[Code scan] Make RunAbacus input-file discovery restore cwd on parse failures

[njzjz]

This issue is a result of a Codex global code scan of deepmodeling/fpop at commit b05b337590c31a5237b2dcbd9c0833b841c08cd4.

Relevant code:

fpop/fpop/abacus.py

Lines 249 to 305 in b05b337

	def get_pporbdpks_from_stru(stru: str= "STRU"):
	"read the label, pp, orb, cell, coord, deepks-descriptor"
	ABACUS_STRU_KEY_WORD = [
	"ATOMIC_SPECIES",
	"NUMERICAL_ORBITAL",
	"LATTICE_CONSTANT",
	"LATTICE_VECTORS",
	"ATOMIC_POSITIONS",
	"NUMERICAL_DESCRIPTOR",
	]
	if not os.path.isfile(stru):
	return {}
	with open(stru) as f1: lines = f1.readlines()
	def get_block(keyname):
	block = []
	for i,line in enumerate(lines):
	if line.strip() == "": continue
	elif line.split('#')[0].strip() == keyname:
	for ij in range(i+1,len(lines)):
	if lines[ij].strip() == "": continue
	elif lines[ij].strip() in ABACUS_STRU_KEY_WORD:
	return block
	else:
	block.append(lines[ij])
	return block
	return None
	atomic_species = get_block("ATOMIC_SPECIES")
	numerical_orbital = get_block("NUMERICAL_ORBITAL")
	dpks = get_block("NUMERICAL_DESCRIPTOR")
	dpks = None if dpks == None else dpks[0].strip()
	#read species
	pp = []
	labels = []
	mass = []
	if atomic_species:
	for line in atomic_species:
	sline = line.split()
	labels.append(sline[0])
	pp.append(sline[2])
	mass.append(float(sline[1]))
	#read orbital
	if numerical_orbital == None:
	orb = None
	else:
	orb = []
	for line in numerical_orbital:
	orb.append(line.split()[0])
	return {
	"labels": labels,
	"mass": mass,
	"pp":pp,
	"orb":orb,
	"dpks":dpks,}

fpop/fpop/abacus.py

Lines 556 to 596 in b05b337

	class RunAbacus(RunFp):
	def input_files(self,task_path) -> List[str]:
	r'''The mandatory input files to run an abacus task.
	Returns
	-------
	files: List[str]
	A list of madatory input files names.
	'''
	cwd = os.getcwd()
	os.chdir(task_path)
	files = ["INPUT","STRU"]
	if os.path.isfile("KPT"):
	files.append("KPT")
	files_tmp = []
	#read STRU
	stru_data = get_pporbdpks_from_stru("STRU")
	if stru_data != None:
	orb_files = stru_data["orb"]
	pp_files = stru_data["pp"]
	dpks_descriptor = stru_data["dpks"]
	files_tmp += pp_files
	if orb_files: files_tmp += orb_files
	if dpks_descriptor: files_tmp += [dpks_descriptor]
	#read INPUT
	input = AbacusInputs.read_inputf("INPUT")
	if "deepks_model" in input: files_tmp += [input["deepks_model"]]
	for ii in files_tmp:
	if os.path.isfile(ii):
	files.append(ii)
	else:
	print("ERROR: file %s is not found" % ii)
	os.chdir(cwd)
	return files

Problem:
RunAbacus.input_files() changes the process working directory with os.chdir(task_path) and restores it only on the successful path. If STRU parsing raises, the caller is left in the task directory.

There are at least two easy ways to trigger this:

1. If STRU is missing, get_pporbdpks_from_stru("STRU") returns {}. input_files() checks if stru_data != None, then indexes stru_data["orb"] and raises KeyError.
2. If a STRU section header has an inline comment, such as NUMERICAL_ORBITAL # comment, get_block() does not strip comments when detecting the next section header. The commented header is treated as an ATOMIC_SPECIES data line and parsing can fail with ValueError: could not convert string to float: '#'.

Minimal reproduction for the second case:

ATOMIC_SPECIES
H 1 H.upf
NUMERICAL_ORBITAL # comment
H.orb
LATTICE_CONSTANT
1

Expected behavior:
RunAbacus.input_files() should restore cwd in a finally block, and STRU parsing failures should be reported as clear missing/invalid input errors instead of leaking process state.