Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Can't build wheel for h5py #346

Open
NilsNyberg opened this issue Feb 6, 2024 · 1 comment
Open

Can't build wheel for h5py #346

NilsNyberg opened this issue Feb 6, 2024 · 1 comment

Comments

@NilsNyberg
Copy link

NilsNyberg commented Feb 6, 2024 •
edited
Loading

I am trying to run this notebook using the dandi jupyterhub:
https://alleninstitute.github.io/openscope_databook/visualization/visualize_neuropixel_probes.html

However, in the first cell, when running:

try:
    from dandi_utils import dandi_stream_open
except:
    !git clone https://github.com/AllenInstitute/openscope_databook.git
    %cd openscope_databook
    %pip install -e .

I get error:

fatal: destination path 'openscope_databook' already exists and is not an empty directory.
/home/jovyan/openscope_databook/docs/visualization/openscope_databook
Obtaining file:///home/jovyan/openscope_databook/docs/visualization/openscope_databook
  Preparing metadata (setup.py) ... done
Collecting ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458 (from databook-utils==1.0.0)
  Using cached ophys_nway_matching-0.6.0-py3-none-any.whl
Collecting ccfwidget==0.5.3 (from databook-utils==1.0.0)
  Using cached ccfwidget-0.5.3-py3-none-any.whl (9.7 kB)
Collecting cebra (from databook-utils==1.0.0)
  Using cached cebra-0.4.0-py2.py3-none-any.whl.metadata (5.8 kB)
Collecting dandi==0.55.1 (from databook-utils==1.0.0)
  Using cached dandi-0.55.1-py3-none-any.whl.metadata (7.6 kB)
Collecting elephant==0.12.0 (from databook-utils==1.0.0)
  Using cached elephant-0.12.0-cp311-cp311-linux_x86_64.whl
Collecting fsspec==2022.11.0 (from databook-utils==1.0.0)
  Using cached fsspec-2022.11.0-py3-none-any.whl (139 kB)
Collecting h5py==3.7 (from databook-utils==1.0.0)
  Using cached h5py-3.7.0.tar.gz (392 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting jupyter==1.0.0 (from databook-utils==1.0.0)
  Using cached jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)
Collecting matplotlib==3.6.2 (from databook-utils==1.0.0)
  Using cached matplotlib-3.6.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.8 MB)
Collecting mpl-interactions==0.22.0 (from databook-utils==1.0.0)
  Using cached mpl_interactions-0.22.0-py3-none-any.whl (47 kB)
Requirement already satisfied: neo==0.12.0 in /opt/conda/lib/python3.11/site-packages (from databook-utils==1.0.0) (0.12.0)
Requirement already satisfied: numpy in /opt/conda/lib/python3.11/site-packages (from databook-utils==1.0.0) (1.24.4)
Collecting nwbwidgets==0.10.0 (from databook-utils==1.0.0)
  Using cached nwbwidgets-0.10.0-py3-none-any.whl (67 kB)
Collecting pandas==1.5.2 (from databook-utils==1.0.0)
  Using cached pandas-1.5.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.0 MB)
Collecting Pillow==9.3.0 (from databook-utils==1.0.0)
  Using cached Pillow-9.3.0-cp311-cp311-manylinux_2_28_x86_64.whl (3.3 MB)
Collecting pynwb==2.2.0 (from databook-utils==1.0.0)
  Using cached pynwb-2.2.0-py3-none-any.whl (126 kB)
Requirement already satisfied: quantities==0.14.1 in /opt/conda/lib/python3.11/site-packages (from databook-utils==1.0.0) (0.14.1)
Collecting scikit-image==0.19.3 (from databook-utils==1.0.0)
  Using cached scikit_image-0.19.3-cp311-cp311-linux_x86_64.whl
Collecting scipy==1.9.3 (from databook-utils==1.0.0)
  Using cached scipy-1.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (33.4 MB)
Requirement already satisfied: statsmodels==0.14.0 in /opt/conda/lib/python3.11/site-packages (from databook-utils==1.0.0) (0.14.0)
Collecting suite2p==0.12.1 (from databook-utils==1.0.0)
  Using cached suite2p-0.12.1-py3-none-any.whl (648 kB)
Collecting tensortools==0.4 (from databook-utils==1.0.0)
  Using cached tensortools-0.4-py3-none-any.whl
Collecting zarr==2.13.3 (from databook-utils==1.0.0)
  Using cached zarr-2.13.3-py3-none-any.whl (191 kB)
Requirement already satisfied: dask in /opt/conda/lib/python3.11/site-packages (from ccfwidget==0.5.3->databook-utils==1.0.0) (2023.10.0)
Collecting ipytree (from ccfwidget==0.5.3->databook-utils==1.0.0)
  Using cached ipytree-0.2.2-py2.py3-none-any.whl (1.3 MB)
Requirement already satisfied: itkwidgets>=0.30.1 in /opt/conda/lib/python3.11/site-packages (from ccfwidget==0.5.3->databook-utils==1.0.0) (0.32.4)
Requirement already satisfied: toolz in /opt/conda/lib/python3.11/site-packages (from ccfwidget==0.5.3->databook-utils==1.0.0) (0.12.0)
Requirement already satisfied: xarray in /opt/conda/lib/python3.11/site-packages (from ccfwidget==0.5.3->databook-utils==1.0.0) (2023.10.1)
Requirement already satisfied: requests in /opt/conda/lib/python3.11/site-packages (from ccfwidget==0.5.3->databook-utils==1.0.0) (2.31.0)
Requirement already satisfied: appdirs in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (1.4.4)
Requirement already satisfied: bidsschematools~=0.7.0 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.7.2)
Requirement already satisfied: click in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (8.1.7)
Requirement already satisfied: click-didyoumean in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.3.0)
Requirement already satisfied: dandischema~=0.8.0 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.8.4)
Requirement already satisfied: etelemetry>=0.2.2 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.3.1)
Requirement already satisfied: fasteners in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.17.3)
Requirement already satisfied: fscacher>=0.3.0 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.4.0)
Requirement already satisfied: hdmf!=3.5.0 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (3.11.0)
Requirement already satisfied: humanize in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (4.8.0)
Requirement already satisfied: interleave~=0.1 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.2.1)
Requirement already satisfied: joblib in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (1.3.2)
Requirement already satisfied: keyring!=23.9.0 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (24.2.0)
Requirement already satisfied: keyrings.alt in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (4.2.0)
Requirement already satisfied: packaging in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (23.2)
Requirement already satisfied: pycryptodomex in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (3.19.0)
Requirement already satisfied: pydantic>=1.9.0 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (1.10.13)
Requirement already satisfied: nwbinspector>=0.4.28 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.4.31)
Requirement already satisfied: pyout!=0.6.0,>=0.5 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.7.3)
Requirement already satisfied: python-dateutil in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (2.8.2)
Requirement already satisfied: ruamel.yaml<1,>=0.15 in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.17.39)
Requirement already satisfied: semantic-version in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (2.10.0)
Requirement already satisfied: tenacity in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (8.2.3)
Requirement already satisfied: zarr-checksum in /opt/conda/lib/python3.11/site-packages (from dandi==0.55.1->databook-utils==1.0.0) (0.4.0)
Requirement already satisfied: six>=1.10.0 in /opt/conda/lib/python3.11/site-packages (from elephant==0.12.0->databook-utils==1.0.0) (1.16.0)
Requirement already satisfied: tqdm in /opt/conda/lib/python3.11/site-packages (from elephant==0.12.0->databook-utils==1.0.0) (4.66.1)
Requirement already satisfied: notebook in /opt/conda/lib/python3.11/site-packages (from jupyter==1.0.0->databook-utils==1.0.0) (7.0.6)
Requirement already satisfied: qtconsole in /opt/conda/lib/python3.11/site-packages (from jupyter==1.0.0->databook-utils==1.0.0) (5.5.0)
Collecting jupyter-console (from jupyter==1.0.0->databook-utils==1.0.0)
  Using cached jupyter_console-6.6.3-py3-none-any.whl (24 kB)
Requirement already satisfied: nbconvert in /opt/conda/lib/python3.11/site-packages (from jupyter==1.0.0->databook-utils==1.0.0) (7.9.2)
Requirement already satisfied: ipykernel in /opt/conda/lib/python3.11/site-packages (from jupyter==1.0.0->databook-utils==1.0.0) (6.25.2)
Requirement already satisfied: ipywidgets in /opt/conda/lib/python3.11/site-packages (from jupyter==1.0.0->databook-utils==1.0.0) (8.1.1)
Requirement already satisfied: contourpy>=1.0.1 in /opt/conda/lib/python3.11/site-packages (from matplotlib==3.6.2->databook-utils==1.0.0) (1.1.1)
Requirement already satisfied: cycler>=0.10 in /opt/conda/lib/python3.11/site-packages (from matplotlib==3.6.2->databook-utils==1.0.0) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /opt/conda/lib/python3.11/site-packages (from matplotlib==3.6.2->databook-utils==1.0.0) (4.43.1)
Requirement already satisfied: kiwisolver>=1.0.1 in /opt/conda/lib/python3.11/site-packages (from matplotlib==3.6.2->databook-utils==1.0.0) (1.4.5)
Requirement already satisfied: pyparsing>=2.2.1 in /opt/conda/lib/python3.11/site-packages (from matplotlib==3.6.2->databook-utils==1.0.0) (3.1.1)
Requirement already satisfied: ipympl in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (0.9.3)
Requirement already satisfied: ipydatagrid in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (1.2.0)
Requirement already satisfied: ipyvolume>=0.6.0a10 in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (0.6.3)
Collecting ipywidgets (from jupyter==1.0.0->databook-utils==1.0.0)
  Using cached ipywidgets-7.8.1-py2.py3-none-any.whl.metadata (1.9 kB)
Requirement already satisfied: plotly in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (5.13.1)
Requirement already satisfied: aiohttp in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (3.8.6)
Requirement already satisfied: tifffile in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (2023.9.26)
Requirement already satisfied: ndx-spectrum in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (0.2.2)
Requirement already satisfied: ndx-icephys-meta in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (0.1.0)
Requirement already satisfied: ndx-grayscalevolume in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (0.0.2)
Requirement already satisfied: trimesh in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (4.0.4)
Requirement already satisfied: importlib-metadata<5.0 in /opt/conda/lib/python3.11/site-packages (from nwbwidgets==0.10.0->databook-utils==1.0.0) (4.13.0)
Requirement already satisfied: pytz>=2020.1 in /opt/conda/lib/python3.11/site-packages (from pandas==1.5.2->databook-utils==1.0.0) (2023.3.post1)
Collecting numpy (from databook-utils==1.0.0)
  Using cached numpy-1.23.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
Requirement already satisfied: setuptools in /opt/conda/lib/python3.11/site-packages (from pynwb==2.2.0->databook-utils==1.0.0) (59.6.0)
Requirement already satisfied: networkx>=2.2 in /opt/conda/lib/python3.11/site-packages (from scikit-image==0.19.3->databook-utils==1.0.0) (3.2)
Requirement already satisfied: imageio>=2.4.1 in /opt/conda/lib/python3.11/site-packages (from scikit-image==0.19.3->databook-utils==1.0.0) (2.31.5)
Requirement already satisfied: PyWavelets>=1.1.1 in /opt/conda/lib/python3.11/site-packages (from scikit-image==0.19.3->databook-utils==1.0.0) (1.4.1)
Requirement already satisfied: patsy>=0.5.2 in /opt/conda/lib/python3.11/site-packages (from statsmodels==0.14.0->databook-utils==1.0.0) (0.5.3)
Requirement already satisfied: natsort in /opt/conda/lib/python3.11/site-packages (from suite2p==0.12.1->databook-utils==1.0.0) (8.4.0)
Collecting rastermap>0.1.0 (from suite2p==0.12.1->databook-utils==1.0.0)
  Using cached rastermap-0.9.4-py3-none-any.whl.metadata (18 kB)
Collecting scanimage-tiff-reader>=1.4.1 (from suite2p==0.12.1->databook-utils==1.0.0)
  Using cached scanimage_tiff_reader-1.4.1.4-cp311-cp311-linux_x86_64.whl
Collecting torch==1.13.1 (from suite2p==0.12.1->databook-utils==1.0.0)
  Using cached torch-1.13.1-cp311-cp311-manylinux1_x86_64.whl (887.4 MB)
Collecting paramiko (from suite2p==0.12.1->databook-utils==1.0.0)
  Using cached paramiko-3.4.0-py3-none-any.whl.metadata (4.4 kB)
Requirement already satisfied: numba>=0.43.1 in /opt/conda/lib/python3.11/site-packages (from suite2p==0.12.1->databook-utils==1.0.0) (0.57.1)
Collecting sbxreader (from suite2p==0.12.1->databook-utils==1.0.0)
  Using cached sbxreader-0.2.2-py3-none-any.whl (19 kB)
Requirement already satisfied: scikit-learn in /opt/conda/lib/python3.11/site-packages (from suite2p==0.12.1->databook-utils==1.0.0) (1.3.1)
Collecting cellpose (from suite2p==0.12.1->databook-utils==1.0.0)
  Using cached cellpose-2.2.3-py3-none-any.whl.metadata (21 kB)
Collecting nd2 (from suite2p==0.12.1->databook-utils==1.0.0)
  Using cached nd2-0.8.1-py3-none-any.whl.metadata (25 kB)
Requirement already satisfied: munkres in /opt/conda/lib/python3.11/site-packages (from tensortools==0.4->databook-utils==1.0.0) (1.1.4)
Requirement already satisfied: asciitree in /opt/conda/lib/python3.11/site-packages (from zarr==2.13.3->databook-utils==1.0.0) (0.3.3)
Requirement already satisfied: numcodecs>=0.10.0 in /opt/conda/lib/python3.11/site-packages (from zarr==2.13.3->databook-utils==1.0.0) (0.11.0)
Requirement already satisfied: typing-extensions in /opt/conda/lib/python3.11/site-packages (from torch==1.13.1->suite2p==0.12.1->databook-utils==1.0.0) (4.8.0)
Collecting nvidia-cuda-runtime-cu11==11.7.99 (from torch==1.13.1->suite2p==0.12.1->databook-utils==1.0.0)
  Using cached nvidia_cuda_runtime_cu11-11.7.99-py3-none-manylinux1_x86_64.whl (849 kB)
Collecting nvidia-cudnn-cu11==8.5.0.96 (from torch==1.13.1->suite2p==0.12.1->databook-utils==1.0.0)
  Using cached nvidia_cudnn_cu11-8.5.0.96-2-py3-none-manylinux1_x86_64.whl (557.1 MB)
Collecting nvidia-cublas-cu11==11.10.3.66 (from torch==1.13.1->suite2p==0.12.1->databook-utils==1.0.0)
  Using cached nvidia_cublas_cu11-11.10.3.66-py3-none-manylinux1_x86_64.whl (317.1 MB)
Collecting nvidia-cuda-nvrtc-cu11==11.7.99 (from torch==1.13.1->suite2p==0.12.1->databook-utils==1.0.0)
  Using cached nvidia_cuda_nvrtc_cu11-11.7.99-2-py3-none-manylinux1_x86_64.whl (21.0 MB)
Requirement already satisfied: wheel in /opt/conda/lib/python3.11/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch==1.13.1->suite2p==0.12.1->databook-utils==1.0.0) (0.41.2)
Collecting literate-dataclasses (from cebra->databook-utils==1.0.0)
  Using cached literate_dataclasses-0.0.6-py3-none-any.whl (5.0 kB)
Collecting argschema==2.0.2 (from ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0)
  Using cached argschema-2.0.2-py2.py3-none-any.whl
Collecting opencv-python<5.0 (from ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0)
  Using cached opencv_python-4.9.0.80-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (20 kB)
Requirement already satisfied: pytest in /opt/conda/lib/python3.11/site-packages (from ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0) (7.4.3)
Collecting pytest-cov (from ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0)
  Using cached pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB)
Requirement already satisfied: jinja2 in /opt/conda/lib/python3.11/site-packages (from ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0) (3.1.2)
Collecting pypdf2 (from ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0)
  Using cached pypdf2-3.0.1-py3-none-any.whl (232 kB)
Collecting marshmallow==3.0.0rc6 (from argschema==2.0.2->ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0)
  Using cached marshmallow-3.0.0rc6-py2.py3-none-any.whl (42 kB)
Requirement already satisfied: pyyaml in /opt/conda/lib/python3.11/site-packages (from bidsschematools~=0.7.0->dandi==0.55.1->databook-utils==1.0.0) (6.0.1)
Requirement already satisfied: jsonschema[format] in /opt/conda/lib/python3.11/site-packages (from dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (4.19.1)
Requirement already satisfied: ci-info>=0.2 in /opt/conda/lib/python3.11/site-packages (from etelemetry>=0.2.2->dandi==0.55.1->databook-utils==1.0.0) (0.3.0)
Requirement already satisfied: zipp>=0.5 in /opt/conda/lib/python3.11/site-packages (from importlib-metadata<5.0->nwbwidgets==0.10.0->databook-utils==1.0.0) (3.17.0)
Requirement already satisfied: bqplot in /opt/conda/lib/python3.11/site-packages (from ipyvolume>=0.6.0a10->nwbwidgets==0.10.0->databook-utils==1.0.0) (0.12.42)
Requirement already satisfied: traittypes in /opt/conda/lib/python3.11/site-packages (from ipyvolume>=0.6.0a10->nwbwidgets==0.10.0->databook-utils==1.0.0) (0.2.1)
Requirement already satisfied: traitlets in /opt/conda/lib/python3.11/site-packages (from ipyvolume>=0.6.0a10->nwbwidgets==0.10.0->databook-utils==1.0.0) (5.11.2)
Requirement already satisfied: ipywebrtc in /opt/conda/lib/python3.11/site-packages (from ipyvolume>=0.6.0a10->nwbwidgets==0.10.0->databook-utils==1.0.0) (0.6.0)
Requirement already satisfied: ipyvuetify in /opt/conda/lib/python3.11/site-packages (from ipyvolume>=0.6.0a10->nwbwidgets==0.10.0->databook-utils==1.0.0) (1.8.10)
Requirement already satisfied: ipyvue>=1.7.0 in /opt/conda/lib/python3.11/site-packages (from ipyvolume>=0.6.0a10->nwbwidgets==0.10.0->databook-utils==1.0.0) (1.10.1)
Requirement already satisfied: pythreejs>=2.4.0 in /opt/conda/lib/python3.11/site-packages (from ipyvolume>=0.6.0a10->nwbwidgets==0.10.0->databook-utils==1.0.0) (2.4.2)
Requirement already satisfied: comm>=0.1.3 in /opt/conda/lib/python3.11/site-packages (from ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (0.1.4)
Requirement already satisfied: ipython-genutils~=0.2.0 in /opt/conda/lib/python3.11/site-packages (from ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (0.2.0)
Collecting widgetsnbextension~=3.6.6 (from ipywidgets->jupyter==1.0.0->databook-utils==1.0.0)
  Using cached widgetsnbextension-3.6.6-py2.py3-none-any.whl.metadata (1.3 kB)
Requirement already satisfied: ipython>=4.0.0 in /opt/conda/lib/python3.11/site-packages (from ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (8.16.1)
Collecting jupyterlab-widgets<3,>=1.0.0 (from ipywidgets->jupyter==1.0.0->databook-utils==1.0.0)
  Using cached jupyterlab_widgets-1.1.7-py3-none-any.whl.metadata (3.7 kB)
Requirement already satisfied: colorcet in /opt/conda/lib/python3.11/site-packages (from itkwidgets>=0.30.1->ccfwidget==0.5.3->databook-utils==1.0.0) (3.0.1)
Requirement already satisfied: itk-core>=5.3.0 in /opt/conda/lib/python3.11/site-packages (from itkwidgets>=0.30.1->ccfwidget==0.5.3->databook-utils==1.0.0) (5.3.0)
Requirement already satisfied: itk-filtering>=5.3.0 in /opt/conda/lib/python3.11/site-packages (from itkwidgets>=0.30.1->ccfwidget==0.5.3->databook-utils==1.0.0) (5.3.0)
Requirement already satisfied: itk-numerics>=5.3.0 in /opt/conda/lib/python3.11/site-packages (from itkwidgets>=0.30.1->ccfwidget==0.5.3->databook-utils==1.0.0) (5.3.0)
Requirement already satisfied: itk-meshtopolydata>=0.10 in /opt/conda/lib/python3.11/site-packages (from itkwidgets>=0.30.1->ccfwidget==0.5.3->databook-utils==1.0.0) (0.10.0)
Requirement already satisfied: ipydatawidgets>=4.0.1 in /opt/conda/lib/python3.11/site-packages (from itkwidgets>=0.30.1->ccfwidget==0.5.3->databook-utils==1.0.0) (4.3.2)
Requirement already satisfied: zstandard in /opt/conda/lib/python3.11/site-packages (from itkwidgets>=0.30.1->ccfwidget==0.5.3->databook-utils==1.0.0) (0.21.0)
Requirement already satisfied: jaraco.classes in /opt/conda/lib/python3.11/site-packages (from keyring!=23.9.0->dandi==0.55.1->databook-utils==1.0.0) (3.3.0)
Requirement already satisfied: SecretStorage>=3.2 in /opt/conda/lib/python3.11/site-packages (from keyring!=23.9.0->dandi==0.55.1->databook-utils==1.0.0) (3.3.3)
Requirement already satisfied: jeepney>=0.4.2 in /opt/conda/lib/python3.11/site-packages (from keyring!=23.9.0->dandi==0.55.1->databook-utils==1.0.0) (0.8.0)
Requirement already satisfied: llvmlite<0.41,>=0.40.0dev0 in /opt/conda/lib/python3.11/site-packages (from numba>=0.43.1->suite2p==0.12.1->databook-utils==1.0.0) (0.40.1)
Requirement already satisfied: entrypoints in /opt/conda/lib/python3.11/site-packages (from numcodecs>=0.10.0->zarr==2.13.3->databook-utils==1.0.0) (0.4)
Requirement already satisfied: s3fs in /opt/conda/lib/python3.11/site-packages (from nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0) (2023.10.0)
Requirement already satisfied: isodate in /opt/conda/lib/python3.11/site-packages (from nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0) (0.6.1)
Requirement already satisfied: blessed in /opt/conda/lib/python3.11/site-packages (from pyout!=0.6.0,>=0.5->dandi==0.55.1->databook-utils==1.0.0) (1.20.0)
INFO: pip is looking at multiple versions of rastermap to determine which version is compatible with other requirements. This could take a while.
Collecting rastermap>0.1.0 (from suite2p==0.12.1->databook-utils==1.0.0)
  Using cached rastermap-0.9.3-py3-none-any.whl.metadata (18 kB)
  Using cached rastermap-0.9.2-py3-none-any.whl.metadata (17 kB)
  Using cached rastermap-0.9.1-py3-none-any.whl.metadata (16 kB)
  Using cached rastermap-0.9.0-py3-none-any.whl.metadata (8.0 kB)
  Using cached rastermap-0.1.3-py3-none-any.whl (80 kB)
Collecting pyqtgraph (from rastermap>0.1.0->suite2p==0.12.1->databook-utils==1.0.0)
  Using cached pyqtgraph-0.13.3-py3-none-any.whl (960 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in /opt/conda/lib/python3.11/site-packages (from requests->ccfwidget==0.5.3->databook-utils==1.0.0) (3.3.0)
Requirement already satisfied: idna<4,>=2.5 in /opt/conda/lib/python3.11/site-packages (from requests->ccfwidget==0.5.3->databook-utils==1.0.0) (3.4)
Requirement already satisfied: urllib3<3,>=1.21.1 in /opt/conda/lib/python3.11/site-packages (from requests->ccfwidget==0.5.3->databook-utils==1.0.0) (2.0.7)
Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.11/site-packages (from requests->ccfwidget==0.5.3->databook-utils==1.0.0) (2023.7.22)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /opt/conda/lib/python3.11/site-packages (from ruamel.yaml<1,>=0.15->dandi==0.55.1->databook-utils==1.0.0) (0.2.7)
Requirement already satisfied: attrs>=17.3.0 in /opt/conda/lib/python3.11/site-packages (from aiohttp->nwbwidgets==0.10.0->databook-utils==1.0.0) (23.1.0)
Requirement already satisfied: multidict<7.0,>=4.5 in /opt/conda/lib/python3.11/site-packages (from aiohttp->nwbwidgets==0.10.0->databook-utils==1.0.0) (6.0.4)
Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /opt/conda/lib/python3.11/site-packages (from aiohttp->nwbwidgets==0.10.0->databook-utils==1.0.0) (4.0.3)
Requirement already satisfied: yarl<2.0,>=1.0 in /opt/conda/lib/python3.11/site-packages (from aiohttp->nwbwidgets==0.10.0->databook-utils==1.0.0) (1.9.2)
Requirement already satisfied: frozenlist>=1.1.1 in /opt/conda/lib/python3.11/site-packages (from aiohttp->nwbwidgets==0.10.0->databook-utils==1.0.0) (1.4.0)
Requirement already satisfied: aiosignal>=1.1.2 in /opt/conda/lib/python3.11/site-packages (from aiohttp->nwbwidgets==0.10.0->databook-utils==1.0.0) (1.3.1)
Collecting opencv-python-headless (from cellpose->suite2p==0.12.1->databook-utils==1.0.0)
  Using cached opencv_python_headless-4.9.0.80-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (20 kB)
Requirement already satisfied: fastremap in /opt/conda/lib/python3.11/site-packages (from cellpose->suite2p==0.12.1->databook-utils==1.0.0) (1.14.0)
Requirement already satisfied: imagecodecs in /opt/conda/lib/python3.11/site-packages (from cellpose->suite2p==0.12.1->databook-utils==1.0.0) (2023.9.18)
Collecting roifile (from cellpose->suite2p==0.12.1->databook-utils==1.0.0)
  Using cached roifile-2024.1.10-py3-none-any.whl.metadata (4.8 kB)
Requirement already satisfied: cloudpickle>=1.5.0 in /opt/conda/lib/python3.11/site-packages (from dask->ccfwidget==0.5.3->databook-utils==1.0.0) (3.0.0)
Requirement already satisfied: partd>=1.2.0 in /opt/conda/lib/python3.11/site-packages (from dask->ccfwidget==0.5.3->databook-utils==1.0.0) (1.4.1)
Requirement already satisfied: py2vega>=0.5 in /opt/conda/lib/python3.11/site-packages (from ipydatagrid->nwbwidgets==0.10.0->databook-utils==1.0.0) (0.6.1)
Requirement already satisfied: debugpy>=1.6.5 in /opt/conda/lib/python3.11/site-packages (from ipykernel->jupyter==1.0.0->databook-utils==1.0.0) (1.8.0)
Requirement already satisfied: jupyter-client>=6.1.12 in /opt/conda/lib/python3.11/site-packages (from ipykernel->jupyter==1.0.0->databook-utils==1.0.0) (8.4.0)
Requirement already satisfied: jupyter-core!=5.0.*,>=4.12 in /opt/conda/lib/python3.11/site-packages (from ipykernel->jupyter==1.0.0->databook-utils==1.0.0) (5.4.0)
Requirement already satisfied: matplotlib-inline>=0.1 in /opt/conda/lib/python3.11/site-packages (from ipykernel->jupyter==1.0.0->databook-utils==1.0.0) (0.1.6)
Requirement already satisfied: nest-asyncio in /opt/conda/lib/python3.11/site-packages (from ipykernel->jupyter==1.0.0->databook-utils==1.0.0) (1.5.8)
Requirement already satisfied: psutil in /opt/conda/lib/python3.11/site-packages (from ipykernel->jupyter==1.0.0->databook-utils==1.0.0) (5.9.5)
Requirement already satisfied: pyzmq>=20 in /opt/conda/lib/python3.11/site-packages (from ipykernel->jupyter==1.0.0->databook-utils==1.0.0) (25.1.1)
Requirement already satisfied: tornado>=6.1 in /opt/conda/lib/python3.11/site-packages (from ipykernel->jupyter==1.0.0->databook-utils==1.0.0) (6.3.3)
Requirement already satisfied: MarkupSafe>=2.0 in /opt/conda/lib/python3.11/site-packages (from jinja2->ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0) (2.1.3)
Requirement already satisfied: prompt-toolkit>=3.0.30 in /opt/conda/lib/python3.11/site-packages (from jupyter-console->jupyter==1.0.0->databook-utils==1.0.0) (3.0.39)
Requirement already satisfied: pygments in /opt/conda/lib/python3.11/site-packages (from jupyter-console->jupyter==1.0.0->databook-utils==1.0.0) (2.16.1)
Requirement already satisfied: beautifulsoup4 in /opt/conda/lib/python3.11/site-packages (from nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (4.12.2)
Requirement already satisfied: bleach!=5.0.0 in /opt/conda/lib/python3.11/site-packages (from nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (6.1.0)
Requirement already satisfied: defusedxml in /opt/conda/lib/python3.11/site-packages (from nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (0.7.1)
Requirement already satisfied: jupyterlab-pygments in /opt/conda/lib/python3.11/site-packages (from nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (0.2.2)
Requirement already satisfied: mistune<4,>=2.0.3 in /opt/conda/lib/python3.11/site-packages (from nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (3.0.1)
Requirement already satisfied: nbclient>=0.5.0 in /opt/conda/lib/python3.11/site-packages (from nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (0.8.0)
Requirement already satisfied: nbformat>=5.7 in /opt/conda/lib/python3.11/site-packages (from nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (5.9.2)
Requirement already satisfied: pandocfilters>=1.4.1 in /opt/conda/lib/python3.11/site-packages (from nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (1.5.0)
Requirement already satisfied: tinycss2 in /opt/conda/lib/python3.11/site-packages (from nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (1.2.1)
Requirement already satisfied: resource-backed-dask-array in /opt/conda/lib/python3.11/site-packages (from nd2->suite2p==0.12.1->databook-utils==1.0.0) (0.1.0)
Requirement already satisfied: jupyter-server<3,>=2.4.0 in /opt/conda/lib/python3.11/site-packages (from notebook->jupyter==1.0.0->databook-utils==1.0.0) (2.8.0)
Requirement already satisfied: jupyterlab-server<3,>=2.22.1 in /opt/conda/lib/python3.11/site-packages (from notebook->jupyter==1.0.0->databook-utils==1.0.0) (2.25.0)
Requirement already satisfied: jupyterlab<5,>=4.0.2 in /opt/conda/lib/python3.11/site-packages (from notebook->jupyter==1.0.0->databook-utils==1.0.0) (4.0.7)
Requirement already satisfied: notebook-shim<0.3,>=0.2 in /opt/conda/lib/python3.11/site-packages (from notebook->jupyter==1.0.0->databook-utils==1.0.0) (0.2.3)
Collecting bcrypt>=3.2 (from paramiko->suite2p==0.12.1->databook-utils==1.0.0)
  Using cached bcrypt-4.1.2-cp39-abi3-manylinux_2_28_x86_64.whl.metadata (9.5 kB)
Requirement already satisfied: cryptography>=3.3 in /opt/conda/lib/python3.11/site-packages (from paramiko->suite2p==0.12.1->databook-utils==1.0.0) (41.0.4)
Collecting pynacl>=1.5 (from paramiko->suite2p==0.12.1->databook-utils==1.0.0)
  Using cached PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB)
Requirement already satisfied: iniconfig in /opt/conda/lib/python3.11/site-packages (from pytest->ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0) (2.0.0)
Requirement already satisfied: pluggy<2.0,>=0.12 in /opt/conda/lib/python3.11/site-packages (from pytest->ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0) (1.3.0)
Collecting coverage>=5.2.1 (from coverage[toml]>=5.2.1->pytest-cov->ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458->databook-utils==1.0.0)
  Using cached coverage-7.4.1-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.2 kB)
Requirement already satisfied: qtpy>=2.4.0 in /opt/conda/lib/python3.11/site-packages (from qtconsole->jupyter==1.0.0->databook-utils==1.0.0) (2.4.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in /opt/conda/lib/python3.11/site-packages (from scikit-learn->suite2p==0.12.1->databook-utils==1.0.0) (3.2.0)
Requirement already satisfied: webencodings in /opt/conda/lib/python3.11/site-packages (from bleach!=5.0.0->nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (0.5.1)
Requirement already satisfied: cffi>=1.12 in /opt/conda/lib/python3.11/site-packages (from cryptography>=3.3->paramiko->suite2p==0.12.1->databook-utils==1.0.0) (1.16.0)
Requirement already satisfied: backcall in /opt/conda/lib/python3.11/site-packages (from ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (0.2.0)
Requirement already satisfied: decorator in /opt/conda/lib/python3.11/site-packages (from ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (5.1.1)
Requirement already satisfied: jedi>=0.16 in /opt/conda/lib/python3.11/site-packages (from ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (0.19.1)
Requirement already satisfied: pickleshare in /opt/conda/lib/python3.11/site-packages (from ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (0.7.5)
Requirement already satisfied: stack-data in /opt/conda/lib/python3.11/site-packages (from ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (0.6.2)
Requirement already satisfied: pexpect>4.3 in /opt/conda/lib/python3.11/site-packages (from ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (4.8.0)
Requirement already satisfied: jsonschema-specifications>=2023.03.6 in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (2023.7.1)
Requirement already satisfied: referencing>=0.28.4 in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (0.30.2)
Requirement already satisfied: rpds-py>=0.7.1 in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (0.10.6)
Requirement already satisfied: platformdirs>=2.5 in /opt/conda/lib/python3.11/site-packages (from jupyter-core!=5.0.*,>=4.12->ipykernel->jupyter==1.0.0->databook-utils==1.0.0) (3.11.0)
Requirement already satisfied: anyio>=3.1.0 in /opt/conda/lib/python3.11/site-packages (from jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (4.0.0)
Requirement already satisfied: argon2-cffi in /opt/conda/lib/python3.11/site-packages (from jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (23.1.0)
Requirement already satisfied: jupyter-events>=0.6.0 in /opt/conda/lib/python3.11/site-packages (from jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (0.8.0)
Requirement already satisfied: jupyter-server-terminals in /opt/conda/lib/python3.11/site-packages (from jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (0.4.4)
Requirement already satisfied: overrides in /opt/conda/lib/python3.11/site-packages (from jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (7.4.0)
Requirement already satisfied: prometheus-client in /opt/conda/lib/python3.11/site-packages (from jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (0.17.1)
Requirement already satisfied: send2trash>=1.8.2 in /opt/conda/lib/python3.11/site-packages (from jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (1.8.2)
Requirement already satisfied: terminado>=0.8.3 in /opt/conda/lib/python3.11/site-packages (from jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (0.17.1)
Requirement already satisfied: websocket-client in /opt/conda/lib/python3.11/site-packages (from jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (1.6.4)
Requirement already satisfied: async-lru>=1.0.0 in /opt/conda/lib/python3.11/site-packages (from jupyterlab<5,>=4.0.2->notebook->jupyter==1.0.0->databook-utils==1.0.0) (2.0.4)
Requirement already satisfied: jupyter-lsp>=2.0.0 in /opt/conda/lib/python3.11/site-packages (from jupyterlab<5,>=4.0.2->notebook->jupyter==1.0.0->databook-utils==1.0.0) (2.2.0)
Requirement already satisfied: babel>=2.10 in /opt/conda/lib/python3.11/site-packages (from jupyterlab-server<3,>=2.22.1->notebook->jupyter==1.0.0->databook-utils==1.0.0) (2.13.0)
Requirement already satisfied: json5>=0.9.0 in /opt/conda/lib/python3.11/site-packages (from jupyterlab-server<3,>=2.22.1->notebook->jupyter==1.0.0->databook-utils==1.0.0) (0.9.14)
Requirement already satisfied: fastjsonschema in /opt/conda/lib/python3.11/site-packages (from nbformat>=5.7->nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (2.18.1)
Requirement already satisfied: locket in /opt/conda/lib/python3.11/site-packages (from partd>=1.2.0->dask->ccfwidget==0.5.3->databook-utils==1.0.0) (1.0.0)
Requirement already satisfied: wcwidth in /opt/conda/lib/python3.11/site-packages (from prompt-toolkit>=3.0.30->jupyter-console->jupyter==1.0.0->databook-utils==1.0.0) (0.2.8)
Requirement already satisfied: gast<0.5,>=0.4.0 in /opt/conda/lib/python3.11/site-packages (from py2vega>=0.5->ipydatagrid->nwbwidgets==0.10.0->databook-utils==1.0.0) (0.4.0)
Requirement already satisfied: email-validator>=1.0.3 in /opt/conda/lib/python3.11/site-packages (from pydantic[email]<2.0,>=1.8.1->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (2.1.0.post1)
Requirement already satisfied: soupsieve>1.2 in /opt/conda/lib/python3.11/site-packages (from beautifulsoup4->nbconvert->jupyter==1.0.0->databook-utils==1.0.0) (2.5)
Requirement already satisfied: pyct>=0.4.4 in /opt/conda/lib/python3.11/site-packages (from colorcet->itkwidgets>=0.30.1->ccfwidget==0.5.3->databook-utils==1.0.0) (0.5.0)
Requirement already satisfied: more-itertools in /opt/conda/lib/python3.11/site-packages (from jaraco.classes->keyring!=23.9.0->dandi==0.55.1->databook-utils==1.0.0) (10.1.0)
Requirement already satisfied: fqdn in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (1.5.1)
Requirement already satisfied: isoduration in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (20.11.0)
Requirement already satisfied: jsonpointer>1.13 in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (2.4)
Requirement already satisfied: rfc3339-validator in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (0.1.4)
Requirement already satisfied: rfc3987 in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (1.3.8)
Requirement already satisfied: uri-template in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (1.3.0)
Requirement already satisfied: webcolors>=1.11 in /opt/conda/lib/python3.11/site-packages (from jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (1.13)
Requirement already satisfied: aiobotocore~=2.7.0 in /opt/conda/lib/python3.11/site-packages (from s3fs->nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0) (2.7.0)
INFO: pip is looking at multiple versions of s3fs to determine which version is compatible with other requirements. This could take a while.
Collecting s3fs (from nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0)
  Using cached s3fs-2024.2.0-py3-none-any.whl.metadata (1.6 kB)
  Using cached s3fs-2023.12.2-py3-none-any.whl.metadata (1.6 kB)
  Using cached s3fs-2023.12.1-py3-none-any.whl.metadata (1.6 kB)
  Using cached s3fs-2023.9.2-py3-none-any.whl.metadata (1.6 kB)
Collecting aiobotocore~=2.5.4 (from s3fs->nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0)
  Using cached aiobotocore-2.5.4-py3-none-any.whl.metadata (19 kB)
Collecting s3fs (from nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0)
  Using cached s3fs-2023.9.1-py3-none-any.whl.metadata (1.6 kB)
  Using cached s3fs-2023.9.0-py3-none-any.whl.metadata (1.6 kB)
  Using cached s3fs-2023.6.0-py3-none-any.whl.metadata (1.6 kB)
INFO: pip is still looking at multiple versions of s3fs to determine which version is compatible with other requirements. This could take a while.
  Using cached s3fs-2023.5.0-py3-none-any.whl (28 kB)
  Using cached s3fs-2023.4.0-py3-none-any.whl (28 kB)
  Using cached s3fs-2023.3.0-py3-none-any.whl (27 kB)
Collecting aiobotocore~=2.4.2 (from s3fs->nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0)
  Using cached aiobotocore-2.4.2-py3-none-any.whl (66 kB)
Collecting s3fs (from nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0)
  Using cached s3fs-2023.1.0-py3-none-any.whl (27 kB)
  Using cached s3fs-2022.11.0-py3-none-any.whl (27 kB)
Collecting botocore<1.27.60,>=1.27.59 (from aiobotocore~=2.4.2->s3fs->nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0)
  Using cached botocore-1.27.59-py3-none-any.whl (9.1 MB)
Requirement already satisfied: wrapt>=1.10.10 in /opt/conda/lib/python3.11/site-packages (from aiobotocore~=2.4.2->s3fs->nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0) (1.16.0)
Requirement already satisfied: aioitertools>=0.5.1 in /opt/conda/lib/python3.11/site-packages (from aiobotocore~=2.4.2->s3fs->nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0) (0.11.0)
Requirement already satisfied: sniffio>=1.1 in /opt/conda/lib/python3.11/site-packages (from anyio>=3.1.0->jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (1.3.0)
Requirement already satisfied: pycparser in /opt/conda/lib/python3.11/site-packages (from cffi>=1.12->cryptography>=3.3->paramiko->suite2p==0.12.1->databook-utils==1.0.0) (2.21)
Requirement already satisfied: dnspython>=2.0.0 in /opt/conda/lib/python3.11/site-packages (from email-validator>=1.0.3->pydantic[email]<2.0,>=1.8.1->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (2.4.2)
Requirement already satisfied: parso<0.9.0,>=0.8.3 in /opt/conda/lib/python3.11/site-packages (from jedi>=0.16->ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (0.8.3)
Requirement already satisfied: python-json-logger>=2.0.4 in /opt/conda/lib/python3.11/site-packages (from jupyter-events>=0.6.0->jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (2.0.7)
Requirement already satisfied: rfc3986-validator>=0.1.1 in /opt/conda/lib/python3.11/site-packages (from jupyter-events>=0.6.0->jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (0.1.1)
Requirement already satisfied: ptyprocess>=0.5 in /opt/conda/lib/python3.11/site-packages (from pexpect>4.3->ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (0.7.0)
Requirement already satisfied: param>=1.7.0 in /opt/conda/lib/python3.11/site-packages (from pyct>=0.4.4->colorcet->itkwidgets>=0.30.1->ccfwidget==0.5.3->databook-utils==1.0.0) (2.0.1)
Requirement already satisfied: argon2-cffi-bindings in /opt/conda/lib/python3.11/site-packages (from argon2-cffi->jupyter-server<3,>=2.4.0->notebook->jupyter==1.0.0->databook-utils==1.0.0) (21.2.0)
Requirement already satisfied: arrow>=0.15.0 in /opt/conda/lib/python3.11/site-packages (from isoduration->jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (1.3.0)
Requirement already satisfied: executing>=1.2.0 in /opt/conda/lib/python3.11/site-packages (from stack-data->ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (1.2.0)
Requirement already satisfied: asttokens>=2.1.0 in /opt/conda/lib/python3.11/site-packages (from stack-data->ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (2.4.0)
Requirement already satisfied: pure-eval in /opt/conda/lib/python3.11/site-packages (from stack-data->ipython>=4.0.0->ipywidgets->jupyter==1.0.0->databook-utils==1.0.0) (0.2.2)
Requirement already satisfied: types-python-dateutil>=2.8.10 in /opt/conda/lib/python3.11/site-packages (from arrow>=0.15.0->isoduration->jsonschema[format]->dandischema~=0.8.0->dandi==0.55.1->databook-utils==1.0.0) (2.8.19.14)
Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /opt/conda/lib/python3.11/site-packages (from botocore<1.27.60,>=1.27.59->aiobotocore~=2.4.2->s3fs->nwbinspector>=0.4.28->dandi==0.55.1->databook-utils==1.0.0) (1.0.1)
Collecting urllib3<3,>=1.21.1 (from requests->ccfwidget==0.5.3->databook-utils==1.0.0)
  Using cached urllib3-1.26.18-py2.py3-none-any.whl.metadata (48 kB)
Using cached dandi-0.55.1-py3-none-any.whl (297 kB)
Using cached cebra-0.4.0-py2.py3-none-any.whl (202 kB)
Using cached ipywidgets-7.8.1-py2.py3-none-any.whl (124 kB)
Using cached opencv_python-4.9.0.80-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (62.2 MB)
Using cached cellpose-2.2.3-py3-none-any.whl (173 kB)
Using cached nd2-0.8.1-py3-none-any.whl (75 kB)
Using cached paramiko-3.4.0-py3-none-any.whl (225 kB)
Using cached pytest_cov-4.1.0-py3-none-any.whl (21 kB)
Using cached bcrypt-4.1.2-cp39-abi3-manylinux_2_28_x86_64.whl (698 kB)
Using cached coverage-7.4.1-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (237 kB)
Using cached jupyterlab_widgets-1.1.7-py3-none-any.whl (295 kB)
Using cached widgetsnbextension-3.6.6-py2.py3-none-any.whl (1.6 MB)
Using cached opencv_python_headless-4.9.0.80-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (49.6 MB)
Using cached roifile-2024.1.10-py3-none-any.whl (16 kB)
Using cached urllib3-1.26.18-py2.py3-none-any.whl (143 kB)
Building wheels for collected packages: h5py
  Building wheel for h5py (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for h5py (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [71 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-311
      creating build/lib.linux-x86_64-cpython-311/h5py
      copying h5py/h5py_warnings.py -> build/lib.linux-x86_64-cpython-311/h5py
      copying h5py/__init__.py -> build/lib.linux-x86_64-cpython-311/h5py
      copying h5py/ipy_completer.py -> build/lib.linux-x86_64-cpython-311/h5py
      copying h5py/version.py -> build/lib.linux-x86_64-cpython-311/h5py
      creating build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/selections.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/group.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/vds.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/base.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/compat.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/files.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/filters.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      copying h5py/_hl/dims.py -> build/lib.linux-x86_64-cpython-311/h5py/_hl
      creating build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/__init__.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_h5pl.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_h5.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_filters.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_dtype.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_attrs_data.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_attrs.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_file_image.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_errors.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_datatype.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_file_alignment.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_base.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_completions.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_objects.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/common.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_h5o.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_slicing.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_h5p.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_file2.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_group.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_file.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/conftest.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_attribute_create.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_selections.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_big_endian_file.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_dimension_scales.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_h5t.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_dataset.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      copying h5py/tests/test_h5f.py -> build/lib.linux-x86_64-cpython-311/h5py/tests
      creating build/lib.linux-x86_64-cpython-311/h5py/tests/data_files
      copying h5py/tests/data_files/__init__.py -> build/lib.linux-x86_64-cpython-311/h5py/tests/data_files
      creating build/lib.linux-x86_64-cpython-311/h5py/tests/test_vds
      copying h5py/tests/test_vds/__init__.py -> build/lib.linux-x86_64-cpython-311/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-x86_64-cpython-311/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-x86_64-cpython-311/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-x86_64-cpython-311/h5py/tests/test_vds
      copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.linux-x86_64-cpython-311/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.linux-x86_64-cpython-311/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.linux-x86_64-cpython-311/h5py/tests/data_files
      running build_ext
      Building h5py requires pkg-config unless the HDF5 path is explicitly specified using the environment variable HDF5_DIR. For more information and details, see https://docs.h5py.org/en/stable/build.html#custom-installation
      error: pkg-config probably not installed: FileNotFoundError(2, 'No such file or directory')
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for h5py
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects
Note: you may need to restart the kernel to use updated packages.

Same message when I restart the kernel and try again, or try running code in the cells below. Also same when I try to run other code on the OpenScope website from the dandi jupyterhub (they all start with the same cell).
@stephprince stephprince mentioned this issue Apr 30, 2024
Closed
@rcpeene
Copy link
Collaborator

rcpeene commented Jun 20, 2024

Related issue here to be investigated by Dandihub
dandi/dandi-hub#93

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@NilsNyberg @rcpeene