CODEWITHSUNDEEP
pythoncythonpython-packagingpython-poetry
Theolodus
Theolodus

Reputation: 2172

Poetry add dependency that uses cython

I have a project which needs to depend on the latest commit of pysam, because I'm working in python 3.11.

This means building the package from source, so I do the following:

poetry add git+https://github.com/pysam-developers/pysam

However, I get an error which I think boils down to poetry not including cython in the build environment:

Unable to determine package info for path: /Users/agreen/Library/Caches/pypoetry/virtualenvs/rnacentral-pipeline-GU-1IkEM-py3.11/src/pysam

Fallback egg_info generation failed.

Command ['/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmpw8auvhsm/.venv/bin/python', 'setup.py', 'egg_info'] errored with the following return code 1, and output: 
# pysam: no cython available - using pre-compiled C
Traceback (most recent call last):
  File "/Users/agreen/Library/Caches/pypoetry/virtualenvs/rnacentral-pipeline-GU-1IkEM-py3.11/src/pysam/setup.py", line 345, in <module>
    raise ValueError(
ValueError: no cython installed, but can not find pysam/libchtslib.c.Make sure that cython is installed when building from the repository

Cython is definitely installed, its in the pyproject.toml, and I can call it from the poetry shell, or import it in a python started in the poetry virtualenv. However, If I use the python from the command poetry is running, then indeed cython is not available.

I think I'm missing some configuration of the build, or some extra option to poetry add. The documentation isn't particularly clear about this use of cython - as far as I can tell it's all about using cython in the package I'm writing, which is not quite what I want.

Upvotes: 2

Views: 764

Answers (1)

sinoroc
sinoroc

Reputation: 22305

Cython is a build dependency of pysam, but apparently pysam does not have a pyproject.toml and thus does not declare its build dependencies (Cython and maybe others). So this is a dead end.

If I were you I would build a wheel of pysam myself and tell Poetry to use this wheel until pysam releases wheels for Python 3.11 on PyPI themselves. Or I would use Python 3.10.

It seems like it is being worked on: https://github.com/pysam-developers/pysam/pull/1168

Upvotes: 2

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