It supports the jupyterlab debugger. But it's not packaged for nixos yet.
Clean up how to specify extensions
Types of extensions:
Jupyter lab extensions
Jupyter server extensions
notebook extensions
bundler extensions (not sure what these are)
Python magics (not really extensions)
Also, we need to specify CLI dependencies for any/all of the above.
Look at how to properly auto-fill whatever is needed for the following:
iPython.packages
jupyterEnvironment.extraPackages
jupyterEnvironment.extraJupyterPath
jupyterEnvironment.extraInputsFrom
Also, I want to be able to run my python from a notebook as well as from the command line.
Clean up how to specify R deps
I have installed an extension that formats code on save. I think it's a
server extensions. To format R code, the formatter appears to rely on the
Python library 'rpy2' as well as the R pkg 'formatR'.
I also have an extension for LSP capabilities. To make it work with R,
I use the R pkg 'languageserver'.
Is it possible to specify these via extraJupyterPath or extraInputsFrom? I
haven't managed to do it, but it should be possible. I tried adding the
following to extraJupyterPath, but none of these seemed to do it:
"${pkgs.R}/lib/R"
"${pkgs.R}/lib/R/library"
"${pkgs.rPackages.formatR}/library"
"${pkgs.rPackages.languageserver}/library"
TODO: Automatically detect which packages need to be specified for extraInputsFrom.
For now, I just manually specify the deps for nbconvert:
extraInputsFrom as specified in one of the lines above gave an error when using direnv:
./.envrc:109: Sourcing: command not found
This is presumably because the dump.env file
./.direnv/wd-86452ccdf0879f88e537141a4809226d/dump.env
is modified when extraInputsFrom has a python package, with the following lines being added:
Sourcing python-remove-tests-dir-hook
Sourcing python-catch-conflicts-hook.sh
Sourcing python-remove-bin-bytecode-hook.sh
Sourcing setuptools-build-hook
Using setuptoolsBuildPhase
Sourcing pip-install-hook
Using pipInstallPhase
Sourcing python-imports-check-hook.sh
Using pythonImportsCheckPhase
Sourcing python-namespaces-hook
Rename directory variables to match what Jupyter uses
TODO: @krassowski/jupyterlab-lsp:signature settings schema could not be found and was not loaded
If JUPYTER_DATA_DIR is made immutable, I get the following error:
Unexpected error while saving file: Untitled.ipynb HTTP 500: Internal Server Error
(Unexpected error while saving file: Untitled.ipynb [Errno 30] Read-only file system: '/nix/store/rjcbrkd1br3d4kckw1m1ppn9ksv6sm0c-my-share-jupyter-0.0.0/notebook_secret')
I also got an error when I created an R ipynb file and tried saving it:
File Save Error for Untitled1.ipynb
Unexpected error while saving file: Untitled1.ipynb HTTP 500: Internal Server Error (Unexpected error while saving file: Untitled1.ipynb attempt to write a readonly database)
That error is possibly because this file changes when we create a new notebook:
.share/jupyter/nbsignatures.db
To identify which files must be mutable, make all dirs mutable and then:
Generating grammar tables from /nix/store/sr8r3k029wvgdbv2zr36wr976dk1lya6-python3-3.8.7-env/lib/python3.8/site-packages/blib2to3/Grammar.txt
Writing grammar tables to /home/ariutta/.cache/black/20.8b1/Grammar3.8.7.final.0.pickle
Writing failed: [Errno 2] No such file or directory: '/home/ariutta/.cache/black/20.8b1/tmppem8fqj6'
I made it go away by manually adding the directory, but shouldn't this be automatic?
Moving this from this file to an issue.
take a look at using xeus-python
It supports the jupyterlab debugger. But it's not packaged for nixos yet.
Clean up how to specify extensions
Types of extensions:
Also, we need to specify CLI dependencies for any/all of the above.
Look at how to properly auto-fill whatever is needed for the following:
Also, I want to be able to run my python from a notebook as well as from the command line.
Clean up how to specify R deps
I have installed an extension that formats code on save. I think it's a server extensions. To format R code, the formatter appears to rely on the Python library 'rpy2' as well as the R pkg 'formatR'. I also have an extension for LSP capabilities. To make it work with R, I use the R pkg 'languageserver'.
Is it possible to specify these via extraJupyterPath or extraInputsFrom? I haven't managed to do it, but it should be possible. I tried adding the following to extraJupyterPath, but none of these seemed to do it:
"${pkgs.R}/lib/R""${pkgs.R}/lib/R/library""${pkgs.rPackages.formatR}/library""${pkgs.rPackages.languageserver}/library"TODO: Automatically detect which packages need to be specified for extraInputsFrom. For now, I just manually specify the deps for nbconvert:
These were some attempts that did not work:
extraInputsFrom as specified in one of the lines above gave an error when using direnv:
This is presumably because the dump.env file ./.direnv/wd-86452ccdf0879f88e537141a4809226d/dump.env is modified when extraInputsFrom has a python package, with the following lines being added:
Rename directory variables to match what Jupyter uses
Errors I have sometimes seen:
If JUPYTER_DATA_DIR is made immutable, I get the following error:
I also got an error when I created an R ipynb file and tried saving it:
That error is possibly because this file changes when we create a new notebook:
.share/jupyter/nbsignatures.db
To identify which files must be mutable, make all dirs mutable and then:
or
It will yield a list similar to this:
When the R or Python kernel are launched, these will be added/modified:
I was getting the following error message:
I made it go away by manually adding the directory, but shouldn't this be automatic?
Some useful Nix queries:
for code formatting, compare nb_black with jupyterlab-code-formatter.
One difference:
nb_black is an IPython Magic (%), whereas jupyterlab-code-formatter is a combo lab & server extension.
https://github.com/ryantam626/jupyterlab_code_formatter
For JupyterLab, call nb_black w/ %load_ext lab_black https://pypi.org/project/nb-black/ https://github.com/dnanhkhoa/nb_black