_list_changes = import_ome_zarr(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         zarr_name=zarr_name,
         grid_y_shape=3,
@@ -198,7 +195,6 @@ def test_import_ome_zarr_image_wrong_channels(tmp_path, zenodo_zarr):
     # Run import_ome_zarr and catch the error
     with pytest.raises(ValueError) as e:
         _ = import_ome_zarr(
-            zarr_urls=[],
             zarr_dir=zarr_dir,
             zarr_name=zarr_name,
             grid_y_shape=3,
@@ -217,7 +213,6 @@ def test_import_ome_zarr_plate_no_ROI_tables(tmp_path, zenodo_zarr):
 
     # Run import_ome_zarr
     image_list_changes = import_ome_zarr(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         zarr_name=zarr_name,
         add_image_ROI_table=False,
@@ -297,7 +292,6 @@ def test_import_ome_zarr_image_BIA(tmp_path):
 
     # Run import_ome_zarr
     image_list_changes = import_ome_zarr(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         zarr_name=zarr_name,
         grid_y_shape=3,

tests/tasks/test_registration.py

@@ -266,7 +266,6 @@ def test_multiplexing_registration(
 
     # # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init_multiplex(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         acquisitions=acquisitions,
         num_levels=num_levels,
@@ -472,7 +471,6 @@ def test_multiplexing_registration_3d(
 
     # # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init_multiplex(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         acquisitions=acquisitions,
         num_levels=num_levels,

tests/tasks/test_unit_1536_well_conversion.py

@@ -55,7 +55,6 @@ def test_1536_ome_zarr_conversion(tmp_path: Path, syn_1536_images: str):
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         image_dirs=[syn_1536_images],
         allowed_channels=allowed_channels,
@@ -118,7 +117,6 @@ def test_1536_multiplexing_ome_zarr_conversion(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init_multiplex(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         acquisitions={"0": acquisition_1, "1": acquisition_2},
         image_extension="png",

tests/tasks/test_unit_task.py

@@ -22,7 +22,7 @@ def test_create_ome_zarr(tmp_path, testdata_path):
     debug(args)
 
     dummy = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[], zarr_dir=zarr_dir, image_dirs=[img_path], **args
+        zarr_dir=zarr_dir, image_dirs=[img_path], **args
     )
     debug(dummy)
 

tests/tasks/test_workflows.py

@@ -83,7 +83,6 @@ def test_create_ome_zarr_fail(tmp_path: Path, zenodo_images: str):
     # Create zarr structure
     with pytest.raises(ValueError):
         _ = cellvoyager_to_ome_zarr_init(
-            zarr_urls=[],
             zarr_dir=zarr_dir,
             image_dirs=[image_dir],
             allowed_channels=tmp_allowed_channels,
@@ -104,7 +103,6 @@ def test_create_ome_zarr_no_images(
     """
     with pytest.raises(ValueError):
         cellvoyager_to_ome_zarr_init(
-            zarr_urls=[],
             zarr_dir=str(tmp_path / "output"),
             image_dirs=[zenodo_images],
             allowed_channels=allowed_channels,
@@ -115,7 +113,6 @@ def test_create_ome_zarr_no_images(
         )
     with pytest.raises(ValueError):
         cellvoyager_to_ome_zarr_init(
-            zarr_urls=[],
             zarr_dir=str(tmp_path / "output"),
             image_dirs=[zenodo_images],
             allowed_channels=allowed_channels,
@@ -155,7 +152,6 @@ def test_yokogawa_to_ome_zarr(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[],
         zarr_dir=str(output_path),
         image_dirs=[str(img_path)],
         allowed_channels=allowed_channels,
@@ -212,7 +208,6 @@ def test_yokogawa_to_ome_zarr(
 
     # Re-run (with overwrite=True for the init task)
     parallelization_list = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[],
         zarr_dir=str(output_path),
         image_dirs=[str(img_path)],
         allowed_channels=allowed_channels,
@@ -232,7 +227,6 @@ def test_yokogawa_to_ome_zarr(
     # Re-run (with overwrite=False for the init task) and fail
     with pytest.raises(OverwriteNotAllowedError):
         cellvoyager_to_ome_zarr_init(
-            zarr_urls=[],
             zarr_dir=str(output_path),
             image_dirs=[str(img_path)],
             allowed_channels=allowed_channels,
@@ -253,7 +247,6 @@ def test_2D_cellvoyager_to_ome_zarr(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[],
         zarr_dir=str(output_path),
         image_dirs=[zenodo_images],
         allowed_channels=allowed_channels,
@@ -484,7 +477,6 @@ def test_MIP_subset_of_images(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[],
         zarr_dir=str(zarr_dir),
         image_dirs=[zenodo_images],
         allowed_channels=allowed_channels,
@@ -554,7 +546,6 @@ def test_illumination_correction(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[],
         zarr_dir=str(zarr_dir),
         image_dirs=[str(img_path)],
         image_extension="png",
@@ -606,7 +597,6 @@ def test_yokogawa_to_ome_zarr_multiplate(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[],
         zarr_dir=str(output_path),
         image_dirs=[img_path_1, img_path_2],
         allowed_channels=allowed_channels,
@@ -671,7 +661,6 @@ def test_cellvoyager_converter_exclusion_patterns(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[],
         zarr_dir=str(output_path),
         image_dirs=[zenodo_images],
         allowed_channels=allowed_channels,

tests/tasks/test_workflows_cellpose_segmentation.py

@@ -451,7 +451,6 @@ def test_workflow_with_per_well_labeling_2D(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init(
-        zarr_urls=[],
         zarr_dir=str(zarr_dir),
         image_dirs=[str(img_path)],
         image_extension="png",

tests/tasks/test_workflows_multiplexing.py

@@ -82,7 +82,6 @@ def test_multiplexing_create_ome_zarr_fail(
     debug(zenodo_images_multiplex)
     with pytest.raises(ValueError):
         _ = cellvoyager_to_ome_zarr_init_multiplex(
-            zarr_urls=[],
             zarr_dir=zarr_dir,
             acquisitions=acquisitions,
             num_levels=num_levels,
@@ -132,7 +131,6 @@ def test_multiplexing_compute(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init_multiplex(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         acquisitions=acquisitions,
         num_levels=num_levels,
@@ -145,7 +143,6 @@ def test_multiplexing_compute(
 
     # Run again, with overwrite=True
     parallelization_list_2 = cellvoyager_to_ome_zarr_init_multiplex(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         acquisitions=acquisitions,
         num_levels=num_levels,
@@ -159,7 +156,6 @@ def test_multiplexing_compute(
     # Run again, with overwrite=False
     with pytest.raises(OverwriteNotAllowedError):
         _ = cellvoyager_to_ome_zarr_init_multiplex(
-            zarr_urls=[],
             zarr_dir=zarr_dir,
             acquisitions=acquisitions,
             num_levels=num_levels,
@@ -246,7 +242,6 @@ def test_non_int_acquisition_key(
     # Create zarr structure
     with pytest.raises(ValueError):
         cellvoyager_to_ome_zarr_init_multiplex(
-            zarr_urls=[],
             zarr_dir=zarr_dir,
             acquisitions=acquisitions,
             num_levels=num_levels,
@@ -275,7 +270,6 @@ def test_multiplexing_arbitrary_acquisition_names(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init_multiplex(
-        zarr_urls=[],
         zarr_dir=zarr_dir,
         acquisitions=acquisitions,
         num_levels=num_levels,
@@ -373,7 +367,6 @@ def test_multiplexing_MIP(
 
     # Create zarr structure
     parallelization_list = cellvoyager_to_ome_zarr_init_multiplex(
-        zarr_urls=[],
         zarr_dir=str(zarr_dir),
         acquisitions=acquisitions,
         num_levels=num_levels,