Blackified

fah_xchem/compute/compound_series.py

@@ -11,32 +11,30 @@ class CompoundSeriesUpdate(BaseModel):
     Can include any set of fields as needed to update a CompoundSeries.
 
     """
+
     metadata: CompoundSeriesMetadata = None
     compounds: List[Compound] = None
     transformations: List[Transformation] = None
 
 
 class CompoundSeries(BaseModel):
-    """A compound series; the core object of operation in fah-xchem.
+    """A compound series; the core object of operation in fah-xchem."""
 
-    """
     metadata: CompoundSeriesMetadata = Field(
-        ...,
-        description="Metadata for the whole compound series"
+        ..., description="Metadata for the whole compound series"
     )
     compounds: List[Compound] = Field(
-        ...,
-        description="List of compounds comprising the compound series"
+        ..., description="List of compounds comprising the compound series"
     )
     transformations: List[Transformation] = Field(
         ...,
-        description="List of transformations performed between compounds within the compound series"
+        description="List of transformations performed between compounds within the compound series",
     )
 
     def update_experimental_data(
-            self,
-            metadata: List[CompoundMetadata],
-        ) -> None:
+        self,
+        metadata: List[CompoundMetadata],
+    ) -> None:
         """Update experimental data for compounds in the CompoundSeries.
 
         Compound instances in `self.compounds` will be replaced as necessary.
@@ -54,12 +52,14 @@ def update_experimental_data(
         for compound in self.compounds:
             metadata_update = metadata_d.get(compound.metadata.compound_id)
 
-            if metadata_update: 
+            if metadata_update:
                 metadata_current = compound.metadata.dict()
-                metadata_current['experimental_data'].update(metadata_update.experimental_data)
+                metadata_current["experimental_data"].update(
+                    metadata_update.experimental_data
+                )
 
                 compound_current = compound.dict()
-                compound_current['metadata'] = metadata_current
+                compound_current["metadata"] = metadata_current
 
                 new_compounds.append(Compound(**compound_current))
             else:

fah_xchem/external/base.py

@@ -7,20 +7,19 @@
 
 
 class ExternalData(BaseModel):
-    """Mixin class for external data interfaces.
+    """Mixin class for external data interfaces."""
 
-    """
     data_dir: Path = Field(
         ...,
-        description="Data directory; retrieved data will be deposited here, can be pre-existing")
+        description="Data directory; retrieved data will be deposited here, can be pre-existing",
+    )
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
         # create data directory if not present
         self.data_dir.mkdir(parents=True, exist_ok=True)
 
-
     @staticmethod
     def _download_url(url, save_path, headers=None, chunk_size=128, message=None):
         """
@@ -29,10 +28,11 @@ def _download_url(url, save_path, headers=None, chunk_size=128, message=None):
         # Create directory
         base_path, filename = os.path.split(save_path)
         os.makedirs(base_path, exist_ok=True)
-    
+
         r = requests.get(url, stream=True, headers=headers)
-        with open(save_path, 'wb') as fd:
-            nchunks = int(int(r.headers['Content-Length'])/chunk_size)
-            for chunk in track(r.iter_content(chunk_size=chunk_size), message,
-                               total=nchunks):
+        with open(save_path, "wb") as fd:
+            nchunks = int(int(r.headers["Content-Length"]) / chunk_size)
+            for chunk in track(
+                r.iter_content(chunk_size=chunk_size), message, total=nchunks
+            ):
                 fd.write(chunk)