Consider removing FA2 as a dependency as it is not actively maintained and does not pip install from PyPI on Python 3.9+

[dburkhardt]

Describe the bug
To reproduce

1. Have Python 3.9.15
2. Build scenicplus from source
3. Install fails at fa2 dependency due to Problem installing fa2 on Python3.9 bhargavchippada/forceatlas2#34

Workaround:

1. Build fa2 from source
2. Build scenicplus from source

Error output
See bhargavchippada/forceatlas2#34

Additional context

• Last commit to fa2 is from December 2020 and last release is from Jan 2019
• The lead dev of fa2 acknowledges they are not actively maintaining the package: Status / getting things moving again bhargavchippada/forceatlas2#38
• This was also an issue in scenicplus and they removed the dependency: Consider removing FA2 as a dependency as it is not actively maintained and does not pip install from PyPI on Python 3.9+ aertslab/scenicplus#92

[KenjiKamimoto-ac]

@dburkhardt

Thank you for your feedback.
I'll look into it.

CellOracle is developed and tested with Python 3.8 and is not currently guaranteed for Python 3.9.
Can you please use python 3.8 for now? But we will test newer version of python including dependencies as soon as possible!

[dburkhardt]

Hi Kenji, thanks for the prompt response!

Where is fa2 used in the code base? I don't see it when I search.

Regarding 3.8, this is now an outdated release for Python. The current stable release is 3.9 and the latest release is 3.11. If this is the only thing keeping you using an outdated release, why not remove?

[KenjiKamimoto-ac]

The force-directed graph is used in our tutorial preparing celloracle input data.

https://morris-lab.github.io/CellOracle.documentation/notebooks/03_scRNA-seq_data_preprocessing/scanpy_preprocessing_with_Paul_etal_2015_data.html

[dburkhardt]

If it's just in the tutorial for pre-processing scRNA, why not just ask people to install it in the notebook like you do with the ATAC base-grn pre-processing tools cicero and monocle3?

It's not really required to use CellOracle, right? From what I can tell, this is the only thing keeping CellOracle from being compatible with the current stable Python release.

[KenjiKamimoto-ac]

Yes, it is not CellOracle itself. The scRNA-seq data preparation step is a necessary step, and I've listed it on the celloracle requirements, but I can remove it and just recommend user to install fa manually.

The fa2 is not the reason why use python3.8. We are working hard to update the package, but it is always taking time to keep python's latest release. Can you please use python 3.8 for now? We will test the newer version of python, including dependencies, as soon as possible.
Do you have any problem with python3.8? Please let me know if you have another issue. It will help us improve codes!

[KenjiKamimoto-ac]

@dburkhardt

For the celloracle next release, 0.10.16, I will remove fa2 from the requirements and
add instructions to install fa2 manually on the tutorial documentation.
That is a relatively easy task! (I already updated requirement file on github repo.)
I'm planning to release cellorace 0.10.16 next week on PyPI!

I think I still need to check some things to support python3.9 or later, but we will do it as soon as possible.

Sorry for the inconvenience! And thanks a lot for your feedback!

[dburkhardt]

Great! For reference, I'm using CellOracle on Python 3.9.15 and it works fine.