[WIP] Documentation overhaul #309
Conversation
and Checking_smact_validity_of_GNoME.ipynb
…o docs_updates
…o docs_updates
…o docs_updates
WalkthroughThe changes encompass various modifications across multiple files, including updates to documentation, formatting adjustments, enhancements to type hinting, and improvements in error handling. The updates also involve reorganising sections in templates, refining workflows, and expanding documentation to provide clearer guidance on functionalities. Overall, these changes aim to enhance code clarity, maintainability, and usability without altering the core logic of the existing functionalities. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant System
participant Documentation
participant Codebase
User->>System: Request for functionalities
System->>Documentation: Retrieve updated documentation
Documentation-->>User: Provide clear guidance
User->>Codebase: Execute functions
Codebase-->>User: Return results
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Actionable comments posted: 6
Outside diff range, codebase verification and nitpick comments (7)
requirements-dev.txt (1)
4-8: Review the addition of new development tools.New tools have been added (
ruff,pyright,codespell,blacken-docs,nbstripout). Each tool serves a specific purpose:
ruff: A fast Python linter, potentially replacingblackandisort.pyright: A static type checker for Python, enhancing type hinting.codespell: For spelling checks in the code, improving readability.blacken-docs: To format code blocks in documentation.nbstripout: To clean notebooks before committing, useful for projects involving Jupyter notebooks.Ensure that these tools integrate well with the existing development workflow and check their compatibility with the Python version used.
docs/requirements.in (1)
5-6: Assess the addition of new documentation packages.New packages have been added:
sphinx-book-theme: Enhances the visual presentation of the documentation.myst-nb: Allows for the inclusion of Jupyter notebooks in the Sphinx documentation.These additions suggest a focus on improving the interactivity and visual appeal of the documentation. Ensure that these packages are compatible with the Sphinx version used and that they integrate well with the existing documentation structure.
docs/tutorials/oxidation_states.ipynb (1)
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64-127: Complex data processing logic for composition generation.The code cell efficiently uses regular expressions and list comprehensions to generate plausible compositions. However, the complexity of the logic could be challenging for beginners. Adding detailed comments explaining each step would enhance understanding and maintainability.
Add detailed comments within the code to explain the purpose and functionality of each major step, especially the regular expressions and list comprehensions, to make the code more accessible to beginners.
docs/tutorials/smact_validity_of_GNoMe.ipynb (1)
Line range hint
17-37: Code Cell: Package Installation and Environment CheckThis cell handles the installation of necessary packages and checks if the notebook is being run in a Google Colab environment. The use of conditional statements to handle different environments (Colab vs. others) is a good practice. However, the installation command for
pandarallelis outside the conditional block, which means it will run regardless of the environment. Consider moving it inside theif IN_COLABblock to avoid unnecessary installations when not in Colab.Proposed change to ensure
pandarallelis only installed in the Colab environment:if IN_COLAB: !pip install git+https://github.com/WMD-group/SMACT.git --quiet + !pip install pandarallel --quiet # Required for parallel processing -!pip install pandarallel --quiet # Required for parallel processingexamples/Structure_Prediction/Li-Garnets_SP-Pym-new.ipynb (1)
9-21: Re-evaluate the Removal ofnumpyThe
numpylibrary is used extensively in related files, including those imported in the notebook. Its removal might lead to issues if any imported functions or classes rely on it. Consider re-evaluating its necessity in the notebook.
numpyis used insmact/structure_prediction/mutation.pyand other related files.Removal of
jsonis JustifiedThe
from_json()method is defined within the codebase and does not require thejsonlibrary, so its removal is justified.
from_json()is defined insmact/structure_prediction/mutation.py.Verify
loggingDependenciesWhile
loggingis used in several files, there is no direct evidence of its necessity in the notebook. Verify if there are any indirect dependencies that might require it.
loggingis used in various files but not directly in the notebook.Analysis chain
Review Import Statements
The addition of
from __future__ import annotationsis beneficial for forward compatibility with type hinting in Python. However, the removal ofnumpyand other libraries likejson,logging, etc., should be carefully evaluated to ensure that their absence does not break any existing functionality in the notebook. If these libraries are not used in the notebook, their removal is justified to clean up the code.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify if removed libraries are still referenced in the notebook. # Test: Search for removed libraries usage. Expect: No occurrences. rg --type py 'numpy|json|logging' examples/Structure_Prediction/Li-Garnets_SP-Pym-new.ipynbLength of output: 130
Script:
#!/bin/bash # Description: Verify the origin of `from_json()` and check for any indirect dependencies on `numpy` and `logging`. # Check if `from_json` is defined in the codebase and its origin. rg 'def from_json' --type py # Check for any indirect dependencies on `numpy` and `logging`. rg 'numpy|logging' --type pyLength of output: 2095
smact/structure_prediction/utilities.py (1)
Line range hint
94-117: Refined type hints and error handling inconvert_next_gen_mprest_data.The
convert_next_gen_mprest_datafunction now uses the updated Python 3.10 syntax for type hints, simplifying the previous complex type hinting. The function's error handling logs a warning before raising an exception, which is a good practice as it provides debug information before terminating the operation. However, the exception handling could be more specific by catching a more precise exception rather than a general one. This would improve the robustness and maintainability of the error handling.Consider refining the exception handling to catch specific exceptions related to the operation, which would provide clearer error information and potentially allow for more granular error recovery strategies.
- except: + except KeyError as e: # or another specific exception relevant to `doc.dict` logger.warn(f"Could not convert input:\n {doc}\n to a dictionary.") raise TypeError("Input is not an MPDataDoc object.") from esmact/structure_prediction/mutation.py (1)
Line range hint
113-148: Refined lambda table population and error handling in_populate_lambda.The
_populate_lambdamethod in theCationMutatorclass ensures that the lambda table is fully populated and handles NaN values and symmetry. The method uses a combination of custom functions to add alpha values and mirror lambda values, which is a robust approach to maintaining the integrity of the lambda table. However, the error handling could be improved by catching specific exceptions rather than using a generalexceptblock.Consider refining the exception handling to catch specific exceptions that are relevant to the operations performed within the method. This would provide clearer error information and potentially allow for more granular error recovery strategies.
- except KeyError: + except KeyError as e: # or another specific exception relevant to the lambda table operations add_alpha(s1, s2)
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files ignored due to path filters (26)
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Files selected for processing (80)
- .github/pull_request_template.md (1 hunks)
- .github/release.yml (1 hunks)
- .github/workflows/ci.yml (2 hunks)
- .github/workflows/combine-prs.yml (4 hunks)
- .github/workflows/publish-to-pypi.yml (1 hunks)
- .gitignore (1 hunks)
- .pre-commit-config.yaml (1 hunks)
- .readthedocs.yaml (1 hunks)
- README.md (2 hunks)
- dev_docs/contribution_guidelines.md (1 hunks)
- dev_docs/design_docs/StructurePredictor.md (1 hunks)
- docs/conf.py (4 hunks)
- docs/examples.rst (1 hunks)
- docs/examples/compound_electroneg.ipynb (1 hunks)
- docs/examples/distorter.ipynb (1 hunks)
- docs/examples/doper.ipynb (1 hunks)
- docs/examples/elements_and_species.ipynb (1 hunks)
- docs/examples/filter.ipynb (1 hunks)
- docs/examples/lists.ipynb (1 hunks)
- docs/examples/oxidation_states.ipynb (1 hunks)
- docs/examples/validity.ipynb (1 hunks)
- docs/index.rst (3 hunks)
- docs/introduction.rst (2 hunks)
- docs/requirements.in (1 hunks)
- docs/requirements.txt (2 hunks)
- docs/smact.dopant_prediction.doper.rst (1 hunks)
- docs/smact.dopant_prediction.rst (2 hunks)
- docs/smact.properties.rst (1 hunks)
- docs/tutorials.rst (1 hunks)
- docs/tutorials/crystal_space.ipynb (1 hunks)
- docs/tutorials/crystal_space_visualisation.ipynb (14 hunks)
- docs/tutorials/oxidation_states.ipynb (14 hunks)
- docs/tutorials/smact_generation_of_solar_oxides.ipynb (1 hunks)
- docs/tutorials/smact_validity_of_GNoMe.ipynb (6 hunks)
- examples/Structure_Prediction/Garnet_Database.ipynb (16 hunks)
- examples/Structure_Prediction/Li-Garnet_Generator.ipynb (20 hunks)
- examples/Structure_Prediction/Li-Garnets_SP-Pym-new.ipynb (37 hunks)
- paper.md (1 hunks)
- pyproject.toml (1 hunks)
- requirements-dev.txt (1 hunks)
- requirements.txt (8 hunks)
- setup.py (1 hunks)
- smact/init.py (17 hunks)
- smact/benchmarking/pymatgen_benchmark.py (2 hunks)
- smact/benchmarking/smact_benchmark.py (2 hunks)
- smact/benchmarking/utilities.py (2 hunks)
- smact/builder.py (3 hunks)
- smact/data/oxidation_state_probability_table.json (1 hunks)
- smact/data/solid_properties.txt (1 hunks)
- smact/data_loader.py (29 hunks)
- smact/distorter.py (4 hunks)
- smact/dopant_prediction/init.py (1 hunks)
- smact/dopant_prediction/doper.py (11 hunks)
- smact/lattice.py (4 hunks)
- smact/lattice_parameters.py (12 hunks)
- smact/mainpage.py (1 hunks)
- smact/oxidation_states.py (6 hunks)
- smact/properties.py (7 hunks)
- smact/screening.py (17 hunks)
- smact/structure_prediction/init.py (1 hunks)
- smact/structure_prediction/database.py (14 hunks)
- smact/structure_prediction/mutation.py (20 hunks)
- smact/structure_prediction/prediction.py (10 hunks)
- smact/structure_prediction/probability_models.py (5 hunks)
- smact/structure_prediction/structure.py (23 hunks)
- smact/structure_prediction/utilities.py (4 hunks)
- smact/tests/files/CaTiO3.json (1 hunks)
- smact/tests/files/Fe3O4.json (1 hunks)
- smact/tests/files/NaCl.json (1 hunks)
- smact/tests/files/mp-540839_CsPbI3_oxi.json (1 hunks)
- smact/tests/files/pymatgen_structure.json (1 hunks)
- smact/tests/files/test_lambda_tab.json (1 hunks)
- smact/tests/test_core.py (10 hunks)
- smact/tests/test_doper.py (2 hunks)
- smact/tests/test_structure.py (17 hunks)
- smact/utils/init.py (1 hunks)
- smact/utils/band_gap_simple.py (1 hunks)
- smact/utils/download_compounds_with_mp_api.py (4 hunks)
- smact/utils/generate_composition_with_smact.py (5 hunks)
- smact/utils/plot_embedding.py (4 hunks)
Files skipped from review due to trivial changes (28)
- .github/pull_request_template.md
- .github/release.yml
- .github/workflows/ci.yml
- .github/workflows/combine-prs.yml
- .github/workflows/publish-to-pypi.yml
- .gitignore
- docs/examples.rst
- docs/examples/compound_electroneg.ipynb
- docs/smact.dopant_prediction.doper.rst
- docs/smact.dopant_prediction.rst
- docs/smact.properties.rst
- docs/tutorials.rst
- examples/Structure_Prediction/Garnet_Database.ipynb
- examples/Structure_Prediction/Li-Garnet_Generator.ipynb
- smact/benchmarking/pymatgen_benchmark.py
- smact/benchmarking/smact_benchmark.py
- smact/data/solid_properties.txt
- smact/dopant_prediction/init.py
- smact/mainpage.py
- smact/structure_prediction/init.py
- smact/structure_prediction/probability_models.py
- smact/tests/files/NaCl.json
- smact/tests/files/mp-540839_CsPbI3_oxi.json
- smact/tests/files/pymatgen_structure.json
- smact/tests/files/test_lambda_tab.json
- smact/tests/test_core.py
- smact/utils/init.py
- smact/utils/band_gap_simple.py
Additional context used
LanguageTool
dev_docs/contribution_guidelines.md
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Context: ...he steps for a new piece of work can be summarised as follows: 1. Push up or create [an i...(OXFORD_SPELLING_Z_NOT_S)
[style] ~18-~18: Consider removing “of” to be more concise
Context: ...are finished with the work, ensure that all of the unit tests pass on your own machine....(ALL_OF_THE)
[uncategorized] ~25-~25: Possible missing comma found.
Context: ...eral overview of using pull requests on GitHub look [in the GitHub docs](https://help....(AI_HYDRA_LEO_MISSING_COMMA)
dev_docs/design_docs/StructurePredictor.md
[uncategorized] ~8-~8: A comma may be missing after the conjunctive/linking adverb ‘Therefore’.
Context: ..., in terms of interfacing withSMACT. Therefore we propose implement a similar method i...(SENT_START_CONJUNCTIVE_LINKING_ADVERB_COMMA)
[uncategorized] ~39-~39: The abbreviation “e.g.” (= for example) requires two periods.
Context: ... Generate a list of target compositions eg for Ba$_2$OF$_2$ `[Ba2+, O2-, F1-, (2, ...(E_G)
[grammar] ~85-~85: Possible agreement error. The noun ‘database’ seems to be countable.
Context: ...lysis of structures - Simple two field database - Field 1: database key - Field 2: ...(CD_NN)
[uncategorized] ~101-~101: A punctuation mark might be missing here.
Context: ...Fe_2_3+O_3_2-` #### Substitution list [[[targetA],["subs1A","subs2A",...]],[[ta...(AI_EN_LECTOR_MISSING_PUNCTUATION)
[uncategorized] ~104-~104: You might be missing the article “the” here.
Context: ...2A",...]],[[targetB],["subs1B"],...] - target is a list, the target composition - thi...(AI_EN_LECTOR_MISSING_DETERMINER_THE)
paper.md
[style] ~42-~42: Would you like to use the Oxford spelling “revolutionizing”? The spelling ‘revolutionising’ is also correct.
Context: ... The paradigm of data-driven science is revolutionising the materials discovery process. There ...(OXFORD_SPELLING_Z_NOT_S)
[uncategorized] ~44-~44: Possible missing comma found.
Context: ... where sets of element combinations are generated then screened using chemical filters. I...(AI_HYDRA_LEO_MISSING_COMMA)
README.md
[misspelling] ~24-~24: Possible spelling mistake found.
Context: ...a enough, nature will always confess_ - Roland Coase (from 'How should economists choose?') ...(EN_MULTITOKEN_SPELLING_TWO)
[style] ~46-~46: Consider a shorter alternative to avoid wordiness.
Context: ...lied to generated lists of compositions in order to screen for particular properties. These...(IN_ORDER_TO_PREMIUM)
[style] ~66-~66: Would you like to use the Oxford spelling “initialize”? The spelling ‘initialise’ is also correct.
Context: ...es the loading of external data used to initialise the coresmact.Elementand `smact.Spe...(OXFORD_SPELLING_Z_NOT_S)
[grammar] ~79-~79: It looks like ‘collections’ doesn’t match ‘a’. Did you mean “a collection” or just “collections”?
Context: ...rediction**: A submodule which contains a collections of tools for predicting dopants. ## Re...(A_NNS_IN)
[uncategorized] ~89-~89: Possible missing comma found.
Context: ...est stable release can be installed via pip which will automatically set up other P...(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~101-~101: Possible missing comma found.
Context: ....com/WMD-group/SMACT.git For developer installation SMACT can be installed from a copy of t...(AI_HYDRA_LEO_MISSING_COMMA)
[locale-violation] ~113-~113: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ... immediately reflected on the PATH. ## License and attribution Python code and origin...(LICENCE_LICENSE_NOUN_SINGULAR)
[locale-violation] ~115-~115: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ... data tables are licensed under the MIT License. ## Development notes ### Bugs, featu...(LICENCE_LICENSE_NOUN_SINGULAR)
[grammar] ~121-~121: The pronoun ‘they’ must be used with a non-third-person form of a verb.
Context: ...n the issue tracker, especially if they helps us improve the docs! For other queries ...(NON3PRS_VERB)
[style] ~125-~125: Consider a different adverb to strengthen your wording.
Context: ...ac.uk). ### Code contributions We are always looking for ways to make SMACT better a...(ALWAYS_CONSTANTLY)
Markdownlint
dev_docs/design_docs/StructurePredictor.md
79-79: null
No space after hash on atx style heading(MD018, no-missing-space-atx)
Additional comments not posted (215)
requirements-dev.txt (1)
3-3: Ensure continued coverage withpytest-cov.The presence of
pytest-covremains unchanged, which is good as it ensures that testing coverage continues to be a priority. Ensure that the version specified is compatible with the Python version used in the project.docs/requirements.in (1)
4-4: Confirm functionality ofreadthedocs-sphinx-search.The dependency
readthedocs-sphinx-searchremains unchanged, ensuring that search functionality within the documentation continues to operate as intended. Confirm that the version specified is compatible with other Sphinx-related dependencies..readthedocs.yaml (3)
10-10: Confirm configuration and requirements settings.The configuration for Sphinx and the explicit setting of Python requirements are crucial for the correct building of documentation. Ensure that the specified configuration file (
docs/conf.py) and the requirements file (docs/requirements.txt) are correctly set up and contain all necessary configurations and dependencies.Also applies to: 15-15
4-4: Review the operating system update.The operating system has been updated to Ubuntu 22.04. This change is likely to offer improved support and features. Ensure that all dependencies and tools used in the documentation build process are compatible with this new operating system version.
Verification successful
Ubuntu 22.04 Compatibility Verified
The update to Ubuntu 22.04 is compatible with Python 3.10, as specified in the
.readthedocs.yamlfile. This change should not disrupt the documentation build process.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of all tools with Ubuntu 22.04. # Test: List all tools and check compatibility with Ubuntu 22.04. cat .readthedocs.yaml | grep 'tools'Length of output: 45
Script:
#!/bin/bash # Extract the entire tools section from the .readthedocs.yaml file. awk '/tools:/,/^[^ ]/' .readthedocs.yamlLength of output: 128
6-6: Assess the Python version update.The Python version has been updated to 3.10. This update may enhance compatibility with newer libraries and language features. Confirm that all Python dependencies specified in the documentation build process are compatible with Python 3.10.
Verification successful
Python 3.10 Compatibility Confirmed
The specified Python dependencies for the documentation build process are compatible with Python 3.10. Both
setup.pyandpyproject.tomlindicate support for Python 3.10, and there are no conflicting constraints for the dependencies listed indocs/requirements.in.
- Python version compatibility is explicitly stated in both
setup.pyandpyproject.toml.- Dependencies for documentation are listed as optional and align with the supported Python versions.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify compatibility of Python dependencies with Python 3.10. # Test: List all Python dependencies and check compatibility with Python 3.10. cat docs/requirements.inLength of output: 200
Script:
#!/bin/bash # Search for setup.py or pyproject.toml files that might contain Python version compatibility information. fd setup.py fd pyproject.tomlLength of output: 57
Script:
#!/bin/bash # Display the contents of setup.py and pyproject.toml to check for Python version compatibility information. cat setup.py cat pyproject.tomlLength of output: 10596
smact/benchmarking/utilities.py (4)
3-3: Approve the addition of future annotations.The inclusion of
from __future__ import annotationsis a forward-thinking addition, enabling postponed evaluation of type annotations which can help with forward compatibility and potentially improve performance.
25-25: Initialisation ofvaluevariable approved.Initialising
valuetoNonebefore its use in the loop clarifies its scope and initial state, enhancing code readability and maintainability.
31-31: Refactor of logging statement approved.The reformatting of the logging statement into a single line improves readability and conciseness without altering its functionality.
39-39: Simplify conditional assignment forfname.Changing the conditional assignment for
fnamefrom a ternary operation to a straightforwardifcondition simplifies the code and enhances readability. Ensure that this change does not affect the functionality wherefnamemight be explicitly passed asNoneor an empty string, which should still default to "benchmark.log".Verification successful
Simplify conditional assignment for
fname.The suggestion to change the ternary operation to an
ifcondition is valid. The current logic ensures thatfnamedefaults to"benchmark.log"when not explicitly set, and this behaviour will remain intact with the proposed change. Implementing this will enhance readability without affecting functionality.
- Consider changing
fname = fname if fname else "benchmark.log"to a more readableifcondition.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that `fname` is correctly handled when explicitly set to None or an empty string. # Test: Search for explicit `None` or empty string assignments to `fname`. Expect: No occurrences that would break the default assignment. rg --type python -A 5 $'fname=None' smact/benchmarking/utilities.py rg --type python -A 5 $'fname=""' smact/benchmarking/utilities.pyLength of output: 195
Script:
#!/bin/bash # Corrected script to verify that `fname` is correctly handled when explicitly set to None or an empty string. # Test: Search for explicit `None` or empty string assignments to `fname`. Expect: No occurrences that would break the default assignment. rg -t py -A 5 'fname=None' smact/benchmarking/utilities.py rg -t py -A 5 'fname=""' smact/benchmarking/utilities.pyLength of output: 323
smact/lattice.py (2)
Line range hint
8-31: Enhanced docstrings inLatticeclass approved.The updated docstrings provide a clearer and more structured description of the
Latticeclass, its attributes, and methods, which enhances the documentation's clarity and usability.
50-59: Critical improvement to default parameter handling inSiteclass.Changing the default value for
oxidation_statesfrom a mutable list ([0]) toNoneand handling it within the constructor is a significant improvement. This change prevents potential bugs related to mutable default arguments and ensures that each instance ofSitehas its own independent list of oxidation states.docs/index.rst (4)
11-29: New 'Introduction' section approved.The addition of the 'Introduction' section provides a detailed overview of
smact's capabilities and features, enhancing the documentation's informativeness and accessibility for new users.
30-33: New 'Install' section approved.The 'Install' section clearly specifies the installation method via pip, which simplifies the setup process for users and enhances the usability of the documentation.
35-47: New 'License and citation' section approved.The 'License and citation' section adds clarity on the licensing terms and provides references for citing the theory and code associated with
smact. This is crucial for academic and professional use, ensuring users understand how to properly attribute the software.
57-57: New entry 'tutorials' in the table of contents approved.Adding 'tutorials' to the table of contents indicates a structured approach to guiding users through the package's functionalities, which is beneficial for enhancing user engagement and learning.
.pre-commit-config.yaml (8)
12-17: Addition of generic pre-commit hooks.The configuration now includes generic hooks like
check-yaml,end-of-file-fixer, andtrailing-whitespace. These are useful for maintaining basic code hygiene and are a good addition to any project.
18-38: Customised Markdown linting setup.The detailed configuration for
markdownlintwith specific rules disabled and files ignored shows a tailored approach to linting Markdown files. This is beneficial as it allows the project to enforce style guidelines while accommodating specific needs.
46-50: Use ofnbstripoutfor cleaning notebooks.The inclusion of
nbstripoutto clean notebooks before committing is a prudent measure to avoid committing unnecessary data like outputs and empty cells. This helps in keeping the repository clean and focused on source code.
51-57: Spell checking withcodespell.The configuration for
codespellto check spelling in the commit and commit messages is a good practice. It helps maintain the professionalism of the documentation and code comments.
59-63: Static type checking withpyright.The use of
pyrightfor static type checking is an excellent addition, especially for a dynamically typed language like Python. It can significantly reduce runtime errors by catching them at the development stage.
64-67: Documentation formatting withblacken-docs.The continued use of
blacken-docsto format code snippets within documentation ensures consistency between code in the repository and examples in the docs, which is crucial for maintaining accurate and user-friendly documentation.
2-11: Consolidation of linting and formatting tools into Ruff.The introduction of
ruff-pre-commitas a replacement for multiple previous tools (likeisort,black, etc.) is a significant change. This consolidation could improve efficiency but requires verification to ensure it covers all previous functionalities adequately.Verification successful
Ruff Configuration Covers Linting and Formatting
The
rufftool is configured in thepyproject.tomlfile to handle both linting and formatting, which suggests it can replace the functionalities ofisortandblack. The contribution guidelines mention these tools, indicating thatruffshould cover their roles. Ensure that the specific configurations inpyproject.tomlalign with the desired functionalities of the replaced tools.
- Check
pyproject.tomlforruffconfigurations.- Review contribution guidelines for mentions of
isortandblack.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that `ruff` and `ruff-format` cover all functionalities of the replaced tools. # Test: Check the documentation and community feedback on `ruff` to ensure it matches the capabilities of the replaced tools. echo "Check Ruff's documentation and community feedback."Length of output: 113
Script:
#!/bin/bash # Search for any configuration or documentation related to `ruff` and `ruff-format` in the repository. rg 'ruff' -A 5 # Check for mentions of `isort`, `black`, or other tools that `ruff` is supposed to replace. rg 'isort|black' -A 5Length of output: 3484
39-45: Integration of Prettier for code formatting.The use of
prettierwith the--writeargument to edit files in-place is a strong choice for maintaining consistent formatting across different types of files. However, ensure that this aggressive formatting aligns with the project's style guidelines.requirements.txt (5)
5-5: Update to dependency management command.The update to use
pyproject.tomlfor dependency management aligns with modern Python packaging practices and should help in managing dependencies more effectively.
75-76: Major version update forpymatgen.The update from
pymatgen==2023.11.12topymatgen==2024.5.1is a significant version change. It is crucial to ensure that this update does not introduce any breaking changes that could affect the project.
35-35: Update tomontypackage version.The update from
monty==2023.11.3tomonty==2024.7.30should be checked for compatibility with other packages, especiallypymatgen, which relies on it.
39-39: Minor version update formultiprocess.The update from
multiprocess==0.70.15tomultiprocess==0.70.16is a minor version change and likely includes bug fixes or minor improvements. This should generally be safe, but verifying the changelog can provide more context.
115-116: Addition oftyping-extensions.The addition of
typing-extensions==4.12.2is a new dependency. It's important to verify that this package is used effectively within the project and that it aligns with the project's requirements for type hinting.dev_docs/contribution_guidelines.md (2)
1-22: Updated contribution guidelines for clarity.The reformatting of the contribution guidelines enhances clarity and makes the document easier to follow. The steps for contributing are well articulated, promoting a smooth contribution process.
Tools
LanguageTool
[style] ~11-~11: Would you like to use the Oxford spelling “summarized”? The spelling ‘summarised’ is also correct.
Context: ...he steps for a new piece of work can be summarised as follows: 1. Push up or create [an i...(OXFORD_SPELLING_Z_NOT_S)
[style] ~18-~18: Consider removing “of” to be more concise
Context: ...are finished with the work, ensure that all of the unit tests pass on your own machine....(ALL_OF_THE)
23-51: Detailed pull request and development requirements sections.The detailed sections on pull requests and development requirements provide clear instructions for contributors. This helps in maintaining a high standard of contributions and ensures that contributors are well informed about the expectations.
Tools
LanguageTool
[uncategorized] ~25-~25: Possible missing comma found.
Context: ...eral overview of using pull requests on GitHub look [in the GitHub docs](https://help....(AI_HYDRA_LEO_MISSING_COMMA)
setup.py (3)
7-12: Update to author and maintainer information approved.The changes to the author and maintainer information are clear and align with the intent to update contact details. However, please ensure that the provided email addresses are active and correct to avoid issues with package maintenance communications.
Please verify the validity of the email addresses
[email protected]and[email protected]to ensure they are active and correct.
20-21: Centralisation of long description usingREADME.md.The implementation of reading the long description from the
README.mdfile is a good practice. It ensures that the package description remains consistent with the project documentation and enhances maintainability.Also applies to: 28-28
41-41: Addition ofsmact.utilsto package list approved.The inclusion of "smact.utils" in the package list suggests useful expansions to the package's capabilities. Please ensure that all necessary files and submodules are correctly included under this new package directory.
Verify that all necessary files and submodules are included under the
smact.utilspackage to ensure full functionality.docs/examples/elements_and_species.ipynb (3)
4-11: Clear and informative introduction.The markdown cell provides a clear and informative introduction to the element and species classes in the
smactlibrary, which are central to its functionality.
14-37: Effective demonstration of functionality.The code cell effectively demonstrates how to retrieve and display the oxidation states for iron using the
smactlibrary. The output is clear and the code is syntactically correct.
40-45: Informative content on additional features.The markdown cell provides useful information on how additional features like the Shannon radius can be utilised, which is relevant for applications such as radius ratio rules or training neural networks.
smact/tests/test_doper.py (3)
6-6: Transition to pytest framework.The import of
pytestis correct and aligns with the transition fromunittesttopytestas described. This change is crucial for the new testing approach.
20-21: Streamlined logic for charge determination.The changes in lines 20 and 21 enhance readability by removing unnecessary line breaks and consolidating the logic for determining the maximum and minimum charges. This maintains the functionality while improving the clarity of the code.
49-50: Updated exception handling with pytest.The use of
pytest.raisesinstead ofself.assertRaisesis a significant improvement, aligning with the pytest framework. This change not only modernises the test suite but also enhances its flexibility and readability.Also applies to: 52-52
docs/examples/lists.ipynb (3)
8-15: Well-structured markdown for list building explanation.The markdown cell provides a clear and concise explanation of how to build lists and dictionaries within the context of the
smactmodule. This is crucial for users who are new to the module or need a refresher on its capabilities.
35-38: Correct and clear code cell for generating elements.The code cell demonstrates the use of
smact.ordered_elementsto generate a list of elements. This is a practical example that aligns well with the preceding markdown explanation, effectively showing how to implement the described functionality.
68-69: Dictionary creation from element list.This code cell effectively demonstrates how to convert a list of elements into a dictionary, which is a continuation of the workflow described in the markdown cells. It's a practical example that enhances the understanding of
smactfunctionalities.smact/utils/download_compounds_with_mp_api.py (4)
7-7: Inclusion of Optional type hint.The import of
Optionalfrom thetypingmodule is appropriate given the changes to themp_api_keyparameter, allowing it to explicitly acceptNoneor a string. This aligns with Python's type hinting conventions and enhances the clarity of the function's interface.
15-15: Updated function signature with Optional type hint.The function signature for
download_mp_datahas been updated to includeOptional[str]for themp_api_keyparameter. This change is a good practice as it clearly indicates that the parameter can beNone, improving the function's documentation and usability.
28-28: Enhanced documentation structure.The addition of a section header for arguments in the docstring improves the documentation structure, making it easier for users to understand the function's parameters and their defaults. This is a valuable update in the context of the overall documentation overhaul.
46-46: Minor improvements and consistency checks.The changes in these lines include:
- A clear error message when the
MP_API_KEYis not set.- Improved readability and consistency in the creation of combinations of formulae.
- A new print statement that enhances the user's understanding of the process by indicating what data is being downloaded.
- Use of JSON dumping to save data, which is a standard practice for persisting API responses.
These changes collectively improve the function's usability and maintainability.
Also applies to: 54-54, 62-63, 92-92
docs/examples/filter.ipynb (2)
9-13: Review the Markdown Cell for Clarity and CorrectnessThe markdown cell provides a clear introduction to the
smact_filterfunction, explaining its purpose and usage effectively. The explanation is concise and free of typographical errors, enhancing the documentation of the project.
53-68: Review the Code Cell for Syntax and EffectivenessThe code cell demonstrates the usage of the
smact_filterfunction effectively. The import statements are correct, and the function is used in a practical example that matches the explanation given in the markdown cell. The use ofpprintto format the output is appropriate, making the results more readable.smact/distorter.py (3)
12-12: Review the Use of Future AnnotationsThe addition of
from __future__ import annotationsis a modern Python practice that allows for postponed evaluation of type annotations. This change is beneficial as it can improve performance and readability, especially in a module that handles complex data types like this one.
34-38: Review Updated Documentation for Clarity and ConsistencyThe updated documentation across multiple functions (
get_sg,get_inequivalent_sites,make_substitution,build_sub_lattice) includes clearer section headers and improved descriptions. These changes make the documentation more informative and easier to understand, aligning with Python documentation standards.Also applies to: 47-60, 84-96, 111-124
69-75: Review Logic Changes for CorrectnessThe update from
== Truetois Truein the boolean checks within theget_inequivalent_sitesfunction is a more Pythonic way to handle boolean expressions. This change enhances code readability and maintainability without altering the core functionality.Also applies to: 77-77
smact/utils/plot_embedding.py (2)
62-63: Review Type Annotation and Formatting ChangesThe update of type annotations from
List[str]tolist[str]reflects a shift towards using modern Python practices with the built-inlisttype. This change simplifies the type hinting and is correctly applied. The condensation of thesubplot_titlesargument into a single line enhances readability without altering the underlying logic.Also applies to: 72-72
119-119: Review Loop Modification for ClarityThe modification of the loop that adds traces to the figure to iterate directly over
legend_colorssimplifies the code by eliminating the unused second variable. This change streamlines the code and improves its clarity while maintaining the original functionality.smact/utils/generate_composition_with_smact.py (3)
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1-15: Review imports and warning settings.The imports are appropriate and align with the functionality of the script. However, consider reviewing the use of
warnings.simplefilter(action="ignore", category=UserWarning)as it might suppress important warnings that could indicate underlying issues during development.
18-24: Well-implemented function for formula conversion.The
convert_formulafunction is efficiently implemented usingitertools.productand list comprehension. It effectively generates chemical formulas based on the provided stoichiometric combinations.
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55-111: Efficient use of multiprocessing and data handling.The implementation of multiprocessing in this function is well done, enhancing performance for potentially large datasets. The use of
tqdmfor progress tracking and the efficient handling of data structures (like flattening lists and filtering for uniqueness) are commendable.dev_docs/design_docs/StructurePredictor.md (3)
1-9: Suggest grammatical improvement and approve content.The introduction and motivation section clearly outlines the rationale for developing a new structure predictor. However, consider adding a comma after "Therefore" to improve readability:
- Therefore we propose implement a similar method in `SMACT`. + Therefore, we propose implementing a similar method in `SMACT`.Tools
LanguageTool
[uncategorized] ~8-~8: A comma may be missing after the conjunctive/linking adverb ‘Therefore’.
Context: ..., in terms of interfacing withSMACT. Therefore we propose implement a similar method i...(SENT_START_CONJUNCTIVE_LINKING_ADVERB_COMMA)
10-26: Suggest grammatical improvements and approve content.The required features section is well-detailed and informative. Consider the following grammatical improvements for clarity:
- Generate a list of target compositions eg for Ba$_2$OF$_2$ + Generate a list of target compositions e.g., for Ba$_2$OF$_2$Additionally, adjust the noun agreement for "database":
- Simple two field database + Simple two-field database
35-57: Suggest formatting fix and approve content.The proposed workflow and suggested development plan sections are comprehensive and well-structured. Consider addressing the following formatting issue to adhere to Markdown best practices:
- #### Database + #### DatabaseThis change ensures that there is a space after the hash in the heading.
Tools
LanguageTool
[uncategorized] ~39-~39: The abbreviation “e.g.” (= for example) requires two periods.
Context: ... Generate a list of target compositions eg for Ba$_2$OF$_2$ `[Ba2+, O2-, F1-, (2, ...(E_G)
docs/examples/distorter.ipynb (3)
1-12: Approve the introduction to thedistortermodule.The markdown cell provides a well-written introduction to the concept of ion substitution, including relevant historical context and links to further reading. This sets a solid foundation for the rest of the notebook.
14-73: Approve the demonstration of thedistortermodule.The code cell is well-organized and effectively demonstrates the usage of the
distortermodule for ion substitutions. The step-by-step comments enhance readability and understanding, making it easy for users to follow the process.
75-84: Approve the output handling in the notebook.The final code cell effectively demonstrates how to write the distorted structures to a crystal structure file, providing a practical end to the notebook. The mention of the
aseatoms class adds clarity to the type of objects being handled.docs/requirements.txt (1)
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2-230: Review ofrequirements.txtThe updates to
requirements.txtreflect a significant overhaul with the addition of new packages and updates to existing ones. It's crucial to ensure that all packages are compatible with Python 3.10, as indicated by the change in the Python version used for pip-compile. Here are some specific points to consider:
- Version Compatibility: Verify that all the updated and new packages are compatible with Python 3.10. This is crucial to prevent runtime issues due to incompatibilities.
- Dependency Clarity: The comments on dependencies are helpful for understanding package relationships. Ensure these comments are accurate and up-to-date to aid in maintenance and troubleshooting.
- Redundancies and Necessities: Review whether all added packages are necessary for the project's functionality or if some can be considered redundant. This helps in keeping the project lightweight and manageable.
Overall, the changes seem to be well-intended to keep the project dependencies robust and up-to-date. However, thorough testing and verification are recommended to ensure smooth integration and functionality.
smact/properties.py (3)
10-28: Review ofeneg_mullikenFunctionThe updates to the
eneg_mullikenfunction enhance its readability and robustness:
- Type Hinting: The use of the
|operator for type unions is a modern Python feature that improves readability and is correctly implemented here.- Error Handling: Replacing generic exceptions with
TypeErrorprovides clearer semantics and helps in debugging type-related issues more effectively.- Documentation: The documentation is clear and well-structured, providing good insights into the function's purpose and usage.
These changes are well-aligned with Python's best practices and enhance the maintainability of the code.
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35-64: Review ofband_gap_HarrisonFunctionThe
band_gap_Harrisonfunction has been updated to improve clarity and type safety:
- Type Hinting: The introduction of the
|operator for thedistanceparameter enhances the readability and flexibility of the function signature.- Documentation: The documentation is comprehensive, detailing the method's theoretical background and parameters clearly.
- Function Logic: The core logic for estimating the band gap appears to be implemented correctly, assuming the constants and calculations are based on accurate scientific data.
These updates should help in maintaining the function's usability and accuracy in scientific computations.
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91-151: Review ofcompound_electronegFunctionThe
compound_electronegfunction has undergone significant updates to enhance its functionality and user feedback:
- Type Hinting: The use of modern Python syntax for type hints (list with
|operator) improves the function's readability and type safety.- Error Handling: The specific
TypeErrormessages enhance error clarity, making it easier for users to understand and resolve issues related to incorrect input types.- Documentation: The documentation is well-formatted and informative, providing clear guidance on the function's usage and parameters.
These improvements are commendable as they contribute to the robustness and maintainability of the function.
docs/examples/doper.ipynb (1)
1-162: Review ofdoper.ipynbNotebookThe
doper.ipynbnotebook is a well-structured document that provides comprehensive examples of using theDopermodule for dopant prediction:
- Content Quality: The markdown cells are informative, providing clear explanations of the module's functionality and the significance of the outputs.
- Code Quality: The code cells are correctly written, demonstrating the module's capabilities effectively. The use of parameters like
num_dopantsand different plotting options adds to the educational value of the notebook.- Relevance: The examples range from simple to complex scenarios, making the notebook a valuable resource for users at different levels of expertise.
This notebook is a valuable addition to the documentation, enhancing the usability and accessibility of the
Dopermodule.smact/tests/files/CaTiO3.json (1)
1-162: Comprehensive Improvement in JSON Structure Readability and MaintainabilityThe overhaul of the JSON structure in
CaTiO3.jsonsignificantly enhances its readability and maintainability. The clear formatting and detailed entries in thesitesarray improve the ease of parsing and understanding the data. The structure maintains all necessary information without altering the underlying data, which is crucial for users interacting with this data.The changes are well-executed and align with the objectives of making the documentation and data structures more user-friendly and maintainable.
paper.md (1)
1-40: Consistent Formatting in Metadata SectionThe update from single to double quotes in the title of the document is a minor but consistent formatting change that enhances the professional appearance of the document. The rest of the metadata remains unchanged, ensuring consistency and accuracy in the representation of authorship and affiliations.
These changes are purely cosmetic but contribute positively to the overall readability and professional standards of the document.
smact/oxidation_states.py (3)
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28-50: Updated Type Annotations and Streamlined Logic in__init__MethodThe update to the type annotations in the
__init__method of theOxidation_state_probability_finderclass aligns with modern Python practices, enhancing the clarity and maintainability of the code. The use ofdict[tuple[str, str], float] | Noneis more explicit and readable compared to the previousOptional[Dict[Tuple[str, str], float]].The streamlined logic for loading the default probability table when none is provided is clear and efficient, reducing redundancy and improving the readability of the code.
89-108: Simplified Logic inpair_probabilityMethodThe simplification in the
pair_probabilitymethod, where the tuple is directly returned instead of being assigned to a variable first, enhances code clarity and reduces unnecessary variable usage. This change makes the code more concise and easier to follow.The method's functionality remains intact, ensuring that the core logic is preserved while improving the code's maintainability.
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114-166: Enhanced Error Handling and Type Checking incompound_probabilityMethodThe updates to the
compound_probabilitymethod, including the replacement oftype(structure) == listwithisinstance(structure, list), demonstrate a more robust and Pythonic way of type checking. This change enhances the reliability of the code by ensuring that the type checks are more accurate.The error messages have been made more concise, which improves the readability and maintainability of the code. These changes are well-executed and contribute positively to the overall quality of the codebase.
smact/lattice_parameters.py (12)
6-25: Documentation improvements approved forcubic_perovskite.The updated docstring enhances clarity and readability by clearly defining the function's parameters and expected outputs.
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38-72: Documentation improvements approved forwurtzite.The structured docstring for
wurtziteis well-organized, making it easier for users to understand the function's purpose and usage.
79-91: Terminology and documentation updates approved forfcc.The change from "shannon_radius" to "covalent_radius" in the function signature and docstring improves accuracy and clarity. The structured documentation is also well-implemented.
104-116: Documentation and terminology updates approved forbcc.The updates to the
bccfunction's documentation and the terminology change enhance the clarity and accuracy of the information provided.
129-141: Consistent documentation improvements approved forhcp.The structured docstring and terminology updates for the
hcpfunction are consistent with other functions, enhancing clarity and usability.
154-166: Documentation and terminology updates approved fordiamond.The updates to the
diamondfunction's documentation and terminology are well-executed, enhancing clarity and consistency.
179-191: Approved documentation and terminology updates forbct.The
bctfunction's documentation is clear and structured, with appropriate terminology updates enhancing the overall quality.
204-216: Documentation improvements approved forrocksalt.The updated docstring for
rocksaltenhances clarity and readability, making it easier for users to understand the function's purpose and usage.
234-246: Documentation improvements approved forb2.The structured docstring for
b2is well-organized, making it easier for users to understand the function's purpose and usage.
264-276: Documentation improvements approved forzincblende.The structured docstring for
zincblendeenhances clarity and readability, aiding users in understanding the function's purpose and usage.
298-310: Documentation improvements approved forb10.The structured docstring for
b10is well-organized, making it easier for users to understand the function's purpose and usage.
326-338: Documentation improvements approved forstuffed_wurtzite.The structured docstring for
stuffed_wurtziteenhances clarity and readability, aiding users in understanding the function's purpose and usage.docs/tutorials/crystal_space.ipynb (8)
7-8: Clear and concise introduction.The title "Exploring crystal space" effectively sets the stage for the tutorial's content.
14-15: Well-contextualised tutorial overview.The overview provides a clear goal and context for the tutorial, enhancing its educational value by linking to a relevant publication.
21-36: Structured and clear tutorial objectives.The step-by-step breakdown of the tutorial's objectives provides clarity and ensures that learners can easily follow along.
61-62: Enhanced accessibility with Colab badge.Including the "Open in Colab" badge is a user-friendly addition that makes it easier for users to access and run the notebook.
70-81: Robust environment handling and package installation.The code effectively checks if the notebook is running in Google Colab and installs the required packages accordingly, ensuring compatibility and functionality across different environments.
89-91: Verify accessibility of relative import paths.The import statement uses a relative path, which may not be accessible in all environments. Consider verifying or providing instructions for setting up the directory structure when running the notebook locally.
115-116: Appropriate display of DataFrame for verification.Displaying the DataFrame is a good practice to allow users to verify the output of the data generation step.
241-243: Clear transition to next steps.The transition to the next tutorial is well-handled with a direct link. Ensure the linked notebook is accessible and the link is functional.
docs/tutorials/crystal_space_visualisation.ipynb (16)
7-7: Update to Notebook TitleThe title of the notebook has been updated to "Visualising crystal space" to better reflect the focus of the tutorial. This change aligns with the PR's objective to enhance documentation clarity and usability.
14-22: Enhanced Tutorial Introduction and Consistency in TerminologyThe introduction has been expanded to clearly describe the use of dimension reduction techniques for visualising large crystal spaces. The consistent use of lowercase for "element embeddings" and "dimension reduction" improves the professional tone of the documentation.
36-36: Section Title StandardisationThe section title "1. Element embeddings" has been standardised to use title case, which is consistent with other headings in the document. This change enhances the readability and structure of the notebook.
50-51: Addition of Google Colab LinkA new markdown cell has been added to provide a direct link to open the notebook in Google Colab. This is a significant enhancement in terms of accessibility, allowing users to easily access and run the notebook in a cloud environment.
59-71: Conditional Installation Commands for Google ColabThe code has been modified to include a check for Google Colab environment and conditionally install necessary packages if the notebook is run there. This is a thoughtful addition that ensures the notebook can be used seamlessly in different environments.
118-118: Streamlined Code for Reading DataThe code for reading a DataFrame from a pickle file has been streamlined by removing unnecessary line breaks, which improves the readability and maintainability of the code.
128-128: Clarification on Sample SizeThe number of samples for
n_sampleshas been reduced from 3000 to 100, with a comment added to clarify its use in a specific paper. This change makes the tutorial more manageable for users who may not need to process a large dataset initially.
184-191: Refinement in Embedding Dimension Access and Error HandlingThe logic for obtaining the embedding dimension and handling errors during the embedding computation has been refined. These changes improve the robustness and clarity of the code, ensuring that users have a better understanding of how embeddings are handled in the notebook.
225-225: Updated Section Title for Dimension ReductionThe section title has been updated to "2. Dimension reduction" to maintain consistency with the notebook's theme and other section titles. This change helps in keeping the document structured and easy to navigate.
301-301: Enhanced Saving Mechanism for Reduced EmbeddingsThe function
dimension_reductionnow includes a more detailed mechanism for saving reduced embeddings, which includes checking and creating directories as needed. This enhancement improves the usability of the function by handling file system operations more robustly.
319-319: Streamlined Data Retrieval and Reduction ProcessThe process for retrieving and reducing embeddings has been streamlined by updating the file paths and parameters used in the function calls. This change ensures that the notebook's code is more efficient and easier to understand.
334-334: Visualisation Section Title UpdateThe final markdown section title has been updated to "3. Visualisation of the low dimensional embeddings," which better describes the content of the section and aligns with the overall theme of the notebook.
343-343: Import Statement for Plotting FunctionAn import statement has been added for the
plot_reducers_embeddingsfunction, which is used in the visualisation section. This addition is crucial for the functionality of the notebook, ensuring that all necessary functions are available.
365-365: Displaying the PlotThe final line of the notebook ensures that the plot of embeddings is displayed within the notebook interface. This is an essential part of the visualisation process, allowing users to see the results of their data analysis directly.
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371-385: Metadata UpdatesThe kernel and language metadata have been updated to reflect the use of Python 3.9.19. These updates are important for ensuring that the notebook runs correctly in environments that match the specified configurations.
389-389: Notebook Format Minor UpdateThe notebook format minor version has been updated, which is likely to enhance compatibility with newer features of the notebook interface.
docs/conf.py (6)
37-37: Approved: Addition ofmyst_nbextension.The inclusion of the
myst_nbextension is a positive change, enhancing the documentation's capability to include Jupyter notebooks directly. This is particularly useful for tutorials or examples that benefit from live code execution.
40-40: Approved: Settingjupyter_execute_notebooksto "off".Setting
jupyter_execute_notebooksto "off" is a prudent choice, especially for large projects where executing notebooks during documentation builds could be resource-intensive and potentially error-prone.
57-59: Approved: Updates to project metadata.The updates to the project name, copyright, and author fields are correctly implemented. Ensure that these changes are consistently reflected across all project documentation and metadata.
118-120: Approved: Change of HTML theme tosphinx_book_theme.Changing the HTML theme to
sphinx_book_themecan significantly enhance the visual appeal and usability of the documentation. It is recommended to review the visual changes in a staging environment to ensure that all elements are displayed correctly and that the new theme aligns with the project's branding.
164-174: Approved: Addition ofhtml_theme_options.The new
html_theme_optionsare well-configured to enhance repository integration, providing direct links to GitHub and Binder. This enhancement will improve user navigation and accessibility, making it easier for users to access the source code or interact with live examples.
178-184: Approved: Addition ofhtml_contextfor GitHub integration.The configuration added to
html_contextis crucial for enhancing community engagement by allowing users to view and edit the source code directly from the documentation. This is a valuable feature for open-source projects.smact/dopant_prediction/doper.py (5)
33-35: Constructor Type Annotations and Docstring EnhancedThe updates to the type annotations using Python 3.10+ syntax (
tuple[str, ...]andstr | None) enhance clarity and modernise the code. The expanded docstring provides detailed information about the parameters, which improves the documentation quality.Also applies to: 39-42
72-73: Method_get_selectivityType Annotations and Docstring EnhancedThe updates to the type annotations using Python 3.10+ syntax (
list[smact.Element]) enhance clarity and modernise the code. The expanded docstring provides detailed information about the parameters and return type, which improves the documentation quality.
105-105: Method_get_dopantsType Annotations and Docstring EnhancedThe updates to the type annotations using Python 3.10+ syntax (
list[str]) enhance clarity and modernise the code. The expanded docstring provides detailed information about the parameters and return type, which improves the documentation quality.Also applies to: 112-117
160-160: Methodget_dopantsDocstring EnhancedThe expanded docstring provides detailed information about the parameters and return type, which improves the documentation quality and offers clearer guidance on the method's functionality and usage.
Also applies to: 162-173
405-412: Propertyto_tableDocstring AddedThe addition of a docstring to the property
to_tableenhances documentation quality by providing clear information about its functionality.smact/tests/test_structure.py (10)
3-3: Approved use of postponed evaluation of type annotations.The addition of
from __future__ import annotationsallows for postponed evaluation of type annotations, which is beneficial for forward references and generally cleaner code.
14-14: Approved addition ofClassVarforTEST_SPECIES.The explicit use of
ClassVarfor theTEST_SPECIESvariable clarifies that it is intended to be a class-level variable, not an instance variable, which is a good practice for constants used in tests.
74-74: Review ofassertStructAlmostEqualmethod.The method's docstring has been reformatted for clarity, which improves the readability and maintainability of the code. The method signature remains unchanged, ensuring that existing functionality is preserved.
94-94: Review oftest_as_poscarmethod.The method tests the POSCAR generation functionality. The test cases have been streamlined by consolidating function calls into single lines, which enhances readability without altering the underlying logic.
148-148: Review oftest_from_py_struct_icsdmethod.The method tests the generation of
SmactStructurefrom a pymatgen structure using ICSD statistics. The instantiation ofSmactStructureis condensed into a single line, which simplifies the code without changing its functionality.
156-156: Review oftest_has_speciesmethod.The method tests whether a species is present in a
SmactStructure. The test cases are simplified by reducing the number of lines used for instantiatingSmactStructureobjects, which improves code efficiency and readability.
164-164: Review oftest_smactStruc_comp_keymethod.The method tests the generation of a composition key for
SmactStructureobjects. The changes involve simplifying the instantiation ofSmactStructureobjects, which makes the test cases more concise and readable.
194-194: Review oftest_equalitymethod.The method tests the equality determination of
SmactStructureobjects. The formatting of list comprehensions and assertions has been compacted into fewer lines, which enhances the readability of the test cases.
209-209: Review oftest_ele_stoicsmethod.The method tests acquiring element stoichiometries from
SmactStructureobjects. The changes involve compacting the list comprehensions and assertions into fewer lines, which simplifies the code without affecting its functionality.
268-268: Review oftest_db_interfacemethod.The method tests interfacing with a database. The use of
pytest.raiseshas been integrated into thetest_ion_mutationmethod, replacing the previous structure that used a nested context manager, which enhances the clarity of the exception handling.smact/structure_prediction/structure.py (8)
3-3: Approved use of postponed evaluation of type annotations.The addition of
from __future__ import annotationsallows for postponed evaluation of type annotations, which is beneficial for forward references and generally cleaner code.
54-58: Review of__init__method inSmactStructure.The method's type annotations have been updated to use modern Python syntax, enhancing readability and aligning with evolving type hinting practices. The logic within the method remains intact, ensuring that existing functionality is preserved.
121-122: Review of_sanitise_speciesmethod.The method's type annotations have been updated to use modern Python syntax. This change improves the clarity of the type definitions and maintains the method's functionality.
234-234: Review offrom_py_structmethod.The method creates a
SmactStructurefrom a pymatgen Structure object. The type annotations have been updated, and the method includes detailed documentation on the parameters and return type, enhancing the method's clarity and maintainability.
297-297: Review offrom_mpmethod.The method creates a
SmactStructureusing the first Materials Project entry for a composition. The type annotations have been updated, and the method includes detailed documentation on the parameters and return type, enhancing the method's clarity and maintainability.
537-537: Review ofhas_speciesmethod.The method's type annotation for the
speciesparameter has been updated to use modern Python syntax. This change clarifies the expected input type and maintains the method's functionality.
541-541: Review ofget_spec_strsmethod.The method's return type has been updated to use modern Python syntax, enhancing readability and aligning with evolving type hinting practices. The method's functionality remains unchanged.
512-512: Review of_get_ele_stoicsmethod.The method's type annotations have been updated to use modern Python syntax. This change improves the clarity of the type definitions and maintains the method's functionality.
smact/data_loader.py (5)
13-13: Approved use of postponed evaluation of type annotations.The addition of
from __future__ import annotationsallows for postponed evaluation of type annotations, which is beneficial for forward references and generally cleaner code.
351-351: Review oflookup_element_datafunction.The function's type annotations have been updated to include explicit types for the parameters, enhancing the clarity and maintainability of the code. The use of f-strings for string formatting in warning messages improves readability and performance.
309-309: Review oflookup_element_hhisfunction.The function's type annotation for the
symbolparameter has been updated to explicitly specify the expected type asstr. This change clarifies the expected input type and maintains the function's functionality.
688-688: Review oflookup_element_sse2015_datafunction.The function's type annotations have been updated to include explicit types for the parameters, enhancing the clarity and maintainability of the code. The use of f-strings for string formatting in warning messages improves readability and performance.
751-751: Review oflookup_element_sse_pauling_datafunction.The function's type annotation for the
symbolparameter has been updated to explicitly specify the expected type asstr. This change clarifies the expected input type and maintains the function's functionality.docs/tutorials/oxidation_states.ipynb (8)
7-13: Clear and concise introduction to the tutorial.The markdown cell effectively introduces the high-throughput compound design workflow and outlines the steps involved using the SMACT library. This provides clarity and sets the context for the tutorial.
20-20: Useful addition of the Colab badge.Including the "Open in Colab" badge enhances accessibility, allowing users to easily run and interact with the notebook in a cloud-based environment.
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143-181: Effective use of multiprocessing and data display.The code cell efficiently handles the generation of compositions using multiprocessing, which is suitable for large datasets. Displaying the first few entries of the generated data is helpful for immediate verification and understanding of the output format.
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188-205: Clear formula generation and output display.The function to convert composition data into chemical formulas is well-implemented. Displaying the first few formulas provides a clear view of the output, aiding in the verification of the data processing logic.
242-242: Clear explanation of the oxidation states model application.The markdown cell effectively explains how the
Oxidation_state_probability_finderclass is used to compute the likelihood of metal species existing in the presence of specific anions, providing valuable context for the tutorial.
242-247: Efficient computation of compound probabilities.The code cell efficiently computes the probabilities of various compounds using the
compound_probabilitymethod of theOxidation_state_probability_finderclass. The use of list comprehension enhances the performance of the operation.
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252-334: Well-organized display of compound probabilities using DataFrame.The creation of a DataFrame to organize and display the compound probabilities and related data is well-executed. The use of HTML styling in the output enhances the readability and presentation of the data.
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393-441: Effective visualization of compound probabilities.The scatter plot effectively visualizes the number of compounds as a function of the probability threshold. This graphical representation helps in understanding the distribution and trends in the compound probabilities, making the data more accessible.
smact/data/oxidation_state_probability_table.json (1)
1-1322: Comprehensive Review of JSON Data StructureThe transformation of
oxidation_state_probability_table.jsoninto a structured JSON array with 1322 entries significantly enhances the dataset's usability and analytical capabilities. The format appears correct, and the data is well-organized, facilitating easier access and manipulation.Data Integrity and Consistency:
- Ensure that all entries are accurate and consistent with expected values for oxidation states and probabilities.
- Verify that no duplicate entries exist and that the data aligns with known chemical properties.
JSON Format:
- The JSON format is correctly maintained throughout the file, with proper list structures and nesting.
Overall, this update should greatly improve the functionality of the dataset for computational contexts requiring detailed oxidation state information.
docs/tutorials/smact_validity_of_GNoMe.ipynb (8)
5-13: Update to Markdown Cell: Introduction and Colab LinkThe introductory markdown cell has been updated to include a description of the notebook's purpose and a link to open it in Google Colab. This is a useful addition for accessibility and ease of use, allowing users to directly interact with the notebook in a cloud environment.
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41-87: Code Cell: Importing Libraries and Initializing Parallel ProcessingThis cell introduces the
initialize_parallel_processingfunction, which encapsulates the setup for parallel processing usingpandarallel. This is a good example of modular code design, enhancing readability and maintainability. The function is well-documented with a docstring explaining its purpose and usage. The subsequent use of this function to set up parallel processing is clear and effective.
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90-191: Data Loading and Initial AnalysisThis cell loads data from an external CSV file into a pandas DataFrame and performs initial data analysis, displaying information about the DataFrame and its first few entries. The use of
pd.read_csvfor data loading is standard and appropriate. The output includes a styled DataFrame, which enhances the visual presentation of the data in the notebook. This cell is well-structured and provides a good foundation for data-driven analysis in subsequent cells.
214-218: Markdown Cell: Explanation of SMACT Validity FunctionThis markdown cell provides a detailed explanation of the
smact_validityfunction used in the notebook. It clearly outlines the function's limitations regarding elements with mixed valency. This is valuable for understanding the context and limitations of the analyses performed in the notebook.
222-342: Application of SMACT Validity Test and Data PresentationThis cell applies the
smact_validityfunction to the DataFrame and displays the results. The use ofparallel_applyis appropriate for leveraging the parallel processing capabilities set up earlier. The presentation of data usingdf.head()provides a clear view of the modifications made to the DataFrame. This cell effectively demonstrates the application of the SMACT validity test to real data.
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356-391: Visualization of ResultsThis cell creates a horizontal bar plot to visualize the results of the SMACT validity test. The use of
matplotlibfor plotting is standard, and the configuration of the plot, including labels and layout adjustments, is well-executed. The plot provides a clear visual representation of the data, making it easier to understand the distribution of SMACT-valid materials in the GNoME database.
395-400: Conclusion Markdown CellThe conclusion summarises the findings of the notebook, reiterating the utility and limitations of the SMACT validity test. It provides a clear closure to the notebook, summarising the analysis performed and the insights gained. This is a well-written conclusion that effectively wraps up the notebook.
405-419: Metadata Updates: Kernel SpecificationThe metadata of the notebook has been updated to reflect a change in the kernel specification, specifically updating the display name and the Python version. This is important for ensuring that the notebook environment is correctly replicated when others use it. The update from Python 2.7.6 to 3.9.16 is particularly crucial as it ensures compatibility with current libraries and syntax.
examples/Structure_Prediction/Li-Garnets_SP-Pym-new.ipynb (7)
5-5: Reset Execution CountsSetting the execution count to
nullis a common practice when cleaning up a notebook for sharing or publication, ensuring that the notebook appears unrun and prevents execution order confusion.
51-51: Consistent Reset of Execution Counts Across All CellsAll code cells have had their execution counts set to
null. This consistency is crucial for maintaining a clean state of the notebook, especially when preparing for version control or sharing. This change aligns with best practices for notebook maintenance.Also applies to: 142-142, 166-166, 188-188, 214-214, 229-229, 308-308, 327-327, 418-418, 431-431, 457-457, 466-466, 522-522, 550-550, 679-679, 696-696, 710-710, 839-839, 853-853, 871-871, 912-912, 940-940, 965-965, 1100-1100, 1120-1120, 1133-1133, 1142-1142, 1151-1151, 1163-1163, 1183-1183, 1214-1214, 1237-1237
452-452: Streamline Print StatementsCondensing multiple print statements into a single line enhances readability and reduces clutter in the notebook. This change is a good practice for improving the presentation of output in Jupyter notebooks.
498-498: Enhance Code Clarity in LoopThe modification within the loop to include predictions and sorting operations in a more concise manner improves the readability and maintainability of the code. Sorting predictions by a key directly within the loop is efficient and clear.
544-544: Use of Advanced Library FeaturesThe use of
mg.Structure.from_str(...).composition.reduced_formulademonstrates an advanced use of the pymatgen library, which is beneficial for handling complex data structures efficiently. This change likely enhances the functionality and performance of the notebook.
933-933: Visualisation Enhancement with SeabornIntroducing
sns.histplotfor data visualisation is an excellent choice for creating more informative and visually appealing plots. This change utilises Seaborn's capabilities effectively, improving the overall quality of data presentation in the notebook.
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37-37: Finalise Notebook with Visual OutputThe addition of a command to save a visual output to a file is a practical use of matplotlib's capabilities, ensuring that results are not only viewable but also storable for future reference. This is a useful feature for reproducibility and sharing of results.
docs/introduction.rst (4)
21-25: Approve installation instructions.The installation instructions are clear and concise, effectively guiding users on how to install the
smactmodule via pip.
26-38: Approve citation details.The citation details are well-presented, providing clear and direct links to the relevant publications. This section effectively communicates the necessary information for citing the theory and code of
smact.
39-42: Approve content in 'Studies using smact' section.This section effectively lists relevant studies and publications, providing users with additional resources to explore the applications of
smact.
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43-48: Approve references section.The references are well-formatted and provide valuable links for users interested in further exploring the foundational works related to
smact.docs/examples/validity.ipynb (2)
9-17: Well-documented explanation of thesmact_validityfunction.The markdown cell provides a clear and concise explanation of the
smact_validityfunction, detailing the Charge Neutrality and Pauling Electronegativity Tests. This should help users understand the function's purpose and application effectively.
44-62: Effective demonstration of thesmact_validityfunction.The code cell effectively demonstrates the application of the
smact_validityfunction on a dataset of chemical compounds. It includes importing necessary modules, creating a DataFrame, applying the function, and displaying the results, which are crucial for understanding the function's practical use.docs/examples/oxidation_states.ipynb (2)
7-9: Clear introduction to theoxidation_statessubmodule.The markdown cell provides a clear and concise introduction to the
oxidation_statessubmodule, effectively setting the stage for the detailed demonstrations that follow. This helps users understand the context and purpose of the submodule.
66-70: Effective demonstration of retrieving species from the probability table.The code cell effectively demonstrates how to use the
Oxidation_state_probability_finderclass to retrieve and print the species included in the probability table. This is a practical example that shows how to interact with the class to obtain useful information.pyproject.toml (3)
3-3: Updatedrequiresfield in[build-system].The update to specify
setuptools>=65.0.0ensures compatibility with newer features and improvements in the build process. This change aligns with modern Python practices and helps maintain the project's robustness.
6-29: Comprehensive new[project]section.The addition of the
[project]section with detailed metadata including the project name, version, description, and author/maintainer details significantly enhances the project's configuration. This section aids in discoverability, compliance with packaging standards, and provides clear information to users and contributors.
41-50: Well-defineddependenciessection.The updated
dependenciessection with specific package requirements and version constraints ensures that the project operates with compatible library versions. This is crucial for maintaining functionality and avoiding conflicts during installation.smact/structure_prediction/database.py (8)
3-3: Addition of postponed evaluation of type annotations.The import of
from __future__ import annotationsallows for postponed evaluation of type annotations, which is beneficial for avoiding circular imports and improving performance. This is a good practice, especially in complex projects.
12-15: Improved error handling for missingParallelPool.Setting
ParallelPooltoNonein case of anImportErroris a robust way to handle optional dependencies. This change ensures that the application can still function even if the optionalpathoslibrary is not installed.
26-30: Use ofTYPE_CHECKINGfor conditional imports.The use of
TYPE_CHECKINGfrom thetypingmodule to conditionally import modules is a good practice. It helps to avoid runtime performance issues and is particularly useful in avoiding circular imports during type checking.
109-110: Refactor method signature and improve documentation inadd_mp_icsd.The method signature has been updated to use modern Python type hints (
listanddictdirectly instead ofListandDictfromtyping). This aligns with Python 3.9+ type hinting practices. The documentation has been improved to include clearer argument descriptions and return type information, enhancing readability and maintainability.Also applies to: 122-130
191-193: Refactor method signature and documentation inadd_structs.The method now uses modern type hints and includes a default value for
commit_after_eachdirectly in the type hint, which is a cleaner approach. The documentation has been expanded to explain the parameters and return type more clearly, which is beneficial for maintainability and clarity.Also applies to: 197-208
227-238: Improved type annotations and documentation inget_structs.The method's return type has been updated to use the new syntax (
listinstead ofList), which is more concise and preferred in Python 3.9 and later. The documentation now includes better descriptions of the arguments and the return type, improving clarity and usability of the method.
252-264: Updated type annotations and enhanced documentation inget_with_species.The method now uses the simplified type annotations (
listandtuple), making the code cleaner and more aligned with recent Python standards. The documentation improvements provide clearer guidance on the method's usage and expected outcomes, which enhances the code's readability and maintainability.
290-293: Refactorparse_mprestfunction signature and documentation.The function signature has been updated to use modern Python type hints. The documentation has been improved to include a more detailed description of the parameters and the return type. These changes make the function easier to understand and use.
Also applies to: 297-305
smact/structure_prediction/prediction.py (5)
13-13: Addition of postponed evaluation of type annotations.The import of
from __future__ import annotationsallows for postponed evaluation of type annotations, which is beneficial for avoiding circular imports and improving performance. This is a good practice, especially in complex projects.
22-28: Use ofTYPE_CHECKINGfor conditional imports.The use of
TYPE_CHECKINGfrom thetypingmodule to conditionally import modules is a good practice. It helps to avoid runtime performance issues and is particularly useful in avoiding circular imports during type checking.
47-54: Streamlined constructor with improved documentation.The constructor of
StructurePredictorhas been streamlined, and the documentation has been improved for clarity. This includes better descriptions of the parameters, which enhances readability and maintainability.
65-68: Refactor method signature and documentation inpredict_structs.The method now uses modern Python type hints (
listandtupledirectly instead ofListandTuple). The documentation has been reformatted to include clearer section headers for arguments and yields, improving documentation quality and making the method easier to understand and use.Also applies to: 73-83
153-157: Refactor method signature and documentation innary_predict_structs.The method signature has been updated to use modern type hints and includes more flexible default values. The documentation improvements provide clearer guidance on the method's usage and expected outcomes, which enhances the code's readability and maintainability.
Also applies to: 162-171
README.md (8)
15-15: Updated title format.The title has been updated to use a Markdown header format, which enhances visibility and conforms to common Markdown practices for readability.
19-20: Updated links and formatting.The links to documentation and examples have been updated and formatted consistently, ensuring they are easily identifiable and accessible. This improves the usability of the README.
26-26: Added statement of need section.The addition of a "Statement of need" section helps clarify the purpose and the scope of the project, which is beneficial for new users and contributors.
32-37: Improved 'Getting started' section.The "Getting started" section has been reorganized and now includes clearer instructions and links, making it easier for new users to begin using the project.
38-59: Enhanced 'Code features' section.The "Code features" section has been expanded to include more detailed descriptions of the core functionalities and links to relevant documentation. This makes the README more informative and useful for users.
Tools
LanguageTool
[style] ~46-~46: Consider a shorter alternative to avoid wordiness.
Context: ...lied to generated lists of compositions in order to screen for particular properties. These...(IN_ORDER_TO_PREMIUM)
62-80: Updated 'List of modules' and 'Requirements' sections.The "List of modules" section has been reorganized to provide a clearer overview of the available modules. The "Requirements" section has been updated to specify the Python version and required packages, which is crucial for setting up the project.
Tools
LanguageTool
[style] ~66-~66: Would you like to use the Oxford spelling “initialize”? The spelling ‘initialise’ is also correct.
Context: ...es the loading of external data used to initialise the coresmact.Elementand `smact.Spe...(OXFORD_SPELLING_Z_NOT_S)
[grammar] ~79-~79: It looks like ‘collections’ doesn’t match ‘a’. Did you mean “a collection” or just “collections”?
Context: ...rediction**: A submodule which contains a collections of tools for predicting dopants. ## Re...(A_NNS_IN)
87-102: Improved installation instructions.The installation instructions have been clarified and now include commands for different installation methods (pip and conda), which is helpful for users looking to install the project.
Tools
LanguageTool
[uncategorized] ~89-~89: Possible missing comma found.
Context: ...est stable release can be installed via pip which will automatically set up other P...(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~101-~101: Possible missing comma found.
Context: ....com/WMD-group/SMACT.git For developer installation SMACT can be installed from a copy of t...(AI_HYDRA_LEO_MISSING_COMMA)
113-134: Enhanced 'License and attribution' and 'Development notes' sections.The "License and attribution" section has been updated to clearly state the licensing terms. The "Development notes" section now includes more detailed guidance on contributing to the project, reporting bugs, and adding tests, which is beneficial for maintaining project quality.
Tools
LanguageTool
[locale-violation] ~113-~113: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ... immediately reflected on the PATH. ## License and attribution Python code and origin...(LICENCE_LICENSE_NOUN_SINGULAR)
[locale-violation] ~115-~115: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ... data tables are licensed under the MIT License. ## Development notes ### Bugs, featu...(LICENCE_LICENSE_NOUN_SINGULAR)
[grammar] ~121-~121: The pronoun ‘they’ must be used with a non-third-person form of a verb.
Context: ...n the issue tracker, especially if they helps us improve the docs! For other queries ...(NON3PRS_VERB)
[style] ~125-~125: Consider a different adverb to strengthen your wording.
Context: ...ac.uk). ### Code contributions We are always looking for ways to make SMACT better a...(ALWAYS_CONSTANTLY)
smact/tests/files/Fe3O4.json (1)
1-316: Excellent improvement in JSON structure readability and maintainability.The changes to the JSON file have significantly enhanced its readability and maintainability. The detailed and well-organized structure ensures that developers and users can easily understand and interact with the data. The inclusion of clear module and class declarations, along with comprehensive details on lattice parameters and atomic sites, is commendable.
smact/__init__.py (7)
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28-134: Documentation and Type Annotation Enhancements inElementClassThe updates to the
Elementclass include enhanced docstrings and the use of modern Python type annotations (str | None). These changes improve both the readability and maintainability of the code, aligning with current best practices in Python development.
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177-281: Documentation and Type Annotation Enhancements inSpeciesClassThe
Speciesclass has seen similar updates to theElementclass, with improved docstrings and modern type annotations. The explicit handling of theradii_sourceparameter enhances the class's functionality by clearly defining the behaviour for different data sources. These changes contribute to the code's readability and maintainability.
300-306: Updated Type Annotations inordered_elementsFunctionThe function now uses the modern
list[str]annotation for its return type, aligning with current Python best practices and enhancing the code's readability.
323-348: Updated Type Annotations inelement_dictionaryFunctionThe function now uses modern type annotations (
Iterable[str] | Noneandstr | None) for its parameters, which clarifies the expected inputs and enhances the code's readability and maintainability.
354-366: Detailed Documentation inare_eqFunctionThe function includes comprehensive documentation that clearly describes its purpose, parameters, and return type, contributing to the code's usability and maintainability.
428-449: Updated Type Annotations and Detailed Documentation inneutral_ratios_iterFunctionThe function now uses modern type annotations (
list[int]andbool | list[list[int]]) and includes a detailed docstring that explains its complex logic. These changes enhance both the readability and maintainability of the code.
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465-500: Updated Type Annotations and Detailed Documentation inneutral_ratiosFunctionThe function now uses modern type annotations (
list[int]andbool | list[list[int]]) for its parameters and includes detailed documentation that clearly explains its purpose and usage. These changes enhance both the readability and maintainability of the code.smact/structure_prediction/utilities.py (2)
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14-32: Updated type hints and docstrings inparse_specfunction.The function
parse_spechas been updated to use the modern Python 3.10 syntax for type hints, changing fromTupletotuple. The docstring has been enhanced with clearer formatting and section headers, improving readability and structure. This is a positive change that aligns with modern Python practices and enhances the documentation for better user understanding.
46-64: Updated type hints and docstrings inunparse_specfunction.The function
unparse_spechas also been updated to use the modern Python 3.10 syntax for type hints, changing fromTupletotuple. The docstring improvements include clearer formatting and section headers, which enhance readability and provide a structured approach to documentation. These changes are consistent with modern Python standards and improve the clarity of the function's purpose and usage.smact/builder.py (2)
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16-44: Enhanced parameter handling incubic_perovskite.The
cubic_perovskitefunction has been updated to useNoneas default values forcell_parandrepetitionsparameters, replacing the previous mutable default lists. This change prevents unintended side effects associated with mutable default arguments and ensures that each function call receives a fresh list. The implementation within the function to assign default values ifNoneis passed is correctly handled. This is a significant improvement in the function's robustness and prevents potential bugs in future usage.
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52-84: Improved parameter handling and clarity inwurtzite.The
wurtzitefunction mirrors the changes made incubic_perovskite, with the introduction ofNoneas default values forcell_parandrepetitionsto avoid mutable defaults. Additionally, theoxidation_statesvariable has been modified to include negative oxidation states in a more concise manner, improving the clarity and maintainability of the code. These changes enhance the function's parameter handling and maintainability without altering its core functionality.smact/structure_prediction/mutation.py (3)
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39-58: Updated type hints and lambda table handling inCationMutator.__init__.The constructor of the
CationMutatorclass has been updated to use the modern Python 3.10 syntax for union types in thealphaparameter. This change enhances type safety and clarity. The method also includes comprehensive documentation that clearly describes the parameters and their default values, improving the readability and usability of the documentation. The lambda table is populated within the constructor, ensuring that it is fully prepared for use immediately after object instantiation.
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69-108: Enhanced JSON handling and DataFrame conversion inCationMutator.from_json.The
from_jsonstatic method has been updated to handle optional JSON input more robustly, with improved type hints and default handling. The method now usespivot_tableinstead ofpivot, which is more suitable for handling potential duplicates in the data, enhancing the robustness of the DataFrame reshaping. The documentation is clear and provides a good level of detail about the method's functionality and parameters.
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402-426: Improved substitution threshold handling inunary_substitute.The
unary_substitutemethod has been updated to use the modern Python 3.10 syntax for union types in thethreshparameter, enhancing type clarity. The method's documentation is well-structured, providing clear information on the parameters and the yield behavior. This method is crucial for generating new structures based on substitution probabilities, and the updates improve its usability and maintainability.docs/tutorials/smact_generation_of_solar_oxides.ipynb (1)
1-439: Comprehensive Review of the Jupyter NotebookThe notebook is well-structured and provides a clear step-by-step guide for generating quaternary oxide compositions using the SMACT library. Here are some specific observations and suggestions:
Markdown Cells (Lines 1-10, 12-18, 20-25, etc.): The markdown cells are informative and well-written. They provide a clear introduction and guide through the process. It might be beneficial to include links to the SMACT library documentation or related resources for users unfamiliar with the library or its functions.
Code Cells (Lines 28-44, 61-95, etc.): The code cells are generally well-written. However, there are a few areas where improvements could be made:
- Error Handling (Lines 34-43): While there is basic error handling for checking if the notebook is running in Google Colab, it might be useful to expand this to handle other potential issues, such as failed installations or imports.
- Library Imports (Lines 61-95): The imports are well-organized, but it's a good practice to explain why each library or module is needed, possibly in a markdown cell before the imports. This can help users understand the dependencies and their roles.
Use of Multiprocessing (Lines 226-258, 269-306): The use of multiprocessing is a good practice for performance optimization. However, it's crucial to mention the potential pitfalls, such as issues with memory usage or debugging. A small section discussing when and why to use multiprocessing, along with its drawbacks, would be beneficial.
Data Handling and Output (Lines 317-395): The steps for handling data and generating output are clear. However, the notebook could benefit from a discussion on how to handle large datasets effectively, considering memory management and performance.
Reproducibility and Documentation (Lines 401-415): The final section on reproducing results is crucial. It might be helpful to include a version control section for the libraries used, ensuring that the notebook remains functional even if library versions change.
Overall, the notebook is well-prepared and serves as a robust tutorial for users interested in materials science and machine learning applications. Enhancing the documentation with more detailed explanations and potential issues or considerations could make it even more valuable.
smact/screening.py (1)
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1-522: Comprehensive Review of thesmact/screening.pyFileThe modifications in
smact/screening.pyenhance the code's readability and maintainability by adopting Python 3.10's type hinting features. Here are some specific observations and suggestions:
Type Annotations (Lines 27-29, 80-81, etc.): The transition to Python 3.10 type annotations is well-executed. This change not only modernizes the code but also makes it more readable and consistent with current Python best practices.
Function Documentation (Lines 34-56, 127-146, etc.): The docstrings are well-written and provide clear descriptions of the functions' purposes, parameters, and return types. It's crucial to maintain this level of documentation, especially in a library dealing with complex chemical computations.
Logical Refactoring (Lines 57-76, 186-220, etc.): The logical refactoring within functions like
pauling_testandeneg_states_testimproves clarity without altering functionality. This is a good practice as it helps other developers understand and maintain the code more easily.Error Handling and Edge Cases (Lines 432-522): The function
smact_validityincludes comprehensive checks and balances, which is excellent for robustness. However, it would be beneficial to include more detailed error messages or logging to help debug issues when they arise.Performance Considerations (Lines 223-260): While the code is optimized for performance, it's important to periodically review these functions to ensure they remain efficient with newer versions of Python and libraries. Consider adding performance benchmarks or tests to monitor any regressions or improvements over time.
Overall, the changes are positive and contribute significantly to the code's quality. Continuing to focus on documentation, error handling, and performance will ensure the library remains reliable and easy to use.
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "3", | ||
| "metadata": { | ||
| "tags": [] | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "Square planar iron has a Shannon radius of None Angstrom\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "iron_square_planar = smact.Species(\"Fe\", 2, \"4_n\")\n", | ||
| "print(\"Square planar iron has a Shannon radius of %s Angstrom\" % iron_square_planar.shannon_radius)" | ||
| ] |
There was a problem hiding this comment.
Handle or explain the 'None' output.
The code cell correctly demonstrates creating a species with specific properties and retrieving the Shannon radius. However, the output showing "None" for the Shannon radius might be confusing. It would be beneficial to either handle this case in the code or provide an explanation in the markdown to clarify why "None" might appear.
| max_atomic_num: int = 103, | ||
| num_processes: int = None, | ||
| save_path: str = None, | ||
| num_processes: Optional[int] = None, | ||
| save_path: Optional[str] = None, | ||
| ): | ||
| """Generate all possible compositions of a given number of elements and | ||
| """ | ||
| Generate all possible compositions of a given number of elements and | ||
| filter them with SMACT. | ||
|
|
||
| Args: | ||
| ---- | ||
| num_elements: the number of elements in a compound. Defaults to 2. | ||
| max_stoich: the maximum stoichiometric coefficient. Defaults to 8. | ||
| max_atomic_num: the maximum atomic number. Defaults to 103. | ||
| num_processes: the number of processes to use. Defaults to None. | ||
| save_path: the path to save the results. Defaults to None. | ||
|
|
||
| Returns: | ||
| ------- | ||
| _description_ | ||
| """ | ||
|
|
||
| """ |
There was a problem hiding this comment.
Approve function signature changes and suggest documentation completion.
The updates to the function signature with Optional type hints enhance clarity and usability. However, the documentation placeholder _description_ in the Returns section should be completed to provide clear information about what the function returns.
Would you like me to help complete the documentation for this function?
| "## 2. Generating compositions\n", | ||
| "\n", | ||
| "First, we'll create binary chemical compositions using the SMACT filter. The SMACT filter is a smart tool that helps us select compositions based on important chemical rules, such as oxidation states and electronegativity.\n", | ||
| "\n", | ||
| "To generate these compositions, we'll use a function called [`generate_composition_with_smact`](../smact/utils/generate_composition_with_smact.py). This function allows us to enumerate all possible binary compositions and filter them based on the SMACT rules. \n", | ||
| "\n", | ||
| "### Key parameters:\n", | ||
| "- `num_elements`: Number of elements in the composition (e.g., 2 for binary).\n", | ||
| "- `max_stoich`: The maximum ratio of each element (e.g., 8 could mean up to 8 atoms of each element).\n", | ||
| "- `max_atomic_num`: Maximum atomic number for the elements considered\n", | ||
| "- `num_processes`: Number of processes to run in parallel to speed up calculations.\n", | ||
| "- `save_path`: Where to save the generated compositions." |
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Detailed explanation of composition generation.
The cell provides a comprehensive explanation of how to generate binary chemical compositions using the SMACT filter. Consider adding a direct link to the SMACT filter documentation for users who may want more detailed information on the filter itself.
| "df_smact = generate_composition_with_smact(\n", | ||
| " num_elements=2,\n", | ||
| " max_stoich=8,\n", | ||
| " max_atomic_num=103,\n", | ||
| " num_processes=8,\n", | ||
| " save_path=\"data/binary/df_binary_label.pkl\",\n", | ||
| ")" |
There was a problem hiding this comment.
Well-documented parameter usage in function call.
The function call is well-documented with clear parameters. Consider adding error handling to manage potential issues during the data generation process.
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "The structure of mp-540839 CsPbI3:\n", | ||
| "\n", | ||
| "Full Formula (Cs4 Pb4 I12)\n", | ||
| "Reduced Formula: CsPbI3\n", | ||
| "abc : 4.847142 10.650447 18.031199\n", | ||
| "angles: 90.000000 90.000000 90.000000\n", | ||
| "pbc : True True True\n", | ||
| "Sites (20)\n", | ||
| " # SP a b c\n", | ||
| "--- ---- ---- -------- --------\n", | ||
| " 0 Cs+ 0.75 0.581276 0.17212\n", | ||
| " 1 Cs+ 0.25 0.418724 0.82788\n", | ||
| " 2 Cs+ 0.75 0.081276 0.32788\n", | ||
| " 3 Cs+ 0.25 0.918724 0.67212\n", | ||
| " 4 Pb2+ 0.25 0.661849 0.439217\n", | ||
| " 5 Pb2+ 0.75 0.338151 0.560783\n", | ||
| " 6 Pb2+ 0.25 0.161849 0.060783\n", | ||
| " 7 Pb2+ 0.75 0.838151 0.939217\n", | ||
| " 8 I- 0.75 0.837211 0.502045\n", | ||
| " 9 I- 0.25 0.162789 0.497955\n", | ||
| " 10 I- 0.75 0.337211 0.997955\n", | ||
| " 11 I- 0.25 0.662789 0.002045\n", | ||
| " 12 I- 0.25 0.529272 0.612308\n", | ||
| " 13 I- 0.75 0.470728 0.387692\n", | ||
| " 14 I- 0.25 0.029272 0.887692\n", | ||
| " 15 I- 0.75 0.970728 0.112308\n", | ||
| " 16 I- 0.25 0.796317 0.287306\n", | ||
| " 17 I- 0.75 0.203683 0.712694\n", | ||
| " 18 I- 0.25 0.296317 0.212694\n", | ||
| " 19 I- 0.75 0.703683 0.787306\n", | ||
| "\n", | ||
| "The compound probability for CsPbI3 is 1.0.\n" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "stderr", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "/home/codespace/.python/current/lib/python3.10/site-packages/pymatgen/io/cif.py:1186: UserWarning: The default value of primitive was changed from True to False in https://github.com/materialsproject/pymatgen/pull/3419. CifParser now returns the cell in the CIF file as is. If you want the primitive cell, please set primitive=True explicitly.\n", | ||
| " warnings.warn(\n" | ||
| ] | ||
| } | ||
| ], | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Load the structure file\n", | ||
| "# Install the required packages\n", | ||
| "try:\n", | ||
| " import google.colab\n", | ||
| "\n", | ||
| "struct = Structure.from_file(\"mp-540839_CsPbI3_oxi.cif\")\n", | ||
| "print(\"The structure of mp-540839 CsPbI3:\\n\")\n", | ||
| "print(struct)\n", | ||
| " IN_COLAB = True\n", | ||
| "except:\n", | ||
| " IN_COLAB = False\n", | ||
| "\n", | ||
| "if IN_COLAB:\n", | ||
| " !pip install git+https://github.com/WMD-group/SMACT.git --quiet\n", | ||
| "\n", | ||
| "# Get the compound probability for CsPbI3\n", | ||
| "prob = ox_prob_finder.compound_probability(struct)\n", | ||
| "# Imports\n", | ||
| "import re\n", | ||
| "from itertools import combinations\n", | ||
| "\n", | ||
| "print(f\"\\nThe compound probability for CsPbI3 is {prob_compound}.\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Filtering a SMACT search space using the oxidation states model\n", | ||
| "import matplotlib.pyplot as plt\n", | ||
| "import multiprocess\n", | ||
| "import numpy as np\n", | ||
| "import pandas as pd\n", | ||
| "from pymatgen.core import Composition\n", | ||
| "\n", | ||
| "Let's attempt to perform the first steps in a high-throughput compound design workflow which involves:\n", | ||
| "* Generating the search space using SMACT\n", | ||
| "* Filtering the search space using the oxidation states model." | ||
| "import smact\n", | ||
| "from smact import Species, screening\n", | ||
| "from smact.oxidation_states import Oxidation_state_probability_finder" |
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Well-structured dependency management and imports.
The code cell effectively handles the installation of the SMACT library and imports necessary packages. The conditional check for Google Colab is a good practice to ensure compatibility. Consider improving the comments for better clarity on each import's purpose.
Consider adding comments next to each import statement to explain their purpose, enhancing code readability and maintainability.
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Actionable comments posted: 3
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Files selected for processing (14)
- CONTRIBUTING.md (1 hunks)
- README.md (3 hunks)
- docs/conf.py (4 hunks)
- docs/smact.utils.rst (1 hunks)
- docs/tutorials/crystal_space_visualisation.ipynb (14 hunks)
- pyproject.toml (1 hunks)
- setup.py (2 hunks)
- smact/init.py (18 hunks)
- smact/data_loader.py (33 hunks)
- smact/properties.py (9 hunks)
- smact/screening.py (17 hunks)
- smact/tests/test_core.py (11 hunks)
- smact/tests/test_utils.py (2 hunks)
- smact/utils/composition.py (4 hunks)
Files skipped from review due to trivial changes (5)
- CONTRIBUTING.md
- docs/smact.utils.rst
- smact/tests/test_core.py
- smact/tests/test_utils.py
- smact/utils/composition.py
Files skipped from review as they are similar to previous changes (7)
- docs/conf.py
- docs/tutorials/crystal_space_visualisation.ipynb
- setup.py
- smact/init.py
- smact/data_loader.py
- smact/properties.py
- smact/screening.py
Additional context used
LanguageTool
README.md
[misspelling] ~24-~24: Possible spelling mistake found.
Context: ...a enough, nature will always confess_ - Roland Coase (from 'How should economists choose?') ...(EN_MULTITOKEN_SPELLING_TWO)
[style] ~46-~46: Consider a shorter alternative to avoid wordiness.
Context: ...lied to generated lists of compositions in order to screen for particular properties. These...(IN_ORDER_TO_PREMIUM)
[style] ~66-~66: Would you like to use the Oxford spelling “initialize”? The spelling ‘initialise’ is also correct.
Context: ...es the loading of external data used to initialise the coresmact.Elementand `smact.Spe...(OXFORD_SPELLING_Z_NOT_S)
[grammar] ~79-~79: It looks like ‘collections’ doesn’t match ‘a’. Did you mean “a collection” or just “collections”?
Context: ...rediction**: A submodule which contains a collections of tools for predicting dopants. ## Re...(A_NNS_IN)
[locale-violation] ~113-~113: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ... immediately reflected on the PATH. ## License and attribution Python code and origin...(LICENCE_LICENSE_NOUN_SINGULAR)
[locale-violation] ~115-~115: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ... data tables are licensed under the MIT License. ## Development notes ### Bugs, featu...(LICENCE_LICENSE_NOUN_SINGULAR)
[grammar] ~121-~121: The pronoun ‘they’ must be used with a non-third-person form of a verb.
Context: ...n the issue tracker, especially if they helps us improve the docs! For other queries ...(NON3PRS_VERB)
Additional comments not posted (16)
pyproject.toml (7)
3-3: Updated build system requirements.The update to the
requiresfield in the[build-system]section to specify a minimum version ofsetuptools(>=65.0.0) is a good practice. It ensures compatibility with newer features and improvements in the build process.
7-30: Enhanced project metadata.The addition of a comprehensive
[project]section with details such as the project name, version, description, and classification improves the project's discoverability and compliance with packaging standards. The use of classifiers to specify the development status, intended audience, and supported Python versions is particularly beneficial.
41-50: Dependencies specified with version constraints.Specifying dependencies with version constraints, as seen in the
dependenciessection, is crucial for maintaining functionality and avoiding conflicts during installation. This approach ensures that the project operates with compatible library versions.
61-76: Optional dependencies categorised.The creation of new sections for optional dependencies (
[project.optional-dependencies]) categorising development and documentation tools allows users to install additional packages as needed without cluttering the main dependencies. This is a good practice for maintainability and user flexibility.
77-77: Semantic versioning configuration.The introduction of a
[tool.semantic_release]section withversion_variableset to "setup.py:version" indicates the use of semantic versioning based on tags. This is essential for automated release management and helps in maintaining a clear versioning strategy.
83-154: Linting and formatting tools configuration.The addition of
[tool.ruff]with specific configurations for target Python version, line length, and rules to ignore or enforce enhances code quality and consistency across the project. The detailed setup for linting rules, including exclusions and per-file ignores, is well-thought-out and aligns with best practices for maintaining a clean codebase.
171-274: Spell checking configuration.The configuration in
[tool.codespell]to skip certain files and directories and to ignore specific words (mostly chemical elements) is appropriate given the project's domain. This setup helps avoid false positives while ensuring that genuine spelling mistakes are caught.README.md (9)
15-15: Title formatting improved.The reformatting of the title to a Markdown header enhances its visibility and is a good practice for making the README more accessible and professional.
19-20: Documentation and examples links updated.Updating the links to the documentation and examples improves the accessibility of these resources for users. Ensuring that these links are maintained and accurate is crucial for user engagement.
28-29: Statement of need clearly articulated.The "Statement of need" section clearly articulates the demand for functional materials and the project's approach to addressing this need. This section is well-written and effectively communicates the project's value proposition.
32-32: Getting started section enhanced.The "Getting started" section provides clear guidance on how to begin using the project, with links to documentation and examples. This is crucial for new users and contributes to a positive user experience.
38-51: Detailed description of code features.The "Code features" section provides a detailed description of the core functionalities and modules of the project. This is essential for users to understand what the project offers and how to utilise its features effectively.
Tools
LanguageTool
[style] ~46-~46: Consider a shorter alternative to avoid wordiness.
Context: ...lied to generated lists of compositions in order to screen for particular properties. These...(IN_ORDER_TO_PREMIUM)
62-80: Comprehensive list of modules.The "List of modules" section is comprehensive and well-organised, providing a clear overview of the various components of the project. This helps users navigate the project's structure and understand its capabilities.
Tools
LanguageTool
[style] ~66-~66: Would you like to use the Oxford spelling “initialize”? The spelling ‘initialise’ is also correct.
Context: ...es the loading of external data used to initialise the coresmact.Elementand `smact.Spe...(OXFORD_SPELLING_Z_NOT_S)
[grammar] ~79-~79: It looks like ‘collections’ doesn’t match ‘a’. Did you mean “a collection” or just “collections”?
Context: ...rediction**: A submodule which contains a collections of tools for predicting dopants. ## Re...(A_NNS_IN)
81-86: Requirements and installation instructions updated.The "Requirements" and "Installation" sections have been updated to reflect the current dependencies and installation methods. This is crucial for ensuring that users can set up the project successfully.
117-117: Development notes section provides clear guidance.The "Development notes" section provides clear guidance on how to report bugs, request features, and contribute to the project. This is important for fostering a collaborative and responsive community.
137-137: References section reformatted.The "References" section has been reformatted for consistency, ensuring that all citations follow a similar structure. This enhances the professionalism of the document.
| reportPossiblyUnboundVariable = true | ||
| reportUnboundVariable = true | ||
|
|
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Type checking configuration in Pyright.
Setting typeCheckingMode to "off" in [tool.pyright] might be reconsidered. While it reduces overhead during development, enabling type checking could improve code reliability and catch potential bugs early. It's worth discussing the trade-offs with the team.
Consider enabling type checking to improve code reliability. Here's a proposed change:
-typeCheckingMode = "off"
+typeCheckingMode = "basic"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. Thoroughly test & benchmark the code to ensure it meets the requirements.
| typeCheckingMode = "off" | |
| reportPossiblyUnboundVariable = true | |
| reportUnboundVariable = true | |
| typeCheckingMode = "basic" | |
| reportPossiblyUnboundVariable = true | |
| reportUnboundVariable = true | |
|
|
||
| License and attribution | ||
| ----------------------- | ||
| ## License and attribution |
There was a problem hiding this comment.
License section needs localisation correction.
The use of "License" in the section title should be localised to "Licence" to align with British English standards, as the rest of the document uses British English.
Consider localising the term "License" to "Licence" in the section title:
-## License and attribution
+## Licence and attributionCommittable 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. Thoroughly test & benchmark the code to ensure it meets the requirements.
| ## License and attribution | |
| ## Licence and attribution |
Tools
LanguageTool
[locale-violation] ~113-~113: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ... immediately reflected on the PATH. ## License and attribution Python code and origin...(LICENCE_LICENSE_NOUN_SINGULAR)
|
|
||
| *If you torture the data enough, nature will always confess* - Roland Coase (from 'How should economists choose?') | ||
| _If you torture the data enough, nature will always confess_ - Roland Coase (from 'How should economists choose?') |
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Inspirational quote formatting.
The formatting of the inspirational quote adds a personal touch to the README, though it's worth ensuring that the quote is correctly attributed and spelled. The spelling of "Roland Coase" should be verified.
Please verify the spelling of "Roland Coase" in the quote attribution. If it is incorrect, consider the following correction:
-_If you torture the data enough, nature will always confess_ - Roland Coase (from 'How should economists choose?')
+_If you torture the data enough, nature will always confess_ - Ronald Coase (from 'How should economists choose?')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. Thoroughly test & benchmark the code to ensure it meets the requirements.
| _If you torture the data enough, nature will always confess_ - Roland Coase (from 'How should economists choose?') | |
| _If you torture the data enough, nature will always confess_ - Ronald Coase (from 'How should economists choose?') |
Tools
LanguageTool
[misspelling] ~24-~24: Possible spelling mistake found.
Context: ...a enough, nature will always confess_ - Roland Coase (from 'How should economists choose?') ...(EN_MULTITOKEN_SPELLING_TWO)
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #309 +/- ##
===========================================
- Coverage 76.46% 72.42% -4.05%
===========================================
Files 26 30 +4
Lines 2265 2415 +150
===========================================
+ Hits 1732 1749 +17
- Misses 533 666 +133 ☔ View full report in Codecov by Sentry. |
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Files selected for processing (4)
- docs/examples.rst (1 hunks)
- docs/examples/valence_electron_count.ipynb (1 hunks)
- docs/smact.utils.rst (1 hunks)
- docs/tutorials.rst (1 hunks)
Files skipped from review due to trivial changes (1)
- docs/examples.rst
Files skipped from review as they are similar to previous changes (2)
- docs/smact.utils.rst
- docs/tutorials.rst
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docs/examples/valence_electron_count.ipynb (1)
4-18: Well-structured and informative markdown cell.The markdown cell provides a clear and concise introduction to the concept of valence electron concentration (VEC), its importance, and its calculation. The inclusion of a mathematical formula enhances understanding, and the brief mention of the
smactfunction sets the stage for the subsequent code cell.
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "Cu0.5NiAlCoCrFeSi has a VEC of 7.00\n", | ||
| "WNbMoTa has a VEC of 5.50\n", | ||
| "AlCoCrCu0.5FeNi3 has a VEC of 8.20\n", | ||
| "Ca65Mg15Zn20 has a VEC of 4.00\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "import smact.properties\n", | ||
| "\n", | ||
| "formulas = [\"Cu0.5NiAlCoCrFeSi\", \"WNbMoTa\", \"AlCoCrCu0.5FeNi3\",\"Ca65Mg15Zn20\"]\n", | ||
| "\n", | ||
| "valence_electron_concentrations = [smact.properties.valence_electron_count(formula) for formula in formulas]\n", | ||
| "\n", | ||
| "for formula, vec in zip(formulas, valence_electron_concentrations):\n", | ||
| " print(f\"{formula} has a VEC of {vec:.2f}\")" | ||
| ] |
There was a problem hiding this comment.
Suggest adding comments to enhance code clarity.
The code cell correctly demonstrates the calculation of valence electron concentrations using the smact.properties module. However, adding comments to explain each step would enhance readability and maintainability, especially for users unfamiliar with the smact library or the concept of VEC.
Consider adding comments like these:
import smact.properties # Importing the SMACT properties module
# List of chemical formulas for which VEC will be calculated
formulas = ["Cu0.5NiAlCoCrFeSi", "WNbMoTa", "AlCoCrCu0.5FeNi3", "Ca65Mg15Zn20"]
# Calculate VEC for each formula using a list comprehension
valence_electron_concentrations = [smact.properties.valence_electron_count(formula) for formula in formulas]
# Print the VEC for each formula
for formula, vec in zip(formulas, valence_electron_concentrations):
print(f"{formula} has a VEC of {vec:.2f}")
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
…o docs_updates
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Outside diff range, codebase verification and nitpick comments (2)
README.md (2)
Line range hint
81-113: Consider adding commas for clarity.The static analysis tool suggests adding commas in the following places for improved clarity:
Line 89: "The latest stable release can be installed via pip, which will automatically set up other Python packages as required:"
Line 101: "For developer installation, SMACT can be installed from a copy of the source repository (https://github.com/wmd-group/smact); this will be preferred if using experimental code branches."
Apply this diff to add the commas:
-The latest stable release can be installed via pip which will automatically set up other Python packages as required: +The latest stable release can be installed via pip, which will automatically set up other Python packages as required: -For developer installation SMACT can be installed from a copy of the source repository (https://github.com/wmd-group/smact); this will be preferred if using experimental code branches. +For developer installation, SMACT can be installed from a copy of the source repository (https://github.com/wmd-group/smact); this will be preferred if using experimental code branches.Tools
LanguageTool
[misspelling] ~24-~24: Possible spelling mistake found.
Context: ...a enough, nature will always confess_ - Roland Coase (from 'How should economists choose?') ...(EN_MULTITOKEN_SPELLING_TWO)
[style] ~46-~46: Consider a shorter alternative to avoid wordiness.
Context: ...lied to generated lists of compositions in order to screen for particular properties. These...(IN_ORDER_TO_PREMIUM)
[style] ~66-~66: Would you like to use the Oxford spelling “initialize”? The spelling ‘initialise’ is also correct.
Context: ...es the loading of external data used to initialise the coresmact.Elementand `smact.Spe...(OXFORD_SPELLING_Z_NOT_S)
[grammar] ~79-~79: It looks like ‘collections’ doesn’t match ‘a’. Did you mean “a collection” or just “collections”?
Context: ...rediction**: A submodule which contains a collections of tools for predicting dopants. ## Re...(A_NNS_IN)
[uncategorized] ~89-~89: Possible missing comma found.
Context: ...est stable release can be installed via pip which will automatically set up other P...(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~101-~101: Possible missing comma found.
Context: ....com/WMD-group/SMACT.git For developer installation SMACT can be installed from a copy of t...(AI_HYDRA_LEO_MISSING_COMMA)
Line range hint
113-152: Consider making the following changes for consistency and clarity:
Lines 113 and 115: Use the British English spelling "licence" instead of "license" to maintain consistency with the rest of the document.
Line 121: Correct the grammar in the sentence "especially if they helps us improve the docs!" to "especially if they help us improve the docs!".
Apply this diff to make the suggested changes:
-## License and attribution +## Licence and attribution -Python code and original data tables are licensed under the MIT License. +Python code and original data tables are licensed under the MIT Licence. -Please use the [Issue Tracker](https://github.com/WMD-group/smact/issues) to report bugs or request features in the first instance. While we hope that most questions can be answered by searching [the docs](https://smact.readthedocs.io/en/latest/), we welcome new questions on the issue tracker, especially if they helps us improve the docs! For other queries about any aspect of the code, please contact Anthony Onwuli (maintainer) by [e-mail](mailto:[email protected]). +Please use the [Issue Tracker](https://github.com/WMD-group/smact/issues) to report bugs or request features in the first instance. While we hope that most questions can be answered by searching [the docs](https://smact.readthedocs.io/en/latest/), we welcome new questions on the issue tracker, especially if they help us improve the docs! For other queries about any aspect of the code, please contact Anthony Onwuli (maintainer) by [e-mail](mailto:[email protected]).
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Files selected for processing (13)
- README.md (4 hunks)
- docs/conf.py (4 hunks)
- docs/examples/valence_electron_count.ipynb (1 hunks)
- docs/tutorials/crystal_space.ipynb (1 hunks)
- docs/tutorials/crystal_space_visualisation.ipynb (14 hunks)
- pyproject.toml (1 hunks)
- smact/tests/test_utils.py (3 hunks)
- smact/utils/band_gap_simple.py (2 hunks)
- smact/utils/composition.py (4 hunks)
- smact/utils/crystal_space/init.py (1 hunks)
- smact/utils/crystal_space/download_compounds_with_mp_api.py (5 hunks)
- smact/utils/crystal_space/generate_composition_with_smact.py (5 hunks)
- smact/utils/crystal_space/plot_embedding.py (4 hunks)
Files skipped from review due to trivial changes (2)
- smact/utils/band_gap_simple.py
- smact/utils/crystal_space/init.py
Files skipped from review as they are similar to previous changes (5)
- docs/conf.py
- docs/examples/valence_electron_count.ipynb
- docs/tutorials/crystal_space.ipynb
- docs/tutorials/crystal_space_visualisation.ipynb
- smact/utils/composition.py
Additional context used
LanguageTool
README.md
[misspelling] ~24-~24: Possible spelling mistake found.
Context: ...a enough, nature will always confess_ - Roland Coase (from 'How should economists choose?') ...(EN_MULTITOKEN_SPELLING_TWO)
[style] ~46-~46: Consider a shorter alternative to avoid wordiness.
Context: ...lied to generated lists of compositions in order to screen for particular properties. These...(IN_ORDER_TO_PREMIUM)
[style] ~66-~66: Would you like to use the Oxford spelling “initialize”? The spelling ‘initialise’ is also correct.
Context: ...es the loading of external data used to initialise the coresmact.Elementand `smact.Spe...(OXFORD_SPELLING_Z_NOT_S)
[grammar] ~79-~79: It looks like ‘collections’ doesn’t match ‘a’. Did you mean “a collection” or just “collections”?
Context: ...rediction**: A submodule which contains a collections of tools for predicting dopants. ## Re...(A_NNS_IN)
[uncategorized] ~89-~89: Possible missing comma found.
Context: ...est stable release can be installed via pip which will automatically set up other P...(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~101-~101: Possible missing comma found.
Context: ....com/WMD-group/SMACT.git For developer installation SMACT can be installed from a copy of t...(AI_HYDRA_LEO_MISSING_COMMA)
[locale-violation] ~113-~113: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ... immediately reflected on the PATH. ## License and attribution Python code and origin...(LICENCE_LICENSE_NOUN_SINGULAR)
[locale-violation] ~115-~115: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ... data tables are licensed under the MIT License. ## Development notes ### Bugs, featu...(LICENCE_LICENSE_NOUN_SINGULAR)
[grammar] ~121-~121: The pronoun ‘they’ must be used with a non-third-person form of a verb.
Context: ...n the issue tracker, especially if they helps us improve the docs! For other queries ...(NON3PRS_VERB)
Additional comments not posted (28)
smact/utils/crystal_space/download_compounds_with_mp_api.py (6)
18-18: LGTM!The updated type hint
str | None = Nonefor themp_api_keyparameter enhances clarity by explicitly indicating that the parameter can accept either a string orNoneas a valid value.
Line range hint
31-43: LGTM!The addition of the section headers "Args:" and "Returns:" in the docstring improves the documentation structure and readability by clearly separating the description of the function's arguments and return values.
49-49: LGTM!Consolidating the error message for the missing API key into a single line enhances code conciseness and readability.
65-65: LGTM!Adding the print statement before the data retrieval process provides clearer feedback during execution, allowing users to track the progress of the download process for each
formula_anonymous.
94-95: LGTM!Using a context manager (
with open(...) as f:) for file operations ensures that files are properly closed after writing, which is a best practice for resource management and helps prevent resource leaks.
57-57: LGTM!Using
itertools.combinations_with_replacementinstead ofitertools.productensures that the generated combinations of stoichiometric coefficients do not contain duplicates, which helps avoid redundant calculations and improves efficiency.smact/tests/test_utils.py (3)
66-66: LGTM!The formatting changes are approved.
84-90: LGTM!The
test_convert_formulamethod is correctly implemented and covers the expected behaviour of theconvert_formulafunction.
92-94: Verify the purpose of the empty test method.The
test_download_compounds_with_mp_apimethod is empty and does not contain any test logic. Is this intentional?If this is a placeholder for a future test, consider adding a TODO comment to document the intended test case and any dependencies required for its execution.
smact/utils/crystal_space/plot_embedding.py (2)
23-23: Docstring addition looks good!The docstring succinctly describes the purpose of the function, enhancing code readability and maintainability.
70-71: Type hint update and docstring addition look good!
- The type hints for the
reducersandembedding_namesparameters have been updated to align with the newer Python type hinting conventions, improving code clarity.- The docstring succinctly describes the purpose of the function, enhancing code readability and maintainability.
Also applies to: 77-77
smact/utils/crystal_space/generate_composition_with_smact.py (2)
21-31: Excellent improvements to the function signature and docstring!The addition of type hints and the expanded docstring significantly enhance the clarity and maintainability of the code. The changes provide clear guidance on the expected types of the function parameters and the return value, making it easier for future developers to understand and use the function correctly.
The core logic of the function remains unaltered, ensuring that the existing functionality is preserved.
Line range hint
39-138: Great job on enhancing the function signature, docstring, and overall readability!The introduction of type hints for
num_processesandsave_pathparameters clarifies the expected types, allowing for better type checking and reducing potential type-related issues. The updated docstring provides a clearer explanation of the function's purpose and the types of its parameters, making it more user-friendly for other developers.The minor formatting adjustments, such as consolidating list comprehensions and removing unnecessary line breaks, improve the overall readability of the code without altering its functionality. These changes make the code more concise and easier to follow.
The core logic and control flow of the function remain unaffected, ensuring that the existing behaviour is preserved.
pyproject.toml (5)
3-3: LGTM!The change to require a minimum version of
setuptoolsis a good practice to ensure compatibility with newer features and improvements in the build process.
6-52: LGTM!The addition of the
[project]section significantly enhances the project's configuration by providing essential metadata. This includes the project name, version, description, and other details that aid in discoverability, compliance with packaging standards, and maintainability. The specified dependencies ensure that the project operates with compatible library versions, which is crucial for maintaining functionality and avoiding conflicts during installation.
60-83: LGTM!The categorisation of optional dependencies into separate sections, such as
devanddocs, is a good practice. It allows users to install additional packages as needed for development or documentation purposes without cluttering the main dependencies. This enhances the project's usability and maintainability by keeping the core dependencies focused and relevant.
85-86: LGTM!The addition of the
[tool.semantic_release]section is essential for automated release management. It specifies the version variable and the source of the version information (tags). This configuration enables the project to follow semantic versioning principles, which helps in maintaining a consistent and meaningful version numbering scheme. Automated release management based on semantic versioning simplifies the release process and improves the overall maintainability of the project.
88-162: LGTM!The addition of the
[tool.ruff]section enhances code quality and consistency across the project. It specifies the target Python version, line length limit, and a comprehensive list of linting rules to ignore or enforce. This configuration helps maintain a consistent coding style, identifies potential issues, and promotes best practices. The use of a linting tool like Ruff improves the overall maintainability and readability of the codebase.README.md (10)
Line range hint
1-13: LGTM!The badges are correctly formatted and provide useful information about the project.
Tools
LanguageTool
[locale-violation] ~3-~3: License must be spelled with a “c” when used as a noun in British English. Use “licence”.
Context: ...eadthedocs.org/en/latest/?badge=latest) [
15-15: LGTM!The project title is correctly formatted as a top-level heading.
19-20: LGTM!The links to the project's documentation and examples are correctly formatted and provide easy access to these resources.
22-22: LGTM!The image showcasing the SMACT interface is correctly formatted and provides a visual representation of the project.
24-24: Verify the spelling of the quote attribution.The spelling of "Roland Coase" in the quote attribution should be verified. If it is incorrect, consider the following correction:
-_If you torture the data enough, nature will always confess_ - Roland Coase (from 'How should economists choose?') +_If you torture the data enough, nature will always confess_ - Ronald Coase (from 'How should economists choose?')Tools
LanguageTool
[misspelling] ~24-~24: Possible spelling mistake found.
Context: ...a enough, nature will always confess_ - Roland Coase (from 'How should economists choose?') ...(EN_MULTITOKEN_SPELLING_TWO)
28-29: LGTM!The description effectively communicates the project's purpose and capabilities.
30-31: LGTM!The GIF showcasing the usage of the SMACT code is correctly formatted and provides a visual demonstration of how the code can be used.
32-38: LGTM!The information provided on how to get started with the project is clear and helpful. The links to the documentation, examples, and tutorials are correctly formatted and provide easy access to these resources.
40-62: LGTM!The list of features provides a comprehensive overview of the capabilities of the SMACT code. The links to the relevant documentation for each feature are correctly formatted and provide easy access to more detailed information.
Tools
LanguageTool
[style] ~46-~46: Consider a shorter alternative to avoid wordiness.
Context: ...lied to generated lists of compositions in order to screen for particular properties. These...(IN_ORDER_TO_PREMIUM)
64-80: LGTM!The list of modules and their descriptions provide a clear overview of the structure and functionality of the SMACT library.
Tools
LanguageTool
[style] ~66-~66: Would you like to use the Oxford spelling “initialize”? The spelling ‘initialise’ is also correct.
Context: ...es the loading of external data used to initialise the coresmact.Elementand `smact.Spe...(OXFORD_SPELLING_Z_NOT_S)
[grammar] ~79-~79: It looks like ‘collections’ doesn’t match ‘a’. Did you mean “a collection” or just “collections”?
Context: ...rediction**: A submodule which contains a collections of tools for predicting dopants. ## Re...(A_NNS_IN)
Overhauling the documentation
Description
N/A
Closes #67
Closes #297
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
TBC
Test Configuration:
Reviewers
N/A
Checklist:
Summary by CodeRabbit
New Features
README.mdandCONTRIBUTING.mdfiles, facilitating better user navigation and understanding.smactlibrary.smactmodule.Documentation
Chores