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AllenInstitute / openscope_databook

OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈
https://alleninstitute.github.io/openscope_databook
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Can't build wheel for h5py #346

Open NilsNyberg opened 6 months ago

NilsNyberg commented 6 months ago

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)
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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).

rcpeene commented 2 months ago

Related issue here to be investigated by Dandihub https://github.com/dandi/dandi-hub/issues/93