ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it)

[bpavie]

I have just installed CalmAn and get the following error:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[1], [line 28](vscode-notebook-cell:?execution_count=1&line=28)
     26     pass
     27 # import caiman and set up visualization:
---> [28](vscode-notebook-cell:?execution_count=1&line=28) import caiman as cm
     29 from caiman.motion_correction import MotionCorrect
     30 from caiman.source_extraction.cnmf import cnmf, params

File c:\Users\u00xxxxx\.conda\envs\caiman\lib\site-packages\caiman\__init__.py:5
      1 #!/usr/bin/env python
      3 import importlib.metadata
----> [5](file:///C:/Users/u00xxxxx/.conda/envs/caiman/lib/site-packages/caiman/__init__.py:5) from caiman.base.movies import movie, load, load_movie_chain, _load_behavior, play_movie
      6 from caiman.base.timeseries import concatenate
      7 from caiman.cluster import start_server, stop_server

File c:\Users\u0094799\.conda\envs\caiman\lib\site-packages\caiman\base\movies.py:36
     34 import caiman.base.traces
     35 import caiman.mmapping
---> [36](file:///C:/Users/u00xxxxx/.conda/envs/caiman/lib/site-packages/caiman/base/movies.py:36) import caiman.summary_images
     37 import caiman.utils.sbx_utils
     38 import caiman.utils.visualization

File c:\Users\u0094799\.conda\envs\caiman\lib\site-packages\caiman\summary_images.py:18
     16 import caiman
...
     14 from . import online_cnmf

File caiman/source_extraction/cnmf/oasis.pyx:1, in init caiman.source_extraction.cnmf.oasis()

ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).
Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?5d15ebc4-0398-4063-988e-425939fc22d3) or open in a [text editor](command:workbench.action.openLargeOutput?5d15ebc4-0398-4063-988e-425939fc22d3). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...

pip list
Package                   Version
------------------------- -----------
absl-py                   2.3.1
anyio                     4.12.0
argon2-cffi               25.1.0
argon2-cffi-bindings      25.1.0
arrow                     1.4.0
asciitree                 0.3.3
asttokens                 3.0.1
async-lru                 2.0.5
attrs                     25.4.0
av                        16.0.1
babel                     2.17.0
backports.zstd            1.2.0
beautifulsoup4            4.14.3
bleach                    6.3.0
bokeh                     3.8.1
Brotli                    1.2.0
cached-property           1.5.2
caiman                    1.13.0
certifi                   2025.11.12
cffi                      2.0.0
charset-normalizer        3.4.4
colorama                  0.4.6
colorcet                  3.1.0
comm                      0.2.3
contourpy                 1.3.2
coverage                  7.13.0
cycler                    0.12.1
debugpy                   1.8.19
decorator                 5.2.1
defusedxml                0.7.1
exceptiongroup            1.3.1
executing                 2.2.1
fasteners                 0.19
fastjsonschema            2.21.2
filelock                  3.20.1
fonttools                 4.61.1
fqdn                      1.5.1
fsspec                    2025.12.0
h11                       0.16.0
h2                        4.3.0
h5py                      3.15.1
hdmf                      4.1.2
holoviews                 1.22.1
hpack                     4.1.0
httpcore                  1.0.9
httpx                     0.28.1
hyperframe                6.1.0
idna                      3.11
ImageIO                   2.37.2
importlib_metadata        8.7.0
importlib_resources       6.5.2
iniconfig                 2.3.0
ipykernel                 7.1.0
ipyparallel               9.0.2
ipython                   8.37.0
ipywidgets                8.1.8
isoduration               20.11.0
jedi                      0.19.2
Jinja2                    3.1.6
joblib                    1.5.2
json5                     0.12.1
jsonpointer               3.0.0
jsonschema                4.25.1
jsonschema-specifications 2025.9.1
jupyter                   1.1.1
jupyter_bokeh             4.0.5
jupyter_client            8.7.0
jupyter-console           6.6.3
jupyter_core              5.9.1
jupyter-events            0.12.0
jupyter-lsp               2.3.0
jupyter_server            2.17.0
jupyter_server_terminals  0.5.3
jupyterlab                4.5.1
jupyterlab_pygments       0.3.0
jupyterlab_server         2.28.0
jupyterlab_widgets        3.0.16
keras                     3.12.0
kiwisolver                1.4.9
lark                      1.3.1
lazy_loader               0.4
librt                     0.7.4
linkify-it-py             2.0.3
Markdown                  3.10
markdown-it-py            4.0.0
MarkupSafe                3.0.3
matplotlib                3.10.8
matplotlib-inline         0.2.1
mdit-py-plugins           0.5.0
mdurl                     0.1.2
mistune                   3.1.4
ml_dtypes                 0.5.4
mpmath                    1.3.0
msgpack                   1.1.2
munkres                   1.1.4
mypy                      1.19.1
mypy_extensions           1.1.0
namex                     0.1.0
narwhals                  2.14.0
nbclient                  0.10.2
nbconvert                 7.16.6
nbformat                  5.10.4
nest_asyncio              1.6.0
networkx                  3.4.2
notebook                  7.5.1
notebook_shim             0.2.4
numcodecs                 0.13.1
numpy                     2.2.6
opencv-python             4.12.0
opencv-python-headless    4.12.0
optree                    0.18.0
overrides                 7.7.0
packaging                 25.0
pandas                    2.3.3
pandocfilters             1.5.0
panel                     1.8.4
param                     2.3.1
parso                     0.8.5
pathspec                  0.12.1
PeakUtils                 1.3.5
pickleshare               0.7.5
pillow                    12.0.0
PIMS                      0.7
pip                       25.3
platformdirs              4.5.1
pluggy                    1.6.0
prometheus_client         0.23.1
prompt_toolkit            3.0.52
psutil                    7.1.3
pure_eval                 0.2.3
pybind11                  3.0.1
pybind11-global           3.0.1
pycparser                 2.22
Pygments                  2.19.2
pynwb                     3.1.3
pyparsing                 3.2.5
pyqtgraph                 0.14.0
PySide6                   6.10.1
PySocks                   1.7.1
pytest                    9.0.2
pytest-cov                7.0.0
python-dateutil           2.9.0.post0
python-json-logger        2.0.7
pytz                      2025.2
pyviz_comms               3.0.6
PyWavelets                1.8.0
pywin32                   311
pywinpty                  2.0.15
PyYAML                    6.0.3
pyzmq                     27.1.0
referencing               0.37.0
requests                  2.32.5
rfc3339_validator         0.1.4
rfc3986-validator         0.1.1
rfc3987-syntax            1.1.0
rich                      14.2.0
rpds-py                   0.30.0
ruamel.yaml               0.18.16
ruamel.yaml.clib          0.2.14
scikit-image              0.25.2
scikit-learn              1.7.2
scipy                     1.15.3
Send2Trash                1.8.3
setuptools                80.9.0
shiboken6                 6.10.1
six                       1.17.0
slicerator                1.1.0
sniffio                   1.3.1
soupsieve                 2.8
stack_data                0.6.3
sympy                     1.14.0
terminado                 0.18.1
threadpoolctl             3.6.0
tifffile                  2025.5.10
tinycss2                  1.5.1
tomli                     2.3.0
torch                     2.9.1
torchvision               0.24.1
tornado                   6.5.4
tqdm                      4.67.1
traitlets                 5.14.3
typing_extensions         4.15.0
typing_utils              0.1.0
tzdata                    2025.2
uc-micro-py               1.0.3
unicodedata2              17.0.0
uri-template              1.3.0
urllib3                   2.6.2
wcwidth                   0.2.14
webcolors                 25.10.0
webencodings              0.5.1
websocket-client          1.9.0
wheel                     0.45.1
widgetsnbextension        4.0.15
win_inet_pton             1.1.0
xyzservices               2025.11.0
zarr                      2.18.3
zipp                      3.23.0

Any idea ?

Best,
Benjamin

[pgunn]

Hi, how did you install this? Did you build it? If so, did you build it from the dev or main branch?

Only recently did I remove (in dev) the pin on numpy that it be 1.x; all conda versions had that (safe) pin and I've been working on switching it over to numpy2; maybe I missed something. But if you got this built either from main or from the conda packages, that'd be pretty surprising.

[pgunn]

Fixed, I think, in dev with e1da662 (although I am still puzzled how you bumped into this)

[bpavie]

Hi, how did you install this? Did you build it? If so, did you build it from the dev or main branch?

Only recently did I remove (in dev) the pin on numpy that it be 1.x; all conda versions had that (safe) pin and I've been working on switching it over to numpy2; maybe I missed something. But if you got this built either from main or from the conda packages, that'd be pretty surprising.

I did the installation like this:

conda create -n caiman -y python=3.10
conda activate caiman
conda install -y caiman -c conda-forge -c anaconda -c main

The I got the error during the import:

import caiman as cm

[pgunn]

Ah, that's probably not the right thing. You can do all that in one step:

conda create -n caiman -c conda-forge caiman

Maybe your enabling the other channels (which we really don't want enabled) led to the numpy version shift?