Compatibility with Mamba & Micromamba

[epassaro]

Hi! I noticed this extension does not work with micromamba.

My workflow consists of defining alias conda=micromamba and suits almost all my needs.

After looking at manager.py I noticed that the output of micromamba info --json is quite different than the expected one (a lot of different and missing keys).

So my questions are:

1. Is there a known workaround to make this extension work with micromamba?
2. Should I write a patch for this?

Thanks

[ken-lauer]

I have a proof-of-concept here that seems to be working in my deployment, at least: https://github.com/ken-lauer/nb_conda_kernels/tree/enh_micromamba
I expect there would be a fair amount more work to make it acceptable to the maintainers - were micromamba support a thing they would even consider, that is.

[mcg1969]

You might be surprised to hear this but I have no problem with the idea of making this work with micromamba. But I do think it is essential that it be well tested.

[AniAggarwal]

Haven't done much development on neither conda nor mamba but I'm happy to help test or contribute; lmk if you think there is something I can help with.

[mcg1969]

Here's what I think would be required.

• In testbed/build.sh, you would need to make sure that the root conda environment has mamba in it.
• The code would need to be modified, likely following the pattern @ken-lauer has already done, but with the ability to configure whether conda or mamba is preferred. Obviously, if only one is installed, fine, go with that; but if both are installed, it would need to be selectable—if for no other reason than to facilitate testing.
• The tests in the tests section would need to be modified to be able to run either with conda or with mamba, selectably.

[mcg1969]

Keep in mind that nb_conda_kernels deliberately does not assume that it lives in the same environment as conda; instead, it relies on calling it via a subprocess. This assumption needs to be preserved for mamba as well. That way, you can run Jupyter (lab|notebook) from a child environment and it still works properly.

[genghisun]

Any progress?

I tried @ken-lauer 's repo but it didn't work, I don't know if I'm doing something wrong. Here are my steps:

# in micromamba env with jupyter
> git clone https://github.com/ken-lauer/nb_conda_kernels.git
> cd nb_conda_kernels/
> git checkout enh_micromamba
> pip install -e .
> python -m nb_conda_kernels.install --enable
Enabling nb_conda_kernels...
CONDA_PREFIX: /path/to/micromamba/envs/jupyter
Status: enabled
> jupyter lab
[E 2024-05-16 14:33:09.968 ServerApp] [nb_conda_kernels] couldn't call conda:
    [Errno 2] No such file or directory: 'conda'
[I 2024-05-16 14:33:10.004 ServerApp] [nb_conda_kernels] enabled, 0 kernels found
# and the kernels of other micromamba environments doesn't show up in jupyter lab webui

> python -m nb_conda_kernels list
[ListKernelSpecs] ERROR | [nb_conda_kernels] couldn't call conda:
[Errno 2] No such file or directory: 'conda'
[ListKernelSpecs] [nb_conda_kernels] enabled, 0 kernels found
Available kernels:
  python3    /path/to/micromamba/envs/jupyter/share/jupyter/kernels/python3
> jupyter kernelspec list
Available kernels:
  python3    /path/to/micromamba/envs/jupyter/share/jupyter/kernels/python3

[mcg1969]

I am not seeing any work being done on this. External contribution will be required. If nb_conda_kernels is essential for you, you'll need to use conda (with the libmamba solver, of course)!

[ken-lauer]

@genghisun I have conda aliased to micromamba for users on our machines as they're used to typing it. The branch linked above, for better or worse, assumes the same is true. A soft-link in your PATH of conda -> micromamba or just having the binary named conda should work.

I'm well aware that the above wouldn't be acceptable for inclusion into anaconda/nb_conda_kernels - but it's still for my own purposes at the moment. It is working well enough on my HPC cluster but is untested elsewhere.

[genghisun]

@ken-lauer Thanks! I made it after ln -s micromamba .local/bin/conda

[theavey]

looks like there is a WIP PR (#279) for this, but set up a new Jupyter env with mamba=2 and Python=3.13 and found that this my conda kernels were not showing up. Would be happy to see this fixed :)

[YanzhaoW]

I createed the softlink with ln -s ~/.local/bin/micromamba ~/.local/bin/conda but still got an error:

Traceback (most recent call last):
  File "~/micromamba/envs/r3bdev/bin/jupyter-lab", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/jupyter_server/extension/application.py", line 628, in launch_instance
    serverapp = cls.initialize_server(argv=args)
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/jupyter_server/extension/application.py", line 598, in initialize_server
    serverapp.initialize(
    ~~~~~~~~~~~~~~~~~~~~^
        argv=argv or [],
        ^^^^^^^^^^^^^^^^
        starter_extension=cls.name,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
        find_extensions=find_extensions,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/traitlets/config/application.py", line 118, in inner
    return method(app, *args, **kwargs)
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/jupyter_server/serverapp.py", line 2834, in initialize
    self.init_configurables()
    ~~~~~~~~~~~~~~~~~~~~~~~^^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/jupyter_server/serverapp.py", line 2098, in init_configurables
    self.kernel_spec_manager = self.kernel_spec_manager_class(
                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
        parent=self,
        ^^^^^^^^^^^^
    )
    ^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/nb_conda_kernels/manager.py", line 127, in __init__
    "nb_conda_kernels | enabled, %s kernels found.", len(self._conda_kspecs)
                                                         ^^^^^^^^^^^^^^^^^^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/nb_conda_kernels/manager.py", line 389, in _conda_kspecs
    for name, info in self._all_specs().items():
                      ~~~~~~~~~~~~~~~^^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/nb_conda_kernels/manager.py", line 267, in _all_specs
    conda_prefix = self._conda_info['conda_prefix']
                   ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
KeyError: 'conda_prefix'

This seems environment variable CONDA_PREFIX must be defined.

[zhangjiakouzf]

I createed the softlink with ln -s ~/.local/bin/micromamba ~/.local/bin/conda but still got an error:

Traceback (most recent call last):
  File "~/micromamba/envs/r3bdev/bin/jupyter-lab", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/jupyter_server/extension/application.py", line 628, in launch_instance
    serverapp = cls.initialize_server(argv=args)
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/jupyter_server/extension/application.py", line 598, in initialize_server
    serverapp.initialize(
    ~~~~~~~~~~~~~~~~~~~~^
        argv=argv or [],
        ^^^^^^^^^^^^^^^^
        starter_extension=cls.name,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
        find_extensions=find_extensions,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/traitlets/config/application.py", line 118, in inner
    return method(app, *args, **kwargs)
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/jupyter_server/serverapp.py", line 2834, in initialize
    self.init_configurables()
    ~~~~~~~~~~~~~~~~~~~~~~~^^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/jupyter_server/serverapp.py", line 2098, in init_configurables
    self.kernel_spec_manager = self.kernel_spec_manager_class(
                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
        parent=self,
        ^^^^^^^^^^^^
    )
    ^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/nb_conda_kernels/manager.py", line 127, in __init__
    "nb_conda_kernels | enabled, %s kernels found.", len(self._conda_kspecs)
                                                         ^^^^^^^^^^^^^^^^^^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/nb_conda_kernels/manager.py", line 389, in _conda_kspecs
    for name, info in self._all_specs().items():
                      ~~~~~~~~~~~~~~~^^
  File "~/micromamba/envs/r3bdev/lib/python3.13/site-packages/nb_conda_kernels/manager.py", line 267, in _all_specs
    conda_prefix = self._conda_info['conda_prefix']
                   ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
KeyError: 'conda_prefix'

This seems environment variable CONDA_PREFIX must be defined.

the same issue with python3.14 and micromamba