Simplified functions in tutorials and updated some tutorials

[Starlitnightly]

• Fixed a SciPy version compatibility error when using multivelo.
• Added the multi_brain_5k dataset loader to dynamo.sample_data.
• Introduced dyn.pl.trends for plotting gene expression trends (Updated of dynamo 1.4.2 #706).
• Deprecated additional .A attributes on sparse matrices (Updated of dynamo 1.4.2 #706).
• Resolved AnnData version conflicts and added dyn.pl.style() for controlling plot styles.
• Added dyn.pl.jacobian_on_gene_axis to visualize the Jacobian between receptors and effectors (Updated of dynamo 1.4.2 #706).
• Updated the analysis of most probable path predictions.

[Starlitnightly]

We can compare how the tutorial differs before and after the “Most probable path predictions” update:

• Previous tutorial: https://dynamo-release.readthedocs.io/en/latest/tutorials/notebooks/lap_tutorial.html
• Current tutorial: https://dynamo-release-test.readthedocs.io/en/latest/tutorials/notebooks/lap_tutorial.html

[codecov]

Codecov Report

Attention: Patch coverage is 14.06250% with 990 lines in your changes missing coverage. Please review.

Project coverage is 36.80%. Comparing base (0887291) to head (836f788).
Report is 11 commits behind head on master.

Files with missing lines	Patch %	Lines
dynamo/prediction/least_action_path.py	5.66%	383 Missing ⚠️
dynamo/prediction/_tf_eval.py	10.36%	173 Missing ⚠️
dynamo/multivelo/dynamical_chrom_func.py	0.00%	144 Missing ⚠️
dynamo/plot/_trends.py	30.92%	67 Missing ⚠️
dynamo/sample_data.py	10.00%	54 Missing ⚠️
dynamo/pl.py	12.50%	49 Missing ⚠️
dynamo/plot/scVectorField.py	0.00%	24 Missing ⚠️
dynamo/plot/_jacobian.py	17.85%	23 Missing ⚠️
dynamo/utils.py	20.00%	16 Missing ⚠️
dynamo/tools/_enum.py	69.56%	14 Missing ⚠️
... and 10 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #718      +/-   ##
==========================================
- Coverage   37.01%   36.80%   -0.21%     
==========================================
  Files         182      182              
  Lines       34935    35027      +92     
==========================================
- Hits        12931    12892      -39     
- Misses      22004    22135     +131     

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[Copilot]

Pull Request Overview

This pull request primarily improves documentation, adds new plotting functions (trends and jacobian_on_gene_axis), updates compatibility with newer SciPy versions, and simplifies function signatures by removing direct MuData type annotations.

• Fixed compatibility issues (e.g. SciPy version‐based array conversion)
• Added new plotting functionality and deprecated certain attributes
• Simplified type annotations in multiomic functions and updated documentation

Reviewed Changes

Copilot reviewed 33 out of 33 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
dynamo/plot/_trends.py	Added a new function for plotting gene expression trends.
dynamo/plot/_jacobian.py	Introduced a new visualization function to display the Jacobian on gene axis.
dynamo/plot/init.py	Updated exports to include the new trends and jacobian plotting functions.
dynamo/pl.py	Added styling settings and a one-time logo print (ensure prints are intentional).
dynamo/multivelo/old_MultiomicVectorField.py	Simplified the MultiomicVectorField constructor signature; check the isinstance usage.
dynamo/multivelo/old_MultiVelocity.py	Removed MuData type annotations; adjusted related function calls accordingly.
dynamo/multivelo/dynamical_chrom_func.py	Updated sparse matrix access based on SciPy version with appropriate array conversion.
dynamo/MultiVelo.py and other multiomic modules	Updated type annotations and inline MuData imports for consistency.
dynamo/configuration.py	Added documentation improvements and fixed minor comments; check for typos.
docs/conf.py	Added module path debug prints; ensure these prints are not intended for production.
Various GitHub workflows and docs	Updated Python version compatibility and added dynamo-release in requirements.