Files that changed from the base of the PR and between a7946c9 and f7e80f0.

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• .github/pull_request_template.md (1 hunks)
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• .github/workflows/combine-prs.yml (4 hunks)
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• README.md (2 hunks)
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• smact/lattice.py (4 hunks)
• smact/lattice_parameters.py (12 hunks)
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• smact/properties.py (7 hunks)
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• 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)
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• 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)

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• docs/smact.dopant_prediction.rst
• docs/smact.properties.rst
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• smact/benchmarking/smact_benchmark.py
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• smact/utils/band_gap_simple.py

requirements-dev.txt (1)

3-3: Ensure continued coverage with pytest-cov.

The presence of pytest-cov remains 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 of readthedocs-sphinx-search.

The dependency readthedocs-sphinx-search remains 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.yaml file. 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.yaml

Length 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.py and pyproject.toml indicate support for Python 3.10, and there are no conflicting constraints for the dependencies listed in docs/requirements.in.

• Python version compatibility is explicitly stated in both setup.py and pyproject.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.in

Length 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.toml

Length 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.toml

Length of output: 10596

smact/benchmarking/utilities.py (4)

3-3: Approve the addition of future annotations.

The inclusion of from __future__ import annotations is a forward-thinking addition, enabling postponed evaluation of type annotations which can help with forward compatibility and potentially improve performance.

---

25-25: Initialisation of value variable approved.

Initialising value to None before 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 for fname.

Changing the conditional assignment for fname from a ternary operation to a straightforward if condition simplifies the code and enhances readability. Ensure that this change does not affect the functionality where fname might be explicitly passed as None or 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 if condition is valid. The current logic ensures that fname defaults 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 readable if condition.

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.py

Length 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.py

Length of output: 323

smact/lattice.py (2)

Line range hint 8-31: Enhanced docstrings in Lattice class approved.

The updated docstrings provide a clearer and more structured description of the Lattice class, its attributes, and methods, which enhances the documentation's clarity and usability.

---

50-59: Critical improvement to default parameter handling in Site class.

Changing the default value for oxidation_states from a mutable list ([0]) to None and handling it within the constructor is a significant improvement. This change prevents potential bugs related to mutable default arguments and ensures that each instance of Site has 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, and trailing-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 markdownlint with 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 of nbstripout for cleaning notebooks.

The inclusion of nbstripout to 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 with codespell.

The configuration for codespell to 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 with pyright.

The use of pyright for 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 with blacken-docs.

The continued use of blacken-docs to 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-commit as a replacement for multiple previous tools (like isort, 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 ruff tool is configured in the pyproject.toml file to handle both linting and formatting, which suggests it can replace the functionalities of isort and black. The contribution guidelines mention these tools, indicating that ruff should cover their roles. Ensure that the specific configurations in pyproject.toml align with the desired functionalities of the replaced tools.

• Check pyproject.toml for ruff configurations.
• Review contribution guidelines for mentions of isort and black.

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 5

Length of output: 3484

---

39-45: Integration of Prettier for code formatting.

The use of prettier with the --write argument 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.toml for dependency management aligns with modern Python packaging practices and should help in managing dependencies more effectively.

---

75-76: Major version update for pymatgen.

The update from pymatgen==2023.11.12 to pymatgen==2024.5.1 is 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 to monty package version.

The update from monty==2023.11.3 to monty==2024.7.30 should be checked for compatibility with other packages, especially pymatgen, which relies on it.

---

39-39: Minor version update for multiprocess.

The update from multiprocess==0.70.15 to multiprocess==0.70.16 is 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 of typing-extensions.

The addition of typing-extensions==4.12.2 is 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 using README.md.

The implementation of reading the long description from the README.md file 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 of smact.utils to 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.utils package 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 smact library, 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 smact library. 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 pytest is correct and aligns with the transition from unittest to pytest as 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.raises instead of self.assertRaises is 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 smact module. 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_elements to 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 smact functionalities.

smact/utils/download_compounds_with_mp_api.py (4)

7-7: Inclusion of Optional type hint.

The import of Optional from the typing module is appropriate given the changes to the mp_api_key parameter, allowing it to explicitly accept None or 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_data has been updated to include Optional[str] for the mp_api_key parameter. This change is a good practice as it clearly indicates that the parameter can be None, 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_KEY is 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 Correctness

The markdown cell provides a clear introduction to the smact_filter function, 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 Effectiveness

The code cell demonstrates the usage of the smact_filter function 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 of pprint to format the output is appropriate, making the results more readable.

smact/distorter.py (3)

12-12: Review the Use of Future Annotations

The addition of from __future__ import annotations is 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 Consistency

The 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 Correctness

The update from == True to is True in the boolean checks within the get_inequivalent_sites function 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 Changes

The update of type annotations from List[str] to list[str] reflects a shift towards using modern Python practices with the built-in list type. This change simplifies the type hinting and is correctly applied. The condensation of the subplot_titles argument into a single line enhances readability without altering the underlying logic.

Also applies to: 72-72

---

119-119: Review Loop Modification for Clarity

The modification of the loop that adds traces to the figure to iterate directly over legend_colors simplifies 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)

Line range hint 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_formula function is efficiently implemented using itertools.product and list comprehension. It effectively generates chemical formulas based on the provided stoichiometric combinations.

---

Line range hint 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 tqdm for 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 with SMACT. 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
+ #### Database

This 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 the distorter module.

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 the distorter module.

The code cell is well-organized and effectively demonstrates the usage of the distorter module 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 ase atoms class adds clarity to the type of objects being handled.

docs/requirements.txt (1)

Line range hint 2-230: Review of requirements.txt

The updates to requirements.txt reflect 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 of eneg_mulliken Function

The updates to the eneg_mulliken function 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 TypeError provides 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.

---

Line range hint 35-64: Review of band_gap_Harrison Function

The band_gap_Harrison function has been updated to improve clarity and type safety:

• Type Hinting: The introduction of the | operator for the distance parameter 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.

---

Line range hint 91-151: Review of compound_electroneg Function

The compound_electroneg function 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 TypeError messages 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 of doper.ipynb Notebook

The doper.ipynb notebook is a well-structured document that provides comprehensive examples of using the Doper module 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_dopants and 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 Doper module.

smact/tests/files/CaTiO3.json (1)

1-162: Comprehensive Improvement in JSON Structure Readability and Maintainability

The overhaul of the JSON structure in CaTiO3.json significantly enhances its readability and maintainability. The clear formatting and detailed entries in the sites array 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 Section

The 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)

Line range hint 28-50: Updated Type Annotations and Streamlined Logic in __init__ Method

The update to the type annotations in the __init__ method of the Oxidation_state_probability_finder class aligns with modern Python practices, enhancing the clarity and maintainability of the code. The use of dict[tuple[str, str], float] | None is more explicit and readable compared to the previous Optional[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 in pair_probability Method

The simplification in the pair_probability method, 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.

---

Line range hint 114-166: Enhanced Error Handling and Type Checking in compound_probability Method

The updates to the compound_probability method, including the replacement of type(structure) == list with isinstance(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 for cubic_perovskite.

The updated docstring enhances clarity and readability by clearly defining the function's parameters and expected outputs.

---

Line range hint 38-72: Documentation improvements approved for wurtzite.

The structured docstring for wurtzite is well-organized, making it easier for users to understand the function's purpose and usage.

---

79-91: Terminology and documentation updates approved for fcc.

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 for bcc.

The updates to the bcc function's documentation and the terminology change enhance the clarity and accuracy of the information provided.

---

129-141: Consistent documentation improvements approved for hcp.

The structured docstring and terminology updates for the hcp function are consistent with other functions, enhancing clarity and usability.

---

154-166: Documentation and terminology updates approved for diamond.

The updates to the diamond function's documentation and terminology are well-executed, enhancing clarity and consistency.

---

179-191: Approved documentation and terminology updates for bct.

The bct function's documentation is clear and structured, with appropriate terminology updates enhancing the overall quality.

---

204-216: Documentation improvements approved for rocksalt.

The updated docstring for rocksalt enhances clarity and readability, making it easier for users to understand the function's purpose and usage.

---

234-246: Documentation improvements approved for b2.

The structured docstring for b2 is well-organized, making it easier for users to understand the function's purpose and usage.

---

264-276: Documentation improvements approved for zincblende.

The structured docstring for zincblende enhances clarity and readability, aiding users in understanding the function's purpose and usage.

---

298-310: Documentation improvements approved for b10.

The structured docstring for b10 is well-organized, making it easier for users to understand the function's purpose and usage.

---

326-338: Documentation improvements approved for stuffed_wurtzite.

The structured docstring for stuffed_wurtzite enhances 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 Title

The 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 Terminology

The 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 Standardisation

The 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 Link

A 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 Colab

The 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 Data

The 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 Size

The number of samples for n_samples has 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 Handling

The 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 Reduction

The 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 Embeddings

The function dimension_reduction now 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 Process

The 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 Update

The 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 Function

An import statement has been added for the plot_reducers_embeddings function, 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 Plot

The 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.

---

Line range hint 371-385: Metadata Updates

The 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 Update

The 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 of myst_nb extension.

The inclusion of the myst_nb extension 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: Setting jupyter_execute_notebooks to "off".

Setting jupyter_execute_notebooks to "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 to sphinx_book_theme.

Changing the HTML theme to sphinx_book_theme can 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 of html_theme_options.

The new html_theme_options are 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 of html_context for GitHub integration.

The configuration added to html_context is 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 Enhanced

The updates to the type annotations using Python 3.10+ syntax (tuple[str, ...] and str | 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_selectivity Type Annotations and Docstring Enhanced

The 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_dopants Type Annotations and Docstring Enhanced

The 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: Method get_dopants Docstring Enhanced

The 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: Property to_table Docstring Added

The addition of a docstring to the property to_table enhances 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 annotations allows for postponed evaluation of type annotations, which is beneficial for forward references and generally cleaner code.

---

14-14: Approved addition of ClassVar for TEST_SPECIES.

The explicit use of ClassVar for the TEST_SPECIES variable 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 of assertStructAlmostEqual method.

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 of test_as_poscar method.

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 of test_from_py_struct_icsd method.

The method tests the generation of SmactStructure from a pymatgen structure using ICSD statistics. The instantiation of SmactStructure is condensed into a single line, which simplifies the code without changing its functionality.

---

156-156: Review of test_has_species method.

The method tests whether a species is present in a SmactStructure. The test cases are simplified by reducing the number of lines used for instantiating SmactStructure objects, which improves code efficiency and readability.

---

164-164: Review of test_smactStruc_comp_key method.

The method tests the generation of a composition key for SmactStructure objects. The changes involve simplifying the instantiation of SmactStructure objects, which makes the test cases more concise and readable.

---

194-194: Review of test_equality method.

The method tests the equality determination of SmactStructure objects. The formatting of list comprehensions and assertions has been compacted into fewer lines, which enhances the readability of the test cases.

---

209-209: Review of test_ele_stoics method.

The method tests acquiring element stoichiometries from SmactStructure objects. The changes involve compacting the list comprehensions and assertions into fewer lines, which simplifies the code without affecting its functionality.

---

268-268: Review of test_db_interface method.

The method tests interfacing with a database. The use of pytest.raises has been integrated into the test_ion_mutation method, 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 annotations allows for postponed evaluation of type annotations, which is beneficial for forward references and generally cleaner code.

---

54-58: Review of __init__ method in SmactStructure.

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_species method.

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 of from_py_struct method.

The method creates a SmactStructure from 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 of from_mp method.

The method creates a SmactStructure using 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 of has_species method.

The method's type annotation for the species parameter has been updated to use modern Python syntax. This change clarifies the expected input type and maintains the method's functionality.

---

541-541: Review of get_spec_strs method.

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_stoics method.

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 annotations allows for postponed evaluation of type annotations, which is beneficial for forward references and generally cleaner code.

---

351-351: Review of lookup_element_data function.

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 of lookup_element_hhis function.

The function's type annotation for the symbol parameter has been updated to explicitly specify the expected type as str. This change clarifies the expected input type and maintains the function's functionality.

---

688-688: Review of lookup_element_sse2015_data function.

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 of lookup_element_sse_pauling_data function.

The function's type annotation for the symbol parameter has been updated to explicitly specify the expected type as str. 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.

---

Line range hint 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.

---

Line range hint 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_finder class 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_probability method of the Oxidation_state_probability_finder class. The use of list comprehension enhances the performance of the operation.

---

Line range hint 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.

---

Line range hint 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 Structure

The transformation of oxidation_state_probability_table.json into 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 Link

The 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.

---

Line range hint 41-87: Code Cell: Importing Libraries and Initializing Parallel Processing

This cell introduces the initialize_parallel_processing function, which encapsulates the setup for parallel processing using pandarallel. 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.

---

Line range hint 90-191: Data Loading and Initial Analysis

This 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_csv for 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 Function

This markdown cell provides a detailed explanation of the smact_validity function 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 Presentation

This cell applies the smact_validity function to the DataFrame and displays the results. The use of parallel_apply is appropriate for leveraging the parallel processing capabilities set up earlier. The presentation of data using df.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.

---

Line range hint 356-391: Visualization of Results

This cell creates a horizontal bar plot to visualize the results of the SMACT validity test. The use of matplotlib for 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 Cell

The 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 Specification

The 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 Counts

Setting the execution count to null is 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 Cells

All 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 Statements

Condensing 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 Loop

The 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 Features

The use of mg.Structure.from_str(...).composition.reduced_formula demonstrates 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 Seaborn

Introducing sns.histplot for 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.

---

Line range hint 37-37: Finalise Notebook with Visual Output

The 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 smact module 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.

---

Line range hint 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 the smact_validity function.

The markdown cell provides a clear and concise explanation of the smact_validity function, 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 the smact_validity function.

The code cell effectively demonstrates the application of the smact_validity function 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 the oxidation_states submodule.

The markdown cell provides a clear and concise introduction to the oxidation_states submodule, 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_finder class 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: Updated requires field in [build-system].

The update to specify setuptools>=65.0.0 ensures 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-defined dependencies section.

The updated dependencies section 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 annotations allows 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 missing ParallelPool.

Setting ParallelPool to None in case of an ImportError is a robust way to handle optional dependencies. This change ensures that the application can still function even if the optional pathos library is not installed.

---

26-30: Use of TYPE_CHECKING for conditional imports.

The use of TYPE_CHECKING from the typing module 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 in add_mp_icsd.

The method signature has been updated to use modern Python type hints (list and dict directly instead of List and Dict from typing). 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 in add_structs.

The method now uses modern type hints and includes a default value for commit_after_each directly 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 in get_structs.

The method's return type has been updated to use the new syntax (list instead of List), 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 in get_with_species.

The method now uses the simplified type annotations (list and tuple), 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: Refactor parse_mprest function 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 annotations allows 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 of TYPE_CHECKING for conditional imports.

The use of TYPE_CHECKING from the typing module 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 StructurePredictor has 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 in predict_structs.

The method now uses modern Python type hints (list and tuple directly instead of List and Tuple). 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 in nary_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 core smact.Element and `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)

Line range hint 28-134: Documentation and Type Annotation Enhancements in Element Class

The updates to the Element class 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.

---

Line range hint 177-281: Documentation and Type Annotation Enhancements in Species Class

The Species class has seen similar updates to the Element class, with improved docstrings and modern type annotations. The explicit handling of the radii_source parameter 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 in ordered_elements Function

The 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 in element_dictionary Function

The function now uses modern type annotations (Iterable[str] | None and str | None) for its parameters, which clarifies the expected inputs and enhances the code's readability and maintainability.

---

354-366: Detailed Documentation in are_eq Function

The 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 in neutral_ratios_iter Function

The function now uses modern type annotations (list[int] and bool | list[list[int]]) and includes a detailed docstring that explains its complex logic. These changes enhance both the readability and maintainability of the code.

---

Line range hint 465-500: Updated Type Annotations and Detailed Documentation in neutral_ratios Function

The function now uses modern type annotations (list[int] and bool | 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)

Line range hint 14-32: Updated type hints and docstrings in parse_spec function.

The function parse_spec has been updated to use the modern Python 3.10 syntax for type hints, changing from Tuple to tuple. 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 in unparse_spec function.

The function unparse_spec has also been updated to use the modern Python 3.10 syntax for type hints, changing from Tuple to tuple. 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)

Line range hint 16-44: Enhanced parameter handling in cubic_perovskite.

The cubic_perovskite function has been updated to use None as default values for cell_par and repetitions parameters, 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 if None is passed is correctly handled. This is a significant improvement in the function's robustness and prevents potential bugs in future usage.

---

Line range hint 52-84: Improved parameter handling and clarity in wurtzite.

The wurtzite function mirrors the changes made in cubic_perovskite, with the introduction of None as default values for cell_par and repetitions to avoid mutable defaults. Additionally, the oxidation_states variable 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)

Line range hint 39-58: Updated type hints and lambda table handling in CationMutator.__init__.

The constructor of the CationMutator class has been updated to use the modern Python 3.10 syntax for union types in the alpha parameter. 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.

---

Line range hint 69-108: Enhanced JSON handling and DataFrame conversion in CationMutator.from_json.

The from_json static method has been updated to handle optional JSON input more robustly, with improved type hints and default handling. The method now uses pivot_table instead of pivot, 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.

---

Line range hint 402-426: Improved substitution threshold handling in unary_substitute.

The unary_substitute method has been updated to use the modern Python 3.10 syntax for union types in the thresh parameter, 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 Notebook

The 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:

1. 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.

2. 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.

3. 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.

4. 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.

5. 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)

Line range hint 1-522: Comprehensive Review of the smact/screening.py File

The modifications in smact/screening.py enhance the code's readability and maintainability by adopting Python 3.10's type hinting features. Here are some specific observations and suggestions:

1. 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.

2. 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.

3. Logical Refactoring (Lines 57-76, 186-220, etc.): The logical refactoring within functions like pauling_test and eneg_states_test improves clarity without altering functionality. This is a good practice as it helps other developers understand and maintain the code more easily.

4. Error Handling and Edge Cases (Lines 432-522): The function smact_validity includes 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.

5. 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.

Files that changed from the base of the PR and between f7e80f0 and 2369591.

• 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)

• CONTRIBUTING.md
• docs/smact.utils.rst
• smact/tests/test_core.py
• smact/tests/test_utils.py
• smact/utils/composition.py

• docs/conf.py
• docs/tutorials/crystal_space_visualisation.ipynb
• setup.py
• smact/init.py
• smact/data_loader.py
• smact/properties.py
• smact/screening.py

pyproject.toml (7)

3-3: Updated build system requirements.

The update to the requires field in the [build-system] section to specify a minimum version of setuptools (>=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 dependencies section, 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 with version_variable set 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 core smact.Element and `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.

Files that changed from the base of the PR and between 2369591 and b753b8c.

• docs/examples.rst (1 hunks)
• docs/examples/valence_electron_count.ipynb (1 hunks)
• docs/smact.utils.rst (1 hunks)
• docs/tutorials.rst (1 hunks)

• docs/examples.rst

• docs/smact.utils.rst
• docs/tutorials.rst

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 smact function sets the stage for the subsequent code cell.

Files that changed from the base of the PR and between b753b8c and 0c21a6c.

• docs/conf.py (4 hunks)

• docs/conf.py

Files that changed from the base of the PR and between 0c21a6c and e959684.

• docs/introduction.rst (2 hunks)

• docs/introduction.rst