dynamo-release

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Migrate to Numpy 2.0.0

1

Numpy made a [major release](https://numpy.org/doc/stable/release/2.0.0-notes.html) with a large number of breaking changes one week ago. We need to update our API accordingly.

Sichao25

Debug `pl.circosPlot()`

1

Bug: description: The latest changes in Matplotlib require specifying the axes when creating a colorbar, which is causing an error in `nxviz.annotate.node_colormapping`

Sichao25

See this [issue](https://github.com/aristoteleo/dynamo-release/issues/680).

Sichao25

gene names missing when using dyn.pl.highest_frac_genes

1

orient ='h' is ok but 'v' is problematic. probably there should be get_xlim and get_xticks https://github.com/aristoteleo/dynamo-release/blob/2e7eb21b22c20e385853fbfb1a32aba745627e3f/dynamo/plot/preprocess.py#L936 and https://github.com/aristoteleo/dynamo-release/blob/2e7eb21b22c20e385853fbfb1a32aba745627e3f/dynamo/plot/preprocess.py#L937 ``` dyn.pl.highest_frac_genes(adata, figsize=(6, 4),orient='v') ``` 

chansigit

Input X contains NaN.

5

dyn.tl.cell_velocities(adata, method='kmc', other_kernels_dict={'transform': 'sqrt'}) raise 'Input X contains NaN.'

christophechu

LinAlgError when running dyn.tl.dynamics()

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### Discussed in https://github.com/aristoteleo/dynamo-release/discussions/423 Originally posted by **Ckenen** September 21, 2022 When I run dyn.tl.dynamics(adata, group="group", NTR_vel=True), it will raise LinAlgError: SVD did not converge. However, if I do not...

nprashant2001

Failed building wheel for louvain when I tried to install dynamo-release

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Hi Xiaojie, I have trouble installing dynamo-release. I used pip install command and the installation interrupted because of failed building wheel for louvain. I did the screen shot and attach...

ruifengy

Can't get dyn.tl.dynamics(adata) to work

2

- [x] I am sure this issue is not simply a general python programming problem (if so, please google the answers). - [x] I have searched github issues and confirm...

wodigraf

Dropbox link in ERCC relative2abs is no longer available.

1

a minor issue: the dropbox link to the ERCC file became invalid. https://github.com/aristoteleo/dynamo-release/blob/a5a199886f83b96983858d1c1f81ea358ce9b62d/dynamo/preprocessing/utils.py#L844

chansigit

Optimize the display of the tutorial page and add `adjust_legend` argument

2

The new tutorial could be found in https://dynamo-release-test.readthedocs.io/en/latest/index.html. 1. It is important to note that the notebook for this tutorial depends on [dynamo-tutorials](https://github.com/aristoteleo/dynamo-tutorials/), but there are some issues related to...

Starlitnightly