Develop #69
Develop #69
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…atching value types (`str` and `bool` etc) with their mismatching INCARs
…and informatively warn user when incorrect values present
… efficient, robust, general improvements
…roject) is actually the primitive structure
…ue until its next release (see materialsproject/pymatgen-analysis-defects#188)
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All tests passed on previous run, merging |
WalkthroughThe recent updates focus on refining GitHub workflows, enhancing Python package configurations, and improving the robustness and functionality of the Changes
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Actionable comments posted: 9
Out of diff range and nitpick comments (8)
doped/utils/supercells.py (1)
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750-1000: Complex functionfind_ideal_supercellis well-implemented with comprehensive documentation.The function handles a complex algorithm with multiple helper functions and conditional paths. Consider refactoring to split this function into smaller sub-functions for each major step to enhance readability and maintainability.
tests/test_chemical_potentials.py (2)
93-126: Consider adding more detailed comments explaining the purpose of each assertion and the expected outcomes. This will enhance the readability and maintainability of the test cases, especially for complex checks involving chemical potentials and warnings.
269-271: Ensure that the error messages are clear and provide sufficient information to the user about what went wrong and how to resolve it. Consider enhancing the error message to guide the user more effectively.tests/test_vasp.py (5)
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54-82: Ensure that the paths used insetUpare dynamically generated to avoid hard-coded paths which might not be universally applicable.- self.data_dir = os.path.join(os.path.dirname(__file__), "data") + self.data_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "data")
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54-54: Consider mocking_potcars_availablein your tests to ensure consistent test behavior across different environments.
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300-466: Ensure that test methods liketest_neutral_defect_dict_setandtest_charged_defect_incarinclude comprehensive assertions to cover all edge cases.
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454-466: Avoid redundancy by reusingsetUpfromDefectDictSetTestwithout redefining it unless necessary. Consider using inheritance or composition if setup code needs to be shared across test classes.
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454-466: Add more detailed assertions in methods liketest_initialisation_and_writingto ensure that all aspects ofDefectRelaxSetinitialization are correctly tested.
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Files selected for processing (23)
- .github/workflows/JOSS_draft-PDF.yaml (1 hunks)
- .github/workflows/pip_install_test.yml (2 hunks)
- .github/workflows/release.yml (1 hunks)
- .github/workflows/test.yml (3 hunks)
- .readthedocs.yaml (1 hunks)
- CHANGELOG.rst (1 hunks)
- CITATION.cff (1 hunks)
- README.md (4 hunks)
- docs/Dev_ToDo.md (3 hunks)
- docs/Installation.rst (1 hunks)
- docs/Troubleshooting.rst (1 hunks)
- docs/conf.py (1 hunks)
- docs/index.rst (5 hunks)
- doped/analysis.py (3 hunks)
- doped/chemical_potentials.py (16 hunks)
- doped/utils/legacy_corrections.py (1 hunks)
- doped/utils/parsing.py (6 hunks)
- doped/utils/supercells.py (1 hunks)
- doped/vasp.py (1 hunks)
- pyproject.toml (2 hunks)
- tests/test_chemical_potentials.py (7 hunks)
- tests/test_generation.py (13 hunks)
- tests/test_vasp.py (6 hunks)
Files not reviewed due to errors (1)
- docs/Dev_ToDo.md (no review received)
Files skipped from review due to trivial changes (5)
- CITATION.cff
- docs/Installation.rst
- docs/Troubleshooting.rst
- docs/conf.py
- pyproject.toml
Additional Context Used
LanguageTool (31)
README.md (4)
Near line 8: Although a hyphen is possible, it is not necessary in a compound modifier in which the first word is an adverb that ends in ‘ly’.
Context: ...ducible, user-friendly yet powerful and fully-customisable manner. Tutorials showing the code fun...
Near line 15: Although a hyphen is possible, it is not necessary in a compound modifier in which the first word is an adverb that ends in ‘ly’.
Context: ...ures All features and functionality are fully-customisable: - Supercell Generation: Generate a...
Near line 23: Although a hyphen is possible, it is not necessary in a compound modifier in which the first word is an adverb that ends in ‘ly’.
Context: ...ections, etc. -PythonInterface: Fully-customisable, modularPythonAPI. Plug-and-play w/...
Near line 48: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...i.org/10.21105/joss.06433). Journal of Open Source Software 9 (96), 6433, 2024 ## `S...docs/Dev_ToDo.md (27)
Near line 6: A comma may be missing after the conjunctive/linking adverb ‘Also’.
Context: ...of code out ofinterfacesubpackage?) Also can see https://github.com/materialspro...
Near line 7: Two successive sentences begin with the same adverb. Consider rewording the sentence or use a thesaurus to find a synonym.
Context: .../phases.py for 2D chempot plotting. - Also seeCs2SnTiI6notebooks for template ...
Near line 15: This phrase is redundant. Consider using “outside”.
Context: ...e plot - Don't show transition levels outside of the bandgap (or within a certain range ...
Near line 16: To form a complete sentence, be sure to include a subject.
Context: ...iscussion and CdTe pyscfermi notebooks. Would be easy to implement if auto degeneracy...
Near line 19: If ‘want’ is used as a verb, it usually requires the infinitive.
Context: ...a of theAiiDA-defectspreprint, want plotting tools like this - Can we add an option ...
Near line 20: Except for inverted sentences, ‘Can we’ requires a question mark at the end of the sentence.
Context: ...defect-structures) – seems quite useful tbf ## Housekeeping - Tutorials general st...
Near line 29: Unpaired symbol: ‘(’ seems to be missing
Context: ... but smaller for VCd bipolaron in CdTe))). - Add our recommended workflow (gam...
Near line 33: In American English, abbreviations like “etc.” require a period.
Context: ...state behaviour being a bit more common etc). If the user wants to add bandfilling ...
Near line 33: Modal verbs like ‘can’ or ‘will’ require the following verb to be in its base form.
Context: ...bandfilling corrections, they can still doing this by calculating it themselves and a...
Near line 40: Although a hyphen is possible, it is not necessary in a compound modifier in which the first word is an adverb that ends in ‘ly’.
Context: ... of a VASP dielectric calculation if an oddly-defined primitive cell is used) -vasp_ncl...
Near line 42: If the ‘because’ clause is essential to the meaning, do not use a comma before the clause.
Context: ... Often can't useNKREDwithvasp_std, because we don't know beforehand the kpts in th...
Near line 44: Although a hyphen is possible, it is not necessary in a compound modifier in which the first word is an adverb that ends in ‘ly’.
Context: ...kpoints, due to memory limitations. - Readily-usable in conjunction withatomate,AiiDA(...
Near line 44: ‘in conjunction with’ might be wordy. Consider a shorter alternative.
Context: ... memory limitations. - Readily-usable in conjunction withatomate,AiiDA(-defects),vise, `...
Near line 46: Do not use a colon (:) before a series that is introduced by a preposition (‘with’). Remove the colon or add a noun or a noun phrase after the preposition.
Context: ...onal dependencies. - Workflow diagram with: https://twitter.com/Andrew_S_Rosen/stat...
Near line 47: As an alternative to the over-used intensifier ‘very’, consider replacing this phrase.
Context: ...an sometimes be worth doing if you have a very large supercell for speed up, but it's impo...
Near line 47: As an alternative to the over-used intensifier ‘very’, consider replacing this phrase.
Context: ...only do if you're a power user and have a very large supercell. - Show usage of `get_conv_...
Near line 51: In American English, abbreviations like “etc.” require a period.
Context: ...put structure,generate_supercelletc), but conventional cell should always b...
Near line 57: This phrase is redundant. Consider writing “cancel”.
Context: ...ts that the SOC effects on total energy cancel out for chemical potential calculations...
Near line 69: Qualifiers like “somewhat” can weaken your message and make your writing sound uncertain. Consider removing it or choosing an alternative to sound more confident.
Context: ...ral, the correction terms should follow somewhat consistent trends (for a given charge s...
Near line 69: It appears that only one verb is needed.
Context: ... something odd is happening there. This is can be fairly easily scanned with `get_form...
Near line 70: Use a comma before “and” if it connects two independent clauses (unless they are closely connected and short).
Context: ...The Wyckoff analysis code is very useful and no other package can do this afaik. See...
Near line 75: Consider adding a comma here.
Context: ...s and can fail in weird cases. As always please consider if these charge states are ...
Near line 76: In American English, abbreviations like “etc.” require a period.
Context: ...mmetry, amphoteric, mixed-valence cases etc!) - Note cases where we expect defa...
Near line 77: Consider changing the order of words to improve your wording.
Context: ...s where we expect default charge states to not be appropriate (e.g. mixed ionic-covale...
Near line 82: In American English, abbreviations like “etc.” require a period.
Context: ...tum/magnetic defects, d-orbital defects etc), in which case you can manually adjust...
Near line 84: In American English, abbreviations like “etc.” require a period.
Context: ...lay around withprobability_thresholdetc). - Should flick through other defect c...
Near line 94: In American English, abbreviations like “etc.” require a period.
Context: ...lso group defects for the concentration etc functions, currently doesn't (e.g. `CdT...
Additional comments not posted (41)
.readthedocs.yaml (2)
9-9: Update to Ubuntu 22.04 aligns with modern best practices for OS support.
11-11: Update to Python 3.11 ensures compatibility with the latest Python features and security patches..github/workflows/JOSS_draft-PDF.yaml (2)
13-13: Upgrade toactions/checkout@v4enhances security and adds new features.
21-21: Upgrade toactions/upload-artifact@v5provides improvements in artifact handling and performance..github/workflows/test.yml (4)
16-22: Updated matrix configurations to include newer operating systems and Python versions, enhancing test coverage.
27-27: Upgrade toactions/checkout@v4ensures the use of the latest features and security updates.
29-29: Upgrade toactions/setup-python@v5ensures compatibility with the latest Python releases and features.
57-57: Upgrade toactions/upload-artifact@v4provides better performance and reliability in artifact uploads..github/workflows/pip_install_test.yml (4)
21-27: Updated matrix configurations to exclude unsupported Python versions on macOS-14, ensuring compatibility and preventing unnecessary failures.
32-32: Upgrade toactions/checkout@v4ensures the use of the latest features and security updates.
34-34: Upgrade toactions/setup-python@v5ensures compatibility with the latest Python releases and features.
63-63: Upgrade toactions/upload-artifact@v4provides better performance and reliability in artifact uploads..github/workflows/release.yml (3)
19-19: Upgrade toactions/checkout@v4enhances security and adds new features.
21-21: Upgrade toactions/setup-python@v5ensures compatibility with the latest Python features and security patches.
23-23: Setting the Python version explicitly to 3.11 in the release workflow ensures that the latest Python version is used for building and publishing, aligning with best practices.doped/utils/legacy_corrections.py (1)
47-47: Changing the return format to a dictionary enhances data handling and integration with other parts of the software, allowing for more structured and accessible correction data.CHANGELOG.rst (1)
4-10: The changelog effectively documents significant updates and improvements in version 2.4.2, providing clear information on changes and enhancements made to the software.README.md (3)
6-6: Adding a DOI badge enhances the visibility and accessibility of the academic paper associated with the software, providing a direct link for citation.
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10-29: The updates to the tutorials and key features sections provide clearer, more detailed information on the software's capabilities and usage, enhancing user understanding and engagement.
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46-65: The updated citation section provides comprehensive details on how to properly cite the software in academic work, which is crucial for acknowledging the software's contribution to research.docs/index.rst (4)
27-27: Ensure the JOSS paper link is accessible
The link to the JOSS paper is crucial for users to access relevant research. Verify that this link is accessible and directs users to the intended resource.#!/bin/bash # Description: Check if the JOSS paper link is accessible. curl -o /dev/null -s -w "%{http_code}\n" https://doi.org/10.21105/joss.06433
51-59: Confirm the target URL for the JOSS paper image
The image link in the documentation should correctly point to the intended JOSS paper. Confirm that the target URL is correct and the resource is available.#!/bin/bash # Description: Verify the target URL for the JOSS paper image. curl -o /dev/null -s -w "%{http_code}\n" https://doi.org/10.21105/joss.06433
72-72: Update the citation year to match the publication year
The citation entry for the JOSS paper mentions the year as 2024, which should be consistent with the actual publication year. If the paper is indeed published in 2024, this is correct; otherwise, update the year accordingly.#!/bin/bash # Description: Check the publication year of the JOSS paper. curl -s https://doi.org/10.21105/joss.06433 | grep -oP 'Published:\s+\K\d{4}'
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92-106: Review the consistency of publication years in the cited studies
The publication years for the cited studies range from 2022 to 2024. Ensure that these years are accurate and reflect the actual publication dates of the respective papers.#!/bin/bash # Description: Verify the publication years for the cited studies. # Example command to check one of the publication years. curl -s https://doi.org/10.1002/adma.202400343 | grep -oP 'Published:\s+\K\d{4}'doped/utils/supercells.py (3)
75-76: Updated function call tolattice.get_points_in_spherewith conversion to list.This change ensures that the output from
get_points_in_sphereis explicitly converted to a list, which might be necessary for subsequent operations like sorting. This is a good practice to avoid potential issues with lazy evaluation in Python where the returned object could be an iterator.
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15-23: Functionget_min_image_distancecorrectly delegates computation to a helper function.This is a good example of modular code design, where the main function serves as an interface, and the actual computation is handled by a more specialized function. This enhances readability and maintainability.
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58-92: Robust implementation of_get_min_image_distance_from_matrix.The function is well-documented and includes appropriate error handling for edge cases, such as a minimum image distance of zero or less. This prevents potential runtime errors and ensures the function's reliability.
tests/test_chemical_potentials.py (1)
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580-711: Ensure that the test cases cover all relevant scenarios, including edge cases and potential error conditions. This will help improve the robustness of the module and prevent future regressions.#!/bin/bash # Description: Verify that all edge cases and error conditions are covered in the test cases for CSV output functionality. # Test: Search for test cases covering edge cases and error conditions. rg --type python $'test_to_csv'tests/test_vasp.py (2)
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84-86: Verify the implementation ofif_present_rmto ensure it handles exceptions properly when attempting to remove non-existent directories.#!/bin/bash # Description: Check the implementation of `if_present_rm`. # Test: Search for the function definition and usage. Expect: Proper exception handling. rg --type python $'if_present_rm'
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468-472: Ensure thattearDowninDefectRelaxSetTestremoves all files and directories created during the tests to prevent any side effects on subsequent tests.#!/bin/bash # Description: Verify cleanup process in `tearDown`. # Test: Check for residual files after tests run. Expect: No residual files. find . -type f -name 'test_*'doped/chemical_potentials.py (3)
21-21: Update toUnconvergedVASPWarningimport is consistent with the summary.
25-25: The addition ofget_vasprunto imports aligns with the summary's mention of import changes in this file.
332-332: Ensure that theSETTINGSobject properly handles thePMG_MAPI_KEYretrieval as expected.#!/bin/bash # Description: Verify the handling of `PMG_MAPI_KEY` in the `SETTINGS` object. # Test: Search for the SETTINGS usage. Expect: Proper handling of PMG_MAPI_KEY. rg --type python $'SETTINGS.get("PMG_MAPI_KEY")'doped/analysis.py (1)
44-44: Ensure the newly imported functiondefect_charge_from_vasprunis used correctly.#!/bin/bash # Description: Verify the usage of `defect_charge_from_vasprun` in the file. # Test: Search for the function usage. Expect: Correct usage with appropriate arguments. rg --type py 'defect_charge_from_vasprun' doped/analysis.pydoped/vasp.py (7)
84-84: Update exception handling to includeRuntimeErroras per the latestpymatgenrelease.
88-88: Ensure that the loop correctly handles the potential functional choices without causing an infinite loop or missing potential valid configurations.#!/bin/bash # Description: Check the loop logic for setting `potcar_functional`. # Test: Review the logic manually and ensure all paths are covered. echo "Manual review required for loop logic in _test_potcar_functional_choice function."
84-84: Ensure robust handling of encoding errors in theDopedKpointsclass.
84-84: Review the initialization and configuration logic inDopedDictSetto ensure it correctly integrates user settings with defaults.#!/bin/bash # Description: Verify the integration of user settings in `DopedDictSet`. # Test: Check the constructor logic and property methods. echo "Manual review required for constructor and properties in DopedDictSet class."
84-84: Ensure that theincarproperty inDefectDictSetcorrectly handles charge states and other INCAR settings for defect calculations.#!/bin/bash # Description: Check the `incar` property logic in `DefectDictSet`. # Test: Review the handling of charge states and INCAR adjustments. echo "Manual review required for incar property in DefectDictSet class."
84-84: Review the configuration of VASP input files inDefectRelaxSetto ensure they are correctly set up for defect relaxation calculations.#!/bin/bash # Description: Verify the setup of VASP input files in `DefectRelaxSet`. # Test: Check each property method for correct configuration. echo "Manual review required for VASP input file configuration in DefectRelaxSet class."
84-84: Ensure efficient and correct handling of multiple defect calculations inDefectsSet, particularly the use of multiprocessing.#!/bin/bash # Description: Check the multiprocessing implementation in `DefectsSet`. # Test: Review the logic for handling multiple defects and the use of multiprocessing. echo "Manual review required for multiprocessing implementation in DefectsSet class."
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