ImportError: cannot import name 'Protocol' from 'typing'

[hl-xue]

Hello,

Thanks for the nice pipeline!

I am encountering some issues when running it on your test data.

I cloned your Github main branch and then manually commented the line

  - igraph<0.10

in envs/scib-pipeline-R4.0.yml following an error during installation and the instructions here.

But when I ran the workflow, I got this error:

ImportError: cannot import name 'Protocol' from 'typing'
Traceback (most recent call last):
  File "scripts/integration/runIntegration.py", line 67, in <module>
    runIntegration(file, out, run, hvg, batch, celltype)
  File "scripts/integration/runIntegration.py", line 22, in runIntegration
    integrated = method(adata, batch, celltype)
...

By looking into miniconda3/envs/scib-pipeline-R4.0/lib/python3.7/typing.py, I found a mentioning of:

* The public counterpart of the generics API consists of two classes: Generic and Protocol
  (the latter is currently private, but will be made public after PEP 544 acceptance).

Then I found here that the PEP 544 was supported since Python 3.8.

However, when I tried to change

- python>=3.7

to

- python>=3.8

in the envs/scib-pipeline-R4.0.yml and update the environment, I got a confliction

The following packages are incompatible
├─ bbknn 1.3.9**  is installable with the potential options
│  ├─ bbknn 1.3.9 would require
│  │  ├─ python >=2.7,<2.8.0a0 , which can be installed;
│  │  └─ python_abi 2.7.* *_cp27mu, which can be installed;
│  ├─ bbknn 1.3.9 would require
│  │  ├─ python >=3.6,<3.7.0a0 , which can be installed;
│  │  └─ python_abi 3.6.* *_cp36m, which can be installed;
│  └─ bbknn 1.3.9 would require
│     ├─ python >=3.7,<3.8.0a0 , which can be installed;
│     └─ python_abi 3.7.* *_cp37m, which can be installed;
└─ python >=3.8  is uninstallable because there are no viable options
   ├─ python [3.10.0|3.10.10|...|3.9.7] conflicts with any installable versions previously reported;
   ├─ python [3.10.0|3.10.1|...|3.10.9] would require
   │  └─ python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported;
   ├─ python [3.11.0|3.11.1|3.11.2|3.11.3|3.11.4] would require
   │  └─ python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported;
   ├─ python [3.8.0|3.8.1] would require
   │  └─ python_abi * *_cp38, which conflicts with any installable versions previously reported;
   ├─ python [3.8.10|3.8.12|...|3.8.8] would require
   │  └─ python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported;
   └─ python [3.9.0|3.9.1|...|3.9.9] would require
      └─ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported.

Do you know how should I solve this please?
Also, I would suggest to have a pre-build docker or singularity image of this pipeline if possible, in which anyone can launch the benchmarking without package installation.

[skim245]

@hl-xue did you resolve this issue?
I also face the same error when I try to run the pipeline to include the methods: scanvi, scgen and scvi.
seems like the Protocol from typing is incompatible with Python 3.7