style corrections

mantis/tests/test_analysis/test_affine.py

@@ -59,6 +59,7 @@ def test_3d_translation():
         result[3:10, 0:9, 0:6] == 1
     )  # Test if the shifts where going to the right direction
 
+
 @pytest.mark.parametrize(
     "function_to_test, parameters",
     [
@@ -88,4 +89,3 @@ def test_3d_translation():
 def test_error(function_to_test, parameters):
     with pytest.raises(ValueError):
         function_to_test(**parameters)
-

mantis/tests/test_analysis/test_analysis_settings.py

@@ -151,4 +151,4 @@ def test_example_stabilize_timelapse_settings(example_stabilize_timelapse_settin
 )
 def test_derror(class_to_test, parameters):
     with pytest.raises(ValueError):
-        class_to_test(**parameters)
+        class_to_test(**parameters)

mantis/tests/test_analysis/test_deskew.py

@@ -9,6 +9,7 @@
     get_deskewed_data_shape,
 )
 
+
 def test_average_n_slices():
     data = np.array(
         [[[1, 2], [3, 4]], [[5, 6], [7, 8]], [[9, 10], [11, 12]], [[13, 14], [15, 16]]]
@@ -88,4 +89,3 @@ def test_deskew_data():
 def test_error(function_to_test, parameters):
     with pytest.raises(ValueError):
         function_to_test(**parameters)
-

mantis/tests/test_analysis/test_stich.py

@@ -1,17 +1,16 @@
 import tempfile
 
 from pathlib import Path
-import dask.array as da
+from unittest.mock import patch
+
 import numpy as np
 import pandas as pd
 import pytest
-import zarr
 
 from iohub import open_ome_zarr
 
 from mantis.analysis.AnalysisSettings import ProcessingSettings
 from mantis.analysis.stitch import (
-    _stitch_images,
     blend,
     cleanup_shifts,
     compute_total_translation,
@@ -24,7 +23,6 @@
     preprocess_and_shift,
     process_dataset,
     shift_image,
-    stitch_shifted_store,
 )
 
 
@@ -137,7 +135,6 @@ def test_compute_total_translation():
     assert "biahub" in str(record.list[0].message), "Deprecation warning was not found."
 
 
-
 def test_cleanup_shifts():
     csv_filepath = '/fake/path/to/shifts.csv'
     pixel_size_um = 0.5

mantis/tests/test_cli/test_deskew_cli.py

@@ -31,4 +31,3 @@ def test_deskew_cli(tmp_path, example_plate, example_deskew_settings):
     assert output_path.exists()
     assert result.exit_code == 0
     assert "biahub" in str(record.list[0].message), "Deprecation warning was not found."
-

mantis/tests/test_cli/test_estimate_bleaching_cli.py

@@ -26,4 +26,3 @@ def test_estimate_bleaching_cli(tmp_path, example_plate):
     assert output_path.exists()
     assert result.exit_code == 0
     assert "biahub" in str(record.list[0].message), "Deprecation warning was not found."
-

mantis/tests/test_cli/test_register_cli.py

@@ -1,7 +1,6 @@
 import numpy as np
 import pytest
 
-
 from click.testing import CliRunner
 from numpy import testing
 

mantis/tests/test_cli/test_update_scale_metadata.py

@@ -1,6 +1,7 @@
-import pytest
 import os
 
+import pytest
+
 from click.testing import CliRunner
 
 from mantis.cli.main import cli