style: format code, Jupyter Notebook(s), and Python imports with ruff

Author: JoshLoecker

main/como/create_context_specific_model.py

@@ -172,7 +172,7 @@ def _gene_rule_logical(gpr_expression: str, level: int = 0) -> str:
         inner_string = inner_string.replace("[", "")
         inner_string = inner_string.replace("]", "")
 
-    expression_out = f"{gpr_expression[:loc_l]}{inner_string}{gpr_expression[loc_r + 1:]}"
+    expression_out = f"{gpr_expression[:loc_l]}{inner_string}{gpr_expression[loc_r + 1 :]}"
     expression_out = _gene_rule_logical(expression_out, level + 1)
 
     return expression_out
@@ -384,7 +384,7 @@ def _map_expression_to_reaction(
             continue
         for gid in gene_ids:
             if gid in gene_expressions.index:
-                rep_val = f' {gene_expressions.at[gid, "active"]} '
+                rep_val = f" {gene_expressions.at[gid, 'active']} "
             else:
                 rep_val = f" {unknown_val!s} "
             gene_reaction_rule = f" {gene_reaction_rule} "  # pad white space to prevent gene matches inside floats

main/como/rnaseq.py

@@ -418,8 +418,7 @@ def zfpkm_transform(
     cores = multiprocessing.cpu_count() - 2
     logger.debug(f"Processing {total:,} samples through zFPKM transform using {cores} cores")
     logger.debug(
-        f"Will update every {update_per_step:,} steps as this is approximately "
-        f"{update_every_percent:.1%} of {total:,}"
+        f"Will update every {update_per_step:,} steps as this is approximately {update_every_percent:.1%} of {total:,}"
     )
 
     with Pool(processes=cores) as pool: