search

ISA-tools / mzml2isa

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure
GNU General Public License v3.0
12 stars 6 forks source link

add support for Python 3.10 #47

Closed proccaserra closed 1 year ago

proccaserra commented 1 year ago

requires upgrading Pronto ontology parsing component from v=0.12 to v2.5.0

currently, code breaks here: https://github.com/ISA-tools/mzml2isa/blob/acf4220d000418776006b3c89c1014c4f658c30d/mzml2isa/mzml.py#L105

@althonos @Tomnl any hint regarding the pronto changes?

althonos commented 1 year ago

I'll have a look, I think I need to cache some more things wrt pronto because of performance issues with the newer versions :+1:

proccaserra commented 1 year ago

@althonos Thx for the super swift feedback! We are looking at making a release of the ISA-API and adding support for 3.10. @terazus has a fix for pronto 0.12.2 (see below) but since pronto is at 2.5.0 (scream) ! makes little sense to send a PR :).

Line 28: Class Ontology( collections.abc.mappings) instead of Class Ontology(collections.mappings) in Ontology.py in the library.

So we have a fix but can't release.

Please let us how busy you are the moment! ATB

terazus commented 1 year ago

Hello, The problem seems to be originating from the version of pronto that mzml2isa uses. It's old and a bit outdated but can be easily modified to fit our needs. The version of pronto is 0.12.2. In Ontology.py the Ontology class inheritance needs to be changed from collections.mapping to collections.abc.mapping or typing.mapping.

Hope this can help to make a quick fix.

althonos commented 1 year ago

Do you want me to make a new release?

proccaserra commented 1 year ago

@althonos only if you have time ! either way, many thanks for the quick fix to the library.

Tomnl commented 1 year ago

Thanks @althonos for sorting this!