clean the requirements #276
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pydivsufsort is not stable in some OS versions (or systems), so we did not include it as the default reqs. |
| dask==2024.8.0 | ||
| dask_expr==1.1.10 | ||
| pyahocorasick==2.1.0 | ||
| pyteomics==4.7.5 | ||
| lxml==5.3.0 | ||
| lxml==5.3.0 # required by pyteomics |
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Can we still support mzml if we remove it?
I would not want to build and maintain our own mzml reader. But otherwise I’m happy to remove it.
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Maybe it is better to import pyteomics only when we call mzml functionalities. This will not interrupt default workflow if pyteomics has issues.
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This requires by PepXML right? Not pyteomics? Otherwise we can move it into alpharaw
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the error message requiring lxml came from pepxml, yes ..
but pyteomics should be stable if we fix the version, right (like pyteomics==4.7.5)?
on the other hand, people typically use the "loose" version (right, @GeorgWa ;-) )
we could have a separate extra alphabase[mzml] (and [mzml-stable]), such that only then pyteomics and lxml will be installed?
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okay, after some more investigation:
at least alpharaw & peptdeep also have pyteomics/lxml dependency .. so we would make it optional also there (otherwise there's not too much gain)
and: do we want to make it optional at all? are we aware of any downstream packages that always require the mzml extra?
@jalew188 @GeorgWa
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I think mzml will be replaced by binary storage such as hdf5... So I prefer to make it optional. We can support it in the released installers.
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alright, as there's little value (for now) in making mzml optional here, but added complexity, I chose to revert this change for now ..
# Conflicts: # alphabase/psm_reader/msfragger_reader.py # requirements/requirements_development.txt
Clean some unused dependencies
@jalew188 what about pydivsufsort ? this is used by lcp_digest.py but was already commented?