Sichao25

Missing LinearODE methods in mix_kin_deg and mix_pulse_chase experiments.

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...

Bug on 3D plots

1

- [ ] The 3D vectors implemented by Plotly don't support customized coloring. Now it utilizes the [built-in color scales](https://plotly.com/python/builtin-colorscales/) for continuous coloring. We should support coloring by a given...

Implement code quality check

1

Check code quality with `black` and `isort` in workflow instead of flake8.

Automatically generated release notes

2

Investigating the possibility of automatically generating release notes. The guide is [here](https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes).

Further optimize Preprocessor

2

- [ ] Allow chunked input - [ ] Speed up with techniques like multiprocessing, numba - [ ] Modualize `select_genes_monocle`

Improvement of Test Files

2

As part of our ongoing effort to enhance the quality and reliability of our project, we should improve our test files to make them well-structured and comprehensive. - [x] Remove...

None object in dictionary will be ignored when saving to h5ad

3

It seems that if we initialize the value in a dictionary `adata.uns[key]` with None, it will be ignored when saving to h5ad. As a result, when we load the file,...

kmc velocity projection method raise ValueError

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...