Add Octave packages to Binder

[AntoinePrv]

Close #69

[AntoinePrv]

Surprising error on Binder. Same command works locally and in the Binder terminal.

error: 'pkg' undefined near line 1, column 1

[gllmflndn]

I think the 'pkg' undefined issue corresponds to the same one I came across last week: https://octave.discourse.group/t/towards-a-better-jupyter-kernel-and-integration-in-the-jupyterlite-ecosystem/3356/10 My guess is that the directories listed in the Octave path are incorrect and none of the core functions can be found.

[AntoinePrv]

Hi @gllmflndn, thanks for chipping in! In this case, I resolved it by putting some double quotation around the install instructions. Now I have that working but I'm still having issues making Octave inside Docker find the conda-forge compilers.

[rapgenic]

Try deactivating and then reactivating the conda environment. I used to close and reopen the shell to solve that problem, which occurred when I did conda install fortran-compiler and then run octave and pkg install -forge control.

Also I see that you wrote source .bsahrc instead of source .bashrc ....

[gllmflndn]

Hi @AntoinePrv and @rapgenic, could you give more details about how to deactivate and reactivate the conda environment within postBuild? I tried the following but that's definitely not right:

  conda init bash
  source ~/.bashrc
  conda activate notebook

[AntoinePrv]

@gllmflndn I'm still trying to figure this out :)

[gllmflndn]

Thank you @AntoinePrv ! Sorry for sounding impatient, I am very much looking forward to this and thank you for working on it. Unfortunately I don't know enough of conda/mamba to figure out the solution.

If "1+1" works in Octave but not "pkg install" that's because path() returns empty instead of all of the default paths to Octave functions. This is probably because the ones that Octave uses do not exist and path() only displays valid ones. The situation is equivalent to starting Octave with octave --no-init-path. The invalid paths I see when compiling within postBuild are:

/home/conda/feedstock_root/build_artifacts/octave_1663939771504/_build_env/bin/x86_64-conda-linux-gnu-cc
/home/conda/feedstock_root/build_artifacts/octave_1663939771504/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include

[AntoinePrv]

@gllmflndn I found a working solution with micromamba (already installed in the Binder image)

micromamba run -n notebook octave-cli --eval 'pkg install -forge symbolic control signal'

Provided the build/run dependencies (such as compilers) are properly given in ./binder/environment.yml.

[gllmflndn]

Thanks @AntoinePrv it seems to work for me! Paths during compilation are now starting with /srv/conda/envs/notebook/. I still notice some paths such as /home/conda/feedstock_root/build_artifacts/octave_1663939771504/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib during linking but it seems to run anyway.

One minor issue (in my case) I notice is that I use the shell function in a Makefile, spawning a new shell, and the micromamba environment is not available there. Ideally, would there be a way to have everything in postBuild running implicitly in the notebook environment without having to explicitly prepend everything with micromamba run -n notebook?