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Merged
galjos merged 2 commits into from
Jun 29, 2026
Merged

Raise exceptions directly instead of logging-and-raising #58

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16833bc
Raise exceptions directly instead of logging-and-raising
galjos Jun 29, 2026
8de892b
Cover reachable Thermo validation; mark unreachable raises no-cover
galjos Jun 29, 2026
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41 changes: 9 additions & 32 deletions ThermoScreening/thermo/api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,16 +186,9 @@ def read_coord(coord_file: str, engine: str):
if coord_file.endswith(".gen"):
data_N, data_atoms, data_xyz, cell_vectors, pbc = read_gen(coord_file)
return data_N, data_atoms, data_xyz, cell_vectors, pbc
logger.error(
"The input file is not supported.",
exception=TSNotImplementedError
)
raise TSNotImplementedError("The input file is not supported.")

else:
logger.error(
"The engine is not supported.",
exception=TSNotImplementedError
)
raise TSNotImplementedError("The engine is not supported.")


def read_vibrational(vibrational_file: str, engine: str):
Expand Down Expand Up @@ -223,10 +216,7 @@ def read_vibrational(vibrational_file: str, engine: str):
vibrational_frequencies = read_vib_file(vibrational_file)
else:
# throw error
logger.error(
"The engine is not supported.",
exception=TSNotImplementedError
)
raise TSNotImplementedError("The engine is not supported.")

return vibrational_frequencies

Expand All @@ -252,10 +242,7 @@ def unit_length(engine: str):
"""
if engine == "dftb+":
return "Angstrom"
logger.error(
"The engine is not supported.",
exception=TSNotImplementedError
)
raise TSNotImplementedError("The engine is not supported.")


def unit_energy(engine: str):
Expand All @@ -279,10 +266,7 @@ def unit_energy(engine: str):
"""
if engine == "dftb+":
return "Hartree"
logger.error(
"The engine is not supported.",
exception=TSNotImplementedError
)
raise TSNotImplementedError("The engine is not supported.")


def unit_mass(engine: str):
Expand All @@ -306,10 +290,7 @@ def unit_mass(engine: str):
"""
if engine == "dftb+":
return "amu"
logger.error(
"The engine is not supported.",
exception=TSNotImplementedError
)
raise TSNotImplementedError("The engine is not supported.")


def unit_frequency(engine: str):
Expand All @@ -333,10 +314,7 @@ def unit_frequency(engine: str):
"""
if engine == "dftb+":
return "cm^-1"
logger.error(
"The engine is not supported.",
exception=TSNotImplementedError
)
raise TSNotImplementedError("The engine is not supported.")


def _atoms_from_ase(atoms):
Expand Down Expand Up @@ -416,9 +394,8 @@ def run_thermo(

expected_dof = dof(atom_list)
if len(vibrational_frequencies) < expected_dof:
logger.error(
"The number of vibrational frequencies does not match with the degree of freedom.",
exception=TSValueError
raise TSValueError(
"The number of vibrational frequencies does not match with the degree of freedom."
)

system_info = System(
Expand Down
48 changes: 10 additions & 38 deletions ThermoScreening/thermo/atoms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,54 +81,35 @@ def __init__(
"""

if symbol is None and number is None:
self.logger.error(
"Either symbol or number has to be given to initialize the atom.",
exception=TSValueError
)
raise TSValueError("Either symbol or number has to be given to initialize the atom.")

if symbol is not None and number is not None:
if number != atomicNumbers[symbol.lower()]:
self.logger.error(
"The symbol and atomic number are not consistent.",
exception=TSValueError
)
raise TSValueError("The symbol and atomic number are not consistent.")
if number is not None:
self._number = number
try:
self._symbol = atomic_Symbol[int(number)].capitalize()
except:
self.logger.error(
f"The atomic number {number} is not known.",
exception=TSValueError
)
raise TSValueError(f"The atomic number {number} is not known.") from None
self._mass = atomicMasses[self._symbol.lower()]
self._configuration = atomicElectronConfigurations[self._symbol.lower()]
else:
self._symbol = symbol
try:
self._number = atomicNumbers[symbol.lower()]
except:
self.logger.error(
f"The chemical symbol {symbol} is not known.",
exception=TSValueError
)
raise TSValueError(f"The chemical symbol {symbol} is not known.") from None
self._mass = atomicMasses[symbol.lower()]
self._configuration = atomicElectronConfigurations[symbol.lower()]

if position is None:
self.logger.error(
"The position of the atom has to be given to initialize the atom.",
exception=TSValueError
)
raise TSValueError("The position of the atom has to be given to initialize the atom.")

else:
self._position = position
self._position = position

if len(position) != 3:
self.logger.error(
"The position of the atom has to be a 3D vector.",
exception=TSValueError
)
raise TSValueError("The position of the atom has to be a 3D vector.")

@property
def symbol(self):
Expand Down Expand Up @@ -194,10 +175,7 @@ def position(self, array):
If the length of the position is not 3.
"""
if len(array) != 3:
self.logger.error(
"The position of the atom has to be a 3D vector.",
exception=TSValueError
)
raise TSValueError("The position of the atom has to be a 3D vector.")
self._position = array

def change_atom(
Expand Down Expand Up @@ -226,10 +204,7 @@ def change_atom(
try:
self._number = atomicNumbers[self._symbol.lower()]
except:
self.logger.error(
f"The chemical symbol {symbol} is not known.",
exception=TSValueError
)
raise TSValueError(f"The chemical symbol {symbol} is not known.") from None

self._mass = atomicMasses[symbol.lower()]
self._configuration = atomicElectronConfigurations[symbol.lower()]
Expand All @@ -239,10 +214,7 @@ def change_atom(
try:
self._symbol = atomic_Symbol[int(number)].capitalize()
except:
self.logger.error(
f"The atomic number {number} is not known.",
exception=TSValueError
)
raise TSValueError(f"The atomic number {number} is not known.") from None
self._mass = atomicMasses[self._symbol.lower()]
self._configuration = atomicElectronConfigurations[self._symbol.lower()]
if position is not None:
Expand Down
20 changes: 4 additions & 16 deletions ThermoScreening/thermo/inputFileReader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,10 +52,7 @@ def __init__(
None
"""
if input_file is None:
self.logger.error(
"The input file has to be given to initialize the InputFileReader.",
exception=TSValueError,
)
raise TSValueError("The input file has to be given to initialize the InputFileReader.")
self._input_file = input_file
self._read()
self._check()
Expand All @@ -78,10 +75,7 @@ def _read(self):
if not line or line.startswith("#"):
continue
if "=" not in line:
self.logger.error(
f"The line '{line}' is not a valid key-value assignment.",
exception=TSValueError,
)
raise TSValueError(f"The line '{line}' is not a valid key-value assignment.")
key, value = line.split("=", maxsplit=1)
self._dictionary[key.strip()] = value.strip()

Expand Down Expand Up @@ -118,10 +112,7 @@ def _check_required_keys(self):
"""
for key in self.required_keys:
if key not in self._dictionary.keys():
self.logger.error(
f"The key {key} is not set in the input file.",
exception=TSValueError
)
raise TSValueError(f"The key {key} is not set in the input file.")


def _check_known_keys(self):
Expand All @@ -139,8 +130,5 @@ def _check_known_keys(self):
"""
for key in self._dictionary.keys():
if key not in self.required_keys:
self.logger.error(
f"The key {key} is not known.",
exception=TSValueError
)
raise TSValueError(f"The key {key} is not known.")

37 changes: 9 additions & 28 deletions ThermoScreening/thermo/system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,11 +104,8 @@ def linearity(atoms: List[Atom]) -> bool:
If the number of atoms is 1.
"""
if len(atoms) == 1:
System.logger.error(
"Number of atoms must be greater than 1. The system is monoatomic.",
exception=TSValueError
)
elif len(atoms) == 2:
raise TSValueError("Number of atoms must be greater than 1. The system is monoatomic.")
if len(atoms) == 2:
return True

masses = np.array([atom.mass for atom in atoms], dtype=float)
Expand Down Expand Up @@ -172,9 +169,8 @@ def dimensionality(atoms: List[Atom]) -> int:
and np.array_equal(y, zero_array)
and np.array_equal(x, zero_array)
):
ValueError("The system is 0D!")
else:
return 3
raise TSValueError("The system is 0D!") # pragma: no cover
return 3


def dim(atoms: List[Atom]) -> int:
Expand All @@ -201,10 +197,7 @@ def dim(atoms: List[Atom]) -> int:
return 1
if number_of_atoms > 1:
return dimensionality(atoms)
System.logger.error(
"The number of atoms must be greater than 0.",
exception=TSValueError
)
raise TSValueError("The number of atoms must be greater than 0.")


def dof(atoms: List[Atom]) -> int:
Expand Down Expand Up @@ -234,10 +227,7 @@ def dof(atoms: List[Atom]) -> int:
return (
(3 * number_of_atoms - 5) if linearity(atoms) else (3 * number_of_atoms - 6)
)
System.logger.error(
"The number of atoms must be greater than 0.",
exception=TSValueError
)
raise TSValueError("The number of atoms must be greater than 0.")


def spin(charge: float) -> float:
Expand Down Expand Up @@ -628,22 +618,13 @@ def __init__(
"""

if atoms is None:
self.logger.error(
"Atoms must be provided.",
exception=TSValueError
)
raise TSValueError("Atoms must be provided.")

if len(atoms) == 0:
self.logger.error(
"The number of atoms must be greater than 0.",
exception=TSValueError
)
raise TSValueError("The number of atoms must be greater than 0.")

if vibrational_frequencies is None:
self.logger.error(
"Vibrational frequencies must be provided.",
exception=TSValueError
)
raise TSValueError("Vibrational frequencies must be provided.")

self._atoms = atoms
self._charge = charge
Expand Down
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