jupyter-kernelspec-update

#!/usr/bin/env python

import json
import os
import pathlib
import shutil
import subprocess
import sys


def add_python(bindir, name=None):
    """
    Add Python from the bindir folder as a jupyter kernel.
    Environments can be managed with conda or venv (install python and ipykernel).
    """
    name = name + '-python3' if name is not None else 'python3'
    cmd = ['ipykernel', 'install', '--user', '--name', name, '--display-name', name]
    cmd = [bindir / 'python', '-m'] + cmd
    try:
        subprocess.run(cmd, capture_output=True, text=True, check=True)
        print(f'  Python: kernel added as {name}')
    except FileNotFoundError as e:
        print(e)
        print('  Python: Python not installed')
    except subprocess.CalledProcessError as e:
        if 'No module named ipykernel' in e.stderr:
            print('  Python: ipykernel not installed')
            # run pip install ipykernel
            # run conda install ipykernel
        else:
            raise e


def add_octave(bindir, name=None):
    """
    Add Octave from the bindir folder as a jupyter kernel.
    Environments can be managed with conda (install octave, python, octave_kernel).
    """
    name = name + '-octave' if name is not None else 'octave'
    cmd = ['octave_kernel', 'install', '--user', '--name', name]
    cmd = [bindir / 'python', '-m'] + cmd
    try:
        subprocess.run(cmd, capture_output=True, text=True, check=True)
        print(f'  Octave: kernel added as {name}')
        # TODO: can't set display-name, https://github.com/Calysto/metakernel/issues/200
        with open(KERNEL_DIR / name / 'kernel.json', 'r') as f:
            kernelspec = json.load(f)
        kernelspec['display_name'] = name
        with open(KERNEL_DIR / name / 'kernel.json', 'w') as f:
            f.write(json.dumps(kernelspec, indent=1))
    except FileNotFoundError:
        print('  Octave: Python not installed')
    except subprocess.CalledProcessError as e:
        if 'No module named octave_kernel' in e.stderr:
            print('  Octave: octave_kernel not installed')
            # run pip install octave_kernel
            # conda install octave_kernel
        else:
            raise e


def add_r(bindir, name=None):
    """
    Add R from the bindir folder as a jupyter kernel.
    Environments can be managed with conda (install R and IRkernel).
    """
    name = name + '-r' if name is not None else 'r'
    cmd = f'IRkernel::installspec(name = "{name}", displayname = "{name}")'
    cmd = [bindir / 'R', '--slave', '-e', cmd]
    try:
        subprocess.run(cmd, capture_output=True, text=True, check=True)
        print(f'  R: kernel added as {name}')
    except FileNotFoundError:
        print('  R: R not installed')
    except subprocess.CalledProcessError as e:
        if "there is no package called ‘IRkernel’" in e.stderr:
            print('  R: IRkernel not installed')
            # run R -q -e "install.packages('IRkernel')"
            # run conda install r-irkernel
        else:
            raise e


def add_julia(bindir, name=None):
    """
    Add Julia from the bindir folder as a jupyter kernel.
    Environments are managed by starting jupyter in the project folder, where the environment spec resides.
    https://stackoverflow.com/questions/60406075/how-to-set-julia-environment-for-ijulia-jupyter-notebook
    """
    name = name + '-julia' if name is not None else 'julia'
    cmd = f'import IJulia; IJulia.installkernel("{name}")'
    cmd = [bindir / 'julia', '-e', cmd]
    try:
        subprocess.run(cmd, capture_output=True, text=True, check=True)
        print(f'  Julia: kernel added as {name}')
    except FileNotFoundError:
        print('  Julia: Julia not installed')
    except subprocess.CalledProcessError as e:
        if 'Package IJulia not found' in e.stderr:
            print('  Julia: IJulia not installed')
            # run julia -e 'import Pkg; Pkg.add("IJulia")'
        else:
            raise e


def add_all_languages(bindir, name=None):
    print(f'Adding {bindir}')
    add_python(bindir, name)
    add_octave(bindir, name)
    add_r(bindir, name)
    add_julia(bindir, name)


def add_conda_envs(venvdir):
    for venv in os.listdir(venvdir):
        if venv == '.conda_envs_dir_test':
            continue
        add_all_languages(venvdir / venv / 'bin', venv)


def add_python_envs(venvdir):
    for venv in os.listdir(venvdir):
        bindir = venvdir / venv / 'bin'
        print(f'Adding {bindir}')
        config = dict()
        with open(venvdir / venv / 'pyvenv.cfg', 'rt') as f:
            for line in f:
                name, _, value = line.partition("=")
                config[name.strip()] = value.strip()
        if config['version'][:3] != sys.version[:3]:
            print(f"  Error: env created with python {config['version']}")
            continue
        if config['include-system-site-packages'] == 'true':
            print('  Warning: env has access to system packages')
        add_python(bindir, venv)


if __name__ == '__main__':

    KERNEL_DIR = pathlib.Path('/home/michael/.local/share/jupyter/kernels/')
    shutil.rmtree(KERNEL_DIR, ignore_errors=True)
    KERNEL_DIR.mkdir()

    # add_all_languages(pathlib.Path('/usr/bin'))
    # shadows /usr/share/jupyter/kernels/python3/ from python-ipykernel
    # => issue: jupyter will use system python if installed in an environment
    # shadows /usr/share/jupyter/kernels/octave/ from jupyter-octave_kernel
    add_r(pathlib.Path('/usr/bin'))
    add_julia(pathlib.Path('/usr/bin'))

    add_conda_envs(pathlib.Path('/home/michael/.conda/envs/'))
    add_python_envs(pathlib.Path('/home/michael/venv/'))

    subprocess.run(['jupyter', 'kernelspec', 'list'], check=True)