coderabbitai[bot]
commented
2 months ago Walkthrough
## Walkthrough The updates primarily involved restructuring import statements to improve code readability and maintainability. Imports were moved from the global scope to within specific methods or functions, localizing dependencies where they are used. This change impacts various files related to elasticity calculations, VASP input/output handling, crystal structure generation, and defect generation. The codebase now ensures more modular and efficient import management. ## Changes | File Path | Change Summary | |------------------------------------|-------------------------------------------------------------------------------------------------------------| | `dpgen/auto_test/Elastic.py` | Reorganized imports within methods for elasticity calculations and VASP handling. | | `dpgen/auto_test/Gamma.py` | Moved imports to within `make_confs` and `__gen_slab_ase`, added path existence check in `make_confs`. | | `dpgen/auto_test/Interstitial.py` | Localized imports within `make_confs` method. | | `dpgen/auto_test/Surface.py` | Moved imports into `make_confs` method. | | `dpgen/auto_test/VASP.py` | Localized imports within `make_potential_files` and `make_input_file` methods. | | `dpgen/auto_test/Vacancy.py` | Localized imports within `make_confs` method. | | `dpgen/auto_test/gen_confs.py` | Localized imports within `test_fit`, `gen_element`, and `gen_alloy` functions. | | `dpgen/auto_test/lib/abacus.py` | Removed unused import, localized import within `stru2Structure` function. | | `dpgen/auto_test/lib/crys.py` | Localized imports within various functions for creating crystal structures. | | `dpgen/auto_test/lib/vasp.py` | Localized imports within `make_vasp_kpoints_from_incar` function. | | `dpgen/auto_test/mpdb.py` | Localized imports within `check_apikey` function. | | `dpgen/data/gen.py` | Localized imports within various functions for generating supercells and VASP input files. | | `dpgen/data/surf.py` | Localized imports within `poscar_elong` and `make_super_cell_pymatgen` functions. | | `dpgen/database/entry.py` | Localized import within `__init__` method of `Entry` class. | | `dpgen/database/vasp.py` | Localized imports within methods related to VASP input files handling. | | `dpgen/generator/lib/ele_temp.py` | Localized imports within `_get_incar_ele_temp` and `_get_incar_nbands` methods. | | `dpgen/generator/lib/vasp.py` | Localized import within `incar_upper` function. | | `dpgen/generator/run.py` | Localized imports within `make_vasp_incar_ele_temp` and `make_fp_vasp_kp` functions. | | `pyproject.toml` | Updated linting configurations, added banned module-level import for `pymatgen`, and extended per-file ignores for rule `TID253`. |Recent review details
**Configuration used: CodeRabbit UI** **Review profile: CHILL**Commits
Files that changed from the base of the PR and between 8f7829477c1d2d1b3ecc414685ebbec84a09f4bd and 8c541b7eb7b6130ee1eb9e8ba15db63301cda75e.Files selected for processing (19)
* dpgen/auto_test/Elastic.py (4 hunks) * dpgen/auto_test/Gamma.py (3 hunks) * dpgen/auto_test/Interstitial.py (2 hunks) * dpgen/auto_test/Surface.py (2 hunks) * dpgen/auto_test/VASP.py (3 hunks) * dpgen/auto_test/Vacancy.py (2 hunks) * dpgen/auto_test/gen_confs.py (4 hunks) * dpgen/auto_test/lib/abacus.py (2 hunks) * dpgen/auto_test/lib/crys.py (5 hunks) * dpgen/auto_test/lib/vasp.py (2 hunks) * dpgen/auto_test/mpdb.py (1 hunks) * dpgen/data/gen.py (4 hunks) * dpgen/data/surf.py (4 hunks) * dpgen/database/entry.py (2 hunks) * dpgen/database/vasp.py (4 hunks) * dpgen/generator/lib/ele_temp.py (2 hunks) * dpgen/generator/lib/vasp.py (2 hunks) * dpgen/generator/run.py (3 hunks) * pyproject.toml (2 hunks)Files skipped from review due to trivial changes (1)
* dpgen/auto_test/lib/abacus.pyAdditional comments not posted (41)
dpgen/auto_test/mpdb.py (1)
`9-10`: **LGTM! Import localized within the function.** The import of `MPRester` and `MPRestError` within the function scope improves module loading efficiency and avoids unnecessary imports when the function is not called.dpgen/auto_test/lib/crys.py (7)
`5-6`: **LGTM! Import localized within the function.** The import of `Structure` within the function scope improves module loading efficiency and avoids unnecessary imports when the function is not called. --- `13-15`: **LGTM! Imports localized within the function.** The imports of `Lattice` and `Structure` within the function scope improve module loading efficiency and avoid unnecessary imports when the function is not called. --- `25-27`: **LGTM! Imports localized within the function.** The imports of `Lattice` and `Structure` within the function scope improve module loading efficiency and avoid unnecessary imports when the function is not called. --- `33-35`: **LGTM! Imports localized within the function.** The imports of `Lattice` and `Structure` within the function scope improve module loading efficiency and avoid unnecessary imports when the function is not called. --- `50-52`: **LGTM! Imports localized within the function.** The imports of `Lattice` and `Structure` within the function scope improve module loading efficiency and avoid unnecessary imports when the function is not called. --- `66-68`: **LGTM! Imports localized within the function.** The imports of `Lattice` and `Structure` within the function scope improve module loading efficiency and avoid unnecessary imports when the function is not called. --- `87-89`: **LGTM! Imports localized within the function.** The imports of `Lattice` and `Structure` within the function scope improve module loading efficiency and avoid unnecessary imports when the function is not called.dpgen/generator/lib/ele_temp.py (2)
`88-89`: **LGTM! Import localized within the method.** The import of `Incar` within the method scope improves module loading efficiency and avoids unnecessary imports when the method is not called. --- `95-96`: **LGTM! Import localized within the method.** The import of `Incar` within the method scope improves module loading efficiency and avoids unnecessary imports when the method is not called.dpgen/generator/lib/vasp.py (1)
`133-134`: **LGTM! Import localized within the function.** The import of `Incar` within the function scope improves module loading efficiency and avoids unnecessary imports when the function is not called.dpgen/database/entry.py (1)
`54-55`: **Good practice: Localized import.** Moving the import of `Composition` to within the `__init__` method ensures that `pymatgen` is only imported when an instance of `Entry` is created. This can help avoid unnecessary imports and potential import errors if `pymatgen` is not installed.pyproject.toml (3)
`92-92`: **Good practice: Enforcing linting rules.** Adding the linting rule `TID253` to the `select` list ensures that module-level imports of banned modules are flagged by the linter, promoting better import practices. --- `116-119`: **Good practice: Banning module-level imports.** Adding `pymatgen` to the `banned-module-level-imports` list ensures that module-level imports of `pymatgen` are flagged, aligning with the PR objective to move such imports to runtime. --- `121-122`: **Good practice: Extending per-file ignores.** Adding the rule `TID253` to the per-file ignores for files under `tests/` ensures that test files are not flagged for module-level imports, which might be necessary for testing purposes.dpgen/auto_test/gen_confs.py (3)
`20-21`: **Good practice: Localized import.** Moving the import of `StructureMatcher` to within the `test_fit` function ensures that `pymatgen` is only imported when the function is called. This can help avoid unnecessary imports if the function is not used. --- `52-54`: **Good practice: Localized imports.** Moving the imports of `StructureMatcher` and `MPRester` to within the `gen_element` function ensures that `pymatgen` is only imported when the function is called. This can help avoid unnecessary imports if the function is not used. --- `98-99`: **Good practice: Localized import.** Moving the import of `MPRester` to within the `gen_alloy` function ensures that `pymatgen` is only imported when the function is called. This can help avoid unnecessary imports if the function is not used.dpgen/database/vasp.py (3)
`20-21`: **Good practice: Localized imports.** Moving the imports of `Potcar` and `PotcarSingle` to within the `__init__` method ensures that `pymatgen` is only imported when an instance of `DPPotcar` is created. This can help avoid unnecessary imports if the class is not used. --- `83-84`: **Good practice: Localized import.** Moving the import of `Potcar` to within the `from_file` method ensures that `pymatgen` is only imported when the method is called. This can help avoid unnecessary imports if the method is not used. --- `183-184`: **Good practice: Localized imports.** Moving the imports of `Incar`, `Kpoints`, and `Poscar` to within the `from_directory` method ensures that `pymatgen` is only imported when the method is called. This can help avoid unnecessary imports if the method is not used.dpgen/auto_test/VASP.py (2)
`23-24`: **LGTM! Localized import for `Structure`.** The import of `Structure` has been moved to within the method, which is a good practice for optimizing imports. --- `72-73`: **LGTM! Localized imports for `Incar` and `Kpoints`.** The imports of `Incar` and `Kpoints` have been moved to within the method, which is a good practice for optimizing imports.dpgen/auto_test/Vacancy.py (1)
`78-80`: **LGTM! Localized imports for `VacancyGenerator` and `Structure`.** The imports of `VacancyGenerator` and `Structure` have been moved to within the method, which is a good practice for optimizing imports.dpgen/auto_test/Elastic.py (3)
`51-53`: **LGTM! Localized imports for `DeformedStructureSet`, `Strain`, and `Structure`.** The imports of `DeformedStructureSet`, `Strain`, and `Structure` have been moved to within the method, which is a good practice for optimizing imports. --- `190-191`: **LGTM! Localized imports for `Incar` and `Kpoints`.** The imports of `Incar` and `Kpoints` have been moved to within the method, which is a good practice for optimizing imports. --- `253-255`: **LGTM! Localized imports for `ElasticTensor` and `Stress`.** The imports of `ElasticTensor` and `Stress` have been moved to within the method, which is a good practice for optimizing imports.dpgen/auto_test/Surface.py (1)
`86-88`: **LGTM! Localized imports for `Structure` and `generate_all_slabs`.** The imports of `Structure` and `generate_all_slabs` have been moved to within the method, which is a good practice for optimizing imports.dpgen/auto_test/lib/vasp.py (1)
`505-506`: **LGTM! Imports moved inside the function.** The import statements for `Incar` and `Kpoints` were moved inside the `make_vasp_kpoints_from_incar` function to avoid module-level imports of `pymatgen`. This change ensures that the import is only done when necessary.dpgen/auto_test/Gamma.py (2)
`95-96`: **LGTM! Import moved inside the method.** The import statement for `Structure` was moved inside the `make_confs` method to avoid module-level imports of `pymatgen`. This change ensures that the import is only done when necessary. --- `290-291`: **LGTM! Import moved inside the method.** The import statement for `AseAtomsAdaptor` was moved inside the `__gen_slab_ase` method to avoid module-level imports of `pymatgen`. This change ensures that the import is only done when necessary.dpgen/data/surf.py (3)
`166-167`: **LGTM! Import moved inside the function.** The import statement for `Structure` was moved inside the `poscar_elong` function to avoid module-level imports of `pymatgen`. This change ensures that the import is only done when necessary. --- `215-217`: **LGTM! Imports moved inside the function.** The import statements for `Element`, `Structure`, and `AseAtomsAdaptor` were moved inside the `make_super_cell_pymatgen` function to avoid module-level imports of `pymatgen`. This change ensures that the imports are only done when necessary. --- `404-405`: **LGTM! Import moved inside the function.** The import statement for `Poscar` was moved inside the `poscar_scale` function to avoid module-level imports of `pymatgen`. This change ensures that the import is only done when necessary.dpgen/auto_test/Interstitial.py (1)
`79-81`: **LGTM! Imports moved inside the method.** The import statements for `InterstitialGenerator` and `Structure` were moved inside the `make_confs` method to avoid module-level imports of `pymatgen`. This change ensures that the imports are only done when necessary.dpgen/data/gen.py (4)
`301-302`: **LGTM! Import moved to runtime.** The import of `Structure` from `pymatgen.core` has been moved to runtime, which is appropriate to avoid module-level import issues. --- `345-346`: **LGTM! Import moved to runtime.** The import of `Structure` from `pymatgen.core` has been moved to runtime, which is appropriate to avoid module-level import issues. --- `1449-1450`: **LGTM! Import moved to runtime.** The import of `Incar` from `pymatgen.io.vasp` has been moved to runtime, which is appropriate to avoid module-level import issues. --- `1449-1450`: **LGTM! Import moved to runtime.** The import of `Incar` from `pymatgen.io.vasp` has been moved to runtime, which is appropriate to avoid module-level import issues.dpgen/generator/run.py (2)
`3080-3081`: **LGTM!** The import statement for `Incar` is correctly moved to within the function to avoid unnecessary module-level imports. --- `3159-3160`: **LGTM!** The import statements for `Incar` and `Kpoints` are correctly moved to within the function to avoid unnecessary module-level imports.
codecov[bot]
Pymatgen is still imcompatbile with NumPy 2. Move the import into runtime to fix the documentation builds and prevent potential errors when one uses dpgen without using pymatgen.
Signed-off-by: Jinzhe Zeng jinzhe.zeng@rutgers.edu
Summary by CodeRabbit
pyproject.tomlto include new rules and per-file exceptions.