How poetry add a package along with ignoring dependencies installation?

[mainguyenanhvu]

Hi all,

I would like to use poetry to maintain my codebase. I create a conda env:

conda create -c conda-forge -c psi4 -n test python=3.10 openmm=8.2.0 openmmtools=0.24.2 pymbar=3.0.5 pdbfixer mpich mpi4py rdkit pymol-open-source openmmforcefields openff-toolkit openmoltools openbabel ambertools=24.8 mdanalysis mdtraj psi4 resp

Then, I want to install openrattle via poetry add:

poetry add openprattle

However, it threw an error:

Using version ^1.1.2 for openprattle

Updating dependencies
Resolving dependencies... (1.9s)

Package operations: 2 installs, 0 updates, 0 removals

  - Installing openbabel (3.1.1.1): Failed

PEP517 build of a dependency failed

Backend subprocess exited when trying to invoke build_wheel

    | Command '['/tmp/tmps2g0jzfw/.venv/bin/python', '/home/vumna/.local/share/pypoetry/venv/lib/python3.10/site-packages/pyproject_hooks/_in_process/_in_process.py', 'build_wheel', '/tmp/tmpf0c4bc0g']' returned non-zero exit status 1.
    |
    | /tmp/tmps2g0jzfw/.venv/lib/python3.10/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
    | !!
    |
    |         ********************************************************************************
    |         Please consider removing the following classifiers in favor of a SPDX license expression:
    |
    |         License :: OSI Approved :: GNU General Public License (GPL)
    |
    |         See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
    |         ********************************************************************************
    |
    | !!
    |   self._finalize_license_expression()
    | running bdist_wheel
    | running build
    | running build_ext
    | Warning: invalid version number '3.1.1.1'.
    | Guessing Open Babel location:
    | - include_dirs: ['/tmp/tmps2g0jzfw/.venv/include', '/home/vumna/anaconda3/envs/masterpipeline_dev/include/python3.10', '/usr/local/include/openbabel3']
    | - library_dirs: ['/usr/local/lib']
    | building 'openbabel._openbabel' extension
    | swigging openbabel/openbabel-python.i to openbabel/openbabel-python_wrap.cpp
    | swig -python -c++ -small -O -templatereduce -naturalvar -I/tmp/tmps2g0jzfw/.venv/include -I/home/vumna/anaconda3/envs/masterpipeline_dev/include/python3.10 -I/usr/local/include/openbabel3 -o openbabel/openbabel-python_wrap.cpp openbabel/openbabel-python.i
    |
    | Error: SWIG failed. Is Open Babel installed?
    | You may need to manually specify the location of Open Babel include and library directories. For example:
    |   python setup.py build_ext -I/usr/local/include/openbabel3 -L/usr/local/lib
    |   python setup.py install

Note: This error originates from the build backend, and is likely not a problem with poetry but one of the following issues with openbabel (3.1.1.1)

  - not supporting PEP 517 builds
  - not specifying PEP 517 build requirements correctly
  - the build requirements are incompatible with your operating system or Python version
  - the build requirements are missing system dependencies (eg: compilers, libraries, headers).

You can verify this by running pip wheel --no-cache-dir --use-pep517 "openbabel (==3.1.1.1)".

The author Digichem-Project/openprattle#3 said that I could use pip install --no-deps openprattle to prevent it installing openbabel. This temporarily allows me to work with it.

In the long term, I want to use poetry to maintain stability of my codebase.
Therefore, I would like to ask is there any way to tell poetry add do not re-install openbabel?

Thank you for your help.

[dimbleby]

No