issue with required scanpy = 1.5.1

[mistrm82]

Hi, I am trying to setup a conda environment with libraries listed in requirements.txt.

scanpy 1.5.1 gives the following error as there are no viable options given the version requirements for python 3.8 and anndata

└─ scanpy 1.5.1**  is not installable because it requires
   └─ anndata >=0.7  but there are no viable options
      ├─ anndata [0.7|0.7.1|...|0.7.6] would require
      │  └─ python >=3.6,<3.7.0a0 , which conflicts with any installable versions previously reported;
      ├─ anndata [0.7|0.7.1|...|0.8.0] would require
      │  └─ python >=3.7,<3.8.0a0 , which conflicts with any installable versions previously reported;
      ├─ anndata [0.7.1|0.7.3|...|0.9.2] conflicts with any installable versions previously reported;
      ├─ anndata [0.7.4|0.7.5|...|0.8.0] would require
      │  └─ python >=3.9,<3.10.0a0 , which conflicts with any installable versions previously reported;
      ├─ anndata [0.7.8|0.8.0] would require
      │  └─ python >=3.10,<3.11.0a0 , which conflicts with any installable versions previously reported;
      └─ anndata [0.10.0|0.10.1|...|0.10.9] would require
         └─ python >=3.9  but there are no viable options
            ├─ python [3.10.0|3.10.1|...|3.10.9] conflicts with any installable versions previously reported;
            ├─ python [3.11.0|3.11.1|...|3.12.5] conflicts with any installable versions previously reported;
            ├─ python [3.9.0|3.9.1|...|3.9.9] conflicts with any installable versions previously reported;
            └─ python [3.12.0rc3|3.13.0rc1|3.13.0rc2] would require
               └─ _python_rc, which does not exist (perhaps a missing channel).

[JiazhangCai]

Hi, thanks for your comment! The issue you met seems caused by the incorrect version of anndata, which is a key package for scanpy. I recommend you check if the version meets the requirements of the method.

[mistrm82]

As per the requirements I have anndata 0.6.22.post1 installed - however from my post above you can see that scanpy needs anndata >=0.7

[mistrm82]

HI @JiazhangCai I don't think this requirements file is accurate as I am having many issues with packages

[JiazhangCai]

Hi @mistrm82. Thanks for your comment! I will double-check the files and tutorials and update the file if there are any needed modifications. Besides, the correlated paper will be published soon. A more detailed tutorial will come along soon as well.