clean up flake8 linting issues

dynophores/cli.py

@@ -102,7 +102,7 @@ def _greet():
  with open(logo_path, "r", encoding="ascii") as f:
  print(f.read())
  title_str = f"Dynophores CLI {_version.get_versions()['version']}"
- print(f"\n{title_str:^64}")
+ print(f"\n{title_str: ^64}")
 
 
 def _create_viz(args):
@@ -114,16 +114,16 @@ def _create_viz(args):
 
  dyno_path = Path(args.dyno)
  if not dyno_path.is_dir():
- raise RuntimeError(f"Input is no file or file does not exist: `{dyno_path.absolute()}`")
+ raise RuntimeError(f"Input is no file or file does not exist: {dyno_path.absolute()}")
 
  pdb_path = Path(args.pdb)
  if not pdb_path.is_file():
- raise RuntimeError(f"Input is no file or file does not exist: `{pdb_path.absolute()}`")
+ raise RuntimeError(f"Input is no file or file does not exist: {pdb_path.absolute()}")
 
  if args.dcd is not None:
  dcd_path = Path(args.dcd)
  if not dcd_path.is_file():
- raise RuntimeError(f"Input is no file or file does not exist: `{dcd_path.absolute()}`")
+ raise RuntimeError(f"Input is no file or file does not exist: {dcd_path.absolute()}")
  else:
  dcd_path = None
 
@@ -168,8 +168,8 @@ def _copy_notebook(new_notebook_path):
  new_notebook_path = Path(new_notebook_path)
  if new_notebook_path.suffix != ".ipynb":
  raise RuntimeError(
- f"Input file path must have suffix `.ipynb`. "
- f"Your input: `{new_notebook_path.absolute()}`"
+ f"Input file path must have suffix .ipynb. "
+ f"Your input: {new_notebook_path.absolute()}"
  )
  if not new_notebook_path.exists():
  new_notebook_path.parent.mkdir(parents=True, exist_ok=True)
@@ -179,16 +179,16 @@ def _copy_notebook(new_notebook_path):
  print("\nCopy dynophore notebook to user workspace...")
  copyfile(template_notebook_path, new_notebook_path)
  if new_notebook_path.exists():
- print(f"Dynophore notebook location: `{new_notebook_path.absolute()}`")
+ print(f"Dynophore notebook location: {new_notebook_path.absolute()}")
  else:
  raise RuntimeError(
  f"Could not create dynophore notebook at selected location "
- f"`{new_notebook_path.absolute()}`"
+ f"{new_notebook_path.absolute()}"
  )
  else:
  raise RuntimeError(
  f"Could not find dynophore notebook at expected location "
- f"`{template_notebook_path.absolute()}`."
+ f"{template_notebook_path.absolute()}."
  )
 
 
@@ -200,20 +200,20 @@ def _update_paths_in_notebook(notebook_path, dyno_path, pdb_path, dcd_path=None)
 
  notebook_path = Path(notebook_path)
  if not notebook_path.is_file():
- raise RuntimeError(f"Input is no file or does not exist: `{notebook_path.absolute()}`")
+ raise RuntimeError(f"Input is no file or does not exist: {notebook_path.absolute()}")
 
  dyno_path = Path(dyno_path)
  if not dyno_path.is_dir():
- raise RuntimeError(f"Input is no file or file does not exist: `{dyno_path.absolute()}`")
+ raise RuntimeError(f"Input is no file or file does not exist: {dyno_path.absolute()}")
 
  pdb_path = Path(pdb_path)
  if not pdb_path.is_file():
- raise RuntimeError(f"Input is no file or file does not exist: `{pdb_path.absolute()}`")
+ raise RuntimeError(f"Input is no file or file does not exist: {pdb_path.absolute()}")
 
  if dcd_path is not None:
  dcd_path = Path(dcd_path)
  if not dcd_path.is_file():
- raise RuntimeError(f"Input is no file or file does not exist: `{dcd_path.absolute()}`")
+ raise RuntimeError(f"Input is no file or file does not exist: {dcd_path.absolute()}")
 
  # Replace template filepaths in notebook with user-defined filepaths
  print("\nUpdate filepaths in notebook to user filepaths...")
@@ -260,12 +260,12 @@ def _open_notebook(notebook_path):
  notebook_path = Path(notebook_path)
 
  if not notebook_path.exists():
- raise RuntimeError(f"Input path does not exist: `{notebook_path.absolute()}`")
+ raise RuntimeError(f"Input path does not exist: {notebook_path.absolute()}")
  if not notebook_path.is_file():
- raise RuntimeError(f"Input path is not a file: `{notebook_path.absolute()}`")
+ raise RuntimeError(f"Input path is not a file: {notebook_path.absolute()}")
  if notebook_path.suffix != ".ipynb":
  raise RuntimeError(
- f"Input file path must have suffix `.ipynb`. Your input: `{notebook_path.absolute()}`"
+ f"Input file path must have suffix .ipynb. Your input: {notebook_path.absolute()}"
  )
 
  print("Open dynophore notebook with Jupyter Lab...")

dynophores/viz/view3d/interactive.py

@@ -2,6 +2,8 @@
 Contains NGLview 3D visualizations.
 """
 
+# flake8: noqa
+
 import warnings
 
 import numpy as np