UMAP compatibility issue
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- Python
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Description
Hi everyone, I'm or RStudio trying to use umap and umap-learn to find out immune clusters but since the last umap package update a keep seing this error:
`flowDF_scaled.umap <- umap(flowDF_scaled, method = "umap-learn", verbose = TRUE)
[2022-02-02 10:45:30] calling umap-learn (v0.5.2)
[2022-02-02 10:45:30] setting arguments: 14
Error in py_call_impl(callable, dots$args, dots$keywords) :
TypeError: ufunc 'bitwise_and' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
Detailed traceback:
File "C:\Users\AppData\Local\R-MINI~ 1\envs\R-RETI~ 1\lib\site-packages\umap\umap_.py", line 2772, in fit_transform
self.fit(X, y)
File "C:\Users\AppData\Local\R-MINI~ 1\envs\R-RETI~ 1\lib\site-packages\umap\umap_.py", line 2563, in fit
raise_disconnected_warning(
File "C:\Users\AppData\Local\R-MINI~ 1\envs\R-RETI~ 1\lib\site-packages\umap\umap_.py", line 117, in raise_disconnected_warning
if verbose & (vertices_disconnected == 0) & (edges_removed > 0):
In addition: Warning message:
In detect.umap.learn(config) :
Detected umap-learn 0.5.2 but last supported version is 0.4;
setting arguments to match version 0.4.
To override this behavior, set config$umap_learn_args manually.`
Can anyone help me?
RStudio 2021.09.2+382 "Ghost Orchid" Release (fc9e217980ee9320126e33cdf334d4f4e105dc4f, 2022-01-04)
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
UMAP version 0.2.7
Reticulate version 1.24
UMAP-Learn version 0.5.2
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the reported traceback in umap/umap_.py, especially fit_transform and raise_disconnected_warning. Reproduce the failure with umap-learn 0.5.2 through the R package and compare it with the package's version-detection warning; done means the compatibility behavior is verified and the reported error no longer occurs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, r
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100