Improve the documentation of the Polaris CLI

polaris/cli.py

@@ -1,4 +1,4 @@
-from typing import Optional
+from typing import Annotated, Optional
 
 import typer
 
@@ -10,13 +10,22 @@
 )
 
 
-@app.command("login", help="Log in to the Polaris Hub")
+@app.command("login")
 def login(
-    client_env_file: Optional[str] = None,
-    auto_open_browser: bool = True,
-    overwrite: bool = False,
+    client_env_file: Annotated[
+        Optional[str], typer.Option(help="Environment file to overwrite the default environment variables")
+    ] = None,
+    auto_open_browser: Annotated[
+        bool, typer.Option(help="Whether to automatically open the link in a browser to retrieve the token")
+    ] = True,
+    overwrite: Annotated[
+        bool, typer.Option(help="Whether to overwrite the access token if you are already logged in")
+    ] = False,
 ):
-    """Uses the OAuth2 protocol to gain token-based access to the Polaris Hub API"""
+    """Authenticate to the Polaris Hub.
+
+    This CLI will use the OAuth2 protocol to gain token-based access to the Polaris Hub API.
+    """
     with PolarisHubClient(env_file=client_env_file) as client:
         client.login(auto_open_browser=auto_open_browser, overwrite=overwrite)
 

polaris/curation/_data_curator.py

@@ -230,12 +230,14 @@ def run_data_curation(
         # detect stereo activity cliff, keep or remove
         data = _process_stereoisomer_with_activity_cliff(
             data=data,
-            data_cols=[
-                f"{CLASS_PREFIX}{data_col}" if f"{CLASS_PREFIX}{data_col}" in data.columns else data_col
-                for data_col in data_cols
-            ]
-            if class_thresholds
-            else data_cols,
+            data_cols=(
+                [
+                    f"{CLASS_PREFIX}{data_col}" if f"{CLASS_PREFIX}{data_col}" in data.columns else data_col
+                    for data_col in data_cols
+                ]
+                if class_thresholds
+                else data_cols
+            ),
             mask_stereo_undefined_mols=mask_stereo_undefined_mols,
             **activity_cliff_params if activity_cliff_params is not None else {},
         )

polaris/utils/types.py

@@ -115,9 +115,9 @@ class License(BaseModel):
             Else it is required to manually specify this.
     """
 
-    SPDX_LICENSE_DATA_PATH: ClassVar[
-        str
-    ] = "https://raw.githubusercontent.com/spdx/license-list-data/main/json/licenses.json"
+    SPDX_LICENSE_DATA_PATH: ClassVar[str] = (
+        "https://raw.githubusercontent.com/spdx/license-list-data/main/json/licenses.json"
+    )
 
     id: str
     reference: Optional[HttpUrlString] = None