chore: format

src/orcestradownloader/cli/__init__.py

@@ -1,3 +1,3 @@
 from .cli import DatasetMultiCommand, cli
 
-__all__ = ['DatasetMultiCommand', 'cli']
+__all__ = ['DatasetMultiCommand', 'cli']

src/orcestradownloader/dataset_config.py

@@ -22,32 +22,31 @@ class DatasetConfig:
 	'pharmacosets': DatasetConfig(
 		url='https://orcestra.ca/api/pset/available',
 		cache_file='pharmacosets.json',
-		dataset_type=PharmacoSet
+		dataset_type=PharmacoSet,
 	),
 	'icbsets': DatasetConfig(
 		url='https://orcestra.ca/api/clinical_icb/available',
 		cache_file='icbsets.json',
-		dataset_type=ICBSet
+		dataset_type=ICBSet,
 	),
 	'radiosets': DatasetConfig(
 		url='https://orcestra.ca/api/radioset/available',
 		cache_file='radiosets.json',
-		dataset_type=RadioSet
+		dataset_type=RadioSet,
 	),
 	'xevasets': DatasetConfig(
 		url='https://orcestra.ca/api/xevaset/available',
 		cache_file='xevasets.json',
-		dataset_type=XevaSet
+		dataset_type=XevaSet,
 	),
 	'toxicosets': DatasetConfig(
 		url='https://orcestra.ca/api/toxicoset/available',
 		cache_file='toxicosets.json',
-		dataset_type=ToxicoSet
+		dataset_type=ToxicoSet,
 	),
 	'radiomicsets': DatasetConfig(
 		url='https://orcestra.ca/api/radiomicset/available',
 		cache_file='radiomicsets.json',
-		dataset_type=RadiomicSet
+		dataset_type=RadiomicSet,
 	),
 }
-

src/orcestradownloader/managers.py

@@ -140,7 +140,7 @@ def get_manager(self, name: str) -> DatasetManager:
 
 	def get_all_managers(self) -> Dict[str, DatasetManager]:
 		return self.registry
-	
+
 	def __repr__(self) -> str:
 		return f'DatasetRegistry(registry={self.registry})'
 
@@ -273,13 +273,13 @@ def list_all(self, pretty: bool = True, force: bool = False) -> None:
 					click.echo(f'{name},{ds_name}')
 
 	def download_by_name(
-		self, 
-		manager_name: str, 
+		self,
+		manager_name: str,
 		ds_name: List[str],
-		directory: Path, 
-		overwrite: bool = False, 
+		directory: Path,
+		overwrite: bool = False,
 		force: bool = False,
-		timeout_seconds: int = 3600
+		timeout_seconds: int = 3600,
 	) -> List[Path]:
 		"""Download a single dataset."""
 		# Fetch data asynchronously
@@ -289,7 +289,7 @@ def download_by_name(
 			log.exception('Error fetching %s: %s', manager_name, e)
 			errmsg = f'Error fetching {manager_name}: {e}'
 			raise ValueError(errmsg) from e
-		
+
 		manager = self.registry.get_manager(manager_name)
 		dataset_list = [manager[ds_name] for ds_name in ds_name]
 
@@ -300,32 +300,36 @@ def download_by_name(
 				raise ValueError(msg)
 			file_path = directory / manager_name / f'{ds.name}.RDS'
 			if file_path.exists() and not overwrite:
-				Console().print(f'[bold red]File {file_path} already exists. Use --overwrite to overwrite.[/]')
+				Console().print(
+					f'[bold red]File {file_path} already exists. Use --overwrite to overwrite.[/]'
+				)
 				sys.exit(1)
 			file_path.parent.mkdir(parents=True, exist_ok=True)
 			file_paths[ds.name] = file_path
-		
+
 		async def download_all(progress: Progress) -> List[Path]:
-			return await asyncio.gather(*[
-				download_dataset(
-					ds.download_link, 
-					file_paths[ds.name], 
-					progress,
-					timeout_seconds=timeout_seconds
-				) 
-				for ds in dataset_list
-			])
-
+			return await asyncio.gather(
+				*[
+					download_dataset(
+						ds.download_link,
+						file_paths[ds.name],
+						progress,
+						timeout_seconds=timeout_seconds,
+					)
+					for ds in dataset_list
+				]
+			)
+
 		with Progress() as progress:
 			return asyncio.run(download_all(progress))
 
 	def download_all(
-		self, 
+		self,
 		manager_name: str,
-		directory: Path, 
-		overwrite: bool = False, 
+		directory: Path,
+		overwrite: bool = False,
 		force: bool = False,
-		timeout_seconds: int = 3600
+		timeout_seconds: int = 3600,
 	) -> List[Path]:
 		"""Download all datasets for a specific manager."""
 		file_paths = []
@@ -335,7 +339,7 @@ def download_all(
 			log.exception('Error fetching %s: %s', manager_name, e)
 			errmsg = f'Error fetching {manager_name}: {e}'
 			raise ValueError(errmsg) from e
-		
+
 		manager = self.registry.get_manager(manager_name)
 		for ds in manager.datasets:
 			if not ds.download_link:
@@ -344,22 +348,26 @@ def download_all(
 				continue
 			file_path = directory / manager_name / f'{ds.name}.RDS'
 			if file_path.exists() and not overwrite:
-				Console().print(f'[bold red]File {file_path} already exists. Use --overwrite to overwrite.[/]')
+				Console().print(
+					f'[bold red]File {file_path} already exists. Use --overwrite to overwrite.[/]'
+				)
 				sys.exit(1)
 			file_path.parent.mkdir(parents=True, exist_ok=True)
 			file_paths.append(file_path)
-		
+
 		async def download_all_datasets(progress: Progress) -> List[Path]:
-			return await asyncio.gather(*[
-				download_dataset(
-					ds.download_link, 
-					file_path, 
-					progress,
-					timeout_seconds=timeout_seconds
-				) 
-				for ds, file_path in zip(manager.datasets, file_paths)
-			])
-
+			return await asyncio.gather(
+				*[
+					download_dataset(
+						ds.download_link,
+						file_path,
+						progress,
+						timeout_seconds=timeout_seconds,
+					)
+					for ds, file_path in zip(manager.datasets, file_paths)
+				]
+			)
+
 		with Progress(
 			'[progress.description]{task.description}',
 			BarColumn(),
@@ -385,7 +393,10 @@ def __getitem__(self, name: str) -> DatasetManager:
 			msg += f' Available managers: {", ".join(self.names())}'
 			raise ValueError(msg) from se
 
-async def download_dataset(download_link: str, file_path: Path, progress: Progress, timeout_seconds: int = 3600) -> Path:
+
+async def download_dataset(
+	download_link: str, file_path: Path, progress: Progress, timeout_seconds: int = 3600
+) -> Path:
 	"""Download a single dataset.
 
 	Called by the UnifiedDataManager.download_by_name method
@@ -395,14 +406,16 @@ async def download_dataset(download_link: str, file_path: Path, progress: Progre
 		try:
 			async with session.get(download_link) as response:
 				total = int(response.headers.get('content-length', 0))
-				task = progress.add_task(f"[cyan]Downloading {file_path.name}...", total=total)
+				task = progress.add_task(
+					f'[cyan]Downloading {file_path.name}...', total=total
+				)
 				with file_path.open('wb') as f:
 					async for chunk in response.content.iter_chunked(8192):
 						f.write(chunk)
 						progress.update(task, advance=len(chunk))
 		except asyncio.TimeoutError:
-			Console().print(f'[bold red]Timeout while downloading {file_path.name}. Please try again later.[/]')
+			Console().print(
+				f'[bold red]Timeout while downloading {file_path.name}. Please try again later.[/]'
+			)
 			raise
 	return file_path
-
-

src/orcestradownloader/models/base.py

@@ -178,9 +178,7 @@ def print_summary(self, title: str | None = None) -> None:
 
 		This method uses Rich to display a well-formatted table of the record's attributes.
 		"""
-		table = Table(
-			title=title if title else f'{self.__class__.__name__} Summary'
-		)
+		table = Table(title=title if title else f'{self.__class__.__name__} Summary')
 
 		table.add_column('Field', style='bold cyan', no_wrap=True)
 		table.add_column('Value', style='magenta')
@@ -195,16 +193,23 @@ def print_summary(self, title: str | None = None) -> None:
 		table.add_row('Dataset Name', self.dataset.name)
 		table.add_row('Dataset Version', self.dataset.version_info.version)
 		table.add_row(
-				'Dataset Type',
-				self.dataset.version_info.dataset_type.name if self.dataset.version_info.dataset_type else 'N/A',
+			'Dataset Type',
+			self.dataset.version_info.dataset_type.name
+			if self.dataset.version_info.dataset_type
+			else 'N/A',
 		)
 		table.add_row(
 			'Available Datatypes',
 			', '.join(self.datatypes) if self.datatypes else 'N/A',
 		)
 		table.add_row(
 			'Publications',
-			', '.join([f"{pub.citation} ({pub.link})" for pub in self.dataset.version_info.publication])
+			', '.join(
+				[
+					f'{pub.citation} ({pub.link})'
+					for pub in self.dataset.version_info.publication
+				]
+			),
 		)
 
 		console = Console()