No such file or directory: 'conda'

[cgahr]

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Description

On my system, I have only mamba installed and not conda. When running jupyter notebook, jupyter lab or gator, I get the following error message (sorry for the formatting, I tried to fix it as good as possible):

[E 2024-03-07 16:01:47.247 ServerApp.mamba_gator] Error for task 
{
  'type': 'FileNotFoundError', 
  'error': "[Errno 2] No such file or directory: 'conda'", 
  'message': "FileNotFoundError(2, 'No such file or directory')", 
  'traceback': []}

traceback:

  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/site-packages/mamba_gator/handlers.py", line 96, in execute_task
    result = await f(*args)
             ^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/site-packages/mamba_gator/handlers.py", line 380, in update_available
    answer = await env_manager.list_available()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/site-packages/mamba_gator/envmanager.py", line 595, in list_available
    ans = await self._execute(self.manager, "search", "--json")
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/site-packages/mamba_gator/envmanager.py", line 151, in _execute
    process = await current_loop.run_in_executor(
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/subprocess.py", line 1026, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/subprocess.py", line 1953, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)

Furthermore, no environments are shown!

The error itself is not unexpected (at least for me), since I don't have conda installed on my system, I only have mamba!

However, my understanding was that I don't need conda to rungator.

This seems to be a bug to be, but any help is appreciated!

EDIT: I looked through envmanager.py and might have found a possible issue. In line 200, you call which mamba to get the executable of mamba. In my case, I installed mamba via nix, which only provides micromamba. For ease of usage, I aliased mamba to micromamba. In this case however, line 200 return mamba: aliased to micromamba which breaks the command.

EDIT 2: I created a script mamba which correctly resolves to the micromamba executable. Now I get the following error (in the jupyter log):

  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/site-packages/mamba_gator/handlers.py", line 96, in execute_task
    result = await f(*args)
             ^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/site-packages/mamba_gator/handlers.py", line 380, in update_available
    answer = await env_manager.list_available()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/site-packages/mamba_gator/envmanager.py", line 595, in list_available
    ans = await self._execute(self.manager, "search", "--json")
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/site-packages/mamba_gator/envmanager.py", line 151, in _execute
    process = await current_loop.run_in_executor(
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/subprocess.py", line 1026, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/cgahr/micromamba/envs/notebook/lib/python3.12/subprocess.py", line 1953, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)

Reproduce

1. Install environment (below)
2. Run jupyter notebook, jupyter lab or gator
3. Don't find any mamba environment

# environment.yml
name: notebook
channels:
  - conda-forge
  - defaults
dependencies:
  - python>=3.11
  - jupyterlab
  - notebook
  - mamba_gator
  - pip

Expected behavior

Detect all installed environments:

$ mamba env list
  Name            Active  Path
──────────────────────────────────────────────────────────────────────
  base                    /home/cgahr/micromamba
  notebook        *       /home/cgahr/micromamba/envs/notebook
  qmk                     /home/cgahr/micromamba/envs/qmk

Context

• Python package version: 5.2.1
• Extension version:

$ jupyter labextension list
JupyterLab v4.1.3
/home/cgahr/micromamba/envs/notebook/share/jupyter/labextensions
        jupyterlab_pygments v0.3.0 enabled OK (python, jupyterlab_pygments)
        @jupyter-notebook/lab-extension v7.1.1 enabled OK
        @mamba-org/gator-lab v3.1.0 enabled  X (python, mamba_gator)                                                                                                             
                                                                                                             
   The following extensions are outdated:
        @mamba-org/gator-lab
                                                                                                          
   Consider checking if an update is available for these packages.                                                                                                             

• General information:

$ mamba info
                                                                                                                     
       libmamba version : 1.5.4
     micromamba version : 1.5.4
           curl version : libcurl/8.5.0 OpenSSL/3.0.12 zlib/1.3 brotli/1.1.0 zstd/1.5.5 libidn2/2.3.4 libssh2/1.11.0nghttp2/1.57.0
     libarchive version : libarchive 3.7.2 zlib/1.3 liblzma/5.4.5 bz2lib/1.0.8 libzstd/1.5.5
       envs directories : /home/cgahr/micromamba/envs
          package cache : /home/cgahr/micromamba/pkgs
                          /home/cgahr/.mamba/pkgs
            environment : notebook (active)
           env location : /home/cgahr/micromamba/envs/notebook
      user config files : /home/cgahr/.mambarc
 populated config files :
       virtual packages : __unix=0=0
                          __linux=6.2.0=0
                          __glibc=2.38=0
                          __archspec=1=x86_64-v3
               channels :
       base environment : /home/cgahr/micromamba
               platform : linux-64

Command Line Output

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[PaulKGrimes]

I have this same issue with jupyterhub (installed in a micromamba environment, and running as a dedicated user). Setting CONDA_EXE=/opt/mamba/bin/micromamba as an environment variable for the systemd service does not help.

However, after installing mamba_gator in my jupyterhub environment, I'm not getting the same error.

[danyeaw]

Hi @cgahr, if I understand this issue correctly, are you proposing a feature request that Gator supports micromamba? It looks like you are trying to use micromamba as mamba, and Gator doesn't support that currently - so as a fallback it is trying to find Conda.

[psobolewskiPhD]

Ran into this today and can confirm that switching to a miniforge installation with mamba worked just fine. Still it would be nice for this to work with micromamba, because of the simpler installation as a standalone binary.

[cgahr]

It has been a long time so I don't remember all the details since my software stack has changed since.

IIRC I thought that micromamba = mamba, or at least that micromamba should be usable as a replacement for mamba. This wasn't the case, hence the report.

In practice, maybe it would be sufficient to expose a way to configure the mamba/conda/whatever executable.