run.single pdbfile argument ignored

[IAlibay]

Expected

Passing a file and some arguments to run.single should work:

i.e.

import propka.run as pk

mol = pk.single('4LYI.pdb', optargs=['--quiet'])

Actual behaviour

The above worked in 3.1, however moving to 3.2 this leads to a SystemExit caused by agparse.

Causes

From what I can tell, the following are causing this behaviour:

1. single calls loadOptions whose argparse call expects an input_pdb entry.

2. pdbfile is overwritten by the return value of options.filenames.pop(0)

propka/propka/run.py

Line 59 in 01debbf

pdbfile = options.filenames.pop(0)

Possible fix

One quick fix here would be to switch single to have a behaviour similar to what is done in:

propka/tests/test_basic_regression.py

Lines 60 to 84 in 01debbf

	def run_propka(options, pdb_path, tmp_path):
	"""Run PROPKA software.
	Args:
	options: list of PROPKA options
	pdb_path: path to PDB file
	tmp_path: path for working directory
	"""
	options += [str(pdb_path)]
	args = loadOptions(options)
	try:
	_LOGGER.warning(
	"Working in tmpdir {0:s} because of PROPKA file output; "
	"need to fix this.".format(str(tmp_path)))
	cwd = Path.cwd()
	os.chdir(tmp_path)
	parameters = read_parameter_file(args.parameters, Parameters())
	molecule = MolecularContainer(parameters, args)
	molecule = read_molecule_file(str(pdb_path), molecule)
	molecule.calculate_pka()
	molecule.write_pka()
	if args.generate_propka_input:
	molecule.write_propka()
	finally:
	os.chdir(cwd)