lint

Author: sshugsc

pori_python/graphkb/util.py

@@ -127,7 +127,7 @@ def __init__(
 
         # URL check
         if not self.url:
-            raise ValueError("URL to a GraphKB API instance is required")
+            raise ValueError('URL to a GraphKB API instance is required')
 
     @property
     def load(self) -> Optional[float]:
@@ -254,8 +254,8 @@ def login(self, username: str, password: str, pori_demo: bool = False) -> None:
         read_timeout = 61
 
         # KBDEV-1328. Alt. GraphKB login for GSC's PORI online demo
-        if pori_demo or "pori-demo" in self.url:
-            logger.warning("login demo")
+        if pori_demo or 'pori-demo' in self.url:
+            logger.warning('login demo')
             self.login_demo()
 
         # use requests package directly to avoid recursion loop on login failure

pori_python/ipr/main.py

@@ -420,7 +420,7 @@ def ipr_report(
 
     # GKB CONNECTION
     graphkb_conn = GraphKBConnection(graphkb_url) if graphkb_url else GraphKBConnection()
-    logger.info(f"connecting to graphkb: {graphkb_conn.url}")
+    logger.info(f'connecting to graphkb: {graphkb_conn.url}')
 
     graphkb_conn.login(
         graphkb_username if graphkb_username else username,
@@ -499,7 +499,7 @@ def ipr_report(
 
     if include_ipr_variant_text:
         if not ipr_conn:
-            raise ValueError("ipr_url required to include ipr variant text")
+            raise ValueError('ipr_url required to include ipr variant text')
         ipr_comments = get_ipr_analyst_comments(
             ipr_conn,
             gkb_matches,

pori_python/ipr/util.py

@@ -178,30 +178,30 @@ def pandas_falsy(field: Any) -> bool:
 # to allow us to remove otherwise unnecessary biopython dependency
 
 protein_letters_1to3 = {
-    "A": "Ala",
-    "C": "Cys",
-    "D": "Asp",
-    "E": "Glu",
-    "F": "Phe",
-    "G": "Gly",
-    "H": "His",
-    "I": "Ile",
-    "K": "Lys",
-    "L": "Leu",
-    "M": "Met",
-    "N": "Asn",
-    "P": "Pro",
-    "Q": "Gln",
-    "R": "Arg",
-    "S": "Ser",
-    "T": "Thr",
-    "V": "Val",
-    "W": "Trp",
-    "Y": "Tyr",
+    'A': 'Ala',
+    'C': 'Cys',
+    'D': 'Asp',
+    'E': 'Glu',
+    'F': 'Phe',
+    'G': 'Gly',
+    'H': 'His',
+    'I': 'Ile',
+    'K': 'Lys',
+    'L': 'Leu',
+    'M': 'Met',
+    'N': 'Asn',
+    'P': 'Pro',
+    'Q': 'Gln',
+    'R': 'Arg',
+    'S': 'Ser',
+    'T': 'Thr',
+    'V': 'Val',
+    'W': 'Trp',
+    'Y': 'Tyr',
 }
 protein_letters_1to3_extended = {
     **protein_letters_1to3,
-    **{"B": "Asx", "X": "Xaa", "Z": "Glx", "J": "Xle", "U": "Sec", "O": "Pyl"},
+    **{'B': 'Asx', 'X': 'Xaa', 'Z': 'Glx', 'J': 'Xle', 'U': 'Sec', 'O': 'Pyl'},
 }
 
 protein_letters_3to1 = {value: key for key, value in protein_letters_1to3.items()}