mend

tdc/resource/cellxgene_census.py

@@ -2,7 +2,7 @@
 import os
 
 os.environ['KMP_DUPLICATE_LIB_OK'] = "TRUE"
-# TODO: remove 
+# TODO: remove
 import cellxgene_census
 import gget
 import tiledbsoma
@@ -13,14 +13,15 @@ class CensusResource:
     _CENSUS_DATA = "census_data"
     _CENSUS_META = "census_info"
     _FEATURE_PRESENCE = "feature_dataset_presence_matrix"
-    _LATEST_CENSUS = "2023-12-15" # TODO: maybe change to 'latest'
+    _LATEST_CENSUS = "2023-12-15"  # TODO: maybe change to 'latest'
     _HUMAN = "homo_sapiens"
 
     class decorators:
 
         @classmethod
         def check_dataset_is_census_data(cls, func):
             """Sets self.dataset to census_data"""
+
             def check(*args, **kwargs):
                 self = args[0]
                 self.dataset = self._CENSUS_DATA
@@ -31,6 +32,7 @@ def check(*args, **kwargs):
         @classmethod
         def check_dataset_is_census_info(cls, func):
             """Sets self.dataset to census_data"""
+
             def check(*args, **kwargs):
                 self = args[0]
                 self.dataset = self._CENSUS_META
@@ -46,9 +48,11 @@ def slice_checks_X_and_FM(cls, func):
             3. functions requiring a measurement name provide a measurement name
             4. fmt is a valid format
             asserts these requirements hold in input arguments."""
+
             def check(*args, **kwargs):
                 if "upper" in kwargs:
-                    upper, lower = kwargs.get('upper', None), kwargs.get("lower", None)
+                    upper, lower = kwargs.get('upper',
+                                              None), kwargs.get("lower", None)
                     if upper is None or lower is None:
                         raise Exception(
                             "No upper and/or lower bound for slicing was provided. Dataset is too large to fit in memory. \
@@ -57,18 +61,22 @@ def check(*args, **kwargs):
                 fmt = fmt if fmt is not None else "pandas"
                 if "todense" in kwargs:
                     todense = kwargs.get("todense")
-                    kwargs["todense"] = todense if todense is not None else False
+                    kwargs[
+                        "todense"] = todense if todense is not None else False
                     if todense and fmt != "scipy":
                         raise ValueError(
-                            "dense representation only available in scipy format")
+                            "dense representation only available in scipy format"
+                        )
                 measurement_name = kwargs.get("measurement_name")
                 if measurement_name is None:
                     raise Exception("measurement_name was not provided.")
                 elif fmt is not None and fmt not in ["scipy", "pyarrow"]:
                     raise ValueError(
-                        "measurement_matrix only supports 'scipy' or 'pyarrow' format")
+                        "measurement_matrix only supports 'scipy' or 'pyarrow' format"
+                    )
                 kwargs["fmt"] = fmt if fmt is not None else "pandas"
                 return func(*args, **kwargs)
+
             return check
 
     def __init__(self, census_version=None, organism=None):
@@ -238,7 +246,7 @@ def get_cell_count_metadata(self):
                 census_version=self.census_version) as census:
             return census[self.dataset]["summary_cell_counts"]
 
-    @decorators.slice_checks_X_and_FM 
+    @decorators.slice_checks_X_and_FM
     @decorators.check_dataset_is_census_data
     def query_measurement_matrix(self,
                                  value_filter=None,

tdc/test/test_resources.py

@@ -1,16 +1,19 @@
 import os
 import sys
+
 sys.path.append(
     os.path.abspath(os.path.join(os.path.dirname(__file__), "../..")))
 import unittest
 
 from pandas import DataFrame
-# from pyarrow import SparseCOOTensor 
+# from pyarrow import SparseCOOTensor
 from tdc.resource import cellxgene_census
 
+
 class TestResources(unittest.TestCase):
     pass
 
+
 class TestCellXGene(unittest.TestCase):
 
     def setUp(self):
@@ -19,33 +22,40 @@ def setUp(self):
         self.gene_column_names = ["feature_name", "feature_length"]
         self.cell_value_filter = "tissue == 'brain' and sex == 'male'"
         self.cell_column_names = ["assay", "cell_type", "tissue"]
-        
+
     def test_get_cell_metadata(self):
-        obsdf = self.resource.get_cell_metadata(value_filter=self.cell_value_filter,
-                                        column_names=self.cell_column_names,
-                                        fmt="pandas")
+        obsdf = self.resource.get_cell_metadata(
+            value_filter=self.cell_value_filter,
+            column_names=self.cell_column_names,
+            fmt="pandas")
         assert isinstance(obsdf, DataFrame)
-        
+
     def test_get_gene_metadata(self):
-        varpyarrow = self.resource.get_gene_metadata(value_filter=self.gene_value_filter,
-                                                column_names=self.gene_column_names,
-                                                fmt="pyarrow",
-                                                measurement_name="RNA")
+        varpyarrow = self.resource.get_gene_metadata(
+            value_filter=self.gene_value_filter,
+            column_names=self.gene_column_names,
+            fmt="pyarrow",
+            measurement_name="RNA")
         print(varpyarrow)
-        # assert isinstance(varpyarrow, SparseCOOTensor) 
-        
+        # assert isinstance(varpyarrow, SparseCOOTensor)
+
     def test_get_measurement_matrix(self):
         Xslice = self.resource.get_measurement_matrix(upper=5,
-                                                lower=0,
-                                                measurement_name="RNA",
-                                                fmt="scipy",
-                                                todense=True)
+                                                      lower=0,
+                                                      measurement_name="RNA",
+                                                      fmt="scipy",
+                                                      todense=True)
         print("x", Xslice)
-        
+
     def test_get_feature_dataset_presence_matrix(self):
         FMslice = self.resource.get_feature_dataset_presence_matrix(
-            upper=5, lower=0, measurement_name="RNA", fmt="pyarrow", todense=False)
+            upper=5,
+            lower=0,
+            measurement_name="RNA",
+            fmt="pyarrow",
+            todense=False)
         print("f", FMslice)
-
+
+
 if __name__ == "__main__":
-    unittest.main()
+    unittest.main()