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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Issue installing scenicplus #383

Closed jkanche closed 1 month ago

jkanche commented 1 month ago

Describe the bug Installing the package following the instructions in the README results in an error.

To Reproduce

mamba env create --n scenicplus python=3.11 -y
mamba activate scenicplus
git clone https://github.com/aertslab/scenicplus
pip install .

Error output

  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/scenicplus /tmp/pip-install-af_tbwts/scenicplus_e3a745a0e6cc4ddb9d5b75bf4b998d9a
  error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [8 lines of output]
      Collecting numpy>=1.17
        Using cached numpy-1.24.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB)
      Using cached numpy-1.24.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
      Installing collected packages: numpy
      Successfully installed numpy-1.24.4
      error in MACS2 setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Expected end or semicolon (after name and no valid version specifier)
          numpy>=>=1.17
               ^
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

failed

CondaEnvException: Pip failed
jkanche commented 1 month ago

after trying to resolve this a bit: 

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

The conflict is caused by:
    The user requested pyscenic 0.12.1+8.gd2309fe (from git+https://github.com/aertslab/pySCENIC#egg=pyscenic)
    pycistopic 2.0a0 depends on pyscenic
    scenicplus 1.0a1 depends on pyscenic 0.12.1+8.gd2309fe (from git+https://github.com/aertslab/pySCENIC@master)
SeppeDeWinter commented 1 month ago

Hi @jkanche

This issue arrises when MACS2 version <2.2.8 is trying to be installed. You can patch this version of MACS2, see https://github.com/aertslab/scenicplus/issues/101. However, this version should not be installed at all. It is set to version 2.2.9.1 in the requirements.txt file.

I'm also unable to reproduce your issue:


mamba create --name issue_383 python=3.11 -y
mamba activate issue_383
git clone https://github.com/aertslab/scenicplus
cd scenicplus
pip install . --no-cache-dir

Best,

Seppe

jkanche commented 1 month ago

seems like it was caused by another underlying dependency. Thank you for looking into this