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iomega / spec2vec

Word2Vec based similarity measure of mass spectrometry data.
Apache License 2.0
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Update to latest matchms, gensim and poetry buildsystem #95

Open hechth opened 2 months ago

hechth commented 2 months ago

This PR supercedes #93, #90, #74 and also #64 .

This includes the new poetry buildsystem for spec2vec as well as an update to work with the latest version of matchms. I also added support for sparse computations.

So I think once this PR is merged all other PRs can be closed.

hechth commented 2 months ago

@niekdejonge this is ready for review

niekdejonge commented 2 months ago

@hechth Looks good, thanks! I added a few comments, with a few small changes. I did approve the tests running: https://github.com/iomega/spec2vec/actions/runs/10367293699/job/28705599784 but it seems there is still something going wrong with the pyproject.toml file. Or did the tests not run in the latest version of the PR?

hechth commented 2 months ago

@niekdejonge some tests were broken so maybe you can rerun?

hechth commented 2 months ago

No idea what is wrong with the linting, I think it might be actually something with prospector itself.

niekdejonge commented 2 months ago

@hechth linting passes, but I don't have the rights to add secrets to fix the sonarcloud issue. I have now just removed sonarcloud and created an issue #96 to repair this in the future again.

niekdejonge commented 2 months ago

The issue with Pypi is an open issue: https://github.com/pypa/readme_renderer/issues/304