Convert some staticmethod to classmethod
#3710
Conversation
WalkthroughThe recent updates in the pymatgen library focus on transitioning static methods to class methods, incorporating type hinting with Changes
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (invoked as PR comments)
Additionally, you can add CodeRabbit Configration File (
|
|
@coderabbitai review |
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Review Status
Actionable comments generated: 7
Configuration used: CodeRabbit UI
Files selected for processing (13)
- pymatgen/alchemy/transmuters.py (1 hunks)
- pymatgen/analysis/graphs.py (8 hunks)
- pymatgen/core/operations.py (3 hunks)
- pymatgen/io/abinit/pseudos.py (1 hunks)
- pymatgen/io/babel.py (2 hunks)
- pymatgen/io/cp2k/inputs.py (2 hunks)
- pymatgen/io/feff/inputs.py (2 hunks)
- pymatgen/io/pwmat/inputs.py (5 hunks)
- pymatgen/io/vasp/inputs.py (9 hunks)
- pymatgen/phonon/thermal_displacements.py (3 hunks)
- pymatgen/transformations/advanced_transformations.py (1 hunks)
- pymatgen/transformations/standard_transformations.py (3 hunks)
- pymatgen/util/provenance.py (4 hunks)
Files skipped from review due to trivial changes (1)
- pymatgen/transformations/advanced_transformations.py
Additional comments: 26
pymatgen/util/provenance.py (4)
- 79-88: The conversion of
from_dictto a class method inHistoryNodeis correctly implemented. Usingclsallows for better flexibility and inheritance support, aligning with the PR's objectives.- 99-109: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [90-106]
The conversion of
parse_history_nodeto a class method inHistoryNodeis correctly implemented. This change enhances the method's ability to work with inherited classes by utilizingcls.
- 132-139: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [135-142]
The conversion of
from_dictto a class method inAuthoris correctly implemented. This change is consistent with the PR's goal of enhancing class inheritance and flexibility.
- 149-160: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [136-157]
The conversion of
parse_authorto a class method inAuthoris correctly implemented. This method's adaptation to useclsimproves its compatibility with inheritance, aligning with the PR's objectives.pymatgen/io/babel.py (1)
- 333-340: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [336-347]
The conversion of
from_molecule_graphto a class method inBabelMolAdaptoris correctly implemented. Utilizingclsenhances the method's flexibility and inheritance capabilities, which is in line with the PR's objectives.pymatgen/alchemy/transmuters.py (1)
- 294-301: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [297-312]
The conversion of
from_filenamesto a class method inPoscarTransmuteris correctly implemented. However, the return type annotation isStandardTransmuterinstead ofSelf. UsingSelfas the return type would be more consistent with the PR's goal of enhancing class inheritance and flexibility.Consider using
Selfas the return type annotation forfrom_filenamesto better align with the PR's objectives and Python's typing conventions.pymatgen/core/operations.py (1)
- 58-64: The change from
@staticmethodto@classmethodfor thefrom_rotation_and_translationmethod, along with the update of the return type annotation fromSymmOptoSelf, is a positive modification. It aligns with the objective of enhancing flexibility and extensibility by leveraging class inheritance. Good job on making these changes.pymatgen/phonon/thermal_displacements.py (2)
- 18-22: Moving the
import phonopyblock to the top and wrapping it in a try-except block is a good practice for handling optional dependencies. Additionally, addingfrom typing_extensions import Selfis necessary for the changes made in the methodfrom_Ucifto useSelffor type hinting. These changes are well-implemented.- 414-420: The change from
@staticmethodto@classmethodfor thefrom_Ucifmethod, along with the update of the return type annotation from the class name toSelf, is a positive modification. It aligns with the objective of enhancing flexibility and extensibility by leveraging class inheritance. Well done on making these changes.pymatgen/io/pwmat/inputs.py (3)
- 16-16: The import of
Selffromtyping_extensionsis correctly added to support the use ofSelfin type annotations for class methods that return an instance of the class. This aligns with the PR's objective to enhance class design and maintain consistency.- 501-508: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [504-535]
The conversion of
from_structureto a class method in theGenKptclass is correctly implemented. Usingclsinstead of the class nameGenKptwhen returning an instance of the class enhances flexibility and supports inheritance, which is consistent with the PR's objectives.
- 603-610: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [606-618]
The conversion of
from_structureto a class method in theHighSymmetryPointclass is correctly implemented. The use ofclsto return an instance of the class instead of directly referencing the class name is a good practice for enhancing class flexibility and inheritance support.pymatgen/io/feff/inputs.py (1)
- 197-206: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [200-216]
The conversion of
from_cif_filefrom a static method to a class method is correctly implemented and aligns with the objectives of enhancing flexibility and extensibility in the pymatgen codebase. This change allows for better utilization of class inheritance when creating instances, which is a good practice for factory methods like this one.pymatgen/transformations/standard_transformations.py (1)
- 28-28: The import of
Selffromtyping_extensionsis correctly added to support the updated return type annotations. This is a good use of modern Python typing features to enhance code readability and maintainability.pymatgen/io/abinit/pseudos.py (1)
- 111-112: The change from
staticmethodtoclassmethodfor thefrom_filemethod in thePseudoclass is correctly implemented. Usingclsas the first argument allows for more flexible and dynamic instance creation that respects inheritance hierarchies. This modification aligns with the PR objectives to enhance the codebase's flexibility and extensibility.pymatgen/io/cp2k/inputs.py (1)
- 2129-2136: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [273-274]
In the
__eq__method of theSectionclass, the comparisond2.as_dict() == s2.as_dict()may not be the most efficient way to check for equality due to the potential overhead of converting the entire object tree to dictionaries. Consider implementing a more direct comparison method.pymatgen/io/vasp/inputs.py (6)
- 1141-1152: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [1146-1159]
The
gamma_automaticmethod in theKpointsclass correctly implements the creation of an automatic Gamma centered Kpoint grid. It's crucial to ensure that thekptsandshiftarguments are properly validated to prevent invalid configurations.
- 1156-1165: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [1161-1175]
The
monkhorst_automaticmethod in theKpointsclass is implemented correctly for generating an automatic Monkhorst pack Kpoint grid. Similar to previous methods, it's important to validate thekptsandshiftarguments.
- 1172-1181: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [1177-1215]
The
automatic_densitymethod in theKpointsclass provides a way to generate an automatic Kpoint object based on a structure and a kpoint density. This method is crucial for dynamic Kpoint generation. Ensure that thestructureandkppaarguments are validated and that the method correctly handles different lattice types and symmetry considerations.
- 1212-1221: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [1217-1249]
The
automatic_gamma_densitymethod in theKpointsclass is implemented to always use Gamma centered meshes for GW calculations. It's important to ensure that thestructureandkppaarguments are validated and that the method correctly calculates the number of divisions along reciprocal lattice vectors.
- 1267-1278: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [1251-1309]
The
automatic_density_by_lengthsmethod in theKpointsclass allows for specifying k-point density normalized by lattice constants. This method is particularly useful for high-throughput calculations where uniform k-point density across different structures is desired. Ensure that thestructureandlength_densitiesarguments are validated and that the method correctly handles different lattice types and symmetry considerations.
- 1306-1315: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [1311-1340]
The
automatic_linemodemethod in theKpointsclass is designed for generating KPOINTS in line mode, typically used for band structure calculations. It's important to ensure that thedivisionsandibzarguments are validated and that the method correctly handles high symmetry paths.pymatgen/analysis/graphs.py (4)
- 196-203: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [199-216]
The method
with_edgesinStructureGraphhas been correctly converted from a static method to a class method, utilizingclsto call another class methodwith_empty_graph. This change enhances flexibility and inheritance, aligning with the PR's objective. However, there's a minor improvement that can be made to the exception handling for edge tuples.Consider adding more specific error messages for different types of
TypeErrorthat could occur when unpackingedgetuples. This would help in debugging and understanding the exact nature of the error.- raise ValueError("Edges must be given as (from_index, to_index, from_image, to_image) tuples") + if len(edge) != 4: + raise ValueError("Edges must be given as (from_index, to_index, from_image, to_image) tuples") + else: + raise ValueError("Edge indices and images must be integers")
- 250-259: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [253-270]
The conversion of
with_local_env_strategyinStructureGraphto a class method is appropriate and follows the PR's objective. The use ofclsto callwith_empty_graphis consistent with the objective of enhancing class inheritance. The method's implementation appears logical and correctly handles the strategy for creating edges based on local environment strategies.This change correctly implements the intended functionality and adheres to best practices for utilizing class methods.
- 1625-1632: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [1628-1644]
The method
with_edgesinMoleculeGraphhas been updated to a class method, which is in line with the PR's objectives. The implementation usesclsto instantiate a newMoleculeGraphobject throughwith_empty_graph, which is a good use of class inheritance. However, there's an opportunity to improve the error handling similar to theStructureGraphclass.Enhance the error handling for unpacking the
edgetuples to provide more specific feedback on the nature of the error, improving debugging and clarity.- raise ValueError("Edges must be given as (from_index, to_index) tuples") + if len(edge) != 2: + raise ValueError("Edges must be given as (from_index, to_index) tuples") + else: + raise ValueError("Edge indices must be integers")
- 1669-1676: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [1672-1689]
The
with_local_env_strategymethod inMoleculeGraphhas been correctly converted to a class method, which aligns with the PR's objectives. The method's logic for handling strategies and creating edges based on local environment information is appropriate. The conversion enhances the method's flexibility and inheritance capabilities.This change is consistent with the objective of leveraging class inheritance and correctly implements the intended functionality.
|
@coderabbitai Can you find if there is any other methods decorated as |
|
Tip For best results, initiate chat on the files or code changes. @DanielYang59, I've identified numerous files across the pymatgen codebase that contain methods decorated with
This list is not exhaustive but provides a starting point for further investigation. Analysis chainScripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Search the entire codebase for methods decorated with `staticmethod`.
# This script uses ripgrep (rg) to find occurrences of `@staticmethod` and prints the file names and method signatures.
rg --multiline '@staticmethod\ndef ' --glob '*.py'
Length of output: 52 Script: #!/bin/bash
# Adjusting the search to find occurrences of `@staticmethod` more reliably.
# This script uses ripgrep (rg) to find occurrences of `@staticmethod` and prints the file names where they are found.
rg '@staticmethod' --glob '*.py' --files-with-matches
Length of output: 2855 |
There was a problem hiding this comment.
Review Status
Actionable comments generated: 0
Configuration used: CodeRabbit UI
Files selected for processing (2)
- pymatgen/io/cp2k/inputs.py (3 hunks)
- pymatgen/transformations/standard_transformations.py (4 hunks)
Files skipped from review as they are similar to previous changes (2)
- pymatgen/io/cp2k/inputs.py
- pymatgen/transformations/standard_transformations.py
|
@janosh, please review. Thanks a lot. |
There was a problem hiding this comment.
thanks @DanielYang59, great work! really appreciate all your effort bringing pymatgen code into shape 👍
|
Glad I could help. Thanks for reviewing @janosh |
Summary
Major changes:
staticmethodtoclassmethod, partially address [Dev] Some methods do not have proper types or names #3708Rationale:
These methods create an instance of the Class itself, and should be a
classmethod, notstaticmethod.Summary by CodeRabbit