working jupyter notebook with bash, jupytext, nbextensions (osx + linux), and ExecuteTime + TOC2 enabled by default

default.nix

# sets up a working jupyter notebook environment with
# - bash kernel support
# - jupyter_nbextensions_configurator with ExecuteTime enabled
# - jupytext
# tested on
#   - CentOS, macos using nix==2.2.2
#   - docker://ubuntu:latest using nix==2.1.3
# to connect to a remote host via ssh in bash_kernel, use:
#    ssh target-hostname -t 'PS1="[PEXPECT_PROMPT>" bash --norc --noprofile'

with import <nixpkgs> {};

stdenv.mkDerivation rec {
    name = "jupyter-env";
    env = buildEnv {
        name = name;
        paths = buildInputs;
    };
    buildInputs = [
        python3
        openssl
        libxml2
        libffi
        libxslt
        curl  # for curl-config
    ] ++ (if (system == "x86_64-darwin")
        then [ darwin.apple_sdk.frameworks.ApplicationServices ]
        else []);

    shellHook = ''
    unset SOURCE_DATE_EPOCH  # fix for python building
    export PATH=$PATH:${curl.dev}/bin  # provides curl-config; not added to path by default
    export PYCURL_SSL_LIBRARY=openssl

    # shadow $HOME to try to prevent jupyter side effects to/from normal $HOME
    export HOME=$PWD
    export JUPYTER_CONFIG_DIR=$PWD
    function __make-temp-venv() {
        export TEMP_VENV=$(mktemp -d --suffix -venv)
        echo creating temp virtualenv in $TEMP_VENV...
        function cleanup-temp-venv() {
            if [ "x$TEMP_VENV" == "x" ]; then
                return
            fi
            echo cleaning up $TEMP_VENV...
            rm -rf $TEMP_VENV
        }
        trap cleanup-temp-venv EXIT
        export VIRTUAL_ENV=$TEMP_VENV
    }
    function setup-venv() {
        pip install jupyter==1.0.0 bash_kernel==0.7.2
        python -m bash_kernel.install --sys-prefix
        pip install jupyter_contrib_nbextensions==0.5.1 jupytext==1.2.1
        _JUPYTER_NOTEBOOK_CONFIG=$PWD/jupyter_notebook_config.py
        if [ ! -e $_JUPYTER_NOTEBOOK_CONFIG ]; then
            jupyter notebook --generate-config
            echo 'c.NotebookApp.contents_manager_class="jupytext.TextFileContentsManager"' >> $_JUPYTER_NOTEBOOK_CONFIG
        fi
        jupyter contrib nbextension install --sys-prefix
        jupyter nbextensions_configurator enable --sys-prefix
        jupyter nbextension install --py jupyter_nbextensions_configurator --sys-prefix
        jupyter nbextension enable jupyter_nbextensions_configurator --py --sys-prefix
        if [ ! -e $HOME/nbconfig ]; then
            mkdir -p $HOME/nbconfig
            echo '{"nbext_hide_incompat": false}' >> $HOME/nbconfig/common.json
            echo '{"load_extensions": {"execute_time/ExecuteTime": true, "toc2/main": true}}' >> $HOME/nbconfig/notebook.json
        fi
        # sanity checks
        jupyter serverextension list
        jupyter nbextension list
        jupyter kernelspec list
    }
    if [ "x$VIRTUAL_ENV" == "x" ]; then
        echo no VIRTUAL_ENV specified
        __make-temp-venv
    fi
    if [ -e $VIRTUAL_ENV/bin/activate ]; then
        source $VIRTUAL_ENV/bin/activate
    else
        python -m venv $VIRTUAL_ENV
        source $VIRTUAL_ENV/bin/activate
        setup-venv
    fi
    
    function start() {
        if [ $USER == "root" ]; then
            # assume running in docker
            jupyter notebook --ip 0.0.0.0 --allow-root --no-browser $*
        else
            jupyter notebook --no-browser $*
        fi
    }
    '';
}