Introduce Splash Screen with Metadata and Refactor Water Entropy Handling #136
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- incorporate the use of the `Python` library `rich` to enhance the outputs on the terminal - addition of splash screen with metadata using the `CITATION.cff` file - progress bars used to show the progress of each calculation - using `rich` tables to ensure consistency in the output
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- Simplified and unified logging configuration using Rich console - Enabled console output recording for capturing all printed output - Added file handlers for main, error, command, and mdanalysis logs - Implemented method to save buffered console output to file after run - Updated the ability to update logging levels dynamically
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- Additional progress bars have been added to the `build_covariance_matrices` - Additional test cases have been implemented to increase the coverage of functions missed by test cases
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…38-add-splash-screen-metadata
- Unified and simplified progress bar logic across entropy workflows for consistency and clarity - Replaced multiple bars with a single comprehensive progress bar showing current molecule and level - Improved progress titles to reflect specific calculation stages (e.g. building covariance matrices, calculating conformational states) - Renamed molecule label column to "Residue ID" for scientific accuracy and clearer representation
- Use `requests` to get the `CITATION.cff` file from GitHub rather than locally in the project directory - If there are network issues display a minimal splash screen with just ASCII art - Update unit tests to ensure all new functionality is covered
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…clude `requests` in `pyproject.toml` dependencies
… components - Added a new `frame_count` column to the `add_residue_data` function. - Retrieved `frame_count` from `levels.py` and integrated it into `entropy.py` - Included `frame_count` for united atom level entries - Ensured consistent inclusion of frame count in water entropy calculations - Corrected aggregation logic in `_finalize_molecule_results` to ensure accurate summation of entropy values per molecule
- Integrated water entropy into the same group framework as other molecules: - Each water group now gets a proper `group_id`, label, residue count, and atom count - Entropy components (orientational, vibrational-translational, vibrational-rotational) are logged consistently - Updated `_handle_water_entropy` to: - Compute entropy per water group - Exclude water from selection string when `--water-entropy` is enabled - Use MDAnalysis residue names to build accurate group labels - Modified `execute` to: - Separate `water_groups` from `nonwater_groups` - If `water_entropy=True`: handle waters separately and exclude them from later analysis - If `water_entropy=False`: merge water back into non-water groups so they are included in full entropy calculation - Improved `DataLogger` outputs: - Added/cleaned group label mapping table for better tracking - Ensured consistent handling of residue names and frame counts
- Replace manual filtering of water residues with MDAnalysis selection language (`select_atoms("resname WAT")`) for more robust residue handling
- Dynamically determine `residue_group` from Sorient_dict keys, including only residues present in the water selection
- Update group label logging to use the new selection method
- Add unit test `test_calculate_water_entropy_adds_resname` to ensure the `residue_names.add(resname)` path is exercised
3 tasks
…mes))` to ensure the correct range is captured
- Updated `_calculate_water_entropy` and related methods to properly aggregate orientational, translational, and rotational entropy - Incorporated actual water counts from covariances for accurate logging - Revised unit tests to reflect updated method signatures and behaviors, ensuring `add_residue_data` and `add_group_label` calls are correctly tested - Stop adding aggregated water entropy results to the Total Group table, as this is incorrect
jimboid
approved these changes
Aug 22, 2025
jimboid
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Sep 3, 2025
Introduce Splash Screen with Metadata and Refactor Water Entropy Handling
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Summary
This PR adds a rich splash screen to
CodeEntropythat displays program metadata dynamically fetched from theCITATION.cfffile. Additionally, it refactors water entropy handling for more robust and dynamic residue grouping, improving logging and test coverage.Changes
Splash Screen and Metadata
richtables.CITATION.cfffile fetched directly from GitHub.Water Entropy Refactor (Secondary)
select_atoms("resname WAT")) for robust residue handling.residue_groupfromSorient_dictkeys, including only residues present in the water selection.test_calculate_water_entropy_adds_resnameto ensureresidue_names.add(resname)is exercised.Other Improvements
Impact