chore: Refactor code formatting and improve readability

src/nbiatoolkit/nbia.py

@@ -216,8 +216,9 @@ def getBodyPartCounts(
             )
         return bodyparts
 
-    def getStudies(self, Collection : str, PatientID : str = "", StudyInstanceUID : str = ""
-) -> Union[list[dict[str, str]], None]:
+    def getStudies(
+        self, Collection: str, PatientID: str = "", StudyInstanceUID: str = ""
+    ) -> Union[list[dict[str, str]], None]:
         PARAMS = self.parsePARAMS(locals())
 
         response = self.query_api(endpoint=NBIA_ENDPOINTS.GET_STUDIES, params=PARAMS)

src/nbiatoolkit/nbia_cli.py

@@ -1,4 +1,3 @@
-
 import io
 from .nbia import NBIAClient, __version__
 
@@ -27,7 +26,13 @@ def version():
     print("\nAvailable CLI tools: \n")
 
     # run each command with -h to see the available options
-    commands = ["getCollections", "getPatients", "getBodyPartCounts", "getSeries", "downloadSingleSeries"]
+    commands = [
+        "getCollections",
+        "getPatients",
+        "getBodyPartCounts",
+        "getSeries",
+        "downloadSingleSeries",
+    ]
     for command in commands:
         result = subprocess.run([command, "-h"], capture_output=True, text=True)
         output_lines = result.stdout.splitlines()
@@ -39,9 +44,15 @@ def version():
 
     return
 
+
 def general_parser(parser: argparse.ArgumentParser) -> argparse.Namespace:
-    parser.add_argument("-o", "--output", dest="outputfile",
-        action="store", type=argparse.FileType('w', encoding='UTF-8'), help="Output file (tsv works best)",
+    parser.add_argument(
+        "-o",
+        "--output",
+        dest="outputfile",
+        action="store",
+        type=argparse.FileType("w", encoding="UTF-8"),
+        help="Output file (tsv works best)",
     )
 
     parser.add_argument(
@@ -59,6 +70,7 @@ def general_parser(parser: argparse.ArgumentParser) -> argparse.Namespace:
 
     return args
 
+
 # An abstraction of the getCollections and getPatients functions
 # to generalize an interface for the CLI
 def getResults_cli(func, **kwargs) -> None:
@@ -98,6 +110,7 @@ def getResults_cli(func, **kwargs) -> None:
             print(result)
     return
 
+
 # create a helper function that will be used if the user ever uses --output <FILE>.tsv
 # output should be a io.TextIOWrapper object
 def writeResultsToFile(results: List, output: io.TextIOWrapper) -> None:
@@ -125,6 +138,7 @@ def writeResultsToFile(results: List, output: io.TextIOWrapper) -> None:
             output.write(str(result) + "\n")
     return
 
+
 def cli_wrapper(func, **kwargs) -> List[str] | None:
     """
     Wraps a function call with a loading animation.
@@ -156,13 +170,19 @@ def cli_wrapper(func, **kwargs) -> List[str] | None:
 
     return result
 
+
 def getPatients_cli() -> None:
     global query
     query = "patients"
     p = argparse.ArgumentParser(description=f"NBIAToolkit: {query} ")
 
-    p.add_argument("-c", "--collection", action="store",
-                   required=True,type=str,)
+    p.add_argument(
+        "-c",
+        "--collection",
+        action="store",
+        required=True,
+        type=str,
+    )
 
     args = general_parser(p)
 
@@ -174,8 +194,12 @@ def getCollections_cli() -> None:
     query = "collections"
     p = argparse.ArgumentParser(description=f"NBIAToolkit: {query} ")
 
-    p.add_argument("-p", "--prefix",
-        action="store", default="", type=str,
+    p.add_argument(
+        "-p",
+        "--prefix",
+        action="store",
+        default="",
+        type=str,
         help="The prefix to filter collections by, i.e 'TCGA', 'LIDC', 'NSCLC'",
     )
 
@@ -191,13 +215,20 @@ def getBodyPartCounts_cli() -> None:
 
     p = argparse.ArgumentParser(description=f"NBIAToolkit: {query} ")
 
-    p.add_argument("-c", "--collection", dest="collection",
-        action="store", default="", type=str,)
+    p.add_argument(
+        "-c",
+        "--collection",
+        dest="collection",
+        action="store",
+        default="",
+        type=str,
+    )
 
     args = general_parser(p)
 
-
-    return getResults_cli(func=NBIAClient().getBodyPartCounts, Collection=args.collection)
+    return getResults_cli(
+        func=NBIAClient().getBodyPartCounts, Collection=args.collection
+    )
 
 
 def getSeries_cli() -> None:
@@ -207,19 +238,41 @@ def getSeries_cli() -> None:
 
     p = argparse.ArgumentParser(description=f"NBIAToolkit: {query} ")
 
-    p.add_argument("-c", "--collection", dest="collection", action="store",
-        default="", type=str,
+    p.add_argument(
+        "-c",
+        "--collection",
+        dest="collection",
+        action="store",
+        default="",
+        type=str,
     )
 
-    p.add_argument("-p", "--patientID", dest="patientID",
-        action="store", default="", type=str,)
-
-    p.add_argument("-m", "--modality", dest="modality",
-        action="store", default="", type=str,)
+    p.add_argument(
+        "-p",
+        "--patientID",
+        dest="patientID",
+        action="store",
+        default="",
+        type=str,
+    )
 
-    p.add_argument("-study", "--studyInstanceUID", dest="studyInstanceUID",
-        action="store", default="", type=str,)
+    p.add_argument(
+        "-m",
+        "--modality",
+        dest="modality",
+        action="store",
+        default="",
+        type=str,
+    )
 
+    p.add_argument(
+        "-study",
+        "--studyInstanceUID",
+        dest="studyInstanceUID",
+        action="store",
+        default="",
+        type=str,
+    )
 
     p.add_argument(
         "--seriesInstanceUID",
@@ -316,5 +369,3 @@ def downloadSingleSeries_cli() -> None:
         filePattern=args.filePattern,
         overwrite=args.overwrite,
     )
-
-