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Installation fails with conflicting dependencies error#7

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mscheremetjew wants to merge 2 commits into
BioComputingUP:mainfrom
mscheremetjew:main
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Installation fails with conflicting dependencies error#7
mscheremetjew wants to merge 2 commits into
BioComputingUP:mainfrom
mscheremetjew:main

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How to reproduce?

Install Python version 3.12 and source the environment.

When running:
pip install .
within the checkout clone directory, we get the following error:

Error thrown:

When installing MobiDB-lite locally we get the following error:

ERROR: Cannot install -r requirements.txt (line 2) and numpy==2.3.2 because these package versions have conflicting dependencies.

The conflict is caused by:
The user requested numpy==2.3.2
numba 0.61.2 depends on numpy<2.3 and >=1.24

Additionally, some packages in these conflicts have no matching distributions available for your environment:
numpy

To fix this you could try to:

  1. loosen the range of package versions you've specified
  2. remove package versions to allow pip to attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

Suggested fix

We applied a few fixes to the installation configuration, e.g. made optional dependencies mandatory, specified supported Python versions within toml file and also moved all required dependencies to the toml file.

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