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)
$ 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.
Description
On my system, I have only
mamba
installed and notconda
. When runningjupyter notebook
,jupyter lab
orgator
, I get the following error message (sorry for the formatting, I tried to fix it as good as possible):traceback:
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 havemamba
!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 callwhich mamba
to get the executable of mamba. In my case, I installed mamba via nix, which only providesmicromamba
. For ease of usage, I aliasedmamba
tomicromamba
. In this case however, line 200 returnmamba: aliased to micromamba
which breaks the command.EDIT 2: I created a script
mamba
which correctly resolves to themicromamba
executable. Now I get the following error (in the jupyter log):Reproduce
jupyter notebook
,jupyter lab
orgator
Expected behavior
Detect all installed environments:
Context
5.2.1
Extension version:
General information:
Command Line Output
Browser Output