More type annotations #3800
More type annotations #3800
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TestGrainBoundary setUpClass -> setUp, helps language server infer types of class attributes
WalkthroughThe recent updates across various files in the Python library focus on refining method definitions and documentation for improved code clarity and type checking. Changes include adding return type hints, updating docstrings, and transitioning setup methods in the test suite from class-level to instance-level for enhanced flexibility and clarity during testing. Changes
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Actionable comments posted: 16
Out of diff range and nitpick comments (20)
pymatgen/analysis/elasticity/elastic.py (6)
Line range hint
57-63: Ensure proper documentation for constructor parameters.The constructor of
NthOrderElasticTensorlacks detailed documentation for its parametersinput_arrayandcheck_rank. It's crucial for maintainability and usability that all parameters are well-documented, especially in a complex domain like tensor mathematics.
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80-86: Consider optimizing the strain shape conversion.The method
calculate_stressconverts strain from Voigt to full tensor notation if needed. This conversion could be optimized or cached if strains are frequently in Voigt notation to avoid redundant calculations.
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88-94: Clarify the unit conversion inenergy_density.The method
energy_densityincludes a unit conversion step which might not be immediately clear to all users. Consider adding a comment explaining why this conversion is necessary and what units are being converted from and to.
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108-114: Validate tensor shape inElasticTensorconstructor.The constructor of
ElasticTensorshould explicitly check that theinput_arrayis of shape 3x3x3x3. Currently, it relies on the superclass constructor, which does not enforce this specific shape.
Line range hint
116-120: Optimize the calculation ofcompliance_tensor.The property
compliance_tensorcalculates the inverse of the Voigt matrix every time it is accessed. Consider caching this value or using a lazy evaluation pattern to improve performance, especially if this property is accessed frequently.
Line range hint
152-160: Improve error message clarity indirectional_poisson_ratio.The error message "n and m must be orthogonal" in the
directional_poisson_ratiomethod could be more informative. Consider including the values ofnandmin the error message to aid debugging.pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py (4)
685-685: Ensure themp_symbolproperty has a clear docstring.Consider adding a more detailed docstring for the
mp_symbolproperty to explain what an MP symbol is and its relevance.
690-691: Ensure consistency in property descriptions.The docstring for the
ce_symbolproperty could be improved for clarity. Consider specifying what "CE" stands for and how it relates to the MP symbol.
712-712: Clarify the purpose of theIUPAC_symbol_strproperty.The
IUPAC_symbol_strproperty seems redundant since it merely converts theIUPAC_symbolto a string, which is its inherent type. Consider removing this property if it does not serve a specific purpose.
Line range hint
972-997: Review the dictionary construction methods.The methods
get_symbol_name_mappingandget_symbol_cn_mappingcontain duplicate logic. Consider creating a private helper method to reduce code duplication and improve maintainability.+ def _get_mapping(self, key, coordination=None): + geom = {} + for coord_geom in self.cg_list: + if coordination is None or coord_geom.get_coordination_number() == coordination: + geom[getattr(coord_geom, key)] = getattr(coord_geom, key) + return geom - # Replace calls to `get_symbol_name_mapping` and `get_symbol_cn_mapping` with `_get_mapping('mp_symbol')` and `_get_mapping('name')`pymatgen/io/abinit/abiobjects.py (5)
917-917: Ensure thepath_from_structuremethod has a clear docstring.Adding a docstring to the
path_from_structuremethod would improve code readability and maintainability by clearly explaining the purpose and usage of the method.
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1-1: Consider adding type hints to thelattice_from_abivarsfunction.Adding type hints to the function parameters and return type would enhance code readability and maintainability, making it easier to understand the expected types of the inputs and output.
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1-1: Refactor thelattice_from_abivarsfunction to reduce complexity.The function
lattice_from_abivarsis quite complex and handles multiple scenarios. Consider breaking it down into smaller, more focused functions to improve readability and maintainability.
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1-1: Add error handling for missing required keys instructure_from_abivars.The function
structure_from_abivarsassumes that certain keys likeacellandtypatare always present in the input dictionary. Consider adding checks and raising appropriate exceptions if these keys are missing to prevent runtime errors.
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1-1: Optimize the handling of coordinate transformations instructure_from_abivars.The coordinate transformation logic in
structure_from_abivarscould be optimized by extracting it into a separate function or method. This would make the main function cleaner and more focused on its primary responsibility.pymatgen/io/abinit/pseudos.py (1)
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590-625: The function_dict_from_linesis designed to parse formatted text into a dictionary. However, there are a few issues and improvements that can be made:
- The function assumes that
key_numsis iterable, which might not always be the case. It's safer to ensure it's a list or tuple before proceeding.- The error handling could be more descriptive, especially when the lengths of
linesandkey_numsdo not match.- The use of
Namespaceforkwargsis unconventional. A simple dictionary would suffice and be more understandable.- The function modifies
keysin-place, which can lead to unexpected behavior. It's better to create a new list for sanitized keys.- if not isinstance(key_nums, collections.abc.Iterable): - key_nums = list(key_nums) + if not isinstance(key_nums, (list, tuple)): + raise TypeError("key_nums must be a list or tuple") - kwargs = Namespace() + kwargs = {} - keys = "".join(tokens[nk:]).replace("[", "").replace("]", "").split(",") + sanitized_keys = [key.replace("[", "").replace("]", "") for key in tokens[nk:].split(",")] + keys = sanitized_keyspymatgen/analysis/surface_analysis.py (1)
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1293-1307: Add type annotations to the function parameters and return type forentry_dict_from_list.- def entry_dict_from_list(all_slab_entries) -> dict: + def entry_dict_from_list(all_slab_entries: List[SlabEntry]) -> Dict[Tuple, Dict]:This change improves the readability and maintainability of the code by making the expected types of the function parameters and return value explicit.
pymatgen/core/structure.py (3)
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318-327: Consider adding type hints for the__init__method parameters to enhance code readability and maintainability.- def __init__( + def __init__(self,
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349-350: Consider adding type hints for the__init__method parameters to enhance code readability and maintainability.- def __init__( + def __init__(self,
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372-373: Consider adding type hints for the__init__method parameters to enhance code readability and maintainability.- def __init__( + def __init__(self,
| @@ -494,7 +494,7 @@ def wulff_from_chempot( | |||
| symprec=1e-5, | |||
| no_clean=False, | |||
| no_doped=False, | |||
| ): | |||
| ) -> WulffShape: | |||
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Ensure the wulff_from_chempot method handles exceptions or errors gracefully.
Consider adding error handling or logging to manage potential issues with input validation or during execution, such as when delu_dict keys do not match expected symbols or when calculations fail due to unexpected input values.
| values = tokens[:nk] | ||
| # Sanitize keys: In some case we might get strings in the form: foo[,bar] | ||
| keys.replace("[", "").replace("]", "") | ||
| keys = keys.split(",") | ||
| keys = "".join(tokens[nk:]).replace("[", "").replace("]", "").split(",") |
There was a problem hiding this comment.
The handling of the separator in _dict_from_lines function is potentially error-prone. The function checks if the first character of the first key matches the separator but does not handle cases where the separator might not be present, which could lead to incorrect parsing or errors.
- if sep is not None:
- check = keys[0][0]
- if check != sep:
- raise ValueError(f"Expecting separator {sep}, got {check}")
- keys[0] = keys[0][1:]
+ if sep is not None:
+ if not keys[0].startswith(sep):
+ raise ValueError(f"Expecting separator {sep} at the start of {keys[0]}")
+ keys = [key.lstrip(sep) for key in keys]Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| values = tokens[:nk] | |
| # Sanitize keys: In some case we might get strings in the form: foo[,bar] | |
| keys.replace("[", "").replace("]", "") | |
| keys = keys.split(",") | |
| keys = "".join(tokens[nk:]).replace("[", "").replace("]", "").split(",") | |
| values = tokens[:nk] | |
| # Sanitize keys: In some case we might get strings in the form: foo[,bar] | |
| keys = "".join(tokens[nk:]).replace("[", "").replace("]", "").split(",") | |
| if sep is not None: | |
| if not keys[0].startswith(sep): | |
| raise ValueError(f"Expecting separator {sep} at the start of {keys[0]}") | |
| keys = [key.lstrip(sep) for key in keys] |
| @@ -532,7 +532,7 @@ def summary(self): | |||
| return summary | |||
|
|
|||
| @staticmethod | |||
| def _get_data_from_xyz(xyz_path): | |||
| def _get_data_from_xyz(xyz_path) -> list[float]: | |||
There was a problem hiding this comment.
Consider adding error handling for file operations.
The method _get_data_from_xyz opens a file without using a context manager, which could lead to resources not being freed if an exception occurs. Consider using a with statement to handle the file opening and reading.
- with open(xyz_path) as r:
+ with open(xyz_path, 'r') as r:Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| def _get_data_from_xyz(xyz_path) -> list[float]: | |
| def _get_data_from_xyz(xyz_path) -> list[float]: | |
| with open(xyz_path, 'r') as r: |
| @@ -556,7 +556,7 @@ def _get_data_from_xyz(xyz_path): | |||
| return props | |||
|
|
|||
| @staticmethod | |||
| def _get_cm5_data_from_output(ddec_analysis_path): | |||
| def _get_cm5_data_from_output(ddec_analysis_path) -> list[float]: | |||
There was a problem hiding this comment.
Ensure consistent error handling in file operations.
Similar to the previous method, _get_cm5_data_from_output opens a file directly. It's recommended to use a context manager here as well to ensure that the file is properly closed after its contents are processed.
- with open(ddec_analysis_path) as r:
+ with open(ddec_analysis_path, 'r') as r:Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| def _get_cm5_data_from_output(ddec_analysis_path) -> list[float]: | |
| def _get_cm5_data_from_output(ddec_analysis_path) -> list[float]: |
| @@ -497,7 +497,7 @@ def _get_filepath(filename): | |||
| ) | |||
|
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|
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| def bader_analysis_from_path(path: str, suffix: str = ""): | |||
| def bader_analysis_from_path(path: str, suffix: str = "") -> dict[str, Any]: | |||
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Consider refining the error handling for file operations.
The function bader_analysis_from_path uses the glob function to find files but does not handle the case where files are not found effectively. It raises a FileNotFoundError if the CHGCAR file is not found, but similar handling is not present for other critical files like AECCAR0 and AECCAR2. Consider adding explicit error handling for these cases to avoid runtime errors.
- if not aeccar0_path:
+ if aeccar0_path is None:
raise FileNotFoundError("Could not find AECCAR0!")
- if not aeccar2_path:
+ if aeccar2_path is None:
raise FileNotFoundError("Could not find AECCAR2!")Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| def bader_analysis_from_path(path: str, suffix: str = "") -> dict[str, Any]: | |
| def bader_analysis_from_path(path: str, suffix: str = "") -> dict[str, Any]: |
| exp_entries: list of dictionary objects with the following keys/values: { | ||
| "formula": chemical formula, | ||
| "exp energy": formation energy in eV/formula unit, | ||
| "uncertainty": uncertainty in formation energy | ||
| } |
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Consider refactoring compute_corrections to separate data validation from the core computation logic for better maintainability.
| @@ -848,7 +848,7 @@ def __init__(self, permutations_safe_override=False, only_symbols=None): | |||
| only_symbols: Whether to restrict the list of environments to be identified. | |||
| """ | |||
| dict.__init__(self) | |||
| self.cg_list = [] | |||
| self.cg_list: list[CoordinationGeometry] = [] | |||
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Review the initialization of cg_list.
The initialization of cg_list directly within the constructor without checking if the file exists or handling potential JSON parsing errors could lead to runtime exceptions. Consider adding error handling mechanisms.
+ try:
+ with open(cg_file) as file:
+ dd = json.load(file)
+ self.cg_list.append(CoordinationGeometry.from_dict(dd))
+ except (IOError, json.JSONDecodeError) as e:
+ logging.error(f"Failed to load coordination geometry from {cg_file}: {str(e)}")Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| self.cg_list: list[CoordinationGeometry] = [] | |
| try: | |
| with open(cg_file) as file: | |
| dd = json.load(file) | |
| self.cg_list.append(CoordinationGeometry.from_dict(dd)) | |
| except (IOError, json.JSONDecodeError) as e: | |
| logging.error(f"Failed to load coordination geometry from {cg_file}: {str(e)}") |
| for coord_geom in self.cg_list: | ||
| if returned == "cg": | ||
| geom.append(gg) | ||
| geom.append(coord_geom) | ||
| elif returned == "mp_symbol": | ||
| geom.append(gg.mp_symbol) | ||
| geom.append(coord_geom.mp_symbol) | ||
| else: | ||
| for gg in self.cg_list: | ||
| if gg.get_coordination_number() == coordination: | ||
| for coord_geom in self.cg_list: | ||
| if coord_geom.get_coordination_number() == coordination: | ||
| if returned == "cg": | ||
| geom.append(gg) | ||
| geom.append(coord_geom) | ||
| elif returned == "mp_symbol": | ||
| geom.append(gg.mp_symbol) | ||
| geom.append(coord_geom.mp_symbol) |
There was a problem hiding this comment.
Review the method get_geometries.
The method get_geometries can be optimized by removing redundant checks and simplifying the logic. Consider refactoring to improve readability and performance.
- if coordination is None:
- for coord_geom in self.cg_list:
- if returned == "cg":
- geom.append(coord_geom)
- elif returned == "mp_symbol":
- geom.append(coord_geom.mp_symbol)
- else:
- for coord_geom in self.cg_list:
- if coord_geom.get_coordination_number() == coordination:
- if returned == "cg":
- geom.append(coord_geom)
- elif returned == "mp_symbol":
- geom.append(coord_geom.mp_symbol)
+ for coord_geom in self.cg_list:
+ if coordination is None or coord_geom.get_coordination_number() == coordination:
+ geom.append(coord_geom if returned == "cg" else coord_geom.mp_symbol)Committable suggestion
‼️ IMPORTANT
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| for coord_geom in self.cg_list: | |
| if returned == "cg": | |
| geom.append(gg) | |
| geom.append(coord_geom) | |
| elif returned == "mp_symbol": | |
| geom.append(gg.mp_symbol) | |
| geom.append(coord_geom.mp_symbol) | |
| else: | |
| for gg in self.cg_list: | |
| if gg.get_coordination_number() == coordination: | |
| for coord_geom in self.cg_list: | |
| if coord_geom.get_coordination_number() == coordination: | |
| if returned == "cg": | |
| geom.append(gg) | |
| geom.append(coord_geom) | |
| elif returned == "mp_symbol": | |
| geom.append(gg.mp_symbol) | |
| geom.append(coord_geom.mp_symbol) | |
| for coord_geom in self.cg_list: | |
| if coordination is None or coord_geom.get_coordination_number() == coordination: | |
| geom.append(coord_geom if returned == "cg" else coord_geom.mp_symbol) |
| def copy(self) -> Self: | ||
| """Returns a copy of itself. Concrete subclasses should implement this |
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Consider adding type hints for the __init__ method parameters to enhance code readability and maintainability.
- def __init__(
+ def __init__(self,Committable suggestion
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| def copy(self) -> Self: | |
| """Returns a copy of itself. Concrete subclasses should implement this | |
| def copy(self) -> Self: | |
| """Returns a copy of itself. Concrete subclasses should implement this |
| def copy(self) -> Self: | ||
| """Convenience method to get a copy of the molecule. |
There was a problem hiding this comment.
Consider adding type hints for the __init__ method parameters to enhance code readability and maintainability.
- def __init__(
+ def __init__(self,Committable suggestion
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| def copy(self) -> Self: | |
| """Convenience method to get a copy of the molecule. | |
| def copy(self) -> Self: | |
| """Convenience method to get a copy of the molecule. |
…False properties on AbstractTransformation subclasses
…r methods and 'Returns:'->'' for properties
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Actionable comments posted: 14
Out of diff range and nitpick comments (13)
pymatgen/phonon/gruneisen.py (1)
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138-170: Refactor the methodthermal_conductivity_slackfor better readability and efficiency.The method
thermal_conductivity_slackin theGruneisenParameterclass can be refactored for better readability and to avoid redundant calculations. Consider extracting parts of the formula into separate methods or variables.def thermal_conductivity_slack( self, squared: bool = True, limit_frequencies: Literal["debye", "acoustic"] | None = None, theta_d: float | None = None, t: float | None = None, ) -> float: """Calculate the thermal conductivity at the acoustic Debye temperature with the Slack formula, using the average Gruneisen. Adapted from abipy. Args: squared (bool): if True the average is performed on the squared values of the Gruneisen limit_frequencies: if None (default) no limit on the frequencies will be applied. Possible values are "debye" (only modes with frequencies lower than the acoustic Debye temperature) and "acoustic" (only the acoustic modes, i.e. the first three modes). theta_d: the temperature used to estimate the average of the Gruneisen used in the Slack formula. If None the acoustic Debye temperature is used (see acoustic_debye_temp). Will also be considered as the Debye temperature in the Slack formula. t: temperature at which the thermal conductivity is estimated. If None the value at the calculated acoustic Debye temperature is given. The value is obtained as a simple rescaling of the value at the Debye temperature. Returns: The value of the thermal conductivity in W/(m*K) """ assert self.structure is not None, "Structure is not defined." average_mass = np.mean([s.specie.atomic_mass for s in self.structure]) * amu_to_kg if theta_d is None: theta_d = self.acoustic_debye_temp mean_g = self.average_gruneisen(t=theta_d, squared=squared, limit_frequencies=limit_frequencies) f1 = 0.849 * 3 * (4 ** (1 / 3)) / (20 * np.pi**3 * (1 - 0.514 * mean_g**-1 + 0.228 * mean_g**-2)) f2 = (const.k * theta_d / const.hbar) ** 2 f3 = const.k * average_mass * self.structure.volume ** (1 / 3) * 1e-10 / (const.hbar * mean_g**2) thermal_cond = f1 * f2 * f3 if t is not None: thermal_cond *= theta_d / t return thermal_condpymatgen/transformations/standard_transformations.py (2)
399-399: Ensure consistency in method documentation.The method
is_one_to_manyinPartialRemoveSpecieTransformationclass lacks a docstring. Consider adding a brief description to maintain consistency with other methods in the class.
584-584: Ensure consistency in method documentation.The method
is_one_to_manyinOrderDisorderedStructureTransformationclass lacks a docstring. Consider adding a brief description to maintain consistency with other methods in the class.pymatgen/io/cif.py (2)
1611-1612: Ensure thecif_fileproperty inCifWriteris documented.While the property is implemented correctly, adding a docstring would improve code maintainability and clarity, especially for new developers or external contributors who might use this class.
1611-1612: Consider adding a docstring to thecif_fileproperty inCifWriter.A docstring would help clarify the purpose and usage of this property, improving code readability and maintainability.
pymatgen/transformations/advanced_transformations.py (8)
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53-53: Ensure proper documentation for the constructor parameters.Consider adding parameter descriptions in the docstring for
__init__to enhance code readability and maintainability.
Line range hint
59-59: Handle potential division by zero.- num_to_remove = (charge / specie.oxi_state) if specie.oxi_state else 0.0 + if specie.oxi_state == 0: + raise ValueError("Oxidation state cannot be zero for charge balancing.") + num_to_remove = charge / specie.oxi_stateThis change ensures that the code raises an informative error when attempting to divide by zero, which could occur if
specie.oxi_stateis zero.
93-93: Clarify the type oftransformationsparameter.The
transformationsparameter in the constructor should specify the expected type more clearly, possibly using a type hint likeList[AbstractTransformation].
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99-99: Improve error message for clarity.- raise ValueError("SuperTransformation has no single best structure output. Must use return_ranked_list") + raise ValueError("SuperTransformation requires 'return_ranked_list' to be set to an integer to specify the number of structures to return.")This modification provides a clearer instruction on how to use the
return_ranked_listparameter correctly.
Line range hint
183-183: Validater_fractionto prevent logical errors.+ if not (0 <= r_fraction <= 1): + raise ValueError("Replacement fraction must be between 0 and 1.")Adding this validation ensures that the replacement fraction is within a logical range, preventing potential runtime errors or unexpected behavior.
Line range hint
199-199: Handle potential division by zero.- dummy_sp = f"X{charge}{sign}" + if charge == 0: + raise ValueError("Charge cannot be zero when defining a dummy species.") + dummy_sp = f"X{charge}{sign}"This change prevents a division by zero error that could occur later in the code when
chargeis used in calculations.
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328-328: Validatemax_cell_sizeandmax_disordered_sitesto prevent conflicting settings.+ if max_cell_size is not None and max_disordered_sites is not None: + raise ValueError("Specify either 'max_cell_size' or 'max_disordered_sites', not both.")This validation prevents the user from setting both parameters, which are mutually exclusive and could lead to ambiguous behavior.
Line range hint
502-502: Clarify the exception message for unsupported operations.- raise ValueError("SubstitutionPredictorTransformation doesn't support returning 1 structure") + raise ValueError("SubstitutionPredictorTransformation requires 'return_ranked_list' to be set to an integer greater than 1.")This change clarifies the requirements for using the
return_ranked_listparameter, ensuring that users understand it must be an integer greater than 1.
| @@ -506,7 +506,7 @@ def __init__( | |||
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|||
| @property | |||
| def icohplist(self) -> dict[Any, dict[str, Any]]: | |||
| """Returns: icohplist compatible with older version of this class.""" | |||
| """The ICOHP list compatible with older version of this class.""" | |||
There was a problem hiding this comment.
Consider adding a more detailed docstring for the icohplist property.
The current docstring does not provide information about the structure and content of the returned dictionary. Enhancing the docstring would improve code readability and maintainability.
| @@ -520,7 +520,7 @@ def icohplist(self) -> dict[Any, dict[str, Any]]: | |||
|
|
|||
| @property | |||
| def icohpcollection(self): | |||
| """Returns: IcohpCollection object.""" | |||
| """The IcohpCollection object.""" | |||
There was a problem hiding this comment.
Ensure the icohpcollection property has a complete docstring.
The docstring for the icohpcollection property is missing details about the return type and the structure of the returned object. Providing this information would aid developers in understanding the method's purpose and usage.
| @@ -4,7 +4,7 @@ | |||
|
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|||
| import re | |||
| from collections import defaultdict | |||
| from typing import TYPE_CHECKING | |||
| from typing import TYPE_CHECKING, Any | |||
There was a problem hiding this comment.
Consider using more specific type hints for better type checking and clarity.
- from typing import TYPE_CHECKING, Any
+ from typing import TYPE_CHECKING, Any, Dict, List, OptionalCommittable suggestion
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| from typing import TYPE_CHECKING, Any | |
| from typing import TYPE_CHECKING, Any, Dict, List, Optional |
| @@ -520,7 +520,7 @@ def __init__(self, filename): | |||
| filename (str): Filename. | |||
| """ | |||
| self.filename = filename | |||
| self.data: dict[str, list[float] | float] = defaultdict(list) | |||
| self.data: dict[str, Any] = defaultdict(list) | |||
There was a problem hiding this comment.
Ensure that the type hint for data is specified for better code clarity and type checking.
- self.data: dict[str, Any] = defaultdict(list)
+ self.data: Dict[str, List[Any]] = defaultdict(list)Committable suggestion
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| self.data: dict[str, Any] = defaultdict(list) | |
| self.data: Dict[str, List[Any]] = defaultdict(list) |
| return CriticalPointType(self._type) | ||
|
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| def __str__(self): | ||
| return f"Critical Point: {self.type.name} ({self.frac_coords})" | ||
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| @property | ||
| def laplacian(self) -> float: | ||
| """Returns: The Laplacian of the field at the critical point.""" | ||
| """The Laplacian of the field at the critical point.""" |
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Consider adding error handling for cases where the Hessian matrix is not square.
- return np.trace(self.field_hessian)
+ if self.field_hessian.shape == (3, 3):
+ return np.trace(self.field_hessian)
+ else:
+ raise ValueError("Hessian matrix must be 3x3.")Committable suggestion
‼️ IMPORTANT
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| """The Laplacian of the field at the critical point.""" | |
| """The Laplacian of the field at the critical point.""" | |
| if self.field_hessian.shape == (3, 3): | |
| return np.trace(self.field_hessian) | |
| else: | |
| raise ValueError("Hessian matrix must be 3x3.") |
Add documentation for the ellipticity property to clarify its calculation and usage.
- """Most meaningful for bond critical points, can be physically interpreted as e.g.
- degree of pi-bonding in organic molecules. Consult literature for more info.
+ """
+ Ellipticity of the field at the critical point.
+
+ This property is most meaningful for bond critical points and can be physically interpreted, for example,
+ as the degree of pi-bonding in organic molecules. For more detailed information, consult the relevant literature.
+
+ Returns:
+ float: The ellipticity of the field at the critical point.Committable suggestion
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| """The Laplacian of the field at the critical point.""" | |
| """The Laplacian of the field at the critical point. | |
| Ellipticity of the field at the critical point. | |
| This property is most meaningful for bond critical points and can be physically interpreted, for example, | |
| as the degree of pi-bonding in organic molecules. For more detailed information, consult the relevant literature. | |
| Returns: | |
| float: The ellipticity of the field at the critical point. | |
| """ |
Validate the dimensions of the Hessian matrix before computing its trace.
- return np.trace(self.field_hessian)
+ if self.field_hessian.shape == (3, 3):
+ return np.trace(self.field_hessian)
+ else:
+ raise ValueError("Hessian matrix must be 3x3.")Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| """The Laplacian of the field at the critical point.""" | |
| """The Laplacian of the field at the critical point.""" | |
| if self.field_hessian.shape == (3, 3): | |
| return np.trace(self.field_hessian) | |
| else: | |
| raise ValueError("Hessian matrix must be 3x3.") |
| @@ -74,7 +74,7 @@ class HistoryNode(namedtuple("HistoryNode", ["name", "url", "description"])): | |||
| __slots__ = () | |||
|
|
|||
| def as_dict(self) -> dict[str, str]: | |||
| """Returns: Dict.""" | |||
| """Get MSONable dict.""" | |||
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Ensure consistent return types in as_dict method.
The as_dict method in the HistoryNode class should consistently return a dictionary with string keys and values. The current implementation may not handle non-string descriptions properly.
def as_dict(self) -> dict[str, str]:
"""Get MSONable dict."""
- return {"name": self.name, "url": self.url, "description": self.description}
+ return {"name": self.name, "url": self.url, "description": str(self.description)}Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| """Get MSONable dict.""" | |
| def as_dict(self) -> dict[str, str]: | |
| """Get MSONable dict.""" | |
| return {"name": self.name, "url": self.url, "description": str(self.description)} |
| @@ -118,7 +118,7 @@ def __str__(self): | |||
| return f"{self.name} <{self.email}>" | |||
|
|
|||
| def as_dict(self): | |||
| """Returns: MSONable dict.""" | |||
| """Get MSONable dict.""" | |||
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Clarify the expected dictionary structure in as_dict method.
In the as_dict method of the Author class, consider adding a docstring that clearly specifies the structure of the returned dictionary, especially the types of the values.
def as_dict(self) -> dict:
+ """Return a dictionary representation of the Author.
+ Returns:
+ dict: A dictionary with 'name' and 'email' as keys and their corresponding values as strings.
+ """
return {"name": self.name, "email": self.email}Committable suggestion
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| """Get MSONable dict.""" | |
| def as_dict(self) -> dict: | |
| """Return a dictionary representation of the Author. | |
| Returns: | |
| dict: A dictionary with 'name' and 'email' as keys and their corresponding values as strings. | |
| """ | |
| return {"name": self.name, "email": self.email} |
| def atomic_background(self) -> np.ndarray: | ||
| """The atomic background of EELS.""" |
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Add error handling for file operations in atomic_background.
The method atomic_background in the Eels class should include error handling for file operations to manage potential issues with file access or content.
def atomic_background(self) -> np.ndarray:
"""The atomic background of EELS."""
+ try:
+ return self.data[:, 2]
+ except Exception as e:
+ raise RuntimeError("Failed to access atomic background data: " + str(e))Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| def atomic_background(self) -> np.ndarray: | |
| """The atomic background of EELS.""" | |
| def atomic_background(self) -> np.ndarray: | |
| """The atomic background of EELS.""" | |
| try: | |
| return self.data[:, 2] | |
| except Exception as e: | |
| raise RuntimeError("Failed to access atomic background data: " + str(e)) |
| def fine_structure(self) -> np.ndarray: | ||
| """The fine structure of EELS.""" |
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Validate input parameters in fine_structure.
In the fine_structure method of the Eels class, consider validating the input parameters to ensure they meet expected conditions before processing.
def fine_structure(self) -> np.ndarray:
+ if not isinstance(self.data, np.ndarray):
+ raise ValueError("Expected data to be a numpy array")
"""The fine structure of EELS."""
return self.data[:, 3]Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| def fine_structure(self) -> np.ndarray: | |
| """The fine structure of EELS.""" | |
| def fine_structure(self) -> np.ndarray: | |
| """The fine structure of EELS.""" | |
| if not isinstance(self.data, np.ndarray): | |
| raise ValueError("Expected data to be a numpy array") | |
| return self.data[:, 3] |
|
|
||
| @property | ||
| def phdos(self) -> PhononDos: | ||
| """Returns: PhononDos object.""" | ||
| """The phonon DOS (re)constructed from the gruneisen.yaml file.""" |
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Ensure the phdos property correctly handles potential exceptions.
The phdos property in the GruneisenPhononBandStructure class should include error handling to manage cases where the DOS data might be incomplete or malformed.
@property
def phdos(self) -> PhononDos:
+ try:
"""The phonon DOS (re)constructed from the gruneisen.yaml file."""
return PhononDos(self.tdos.frequency_points, self.tdos.dos)
+ except Exception as e:
+ raise RuntimeError("Failed to construct phonon DOS: " + str(e))Committable suggestion
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| """The phonon DOS (re)constructed from the gruneisen.yaml file.""" | |
| @property | |
| def phdos(self) -> PhononDos: | |
| try: | |
| """The phonon DOS (re)constructed from the gruneisen.yaml file.""" | |
| return PhononDos(self.tdos.frequency_points, self.tdos.dos) | |
| except Exception as e: | |
| raise RuntimeError("Failed to construct phonon DOS: " + str(e)) |
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