Skip to content

Fix SyntaxWarning for invalid escape sequences in regex strings #70

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
pmrv merged 1 commit into from
Apr 21, 2026
Merged

Fix SyntaxWarning for invalid escape sequences in regex strings #70

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 9 additions & 9 deletions sphinx_parser/output.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,7 @@ def collect_eval_forces(file_name, index_permutation=None):
_check_permutation(index_permutation)
with open(str(file_name), "r") as f:
file_content = "".join(f.readlines())
n_steps = max(len(re.findall("// --- step \d", file_content, re.MULTILINE)), 1)
n_steps = max(len(re.findall(r"// --- step \d", file_content, re.MULTILINE)), 1)
f_v = ",".join(3 * [r"\s*([\d.-]+)"])

def get_value(term, f=file_content, n=n_steps, p=index_permutation):
Expand Down Expand Up @@ -251,7 +251,7 @@ def get_n_valence(self):
@property
def _log_k_points(self):
start_match = re.search(
"-ik- -x- -y- -z- \| -weight- -nG- -label-",
r"-ik- -x- -y- -z- \| -weight- -nG- -label-",
self.log_file,
)
log_part = self.log_file[start_match.end() + 1 :]
Expand Down Expand Up @@ -287,7 +287,7 @@ def get_volume(self):
def counter(self):
return [
int(re.sub("[^0-9]", "", line.split("=")[0]))
for line in re.findall("F\(.*$", self.log_main, re.MULTILINE)
for line in re.findall(r"F\(.*$", self.log_main, re.MULTILINE)
]

def _get_energy(self, pattern):
Expand All @@ -304,7 +304,7 @@ def get_energy_int(self):
def n_atoms(self):
if self._n_atoms is None:
self._n_atoms = len(
np.unique(re.findall("^Species.*\{", self.log_main, re.MULTILINE))
np.unique(re.findall(r"^Species.*\{", self.log_main, re.MULTILINE))
)
return self._n_atoms

Expand All @@ -313,7 +313,7 @@ def get_forces(self):
Returns:
(numpy.ndarray): Forces of the shape (n_steps, n_atoms, 3)
"""
str_fl = "([-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)"
str_fl = r"([-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)"
pattern = r"Atom: (\d+)\t{" + ",".join(3 * [str_fl]) + r"\}"
arr = np.array(re.findall(pattern, self.log_file))
if len(arr) == 0:
Expand All @@ -331,7 +331,7 @@ def get_magnetic_forces(self):
"""
magnetic_forces = [
float(line.split()[-1])
for line in re.findall("^nu\(.*$", self.log_main, re.MULTILINE)
for line in re.findall(r"^nu\(.*$", self.log_main, re.MULTILINE)
]
if len(magnetic_forces) != 0:
magnetic_forces = np.array(magnetic_forces).reshape(-1, self.n_atoms)
Expand All @@ -342,7 +342,7 @@ def get_magnetic_forces(self):

@property
def n_steps(self):
return len(re.findall("\| SCF calculation", self.log_file, re.MULTILINE))
return len(re.findall(r"\| SCF calculation", self.log_file, re.MULTILINE))

def _parse_band(self, term):
content = re.findall(term, self.log_main, re.MULTILINE)
Expand All @@ -355,7 +355,7 @@ def _parse_band(self, term):
return arr.reshape(shape)

def get_band_energy(self):
return self._parse_band("final eig \[eV\]:(.*)$")
return self._parse_band(r"final eig \[eV\]:(.*)$")

def get_occupancy(self):
return self._parse_band("final focc:(.*)$")
Expand All @@ -365,7 +365,7 @@ def get_convergence(self):
"WARNING: Maximum number of steps exceeded": False,
"Convergence reached.": True,
}
key = "|".join(list(conv_dict.keys())).replace(".", "\.")
key = "|".join(list(conv_dict.keys())).replace(".", r"\.")
items = re.findall(key, self.log_main, re.MULTILINE)
convergence = [conv_dict[k] for k in items]
diff = self.n_steps - len(convergence)
Expand Down
Loading