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

v1.3.2

Update workflow
Remove nxviz dependency

release v1.3.1

Update a new patch for Dynamo ver 1.3

Remove cdlib and KDEpy from the requirement.
Add the sampling number n to the parameters of the topography plotting function.

dynamo-release v1.3.0

Dynamo Ver 1.3.0
Feature Changes
The preprocessing module has been refactored:

Class Preprocessor is recommended for most preprocessing methods and recipes. pp.recipe_monocle, pp.recipe_velocyto has been deprecated (PR 497 PR 500). Check the tutorials here for more instructions.

Normalization has been refactored (PR 474 PR 475): pp.normalize_cell_expr_by_size_factors has been deprecated, and new APIs are:

pp.normalize_cell_expr_by_size_factors -> pp.calc_sz_factor, pp.normalize.

Gene selection has been refactored (PR 474). Now support genes selected by fano factors. APIs are pp.select_genes_monocle and pp.select_genes_by_seurat_recipe.

PCA has been refactored (PR 469). dyn.pp.pca_monocle has been deprecated. The new API is:

pp.pca_monocle -> pp.pca.

sctransform and pearson residuals recipe has been refactored (PR 510 PR 512). Now those advanced methods will only be performed on X layer. Other layers will get normalized by size factors.

Calculation of ntr rate and pp.cell_cycle_scores has been added to the Preprocessor (PR 513). To enable cell cycle scores, set parameter cell_cycle_score_enable to True when initializing the pp.Preprocessor.

Now the size factors normalization will normalize all layers with its own size factors by default (PR 521). To normalize the labeled data with total size factors, we need to set the total_szfactor to total_Size_Factor explicitly.

Multiple new features added, includes genes selection by fano factors (PR 474), external data integration methods (PR 473) and pp.regress_out (PR 470 PR 483 PR 484).

Created more tests for preprocessing module (PR 485).

Replaced adata.obsm["X"] with adata.obsm["X_pca"] (PR 514).

Removed some console output. They can still be displayed with DEBUG logging mode.

Other deprecated APIs include: pp.calc_sz_factor_legacy, pp.filter_cells_legacy, pp.filter_genes_by_outliers_legacy, pp.select_genes_monocle_legacy, pp.select_genes_by_dispersion_general, pp.cook_dist, pp.normalize_cell_expr_by_size_factors. More information can be found on our preprocessing tutorials.

DEBUG
Fixed the bug that save_show_or_return flags not working (PR 414).

Enabled the leiden algorithm to accept the resolution parameters (PR 441).

Fixed the wrong attribute name of anndata object in utils_dimensionReduction.py (PR 458)`

Fixed the dimensionality issue in moments.py (PR 461).

Fixed part of the bug that h5ad file cannot be saved correctly (PR 467).

Fixed the bug that pca_mean will be None under some circumstances (PR 482).

Removing warning message for nxviz (PR 489).

Corrected the norm log-likelihood function (PR 495).

Removed deprecated parameters in gseapy functions (PR 496).

Fixed the bugs that functions will raise error when no fixed points are found in vector field by sampling (PR 501).

Removed unwanted operations in dimension reduction (PR 502).

Tutorial Updates on Readthedocs
Documentation, Tutorials, and readthedocs update:

Update requirements for readthedocs (PR 466).

Update readme (PR 479).

Fixed documentation error caused by importing Literal (PR 486).

Fixed readthedocs error caused by the new version of urllib3 (PR 488).

Other Changes
Docstring and type hints update:

Updated docstring and type hints for tools module (PR 419).

Updated docstring and type hints for vector field module (PR 434).

Updated the docstring and type hints for simulation and predicting module (PR 457).

Update the docstring and type hints for hzplot (PR 456).

v1.2.0

various feature updates / bug fixes since the publication of the paper

v1.1.0

v.1.1.0

update to 1.1.0

v1.0.1-alpha

prepare release for 1.0.9 (1.0.1 tomorrow)

Release v1.0.0

Release 1.0.0