Added output description and python 3.12/3.13 support #734
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- Introduced a new CellTypeClassifier class for cell type classification tasks. - Implemented training, evaluation, and testing methods with support for various data augmentation techniques. - Integrated advanced loss functions and optimizers, including PolyLoss and SAM. - Added functionality for test-time augmentation and probability predictions. - Included normalization methods and model checkpoint loading for enhanced usability.
- Introduced a new import for the monitor tool to track preprocessing steps. - Applied the @monitor decorator to the preprocess_adata method for enhanced progress tracking during data preprocessing.
- Introduced the @monitor decorator in various files to enhance tracking of function execution. - Updated functions in gseapy, fate, least_action_path, perturbation, state_graph, deprecated, pca, cell_velocities, connectivity, dimension_reduction, dynamics, moments, utils, networks, rank_vf, and topography modules. - This addition aims to improve observability and debugging capabilities throughout the codebase.
- Introduced a global flag to control monitor output display and a function to set this preference. - Updated the style function to include a new parameter for showing monitor output. - Removed the @monitor decorator from specific functions to streamline monitoring integration. - Enhanced the StructureWatcher class to conditionally display monitoring information based on the new settings.
- Replaced pkg_resources with importlib.metadata for package version retrieval in conf.py. - Updated DataFrame concatenation from append to pd.concat in simulation.py and temporal.py for improved performance and compatibility. - Removed unused import from trainer.py to clean up the codebase.
- Added Python versions 3.12 and 3.13 to the matrix in the Python package workflow for broader compatibility and testing coverage.
…ine code and improve clarity.
- Removed Python versions 3.12 and 3.13 from the matrix in both the python-package and python-plain-run-test workflows to streamline testing and compatibility.
… modules - Updated NaN constants from np.NAN to np.nan for consistency in diffusion.py. - Enhanced dtype checking in select_cell function to support both int and np.integer types in utils.py. - Changed np.Inf to np.inf in Tang.py for uniformity in floating-point representation.
…ctorField in tests - Improved the _log_to_uns method in StructureWatcher to handle various data types for history logs, ensuring consistent logging in adata.uns. - Updated test data loading in conftest.py to regenerate VectorField if missing from adata.uns for both UMAP and PCA, enhancing test reliability.
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## master #734 +/- ##
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+ Coverage 28.11% 28.20% +0.09%
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Files 295 297 +2
Lines 46721 47399 +678
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+ Hits 13137 13371 +234
- Misses 33584 34028 +444 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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- Improved handling of cell indices in the get_cell_indices_by_name function to accommodate cases where cell names may match multiple entries or be represented as slices or arrays. - Updated test cases to utilize variables for initial and target cell names, enhancing code readability and maintainability.
… method - Changed indexing from clusters[knn.flatten()] to clusters.iloc[knn.flatten()] for correct row selection in fate_bias function. - Updated DataFrame concatenation from pd.merge to pd.concat for improved performance and clarity.
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This pull request introduces several improvements and updates across the codebase to enhance compatibility, maintainability, and monitoring capabilities. The most significant changes include replacing deprecated pandas methods, expanding Python version support in CI, adding function monitoring decorators, and updating documentation build logic.
Key changes:
Pandas compatibility and code modernization
DataFrame.append()calls withpd.concat()throughoutdynamo/external/celldancer/simulation.pyto ensure compatibility with newer pandas versions. [1] [2] [3] [4] [5] [6] [7]np.floattofloatin type conversions indynamo/external/deepvelo/utils/temporal.pyto avoid deprecation warnings. [1] [2]distutilsindynamo/external/deepvelo/trainer/trainer.py.Monitoring and tracking enhancements
@monitordecorator to key analysis and prediction functions (e.g.,enrichr,fate,andecestor,least_action,KO,perturbation, ranking functions,state_graph,tree_model, and preprocessing methods) to enable improved tracking and logging of function calls. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18]show_monitorparameter to thestylefunction indynamo/pl.py, and integrated monitor display preference handling. [1] [2]CI and documentation improvements
importlib.metadatainstead ofpkg_resourcesfor package discovery, aligning with modern Python standards. (docs/conf.py)API and feature expansion
deepvelo,velovi) in themethodargument ofextveloindynamo/tools/_extvelo.py.These changes collectively modernize the codebase, improve observability, and ensure the package remains compatible with the latest Python and pandas releases.