Outdated environemnt files

[VladimirShitov]

Describe the bug

I faced some issues when trying to use an environment file for differential expression analysis. Many of them were caused by an old pertpy version (0.5.0). And a newer version can't be installed because of an old Python requirement (v. 3.9) in the environment file, while the new version of pertpy requires at least 3.10. I find environment files highly valuable (especially those containing R packages) and wish they were up to date.

To Reproduce

Steps to reproduce the behavior:

1. Download the environment file from the chapter "Dealing with conditions"
2. Run conda env create -f differential_gene_expression.yml
3. Try to import the packages from the first cell in the corresponding chapter. I did not succeed.

The following environment file worked for me:

name: differential-gene-expression
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - conda-forge::python=3.10
  - conda-forge::scanpy=1.9.1
  - conda-forge::r-base=4.2.2
  - bioconda::bioconductor-mast=1.24.0
  - bioconda::bioconductor-edger=3.40.0
  - bioconda::bioconductor-singlecellexperiment=1.20.0
  - conda-forge::r-lme4
  - conda-forge::notebook
  - conda-forge::rpy2=3.5.6
  - bioconda::anndata2ri=1.1
  - conda-forge::pip
  - pip:
      - sc-toolbox
      - pertpy==0.9.5

I am, however, not sure that it allows to reproduce the content in the chapter, so I opened an issue instead of PR. Glad to provide more information if needed!

[Zethson]

We are working on updating ALL environments in Q1/Q2 this year. Sorry that this is a pain

[VladimirShitov]

Thanks, looking forward to it!