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compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
https://ms2pip.readthedocs.io
Apache License 2.0
38 stars 18 forks source link

Add support for Python 3.12 (also in bioconda) #230

Open Harry-young-0 opened 2 weeks ago

Harry-young-0 commented 2 weeks ago

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:

LibMambaUnsatisfiableError: Encountered problems while solving:

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:

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

Current channels:

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 commented 2 weeks ago

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 commented 2 weeks ago

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

RalfG commented 5 days ago

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 commented 5 days ago

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).