update formatting standards

Author: Pramesh Sharma

Makefile

@@ -1,5 +1,5 @@
 format:
-	black --line-length 79 .
+	black .
 
 lint:
 	flake8 .

scripts/generate_docs.py

@@ -16,9 +16,7 @@ def generate_help(command, filename):
 
     with open(f"docs/commands/{filename}.md", "w") as doc_file:
         doc_file.write(f"# SSDraw {command} Command\n\n")
-        doc_file.write(
-            f"This section documents the `ssdraw {command}` command.\n\n"
-        )
+        doc_file.write(f"This section documents the `ssdraw {command}` command.\n\n")
         doc_file.write("```bash\n")
         doc_file.write(help_output)
         doc_file.write("```\n")

src/SSDraw/cli.py

@@ -121,9 +121,7 @@ def get_args(
     multi_parser.add_argument(
         "-o", "--output", required=True, help="Name of output directory"
     )
-    multi_parser.set_defaults(
-        func=lambda args: run_multiple_pdbs_on_one_msa(args)
-    )
+    multi_parser.set_defaults(func=lambda args: run_multiple_pdbs_on_one_msa(args))
 
     return parser.parse_args(argv)
 

src/SSDraw/core.py

@@ -67,9 +67,7 @@ def read_consurf_grad(input_file: str) -> T.Tuple[str, T.List[int]]:
 
 def check_consurf_file(file: str) -> T.Optional[str]:
     consurf_pattern = r"^\s*?\d+\s+(\w)\s+\S+\s+\S+\s+(\d)\S*\s+-?\d+.\d+,\s+-?\d+.\d+\s+\d,\d\s+\d+\/\d+\s+\S+"
-    r4s_pattern = (
-        r"^\s*?\d+\s+(\w)\s+(\S+)\s+\[\s*\S+,\s*\S+\]\s+\S+\s+\d+\/\d+"
-    )
+    r4s_pattern = r"^\s*?\d+\s+(\w)\s+(\S+)\s+\[\s*\S+,\s*\S+\]\s+\S+\s+\d+\/\d+"
     with open(file, "r") as f:
         for line in f:
             if re.match(consurf_pattern, line):
@@ -970,9 +968,7 @@ def SSDraw(
     nlines = 1
 
     # Parse color and scoring args
-    CMAP, bvals = parse_color(
-        args, seq_wgaps, pdbseq, bfactors, msa, extra_gaps
-    )
+    CMAP, bvals = parse_color(args, seq_wgaps, pdbseq, bfactors, msa, extra_gaps)
 
     mat = np.tile(NormalizeData(bvals), (100, 1))
 
@@ -1102,11 +1098,7 @@ def SSDraw(
 
     ax.set_aspect(0.5)
 
-    print(
-        "Saving output to {:}.{:}...".format(
-            args.output, args.output_file_type
-        )
-    )
+    print("Saving output to {:}.{:}...".format(args.output, args.output_file_type))
     plt.savefig(
         args.output + "." + args.output_file_type,
         bbox_inches="tight",

src/SSDraw/multi.py

@@ -15,9 +15,7 @@
 import SSDraw.core as SSDraw
 
 
-def SSDraw_layer(
-    fastas, pdbs, names, output_names, output_dir, additional_params
-):
+def SSDraw_layer(fastas, pdbs, names, output_names, output_dir, additional_params):
     nlines = len(pdbs)
 
     # Plot secondary structure chunks
@@ -171,9 +169,7 @@ def SSDraw_layer(
         if loop_coords[j][1][1] > maxsize:
             maxsize = loop_coords[j][1][1]
 
-    fig, ax = plt.subplots(
-        ncols=1, figsize=(sz * 0.7, ((maxsize - minsize) * 0.37))
-    )
+    fig, ax = plt.subplots(ncols=1, figsize=(sz * 0.7, ((maxsize - minsize) * 0.37)))
 
     for i in range(len(output_names)):
         ax.annotate(
@@ -287,9 +283,5 @@ def run_multiple_pdbs_on_one_msa(args):
         additional_params,
     )
 
-    print(
-        "Creating composite image {:}.{:}".format(
-            args.output, output_file_type
-        )
-    )
+    print("Creating composite image {:}.{:}".format(args.output, output_file_type))
     plt.savefig("{:}.{:}".format(args.output, output_file_type))