Issues in MacOS

[odrangel7]

Hi, I am not sure if this has been tested on MacOS but i experience issues when working with the package. Mainly when trying to load mzML files. Perhaps this a known issue?

Best,
Oscar

[roman-bushuiev]

Hi @odrangel7, the package was developed and tested mainly on macOS. Could you specify your issue or provide a minimal example to reproduce it?

[odrangel7]

Thanks for the swift reply. My setup is Sequoia 15.5 installing the environment through terminal using conda. To run the code i used both VS Code and Jupyter notebook. When running the first example, things work fine:
from dreams.api import dreams_embeddings
embs = dreams_embeddings('/Users/odrangel/DreaMS/data/examples/example_5_spectra.mgf')

However, when jumping to the next step:
from dreams.utils.data import MSData
msdata = MSData.from_mzml('/Users/odrangel/DreaMS/data/examples/G87351_1x_BE8_01_26057.mzML')

I obtained this according to the log:
12:23:30.791 [error] Unable to determine site packages path for python /opt/miniconda3/envs/dreams/bin/python (Conda)
12:23:30.793 [info] Process Execution: /opt/miniconda3/envs/dreams/bin/python -c "import ipykernel; print(ipykernel.version); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.file)"
12:23:30.794 [info] Process Execution: /opt/miniconda3/envs/dreams/bin/python -m ipykernel_launcher --f=~/Library/Jupyter/runtime/kernel-v3367b152e3119b0f49d2468bc7efcf37ee7f4e7aa.json
> cwd: /
12:23:31.715 [info] Restarted a006901e-2db0-48c6-b86b-06d8d3f8cf3c
12:23:44.796 [error] Disposing session as kernel process died ExitCode: undefined, Reason:

When working with other functions it is working properly. So as i mention, the issue seems to be related to handling mzML files.
Please let me know if you need further details.

Best,
Oscar

[roman-bushuiev]

Hi Oscar, based on this line 12:23:30.791 [error] Unable to determine site packages path for python /opt/miniconda3/envs/dreams/bin/python (Conda) it looks like some conda environment installation issue. Could you please try to reinstall the environment?

[odrangel7]

Hi again, I tried your suggestion, several times. It face the same issue when loading mzML files. Then i tried other functions to see if I face any other issue and i can see that for example I can load hdf5 and mgf files but when i want to visualize embeddings i face a different issue. Here i attach what i obtained when processing.

Best

[roman-bushuiev]

Hi @odrangel7. Sorry for the late reply, I couldn't respond because of the Metabolomics 2025 conference. How big is your .mzML file? Both errors say that the Jupyter notebook kernel dies which could be simply a result of loading too big files. For example, MassSpecGym_DreaMS file (second error) is quite big: 230k spectra along with their DreaMS embeddings.