coderabbitai[bot]
commented
1 day ago Walkthrough
The pull request introduces several changes across multiple documentation files and Python modules. Key modifications include updates to the Sphinx configuration in docs/conf.py, the addition of new documentation sections for various modules, and restructuring of import paths in Python files. Additionally, the requirements.txt file has been significantly updated with new and modified package dependencies. Changes also include the removal of certain examples from the documentation and enhancements to Jupyter notebooks, particularly in formatting and clarity.
Changes
| File Path | Change Summary |
|---|---|
docs/conf.py |
Renamed variable jupyter_execute_notebooks to nb_execution_mode, commented out html_static_path, added new MOCK_MODULES. |
docs/examples.rst |
Removed entry examples/neutral_combos from toctree. |
docs/examples/doper.ipynb |
Updated header formatting and clarified output description, added new section for plot_dopants. |
docs/smact.utils.crystal_space.download_compounds_with_mp_api.rst |
Added documentation section for download_compounds_with_mp_api. |
docs/smact.utils.crystal_space.generate_composition_with_smact.rst |
Added documentation section for generate_composition_with_smact. |
docs/smact.utils.crystal_space.plot_embedding.rst |
Added documentation section for plot_embedding. |
docs/smact.utils.crystal_space.rst |
Created new documentation file for crystal_space module. |
docs/smact.utils.oxidation.rst |
Created new documentation file for oxidation module. |
docs/smact.utils.rst |
Updated submodules: removed five, added crystal_space and oxidation. |
docs/tutorials/crystal_space.ipynb |
Updated import paths for functions and refined tutorial content. |
docs/tutorials/crystal_space_visualisation.ipynb |
Updated prerequisite reference from crystal_space_with_smact.ipynb to crystal_space.ipynb. |
docs/tutorials/oxidation_states.ipynb |
Changed header from second-level to first-level for prominence. |
requirements.txt |
Added and updated numerous package dependencies, with several packages upgraded to newer versions. |
smact/utils/crystal_space/download_compounds_with_mp_api.py |
Updated import path and corrected save_dir parameter in docstring. |
smact/utils/crystal_space/generate_composition_with_smact.py |
Updated import path, added return type annotations, and expanded docstrings for clarity. |
smact/utils/oxidation.py |
Simplified filename parameter type in write method of ICSD24OxStatesFilter class. |
Possibly related PRs
- #282: Related to changes in
docs/conf.pyand handling of oxidation states in thesmact_validityfunction. - #252: Connects with the introduction of the
smact_validityfunction, which is being modified in the main PR. - #329: Connects with the introduction of new oxidation states and modifications to the
Elementclass. - #336: The addition of a new tutorial for structure prediction complements the main PR's focus on enhancing documentation and functionality.
Suggested labels
enhancement, feature, python, refactor
🐇 In the garden of code, we hop with delight,
New docs and modules, all shining so bright.
With paths rearranged and examples refined,
Our project now sparkles, with treasures to find!
From Sphinx to Jupyter, we dance through the night,
Celebrating changes, oh what a sight! 🌟
📜 Recent review details
**Configuration used: CodeRabbit UI** **Review profile: CHILL**📥 Commits
Reviewing files that changed from the base of the PR and between ac6604f59c9e2d4046962bc4a954cad136bc02b7 and 9c823f4417f35cef1deea1f4631e14afa7f50c36.📒 Files selected for processing (2)
* `.readthedocs.yaml` (1 hunks) * `README.md` (1 hunks)✅ Files skipped from review due to trivial changes (1)
* README.md🔇 Additional comments (2)
.readthedocs.yaml (2)
`16-16`: **Verify the necessity of installing both requirements files** The addition of `requirements.txt` alongside `docs/requirements.txt` could lead to duplicate dependencies or version conflicts. Consider consolidating these files if possible.✅ Verification successful
**Both requirements files serve distinct purposes and should be kept separate** The analysis of both files shows they serve different purposes with minimal overlap: - `requirements.txt` contains the main project dependencies (SMACT, pymatgen, etc.) - `docs/requirements.txt` contains documentation-specific packages (Sphinx, MyST-NB, etc.) 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 `requirements.txt` is necessary as the documentation likely needs access to the main project's code and dependencies to: - Generate API documentation - Execute code examples - Build interactive documentation features🏁 Scripts executed
The following scripts were executed for the analysis: Script: ```shell #!/bin/bash # Description: Check for duplicate dependencies and potential conflicts # Compare requirements files for duplicates echo "Checking for duplicate packages:" comm -12 <(sort requirements.txt) <(sort docs/requirements.txt) # Display both files for manual review echo -e "\nContents of requirements.txt:" cat requirements.txt echo -e "\nContents of docs/requirements.txt:" cat docs/requirements.txt ``` Length of output: 11487Thank 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?
codecov[bot]
Documentation updates
Description
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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.