Getting the error: "numba.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)" when running sc.tl.umap with init_pos='paga'

Hi,

I’m trying to follow the Dahlin18 PAGA tutorial

And in the part where it calls the UMAP function providing it with the PAGA initial points (line 28 in the notebook: sc.tl.umap(adata, init_pos='paga')), I’m getting this error message:

computing UMAP
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/nr/miniconda3/lib/python3.7/site-packages/scanpy/tools/_umap.py", line 145, in umap
    verbose=settings.verbosity > 3,
  File "/home/nr/miniconda3/lib/python3.7/site-packages/umap/umap_.py", line 1005, in simplicial_set_embedding
    verbose=verbose,
  File "/home/nr/miniconda3/lib/python3.7/site-packages/numba/dispatcher.py", line 401, in _compile_for_args
    error_rewrite(e, 'typing')
  File "/home/nr/miniconda3/lib/python3.7/site-packages/numba/dispatcher.py", line 344, in error_rewrite
    reraise(type(e), e, None)
  File "/home/nr/miniconda3/lib/python3.7/site-packages/numba/six.py", line 668, in reraise
    raise value.with_traceback(tb)
numba.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Invalid use of type(CPUDispatcher(<function rdist at 0x7f8ffd913050>)) with parameters (array(float64, 1d, C), array(float32, 1d, C))
Known signatures:
 * (array(float32, 1d, A), array(float32, 1d, A)) -> float32
 * parameterized
[1] During: resolving callee type: type(CPUDispatcher(<function rdist at 0x7f8ffd913050>))
[2] During: typing of call at /home/nr/miniconda3/lib/python3.7/site-packages/umap/umap_.py (795)


File "miniconda3/lib/python3.7/site-packages/umap/umap_.py", line 795:
def optimize_layout(
    <source elided>

                dist_squared = rdist(current, other)
                ^

This is not usually a problem with Numba itself but instead often caused by
the use of unsupported features or an issue in resolving types.

To see Python/NumPy features supported by the latest release of Numba visit:
http://numba.pydata.org/numba-doc/latest/reference/pysupported.html
and
http://numba.pydata.org/numba-doc/latest/reference/numpysupported.html

For more information about typing errors and how to debug them visit:
http://numba.pydata.org/numba-doc/latest/user/troubleshoot.html#my-code-doesn-t-compile

If you think your code should work with Numba, please report the error message
and traceback, along with a minimal reproducer at:
https://github.com/numba/numba/issues/new

I saw a relevant issue on the umap package and even changed line 1138 in umap_.py from embedding to embedding..astype(np.float32, copy=True), but no success.

Any idea?

Thanks!

[ndrubins]

Yes. Within the implementation of the simplicial_set_embedding function in the umap_.py file (in my system it is located at: ~/miniconda3/lib/python3.7/site-packages/umap/umap_.py), I type-casted the embedding objects to astype(np.float32, copy=False) from within the call to the optimize_layout function: lines 1137 and 1138 in umap_.py are thus changed from: embedding, embedding

to: embedding.astype(np.float32, copy=False), embedding.astype(np.float32, copy=False)

[flying-sheep]

Thanks for the info! So lmcinnes/umap#179 needs to be reopened?