Add Crystal Space and Oxidation Utilities to the Documentation #337
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WalkthroughThe pull request introduces several changes across multiple documentation files and Python modules. Key modifications include updates to the Sphinx configuration in Changes
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🔇 Additional comments (2).readthedocs.yaml (2)
The addition of ✅ Verification successfulBoth requirements files serve distinct purposes and should be kept separate The analysis of both files shows they serve different purposes with minimal overlap:
The only shared dependencies are basic utilities (attrs, typing-extensions, etc.) which are common across Python projects and don't pose version conflicts. The addition of
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The inclusion of additional requirements might impact build time and memory usage. Consider monitoring the ReadTheDocs build logs after this change. Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (10)
requirements.txt (1)
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1-375: Consider documenting direct dependencies separatelyThe requirements.txt file contains both direct and transitive dependencies. Consider maintaining a separate requirements-direct.txt file listing only the direct dependencies of the project for better maintainability.
Create a new file
requirements-direct.txtwith only the direct dependencies (those marked with "via SMACT (setup.py)"), then generate requirements.txt from it:+ # Create requirements-direct.txt with: + ase==3.23.0 + dash==2.18.2 + elementembeddings==0.6.1 + # ... other direct dependencies + + # Then generate requirements.txt using: + pip-compile --extra=strict requirements-direct.txt -o requirements.txtdocs/examples/doper.ipynb (3)
14-15: Consider using proper markdown heading instead of bold textFor better document structure and navigation, consider using a proper markdown heading (e.g.,
## Output Format) instead of bold text. This would maintain consistent heading hierarchy and improve the notebook's table of contents generation.-**Output Format** +## Output Format
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1-24: Consider adding error handling examplesThe documentation would benefit from examples demonstrating:
- How to handle invalid ionic species
- Error cases when using incompatible oxidation states
- Edge cases with unusual dopant combinations
This would help users understand the module's behaviour in non-ideal scenarios.
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8-9: Enhance the alternative metrics documentationThe skipspecies metric explanation could be improved by:
- Adding a brief comparison of accuracy between traditional and skipspecies approaches
- Including performance considerations
- Providing guidance on when to use each metric
This would help users make informed decisions about which metric to use for their specific use case.
smact/utils/crystal_space/download_compounds_with_mp_api.py (2)
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16-24: Add type hints to improve code clarity.Consider adding type hints to the function signature for better code maintainability and IDE support.
def download_mp_data( - mp_api_key: str | None = None, - num_elements: int = 2, - max_stoich: int = 8, - save_dir: str = "data/binary/mp_api", - request_interval: float = 0.1, + mp_api_key: str | None = None, + num_elements: int = 2, + max_stoich: int = 8, + save_dir: str = "data/binary/mp_api", + request_interval: float = 0.1, +) -> None:
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89-89: Consider implementing exponential backoff for API requests.The current implementation uses a fixed interval between requests. Consider implementing exponential backoff to better handle potential API rate limits.
- time.sleep(request_interval) + # Implement exponential backoff + retry_count = 0 + while retry_count < 3: + try: + time.sleep(request_interval * (2 ** retry_count)) + break + except Exception as e: + retry_count += 1 + if retry_count == 3: + raise esmact/utils/crystal_space/generate_composition_with_smact.py (2)
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77-86: Consider using context manager for multiprocessing pools.Using a context manager with multiprocessing pools ensures proper cleanup of resources.
- pool = multiprocessing.Pool(processes=multiprocessing.cpu_count() if num_processes is None else num_processes) - compounds = list( - tqdm( - pool.imap_unordered( - partial( - convert_formula, - num_elements=num_elements, - max_stoich=max_stoich, - ), - combinations, - ), - total=len(combinations), - ) - ) - pool.close() - pool.join() + with multiprocessing.Pool(processes=multiprocessing.cpu_count() if num_processes is None else num_processes) as pool: + compounds = list( + tqdm( + pool.imap_unordered( + partial( + convert_formula, + num_elements=num_elements, + max_stoich=max_stoich, + ), + combinations, + ), + total=len(combinations), + ) + )
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115-115: Remove redundantstrict=Falseparameter in zip().The
strictparameter is redundant in Python 3.10+ as it's the default behaviour.- symbols_stoich = zip(res[0], res[2], strict=False) + symbols_stoich = zip(res[0], res[2])docs/tutorials/crystal_space_visualisation.ipynb (2)
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32-38: Consider optimising the embedding computation for large datasets.The current implementation processes embeddings one at a time, which could be inefficient for large datasets. Consider vectorising the computation or processing in batches.
- embeddings = [] - for f in tqdm(formula): - try: - compositional_embedding = CompositionalEmbedding(f, embedding=embedding) - embeddings.append(compositional_embedding.feature_vector(stats=stats)) - except Exception as e: - embeddings.append(np.full(embedding_dim, np.nan)) + def process_batch(formulas, batch_size=100): + for i in range(0, len(formulas), batch_size): + batch = formulas[i:i + batch_size] + yield [ + CompositionalEmbedding(f, embedding=embedding).feature_vector(stats=stats) + if f else np.full(embedding_dim, np.nan) + for f in batch + ] + + embeddings = np.vstack(list(process_batch(formula)))Also applies to: 39-40, 41-42
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148-149: Consider adding error handling for specific exceptions.The dimension reduction implementation could benefit from more specific error handling to provide better feedback to users.
try: reducer = PCA(n_components=n_components, **kwargs) elif reducer == "tsne": reducer = TSNE(n_components=n_components, **kwargs) elif reducer == "umap": reducer = UMAP(n_components=n_components, **kwargs) else: raise ValueError("reducer must be one of ['pca', 'tsne', 'umap']") + try: + reduced_embeddings = reducer.fit_transform(embeddings.values) + except ValueError as e: + raise ValueError(f"Failed to reduce dimensions: {str(e)}") + except MemoryError: + raise MemoryError("Insufficient memory for dimension reduction. Consider reducing the dataset size.")Also applies to: 150-151, 152-153, 154-155, 156-157, 158-159
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📒 Files selected for processing (16)
docs/conf.py(3 hunks)docs/examples.rst(0 hunks)docs/examples/doper.ipynb(1 hunks)docs/smact.utils.crystal_space.download_compounds_with_mp_api.rst(1 hunks)docs/smact.utils.crystal_space.generate_composition_with_smact.rst(1 hunks)docs/smact.utils.crystal_space.plot_embedding.rst(1 hunks)docs/smact.utils.crystal_space.rst(1 hunks)docs/smact.utils.oxidation.rst(1 hunks)docs/smact.utils.rst(1 hunks)docs/tutorials/crystal_space.ipynb(2 hunks)docs/tutorials/crystal_space_visualisation.ipynb(1 hunks)docs/tutorials/oxidation_states.ipynb(1 hunks)requirements.txt(1 hunks)smact/utils/crystal_space/download_compounds_with_mp_api.py(1 hunks)smact/utils/crystal_space/generate_composition_with_smact.py(3 hunks)smact/utils/oxidation.py(1 hunks)
💤 Files with no reviewable changes (1)
- docs/examples.rst
✅ Files skipped from review due to trivial changes (7)
- docs/smact.utils.oxidation.rst
- docs/smact.utils.crystal_space.rst
- docs/smact.utils.crystal_space.download_compounds_with_mp_api.rst
- docs/smact.utils.crystal_space.plot_embedding.rst
- docs/smact.utils.crystal_space.generate_composition_with_smact.rst
- docs/smact.utils.rst
- docs/tutorials/oxidation_states.ipynb
🔇 Additional comments (10)
requirements.txt (1)
224-231: Verify security advisories for pymatgen
The pymatgen package is a critical dependency. Given its recent version (2024.11.13), we should verify there are no known security issues.
✅ Verification successful
pymatgen 2024.11.13 is secure and up-to-date
The version 2024.11.13 of pymatgen being used is secure as it's well above the patched versions for all known vulnerabilities:
- Critical vulnerability (arbitrary code execution) was patched in 2024.2.20
- Moderate vulnerability (ReDoS) was patched in versions after 2022.9.21
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Length of output: 949
docs/examples/doper.ipynb (1)
Line range hint 1-1: Verify integration with Crystal Space functionality
Given that this PR aims to document Crystal Space functions, consider adding examples or references showing how the Doper module integrates with Crystal Space functionality, if applicable.
smact/utils/crystal_space/download_compounds_with_mp_api.py (1)
13-13: LGTM! Import statement has been simplified.
The import statement has been updated to use a more concise path whilst maintaining the same functionality.
smact/utils/crystal_space/generate_composition_with_smact.py (2)
12-12: LGTM! Import statement has been simplified.
The import statement has been updated to use a more concise path whilst maintaining the same functionality.
21-21: LGTM! Return type hints added.
The addition of return type hints improves code clarity and IDE support.
Also applies to: 47-47
docs/tutorials/crystal_space.ipynb (1)
47-47: LGTM! Documentation hyperlinks updated.
The hyperlinks to source files have been updated to reflect the new file structure, improving navigation and documentation clarity.
Also applies to: 130-130
docs/tutorials/crystal_space_visualisation.ipynb (1)
14-14: LGTM: Prerequisite reference updated correctly.
The prerequisite reference has been updated from crystal_space_with_smact.ipynb to crystal_space.ipynb, which aligns with the PR objectives.
docs/conf.py (3)
48-48: LGTM: Configuration updated to use modern Sphinx notebook execution setting.
The change from jupyter_execute_notebooks to nb_execution_mode aligns with current Sphinx-notebook practices.
421-423: LGTM: Mock modules added for documentation build.
The addition of mp_api, mp_api.client, and emmet to MOCK_MODULES is appropriate for handling external dependencies during documentation builds.
157-157: Verify the impact of commenting out static path.
While commenting out html_static_path is valid, ensure that no static assets (CSS, images, etc.) are affected.
✅ Verification successful
Commenting out html_static_path has no impact on the codebase
The verification shows that:
- No
_staticdirectory exists in the repository - The only references to static assets in documentation are images in
dev_docs/design_docs/StructurePredictor.md, which use a different path (../images/) - The only occurrence of
static_pathis the commented line itself inconf.py
Therefore, commenting out the unused html_static_path configuration is safe and won't affect any static assets.
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🛠️ Refactor suggestion
Consider maintaining support for PathLike objects
The change to restrict the filename parameter to only strings reduces API flexibility. Python's path handling typically accepts both string and PathLike objects for better interoperability.
Apply this diff to restore PathLike support:
- filename: str,
+ filename: str | os.PathLike,And update the docstring:
- filename (str): The filename to write the filtered oxidation states list to.
+ filename (str | os.PathLike): The filename to write the filtered oxidation states list to.Also applies to: 122-122
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #337 +/- ##
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- Coverage 77.45% 77.44% -0.01%
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Files 31 31
Lines 2590 2589 -1
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- Hits 2006 2005 -1
Misses 584 584 ☔ View full report in Codecov by Sentry. |
Documentation updates
Description
This PR addresses the following:
Type of change
How Has This Been Tested?
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Documentation
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requirements.txtfile, adding new dependencies and updating existing ones to ensure compatibility and performance..readthedocs.yamlfile to include dependencies fromrequirements.txt.