Refactor/apply isort linting checks

docs/conf.py

@@ -12,9 +12,10 @@
 #
 import os
 import sys
-import dunamai
 from datetime import date
 
+import dunamai
+
 sys.path.insert(0, os.path.abspath(".."))
 
 # Ignore rules regarding import order which is required for sphinx build process

pycytominer/__init__.py

@@ -1,6 +1,7 @@
+from pycytominer import __about__
+
 from .aggregate import aggregate
 from .annotate import annotate
+from .consensus import consensus
 from .feature_select import feature_select
 from .normalize import normalize
-from .consensus import consensus
-from pycytominer import __about__

pycytominer/aggregate.py

@@ -4,10 +4,11 @@
 
 import numpy as np
 import pandas as pd
+
 from pycytominer.cyto_utils import (
-    output,
     check_aggregate_operation,
     infer_cp_features,
+    output,
 )
 
 

pycytominer/annotate.py

@@ -3,14 +3,16 @@
 """
 
 import os
+
 import pandas as pd
+
 from pycytominer.cyto_utils import (
-    output,
+    annotate_cmap,
+    cp_clean,
     infer_cp_features,
     load_platemap,
     load_profiles,
-    annotate_cmap,
-    cp_clean,
+    output,
 )
 
 

pycytominer/consensus.py

@@ -4,10 +4,10 @@
 
 from pycytominer import aggregate
 from pycytominer.cyto_utils import (
-    output,
-    modz,
-    load_profiles,
     check_consensus_operation,
+    load_profiles,
+    modz,
+    output,
 )
 
 

pycytominer/feature_select.py

@@ -2,18 +2,18 @@
 Select features to use in downstream analysis based on specified selection method
 """
 
+from pycytominer.cyto_utils import (
+    drop_outlier_features,
+    get_blocklist_features,
+    infer_cp_features,
+    load_profiles,
+    output,
+)
 from pycytominer.operations import (
     correlation_threshold,
-    variance_threshold,
     get_na_columns,
     noise_removal,
-)
-from pycytominer.cyto_utils import (
-    load_profiles,
-    output,
-    get_blocklist_features,
-    infer_cp_features,
-    drop_outlier_features,
+    variance_threshold,
 )
 
 

pycytominer/normalize.py

@@ -3,10 +3,10 @@
 """
 
 import pandas as pd
-from sklearn.preprocessing import StandardScaler, RobustScaler
+from sklearn.preprocessing import RobustScaler, StandardScaler
 
-from pycytominer.cyto_utils import output, infer_cp_features, load_profiles
-from pycytominer.operations import Spherize, RobustMAD
+from pycytominer.cyto_utils import infer_cp_features, load_profiles, output
+from pycytominer.operations import RobustMAD, Spherize
 
 
 def normalize(

pycytominer/operations/__init__.py

@@ -1,5 +1,5 @@
 from .correlation_threshold import correlation_threshold
-from .variance_threshold import variance_threshold, calculate_frequency
 from .get_na_columns import get_na_columns
-from .transform import Spherize, RobustMAD
 from .noise_removal import noise_removal
+from .transform import RobustMAD, Spherize
+from .variance_threshold import calculate_frequency, variance_threshold

pycytominer/operations/correlation_threshold.py

@@ -4,9 +4,9 @@
 """
 
 from pycytominer.cyto_utils import (
-    infer_cp_features,
-    get_pairwise_correlation,
     check_correlation_method,
+    get_pairwise_correlation,
+    infer_cp_features,
 )
 
 

pycytominer/operations/variance_threshold.py

@@ -4,6 +4,7 @@
 """
 
 import numpy as np
+
 from pycytominer.cyto_utils import infer_cp_features
 
 

pyproject.toml

@@ -146,7 +146,7 @@ select = [
     # flake8-bugbear
     # "B",
     # isort
-    # "I",
+    "I",
     # mccabe
     # "C90",
     # tryceratops
@@ -163,6 +163,7 @@ ignore = [
 # Ignore `E402` and `F401` (unusued imports) in all `__init__.py` files
 "__init__.py" = ["E402", "F401"]
 "tests/*" = ["S101"] # Ignore assert statements in tests
+"pycytominer/cyto_utils/*" = ["I"] # Ignore isort in cyto_utils due to circular imports
 
 [tool.ruff.format]
 preview = true

tests/test_aggregate.py

@@ -1,8 +1,10 @@
 import os
 import tempfile
-import pytest
+
 import numpy as np
 import pandas as pd
+import pytest
+
 from pycytominer import aggregate
 from pycytominer.cyto_utils import infer_cp_features
 

tests/test_annotate.py

@@ -3,6 +3,7 @@
 import tempfile
 
 import pandas as pd
+
 from pycytominer.annotate import annotate
 
 random.seed(123)

tests/test_consensus.py

@@ -1,8 +1,10 @@
 import os
 import random
 import tempfile
+
 import numpy as np
 import pandas as pd
+
 from pycytominer import consensus
 
 random.seed(123)

tests/test_cyto_utils/conftest.py

@@ -3,10 +3,12 @@
 """
 
 import os
-import pandas as pd
 import pathlib
+
+import pandas as pd
 import pytest
 import sqlalchemy
+
 from pycytominer.cyto_utils.cell_locations import CellLocation
 
 

tests/test_cyto_utils/test_DeepProfiler_processing.py

@@ -3,20 +3,20 @@
 """
 
 import os
-import random
-import pytest
-import pandas as pd
 import pathlib
-import numpy.testing as npt
+import random
 
+import numpy.testing as npt
+import pandas as pd
+import pytest
 
+from pycytominer import normalize
+from pycytominer.cyto_utils import infer_cp_features
 from pycytominer.cyto_utils.DeepProfiler_processing import (
-    DeepProfilerData,
     AggregateDeepProfiler,
+    DeepProfilerData,
     SingleCellDeepProfiler,
 )
-from pycytominer import normalize
-from pycytominer.cyto_utils import infer_cp_features
 
 ROOT_DIR = pathlib.Path(__file__).parents[2]
 random.seed(42)

tests/test_cyto_utils/test_annotate_custom.py

@@ -1,8 +1,10 @@
 import os
-import tempfile
 import random
-import pytest
+import tempfile
+
 import pandas as pd
+import pytest
+
 from pycytominer import annotate
 
 random.seed(123)

tests/test_cyto_utils/test_cell_locations.py

@@ -1,11 +1,13 @@
 """This tests the output from CellLocation class"""
 
+from typing import List, Type
+
 import pandas as pd
 import pytest
-from typing import Type, List
-from pycytominer.cyto_utils.cell_locations import CellLocation
 from _pytest.fixtures import FixtureRequest
 
+from pycytominer.cyto_utils.cell_locations import CellLocation
+
 
 def get_metadata_input_dataframe(cell_loc: CellLocation) -> pd.DataFrame:
     """

tests/test_cyto_utils/test_cells.py

@@ -6,15 +6,16 @@
 import numpy as np
 import pandas as pd
 import pytest
+from sqlalchemy import create_engine
+from sqlalchemy.exc import OperationalError
+
 from pycytominer import aggregate, annotate, normalize
 from pycytominer.cyto_utils import (
     get_default_compartments,
     get_default_linking_cols,
     infer_cp_features,
 )
 from pycytominer.cyto_utils.cells import SingleCells, _sqlite_strata_conditions
-from sqlalchemy import create_engine
-from sqlalchemy.exc import OperationalError
 
 random.seed(123)
 

tests/test_cyto_utils/test_collate.py

@@ -1,8 +1,9 @@
 import os
 import pathlib
-import pytest
 
 import pandas as pd
+import pytest
+
 from pycytominer.cyto_utils.collate import collate
 
 # Set constants

tests/test_cyto_utils/test_cp_image_features.py

@@ -1,4 +1,5 @@
 import pandas as pd
+
 from pycytominer.cyto_utils import (
     aggregate_fields_count,
     aggregate_image_features,

tests/test_cyto_utils/test_feature_blocklist.py

@@ -1,5 +1,7 @@
 import pathlib
+
 import pandas as pd
+
 from pycytominer.cyto_utils.features import get_blocklist_features
 
 ROOT_DIR = pathlib.Path(__file__).parents[2]

tests/test_cyto_utils/test_feature_drop_outlier.py

@@ -1,4 +1,5 @@
 import pandas as pd
+
 from pycytominer.cyto_utils.features import drop_outlier_features
 
 # Build data to use in tests

tests/test_cyto_utils/test_feature_infer.py

@@ -1,7 +1,7 @@
-import pytest
 import pandas as pd
-from pycytominer.cyto_utils.features import infer_cp_features
+import pytest
 
+from pycytominer.cyto_utils.features import infer_cp_features
 
 data_df = pd.DataFrame({
     "Cells_Something_Something": [1, 3, 8, 5, 2, 2],

tests/test_cyto_utils/test_features_count_na.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pandas as pd
+
 from pycytominer.cyto_utils import count_na_features
 
 data_df = pd.DataFrame({

tests/test_cyto_utils/test_load.py

@@ -1,15 +1,17 @@
 import os
-import random
-import pytest
 import pathlib
+import random
 import tempfile
+
 import numpy as np
 import pandas as pd
+import pytest
+
 from pycytominer.cyto_utils import (
-    load_profiles,
-    load_platemap,
     load_npz_features,
     load_npz_locations,
+    load_platemap,
+    load_profiles,
 )
 from pycytominer.cyto_utils.load import infer_delim, is_path_a_parquet_file
 

tests/test_cyto_utils/test_modz.py

@@ -1,4 +1,5 @@
 import pandas as pd
+
 from pycytominer.cyto_utils import modz
 from pycytominer.cyto_utils.modz import modz_base
 

tests/test_cyto_utils/test_output.py

@@ -6,6 +6,7 @@
 
 import pandas as pd
 import pytest
+
 from pycytominer.cyto_utils.output import (
     check_compression_method,
     output,

tests/test_cyto_utils/test_single_cell_ingest_utils.py

@@ -1,8 +1,9 @@
 import pytest
+
 from pycytominer.cyto_utils import (
-    get_default_linking_cols,
-    get_default_compartments,
     assert_linking_cols_complete,
+    get_default_compartments,
+    get_default_linking_cols,
     provide_linking_cols_feature_name_update,
 )