knn_smooth_chrom error: umap

[bhhlee]

Hi MultiVelo team,

I have imported in the seurat WNN neighbors distance and idx files as numpy arrays, made sure the cell names matched, but when I try to trun the mv.knn_smooth_chrom() function, I get the following error:

TypingError: Failed in nopython mode pipeline (step: nopython frontend)
No conversion from array(float32, 2d, F) to array(float32, 2d, C) for 'knn_dists', defined at None

File "../../../../envs/scvelo/lib/python3.9/site-packages/umap/umap_.py", line 351:
def nearest_neighbors(
    <source elided>

@numba.njit(
^

During: typing of argument at /data/bhlee/envs/scvelo/lib/python3.9/site-packages/umap/umap_.py (351)

File "../../../../envs/scvelo/lib/python3.9/site-packages/umap/umap_.py", line 351:
def nearest_neighbors(
    <source elided>

@numba.njit(
^

It looks like this used to be an issue with the umap package version, but seems like it should have already been solved: lmcinnes/umap#324

I tried downgrading to another umap version as well, but then I can't important multivelo.

Any idea what is going on?

Much appreciated!

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anndata                   0.10.8                   pypi_0    pypi
anyio                     4.4.0                    pypi_0    pypi
argon2-cffi               23.1.0                   pypi_0    pypi
argon2-cffi-bindings      21.2.0                   pypi_0    pypi
array-api-compat          1.8                      pypi_0    pypi
arrow                     1.3.0                    pypi_0    pypi
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4                    pypi_0    pypi
attrs                     23.2.0                   pypi_0    pypi
babel                     2.15.0                   pypi_0    pypi
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
beautifulsoup4            4.12.3                   pypi_0    pypi
bleach                    6.1.0                    pypi_0    pypi
bzip2                     1.0.8                h4bc722e_7    conda-forge
ca-certificates           2024.7.4             hbcca054_0    conda-forge
certifi                   2024.7.4                 pypi_0    pypi
cffi                      1.16.0                   pypi_0    pypi
charset-normalizer        3.3.2                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.1                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
debugpy                   1.8.2            py39h84cc369_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1                    pypi_0    pypi
exceptiongroup            1.2.2                    pypi_0    pypi
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
fastjsonschema            2.20.0                   pypi_0    pypi
fonttools                 4.53.1                   pypi_0    pypi
fqdn                      1.5.1                    pypi_0    pypi
get-annotations           0.1.2                    pypi_0    pypi
h11                       0.14.0                   pypi_0    pypi
h5py                      3.11.0                   pypi_0    pypi
httpcore                  1.0.5                    pypi_0    pypi
httpx                     0.27.0                   pypi_0    pypi
icu                       75.1                 he02047a_0    conda-forge
idna                      3.7                      pypi_0    pypi
importlib-metadata        8.2.0              pyha770c72_0    conda-forge
importlib-resources       6.4.0                    pypi_0    pypi
importlib_metadata        8.2.0                hd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.18.1                   pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
ipywidgets                7.7.1                    pypi_0    pypi
isoduration               20.11.0                  pypi_0    pypi
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4                    pypi_0    pypi
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.25                   pypi_0    pypi
jsonpointer               3.0.0                    pypi_0    pypi
jsonschema                4.23.0                   pypi_0    pypi
jsonschema-specifications 2023.12.1                pypi_0    pypi
jupyter-events            0.10.0                   pypi_0    pypi
jupyter-lsp               2.2.5                    pypi_0    pypi
jupyter-server            2.14.2                   pypi_0    pypi
jupyter-server-terminals  0.5.3                    pypi_0    pypi
jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2            py39hf3d152e_0    conda-forge
jupyterlab                4.2.4                    pypi_0    pypi
jupyterlab-pygments       0.3.0                    pypi_0    pypi
jupyterlab-server         2.27.3                   pypi_0    pypi
jupyterlab-widgets        3.0.11                   pypi_0    pypi
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5                    pypi_0    pypi
krb5                      1.21.3               h659f571_0    conda-forge
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
legacy-api-wrap           1.4                      pypi_0    pypi
libblas                   3.9.0           23_linux64_openblas    conda-forge
libcblas                  3.9.0           23_linux64_openblas    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 14.1.0               h77fa898_0    conda-forge
libgfortran-ng            14.1.0               h69a702a_0    conda-forge
libgfortran5              14.1.0               hc5f4f2c_0    conda-forge
libgomp                   14.1.0               h77fa898_0    conda-forge
libhwloc                  2.11.1          default_hecaa2ac_1000    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
liblapack                 3.9.0           23_linux64_openblas    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.27          pthreads_hac2b453_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libstdcxx-ng              14.1.0               hc0a3c3a_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.7               he7c6b58_4    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
llvmlite                  0.43.0                   pypi_0    pypi
loompy                    3.0.7                    pypi_0    pypi
markupsafe                2.1.5                    pypi_0    pypi
matplotlib                3.9.1                    pypi_0    pypi
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2                    pypi_0    pypi
multivelo                 0.1.3                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
nbclient                  0.10.0                   pypi_0    pypi
nbconvert                 7.16.4                   pypi_0    pypi
nbformat                  5.10.4                   pypi_0    pypi
ncurses                   6.5                  h59595ed_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
networkx                  3.2.1                    pypi_0    pypi
notebook                  7.2.1                    pypi_0    pypi
notebook-shim             0.2.4                    pypi_0    pypi
numba                     0.60.0           py39h0320e7d_0    conda-forge
numpy                     1.26.4                   pypi_0    pypi
numpy-groupies            0.11.1                   pypi_0    pypi
openssl                   3.3.1                h4bc722e_2    conda-forge
overrides                 7.7.0                    pypi_0    pypi
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    2.2.2                    pypi_0    pypi
pandocfilters             1.5.1                    pypi_0    pypi
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
patsy                     0.5.6                    pypi_0    pypi
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.4.0                   pypi_0    pypi
pip                       24.0               pyhd8ed1ab_0    conda-forge
platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge
prometheus-client         0.20.0                   pypi_0    pypi
prompt-toolkit            3.0.47             pyha770c72_0    conda-forge
prompt_toolkit            3.0.47               hd8ed1ab_0    conda-forge
psutil                    6.0.0            py39hd3abc70_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_0    conda-forge
pycparser                 2.22                     pypi_0    pypi
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pynndescent               0.5.13             pyhff2d567_0    conda-forge
pyparsing                 3.1.2                    pypi_0    pypi
python                    3.9.19          h0755675_0_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
python-json-logger        2.0.7                    pypi_0    pypi
python_abi                3.9                      4_cp39    conda-forge
pytz                      2024.1                   pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
pyzmq                     26.0.3           py39ha1047a2_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1                   pypi_0    pypi
requests                  2.32.3                   pypi_0    pypi
rfc3339-validator         0.1.4                    pypi_0    pypi
rfc3986-validator         0.1.1                    pypi_0    pypi
rpds-py                   0.19.1                   pypi_0    pypi
scanpy                    1.10.2                   pypi_0    pypi
scikit-learn              1.5.1            py39hf7b0125_0    conda-forge
scipy                     1.13.1           py39haf93ffa_0    conda-forge
scvelo                    0.3.2                    pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
send2trash                1.8.3                    pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                71.0.4             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.1                    pypi_0    pypi
soupsieve                 2.5                      pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.14.2                   pypi_0    pypi
stdlib-list               0.10.0                   pypi_0    pypi
tbb                       2021.13.0                pypi_0    pypi
terminado                 0.18.1                   pypi_0    pypi
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tinycss2                  1.3.0                    pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1                    pypi_0    pypi
tornado                   6.4.1            py39hd3abc70_0    conda-forge
tqdm                      4.66.4             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316           pypi_0    pypi
typing_extensions         4.12.2             pyha770c72_0    conda-forge
tzdata                    2024.1                   pypi_0    pypi
umap-learn                0.5.6            py39hf3d152e_0    conda-forge
uri-template              1.3.0                    pypi_0    pypi
urllib3                   2.2.2                    pypi_0    pypi
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.6.0                   pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
websocket-client          1.8.0                    pypi_0    pypi
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        3.6.7                    pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
zeromq                    4.3.5                h75354e8_4    conda-forge
zipp                      3.19.2             pyhd8ed1ab_0    conda-forge