• Fix "lightgray" error in plot_trend
• Address pygam incompatibility with newer scipy versions (automatic skip in tests, user warnings)
• Address fcsparser incompatibility with NumPy 2.0 (automatic skip in tests, user warnings)
• Use different joblib backend in Python 3.12+ with joblib < 1.5 to avoid ResourceTracker warnings
• More convenient cell-name handling for integers (e.g., in spatial data) with automatic type conversion

• update LICENSE file to be consistent with MIT - license
• implement plot_trajectories to show multiple poaths on the UMAP
• Drop leiden dependency to allow Python >= 3.13. igrph is used instead.

• Made pygam an optional dependency that can be installed with pip install palantir[gam] or pip install palantir[full]
• Added proper conditional imports and improved error handling for pygam
• Enhanced run_magic_imputation to return appropriate data types for different inputs
• Updated code to use direct AnnData imports for newer compatibility
• Improved version detection using importlib.metadata with graceful fallbacks
• Fixed Series indexing deprecation warnings in early cell detection functions
• Expanded and standardized documentation with NumPy-style docstrings throughout the codebase
• Added comprehensive type hints to improve code quality and IDE support
• Remove dependency from _ methods in scanpy for plotting.
• add pseudotime_interval argument to control path length in palantir.plot.plot_trajectory

• run_magic_imputation now has a boolean parameter sparse to control output sparsity
• bugfix: run_local_variability for dense expression arrays now runs much faster and more accurate

• avoid devision by zero in select_branch_cells for very small datasets
• make branch selection robust against NaNs
• do not plot unclustered trends (NaN cluster) in plot_gene_trend_clusters

• optional progress bar with progress=True in palantir.utils.run_local_variability
• avoid NaN in local variablility output
• compatibility with scanpy>=1.10.0

• require python>=3.8
• implement CI for testing
• fixes for edge cases discoverd through extended testing
• implement plot_trajectory function to show trajectory on the umap
• scale pseudotime to unit intervall in anndata

• implemented palantir.plot.plot_stats to plot arbitray cell-wise statistics as x-/y-positions.
• reduce memory usgae of palantir.presults.compute_gene_trends
• removed seaborn dependency
• refactor run_diffusion_maps to split out compute_kernel and diffusion_maps_from_kernel
• remove unused dependency tables

New Features

• Enable an AnnData-centric workflow for improved usability and interoperability with other single-cell analysis tools.
• Introduced new utility functions
  • palantir.utils.early_cell To automate fining an early cell based on cell type and diffusion components.
  • palantir.utils.find_terminal_states To automate finding terminal cell states based on cell type and diffusion components.
  • palantir.presults.select_branch_cells To find cells associated to each branch based on fate probability.
  • palantir.plot.plot_branch_selection To inspect the cell to branch association.
  • palantir.utils.run_local_variability To compute local gene expression variability.
  • palantir.utils.run_density A wrapper for mellon.DensityEstimator.
  • palantir.utils.run_density_evaluation Evaluate computed density on a different dataset.
  • palantir.utils.run_low_density_variability. To aggregate local gene expression variability in low density.
  • palantir.plot.plot_branch. To plot branch-selected cells over pseudotime in arbitrary y-postion and coloring.
  • palantir.plot.plot_trend. To plot the gene trend ontop of palantir.plot.plot_branch.
• Added input validation for better error handling and improved user experience.
• Expanded documentation within docstrings, providing additional clarity for users and developers.

Enhancements

• Updated tutorial notebook to reflect the new workflow, guiding users through the updated processes.
• Implemented gene trend computation using Mellon, providing more robust and efficient gene trend analysis.
• Enable annotation in palantir.plot.highight_cells_on_umap.

Changes

• Replaced PhenoGraph dependency with scanpy.tl.leiden for gene trend clustering.
• Deprecated the run_tsne, determine_cell_clusters, and plot_cell_clusters functions. Use corresponding implementations from Scanpy, widely used single-cell analysis library and direct dependecy of Palantir.
• Rename palantir.plot.highight_cells_on_tsne to palantir.plot.highight_cells_on_umap
• Depend on anndata>=0.8.0 to avoid issues writing dataframes in ad.obsm.

Fixes

• Addressed the issue of variability when reproducing results (issue#64), enhancing the reproducibility and reliability of Palantir.

Minor bug fixes.