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lmcinnes / umap

Uniform Manifold Approximation and Projection
BSD 3-Clause "New" or "Revised" License
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Name space collision #439

Open tillea opened 4 years ago

tillea commented 4 years ago

Hi, I intend to package umap for official Debian and stumbled upon another software also called umap inside the Debian Med repository. This looks very unfortunate to me and I consider it a good idea to talk to the authors of "the other umap" where I will file an issue as well. Kind regards, Andreas.

lmcinnes commented 4 years ago

Thanks. This is, indeed, an unfortunate situation. The name space of 4 letter acronyms is, it turns out, relatively small. In this case @hoffmanlab was first to the name; unfortunately I come from a mathematics and pure machine learning background, and was unaware of the use of the name in computational biology. To make matters worse there is also geographic mapping software called umap.

In general, where differentiation is required, this package tends to use "umap-learn" to designate itself as distinct from other uses of umap. In particular, since the @hoffmanlab umap was first I would prefer that they get to keep use of the name if any case of disambiguation is required.

tillea commented 4 years ago

On Mon, May 25, 2020 at 11:04:34AM -0700, Leland McInnes wrote:

Thanks. This is, indeed, an unfortunate situation. The name space of 4 letter acronyms is, it turns out, relatively small. In this case @hoffmanlab was first to the name; unfortunately I come from a mathematics and pure machine learning background, and was unaware of the use of the name in computational biology. To make matters worse there is also geographic mapping software called umap.

I can imagine that there are more name space conflicts in free software in general. But having it in the same fiels makes things extra confusing. My actual motivation was that the Debian Med team is running a COVID-19 effort and umap was suggested - but which one?

In general, where differentiation is required, this package tends to use "umap-learn" to designate itself as distinct from other uses of umap. In particular, since the @hoffmanlab umap was first I would prefer that they get to keep use of the name if any case of disambiguation is required.

I'll take over your suggestion and name the Debian package umap-learn. I'd suggest either to rename the package officially or at least suggest the alternative name more prominently.

Thanks a lot for your quick and helpful response in any case.

PS: tbb belongs to the requirements. I have checked https://pypi.org/project/tbb/ but can not find a link to the source which is needed to create a Debian package. Any hint where to find the source?

lmcinnes commented 4 years ago

I would check with numba -- that is the source of the requirement. It may be no longer needed at this point; I haven't checked recently.

tillea commented 4 years ago

On Mon, May 25, 2020 at 02:32:31PM -0700, Leland McInnes wrote:

I would check with numba -- that is the source of the requirement. It may be no longer needed at this point; I haven't checked recently. umap-learn builds without the tbb requirement and passes its test suite and the example runs as well. Id recommend droping the tbb requirement. I have uploaded umap-learn to the Debian new queue. Kind regards, Andreas.

lmcinnes commented 4 years ago

Thanks for lettingme know. I will likely drop it for the next release or so.