iomega
Update to latest matchms, gensim and poetry buildsystem
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 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?
No idea what is wrong with the linting, I think it might be actually something with prospector itself.
@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.
The issue with Pypi is an open issue: https://github.com/pypa/readme_renderer/issues/304
@hechth This is currently stalled as it is waiting for Gensim 4.4 which should be compatible with numpy>2 and scipy>1.14, which will bring the gensim dependencies in line with matchms dependencies. Then this PR can be merged and spec2vec can be finally updated.
@hechth @niekdejonge gensim 4.4.0 with numpy 2 and Python 3.13 is out (not on conda yet). I added a PR to update versions. Tests are passing.
