OpenMS support

[Arslan-Siraj]

I am trying to add OpenMS support for search engines (.idXML format).
Target to add OpenMS in Oktoberfest.
what I did?

• add openms.py (/spectrum_io/search_result)
  here is dependent pull request initiate OpenMS support spectrum_fundamentals#101

[Arslan-Siraj]

External library pyopenms will require.

[picciama]

Hi @Arslan-Siraj, also thank you here for your contribution. I would also need a unit test so please add it or send me a minimal example file so that I can write one.

[t0mdavid-m]

I think the issue regarding the failing tests is most likely due to this OpenMS/OpenMS#7691. This was fixed in pyopenms 3.2.0.1. Upgrading the version should resolve this.

[picciama]

Hi @t0mdavid-m I cannot install version 3.2.0.1 as it doesn't exist on some package index it seems. I see it in pypi, but I cannot add it to the dependencies as I get:

  RuntimeError

  Unable to find installation candidates for pyopenms (3.2.0.1)

  at ~/miniconda3/envs/oktoberfest/lib/python3.9/site-packages/poetry/installation/chooser.py:74 in choose_for
       70│ 
       71│             links.append(link)
       72│ 
       73│         if not links:
    →  74│             raise RuntimeError(f"Unable to find installation candidates for {package}")
       75│ 
       76│         # Get the best link
       77│         chosen = max(links, key=lambda link: self._sort_key(package, link))
       78│ 

Cannot install pyopenms.

This is why I specifically avoided installing that version. Can you hint me towards the problem?
In my environment, I am using poetry for package dependency management and python 3.9.

[t0mdavid-m]

It looks like we only rebuilt the wheels for windows: https://pypi.org/project/pyopenms/3.2.0.1/#files

Would it be acceptable for you to solve it by setting the requirement to pyopenms>=3.2?

[picciama]

Ok perfect. I realized last time it downloaded version 3.2.0, which still had the problems. This time, it updated to use 3.2.1. I fixed all the remaining issues with tests except the windows issue, which still persists. This has to do with some dynamic DLL linking that doesn't work. Can you check this:

spectrum_io\search_result\openms.py:7: in <module>
    from pyopenms import IdXMLFile, PeptideIdentification, ProteinIdentification
.nox\tests-3-9\lib\site-packages\pyopenms\__init__.py:109: in <module>
    raise e
.nox\tests-3-9\lib\site-packages\pyopenms\__init__.py:67: in <module>
    from ._all_modules import *  # pylint: disable=wildcard-import; lgtm(py/polluting-import)
.nox\tests-3-9\lib\site-packages\pyopenms\_all_modules.py:1: in <module>
    from ._pyopenms_1 import *  # pylint: disable=wildcard-import; lgtm(py/polluting-import)
E   ImportError: DLL load failed while importing _pyopenms_1: A dynamic link library (DLL) initialization routine failed.

needs additional fix

[Arslan-Siraj]

@picciama can you check please? It seems version pyopenms 3.0.0 passed all checks for now.
here merging was done from other branch Arslan-Siraj#5