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Merge pull request #19 from kushalbakshi/codespace
Add DevContainer and tutorial + fix `Segmentation` make + update docs
2 parents 4f53b14 + 5df1a60 commit b23c44c

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‎.cspell.json

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"flagWords": [],
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"allowCompoundWords": true,
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"ignorePaths": [
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"./element_zstack.egg-info/*",
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"./element_array_ephys.egg-info/*",
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"./images/*"
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],
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"words": [
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"acorr",
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"aggr",
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"ascontiguousarray",
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"Alessio",
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"Andreas",
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"apmeta",
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"arange",
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"arithmatex",
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"asarray",
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"astype",
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"Berens",
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"bossdb",
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"CICD",
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"connectome",
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"Connectome",
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"connectomics",
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"DBURLs",
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"autocorrelogram",
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"Axona",
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"bbins",
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"bdist",
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"Binarize",
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"bouton",
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"Brody",
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"Bruker",
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"bshift",
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"Buccino",
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"catgt",
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"cbar",
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"cbin",
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"cdat",
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"chans",
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"Chans",
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"chns",
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"Clust",
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"clusterings",
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"cmap",
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"cnmf",
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"correlogram",
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"correlograms",
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"curations",
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"DANDI",
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"decomp",
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"deconvolution",
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"DISTRO",
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"djbase",
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"dtype",
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"Ecker",
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"ecephys",
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"Eftychios",
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"electrophysiogical",
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"elif",
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"Ephys",
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"Hoenselaar",
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"IACUC",
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"fluo",
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"fneu",
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"Fneu",
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"gblcar",
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"gfix",
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"Giovannucci",
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"Hakan",
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"hdmf",
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"HHMI",
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"hstack",
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"ibllib",
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"ifnull",
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"imax",
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"Imax",
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"IMAX",
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"imec",
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"imread",
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"imro",
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"imrotbl",
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"imshow",
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"Inan",
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"inlinehilite",
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"ipdb",
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"iplane",
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"ipynb",
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"ipywidgets",
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"iscell",
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"Kavli",
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"kcoords",
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"Klusta",
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"Kwik",
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"lfmeta",
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"linenums",
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"masky",
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"mathjax",
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"mdict",
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"Mesoscale",
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"mesoscope",
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"mkdocs",
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"mkdocstrings",
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"ndarrays",
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"neuroglancer",
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"neuroimaging",
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"pngs",
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"Moser",
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"mtscomp",
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"nblocks",
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"nchan",
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"Nchan",
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"nchannels",
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"ndarray",
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"ndepths",
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"ndim",
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"ndimage",
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"Neuralynx",
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"NEURO",
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"neuroconv",
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"Neurodata",
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"Neurolabware",
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"neuropil",
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"Neuropil",
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"Neuropix",
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"neuropixel",
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"NeuroPixels",
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"nfields",
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"nframes",
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"npix",
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"nplanes",
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"nrois",
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"NTNU",
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"nwbfile",
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"NWBHDF",
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"oebin",
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"openephys",
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"openpyxl",
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"Pachitariu",
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"paramsets",
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"phylog",
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"plotly",
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"Pnevmatikakis",
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"PSTH",
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"pykilosort",
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"pymdownx",
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"pynwb",
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"pyopenephys",
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"pyplot",
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"pytest",
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"quantile",
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"Reimer",
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"repolarization",
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"Roboto",
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"roidetect",
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"rois",
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"ROIs",
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"RRID",
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"Rxiv",
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"Sasaki",
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"sbxreader",
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"scipy",
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"sdist",
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"sess",
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"SGLX",
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"Shen",
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"Siapas",
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"Sinz",
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"Siegle",
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"Sitonic",
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"spikeglx",
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"spkcount",
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"spks",
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"Stereotaxic",
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"Sutter",
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"tcat",
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"tickvals",
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"tofile",
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"Tolias",
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"tqdm",
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"usecs",
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"usedb",
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"Vidrio's",
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"vline",
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"vmax",
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"Vmax",
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"voxel",
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"xanchor",
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"xaxes",
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"xaxis",
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"xblock",
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"xcoords",
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"xcorr",
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"xlabel",
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"xlim",
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"xoff",
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"xpix",
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"XPOS",
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"xtick",
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"yanchor",
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"Yatsenko",
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"Zuckerman"
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"yaxes",
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"yaxis",
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"yblock",
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"ycoord",
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"ycoords",
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"ylabel",
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"ylim",
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"yoff",
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"ypix",
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"YPOS",
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"yref",
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"yticks",
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"zpix"
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]
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}

‎.devcontainer/Dockerfile

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FROM python:3.9-slim@sha256:5f0192a4f58a6ce99f732fe05e3b3d00f12ae62e183886bca3ebe3d202686c7f
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ENV PATH /usr/local/bin:$PATH
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ENV PYTHON_VERSION 3.9.17
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RUN \
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adduser --system --disabled-password --shell /bin/bash vscode && \
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# install docker
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apt-get update && \
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apt-get install ca-certificates curl gnupg lsb-release -y && \
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mkdir -m 0755 -p /etc/apt/keyrings && \
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curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg && \
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echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null && \
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apt-get update && \
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apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin -y && \
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usermod -aG docker vscode && \
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apt-get clean
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RUN \
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# dev setup
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apt update && \
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apt-get install sudo git bash-completion graphviz default-mysql-client s3fs procps -y && \
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usermod -aG sudo vscode && \
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echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers && \
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pip install --no-cache-dir --upgrade black pip nbconvert && \
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echo '. /etc/bash_completion' >> /home/vscode/.bashrc && \
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echo 'export PS1="\[\e[32;1m\]\u\[\e[m\]@\[\e[34;1m\]\H\[\e[m\]:\[\e[33;1m\]\w\[\e[m\]$ "' >> /home/vscode/.bashrc && \
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apt-get clean
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COPY ./ /tmp/element-zstack/
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RUN \
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# pipeline dependencies
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apt-get install gcc g++ ffmpeg libsm6 libxext6 -y && \
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pip install --no-cache-dir -e /tmp/element-zstack[elements,tests] && \
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# clean up
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rm -rf /tmp/element-zstack && \
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apt-get clean
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ENV DJ_HOST fakeservices.datajoint.io
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ENV DJ_USER root
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ENV DJ_PASS simple
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ENV VOLUME_ROOT_DATA_DIR /workspaces/element-zstack/example_data
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ENV DATABASE_PREFIX neuro_
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USER vscode
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CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"

‎.devcontainer/devcontainer.json

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{
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"name": "Environment + Data",
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"dockerComposeFile": "docker-compose.yaml",
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"service": "app",
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"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
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"remoteEnv": {
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"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
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},
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"onCreateCommand": "mkdir -p ${VOLUME_ROOT_DATA_DIR} && pip install -e .",
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"postStartCommand": "docker volume prune -f && s3fs ${DJ_PUBLIC_S3_LOCATION} ${VOLUME_ROOT_DATA_DIR} -o nonempty,multipart_size=530,endpoint=us-east-1,url=http://s3.amazonaws.com,public_bucket=1",
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"hostRequirements": {
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"cpus": 4,
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"memory": "8gb",
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"storage": "32gb"
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},
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"forwardPorts": [
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3306
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],
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"customizations": {
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"settings": {
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"python.pythonPath": "/usr/local/bin/python"
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},
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"vscode": {
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"extensions": [
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"ms-python.python@2023.8.0",
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"ms-toolsai.jupyter@2023.3.1201040234"
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]
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}
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}
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}

‎.devcontainer/docker-compose.yaml

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version: "3"
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services:
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app:
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cpus: 4
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mem_limit: 8g
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build:
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context: ..
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dockerfile: ./.devcontainer/Dockerfile
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# image: datajoint/element_array_ephys:latest
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extra_hosts:
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- fakeservices.datajoint.io:127.0.0.1
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environment:
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- DJ_PUBLIC_S3_LOCATION=djhub.vathes.datapub.elements:/workflow-zstack-v1
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devices:
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- /dev/fuse
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cap_add:
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- SYS_ADMIN
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security_opt:
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- apparmor:unconfined
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volumes:
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- ..:/workspaces/element-zstack:cached
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- docker_data:/var/lib/docker # persist docker images
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privileged: true # only because of dind
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volumes:
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docker_data:

‎.github/workflows/release.yaml

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jobs:
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make_github_release:
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uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
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pypi_release:
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needs: make_github_release
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uses: datajoint/.github/.github/workflows/pypi_release.yaml@main
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secrets:
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TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
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TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}
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with:
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UPLOAD_URL: ${{needs.make_github_release.outputs.release_upload_url}}
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mkdocs_release:
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uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
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permissions:

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