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theislab / scib-pipeline

Snakemake pipeline that works with the scIB package to benchmark data integration methods.
MIT License
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igraph version conflict #55

Open cdedonno opened 1 year ago

cdedonno commented 1 year ago

Hey! You might want to update the igraph version requirement, it seems that there is a conflict between what the scib package requires and what is specified here.

INFO: pip is looking at multiple versions of trvaep to determine which version is compatible with other requirements. This could take a while.

The conflict is caused by:
    The user requested igraph<0.10
    scib 1.1.3 depends on igraph>=0.10

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

Pip subprocess error:
  Running command git clone --filter=blob:none --quiet https://github.com/theislab/scib.git /tmp/pip-req-build-tp8ds9mf
ERROR: Cannot install -r /home/carlo.dedonno/git_new/immunai-product/research/2023_02_scib_pipelines/scib-pipeline/envs/condaenv.2_jbkacp.requirements.txt (line 1) and igraph<0.10 because these package versions have conflicting dependencies.
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

failed

CondaEnvException: Pip failed
LuckyMD commented 1 year ago

Thanks for the heads up @cdedonno! Is this just a misspecification @mumichae or are we clashign with trvaep dependencies?

cdedonno commented 1 year ago

For what it's worth, I have just commented out the igraph specification here and I could install the package and run the pipeline on the test data.