Fail to install seacells via conda due to conflicts in environment.yaml

[ChangSuBiostats]

Hi! I tried to install SEACells via option 2, i.e.

conda env create -n seacells --file environment.yaml
conda activate seacells

However, there seems to be conflicts in the specifications, and below are the error messages from conda.

Any insights will be greatly appreciated!!

Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package fa2-0.3.5-py36h8c4c3a4_0 requires python_abi 3.6.* *_cp36m, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ fa2 is installable with the potential options
│  ├─ fa2 0.3.5 would require
│  │  ├─ python >=3.6,<3.7.0a0  with the potential options
│  │  │  ├─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
│  │  │  └─ python 3.6.12 would require
│  │  │     └─ pypy3.6 7.3.3.* , which can be installed;
│  │  └─ python_abi 3.6.* *_cp36m, which can be installed;
│  ├─ fa2 0.3.5 would require
│  │  ├─ python >=3.10,<3.11.0a0 , which can be installed;
│  │  └─ python_abi 3.10.* *_cp310, which can be installed;
│  ├─ fa2 0.3.5 would require
│  │  ├─ python >=3.11,<3.12.0a0 , which can be installed;
│  │  └─ python_abi 3.11.* *_cp311, which can be installed;
│  ├─ fa2 0.3.5 would require
│  │  ├─ python >=3.7,<3.8.0a0 , which can be installed;
│  │  └─ python_abi 3.7.* *_cp37m, which can be installed;
│  ├─ fa2 0.3.5 would require
│  │  ├─ python >=3.8,<3.9.0a0 , which can be installed;
│  │  └─ python_abi 3.8.* *_cp38, which can be installed;
│  └─ fa2 0.3.5 would require
│     ├─ python >=3.9,<3.10.0a0  with the potential options
│     │  ├─ python [3.9.0|3.9.1|...|3.9.9], which can be installed;
│     │  └─ python 3.9.18 would require
│     │     └─ pypy3.9 7.3.13.* , which can be installed;
│     └─ python_abi 3.9.* *_cp39, which can be installed;
├─ louvain >=0.6,!=0.6.2  is installable with the potential options
│  ├─ louvain 0.6.1 would require
│  │  └─ python_abi * *_cp27mu, which conflicts with any installable versions previously reported;
│  ├─ louvain 0.6.1 would require
│  │  └─ python_abi * *_cp35m, which conflicts with any installable versions previously reported;
│  ├─ louvain 0.6.1, which can be installed;
│  ├─ louvain [0.6.1|0.7.0] would require
│  │  └─ python_abi 3.6.* *_cp36m, which can be installed;
│  ├─ louvain 0.6.1 would require
│  │  └─ python_abi 3.6 *_pypy36_pp73, which can be installed;
│  ├─ louvain [0.6.1|0.7.0|0.7.1|0.8.0] would require
│  │  └─ python_abi 3.7.* *_cp37m, which can be installed;
│  ├─ louvain 0.6.1 would require
│  │  └─ python_abi * *_cp37m, which conflicts with any installable versions previously reported;
│  ├─ louvain [0.6.1|0.7.0|0.7.1|0.8.0|0.8.1] would require
│  │  └─ python_abi 3.8.* *_cp38, which can be installed;
│  ├─ louvain 0.6.1 would require
│  │  └─ python_abi * *_cp38, which conflicts with any installable versions previously reported;
│  ├─ louvain [0.6.1|0.7.0|0.7.1|0.8.0|0.8.1] would require
│  │  └─ python_abi 3.9.* *_cp39, which can be installed;
│  ├─ louvain [0.7.1|0.8.0|0.8.1] would require
│  │  └─ python_abi 3.10.* *_cp310, which can be installed;
│  ├─ louvain 0.7.1 would require
│  │  └─ python_abi 3.7 *_pypy37_pp73, which can be installed;
│  ├─ louvain [0.7.1|0.8.0|0.8.1] would require
│  │  └─ python_abi 3.8 *_pypy38_pp73, which can be installed;
│  ├─ louvain [0.7.1|0.8.0|0.8.1] would require
│  │  └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
│  ├─ louvain 0.8.0 would require
│  │  └─ python_abi 3.11.* *_cp311, which can be installed;
│  └─ louvain 0.8.1 would require
│     ├─ python >=3.11,<3.12.0a0 , which can be installed;
│     └─ python_abi 3.11.* *_cp311, which can be installed;
├─ python 3.5**  is not installable because there are no viable options
│  ├─ python [3.5.1|3.5.2|3.5.3|3.5.4|3.5.5] would require
│  │  └─ python_abi * *_cp35m, which conflicts with any installable versions previously reported;
│  └─ python [3.5.4|3.5.5|3.5.6] conflicts with any installable versions previously reported;
└─ python_abi is requested and can be installed.

[ChangSuBiostats]

This error message seems to suggest that python=3.5 is not compatible with other packages, so I also tried installing it with python=3.8. However, if I do that and try to run SEACell_ATAC_analysis.ipynb, executing

SEACells.plot.plot_2D(atac_ad, key='X_umap', colour_metacells=True)

gives the following error:

>>> SEACells.plot.plot_2D(atac_ad, key='X_umap', colour_metacells=True)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'SEACells' has no attribute 'plot'

Running

SEACells.genescores.prepare_multiome_anndata(atac_ad, rna_ad, SEACells_...

also returns similar messages.

By the way, the row of

SEACells.genescores.prepare_multiome_anndata(atac_ad, rna_ad, SEACells_...

in SEACell_ATAC_analysis.ipynb, chunk 14 is cut off on the right in the pdf generated from Jupyter notebook, so one may not be able to reproduce the analysis.

Thanks! Any insights will be appreciated.

[sitarapersad]

Hi! Sorry for the delay in this, will take a look into it and see what's going on with the 'plot' module!