v1.5.3

What's Changed

• Add plot explanation utilities and enhance visualizations by @Starlitnightly in #745
• Bump version from 1.5.2 to 1.5.3 by @Starlitnightly in #746

Full Changelog: v1.5.2...v1.5.3

v1.5.2

What's Changed

• Support NumPy 2.0 with backward compatibility by @Nanguage in #744

New Contributors

• @Nanguage made their first contribution in #744

Full Changelog: v1.5.1...v1.5.2

v1.5.1

Bump version from 1.5.0 to 1.5.1

Release v1.5.0

Changes in this Release

Release v1.5.0

What's Changed

• Fixed 1M cells's error in cell_velocity by @Starlitnightly in #737
• Added more species support to convert the ensembl to symbol by @Starlitnightly in #738
• Fixed some small bug and update the geneid convert tutorial by @Starlitnightly in #739
• Enhance jacobian and sensitivity functions to allow overriding color … by @Starlitnightly in #740
• Updated the version of dynamo to 1.5 by @Starlitnightly in #741

Full Changelog: v1.4.3...v.1.5.0

v1.4.3

What's Changed

• Fix: Add compatibility with anndata >= 0.10 by @NatalieCao323 in #730
• Add SUDE dimension reduction method and update related documentation by @Starlitnightly in #729
• Added celldancer, deepvelo, and latentvelo to dyn.tl.extvelo (#721) by @Starlitnightly in #731
• Added output description and python 3.12/3.13 support by @Starlitnightly in #734
• Added tutorial of external velocity calculation and integration by @Starlitnightly in #735
• Enhance _snapshot method in StructureWatcher to capture detailed colu… by @Starlitnightly in #736

New Contributors

• @NatalieCao323 made their first contribution in #730

Full Changelog: v.1.4.2...v1.4.3

v1.4.2

What's Changed

• Update README.md by @YanshiHu in #704
• Add calc_new_to_total_ratio() in init by @Sichao25 in #671
• Debug duplicate signatures in numba.vectorize() by @Sichao25 in #700
• Debug pl.circosPlot() by @Sichao25 in #682
• Optimize the display of the tutorial page and add adjust_legend argument by @Starlitnightly in #707
• Fixed some issue of readme and added violin_box function (#714) by @Starlitnightly in #715
• Optimize chunked preprocessing by @Sichao25 in #674
• Simplified functions in tutorials and updated some tutorials by @Starlitnightly in #718
• Add temporary anndata version constraint by @Sichao25 in #727

New Contributors

• @YanshiHu made their first contribution in #704
• @Starlitnightly made their first contribution in #707

Full Changelog: v1.4.1...v.1.4.2

Release v1.4.1

What's Changed

• Debug and refactor scPotential in #624
• Replace deprecated np.asscalar() with np.ndarray.item() in #643
• Create chunk option for normalization and gene selection in #598
• Debug state_graph in #630
• Debug jacobian_heatmap() in #653
• Debug .pl.nneighbors() in #644
• Retry codecov upload in #656
• Debug vectorfield given layer input in #619
• Refactor fate() with Trajectory class in #645
• Debug simulation module in #658
• Extra filter after pearson residuals normalization in #665
• Add missing return value to deprecated functions in #663
• Reorganize estimation module in #662
• Debug networks plot in #657
• Refactor scatters() and scatters_interactive() in #654
• Refactor VectorField() function in #620
• Implement pl.plot_connectivity() in #652
• Docstring and type hints for the prediction module in #666
• Update docstr and type hints for External module in #661
• Add doctring and type hints for simulation module in #660
• Docstring and type hints for root folder python files in #667
• Debug the preprocessing of integer matrix input in #664
• Missing return value in .pl.lap_min_time() in #668
• Update matplotlib Colorbar.draw_all() to Colorbar._draw_all() in #669
• Optimize code coverage tests in #605
• Debug test_gradop by in #677
• Constraint on matplotlib version by in #679
• Upgrade code coverage to v4 in #684
• init a branch for updating dependency in #690
• Replace louvain with leiden in #692
• Debug pl.highest_frac_genes() in #681
• Deprecate more sparse matrix .A attributes in #695
• Fix matplotlib version issues and a circular import issue in #686
• Debug set_figure_params in #698
• Debug: shape and name mismatch in cell-wise alpha saving in #697
• Debug: The sizes of the scatter plots are not set correctly in #696

Full Changelog: v1.4.0...v1.4.1

Release v1.4.0

Main feature changes

• Shiny web application for in silico perturbation and least square action path analyses PR 582.
  

• More 3D plots PR 597

  • 3D scatters with Plotly and Pyvista dyn.pl.scatters_interactive().

• 3D vectors and topography with Plotly and Pyvista dyn.pl.cell_wise_vectors_3d(), dyn.pl.topography_3d().

• 3D animation with Pyvista dyn.mv.PyvistaAnim().

• The tools module has been reorganized PR 625

  • Deprecate files dynamo_fitting.py, dynamo_bk.py, dynamics_deprecated.py, utils_moments_deprecated.py.
  • Deprecate legacy functions in construct_velocity_tree.py,pseudotime.py, moments.py, clustering.py.
  • Merge utils_markers.py and markers.py.
  • Merge time_series.py (learns a direct principal graph by integrating the transition matrix between and DDRTree)
    and construct_velocity_tree.py(Integrate pseudotime ordering with velocity to automatically assign the direction
    of the learned trajectory.) to DDRTree_graph.py.
  • Reorganize some functions to utils in the following file: time_series.py, multiomics.py.
  • Rename: DDRTree_py.py to DDRTree.py, psl_py.py to psl.py.

download pdf version of the module graph

• Saved the velocity parameters in adata.varm instead of adata.var PR 579.

• DDRtree based pseudotime and graph learning PR 564 dyn.tl.order_cells(), dyn.tl.construct_velocity_tree().

• Integrated hnswlib fast nearest neighbors method PR 552.

• A helper function to convert the AnnData object from Dynamo to Scvelo, or vice versa PR 551.

• Deprecate infomap clustering PR 555.

Detailed change log and release notes can be found in our Readthedocs.

v1.3.3-alpha

Merge pull request #542 from Sichao25/debug

debug workflow