Add support for Python 3.12 (also in bioconda)

[Harry-young-0]

Hi , sorry if this is dumb. I'm stumbling at the first hurdle of installation. I've followed the documentation, creating a fresh conda environment using: conda create -n ms2rescore_env python=3.12
then: conda activate ms2rescore_env
install ms2rescore goes like this:

(ms2rescore_env) C:\Users\harry\Documents\local_work_folder\sheona_data_output>conda install -c bioconda ms2rescore
Channels:

• bioconda
• defaults
• conda-forge
  Platform: win-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides ms2pip >=4.0.0-dev4 needed by ms2rescore-3.0.0-pyhdfd78af_0

Could not solve for environment specs
The following packages are incompatible
└─ ms2rescore is not installable because there are no viable options
├─ ms2rescore [3.0.0|3.0.0b1|3.0.1] would require
│ └─ ms2pip >=4.0.0-dev4 , which does not exist (perhaps a missing channel);
└─ ms2rescore [3.0.1|3.0.2|3.0.3] would require
└─ ms2pip >=4.0.0-dev8 , which does not exist (perhaps a missing channel).

Figured it might need ms2pip installing separately and got this:
(ms2rescore_env) C:\Users\harry\Documents\local_work_folder\sheona_data_output>conda install -c bioconda ms2pip
Channels:

• bioconda
• defaults
• conda-forge
  Platform: win-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

• ms2pip

Current channels:

• https://conda.anaconda.org/bioconda
• defaults
• https://conda.anaconda.org/conda-forge/noarch
• https://conda.anaconda.org/conda-forge/win-64

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Any ideas? (I'm on windows if that means anything)

[Harry-young-0]

I should add, I get essentially the same error with pip : "note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pandas
Failed to build ms2pip pandas
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (ms2pip, pandas)"

[Harry-young-0]

I may be being an idiot, seen a closed comment saying that ms2pip is not supporting windows anymore. Is this still the case?

[RalfG]

Hi @Harry-young-0,

Thanks for reaching out!

It seems like MS²PIP is only available for Python 3.10 on Bioconda (https://bioconda.github.io/recipes/ms2pip/README.html). I will try to add builds for more Python versions. 3.11 should definitely be supported; 3.12 might depend on the availability of dependencies.

For now, you could try make an environment with Python 3.10.

Let us know if you have further questions.

Best,
Ralf

[RalfG]

Support for Python 3.12 should be added in #228, which adds support for Numpy and Pandas 2. However, those are currently blocked by an incompatibility in pyOpenMS (OpenMS/OpenMS#7600).