execute command before entering conda environment

[cmosig]

On the remote machine I first need to run $(/opt/miniconda3/bin/conda shell.zsh hook) before the conda environment (and conda) can be run. Is there any way to specify that?

[andersy005]

@cmosig, have you tried the -c option?

jupyter-forward username@remote-machine -c '$(/opt/miniconda3/bin/conda shell.zsh hook)'

[cmosig]

Yes, same result. It seems to execute after conda activate, right?

[andersy005]

Yes, same result. It seems to execute after conda activate, right?

if i recall correctly, the command executes before the environment activation

jupyter-forward/jupyter_forward/core.py

Line 206 in 59401a5

command = f'{self.launch_command} {self._prepare_batch_job_script(command)}'

do you mind trying a different command to confirm that this command is getting executed prior to env activation? something like

jupyter-forward username@remote-machine -c 'whoami'

[cmosig]

jupyter-forward username@remote-machine -c 'whoami'

This produces the same result without printing my username. To make sure I didn't miss the small print I ran a diff between both outputs and that returned nothing.

*************************************************************************************** Authenticating ****************************************************************************************
Authenticating user (cmosig) from client (hiding) to remote host ([redacted])
✅ The client is authenticated successfully
********************************************************************************** Verifying shell location ***********************************************************************************
✅ Using shell: /bin/zsh
******************************************************************************** Running Jupyter sanity checks ********************************************************************************
mamba not found
⚠ Mamba check failed: Encountered a bad command exit code!

Command: '/bin/zsh -lc "which mamba"'

Exit code: 1

Stdout: already printed

Stderr: n/a (PTYs have no stderr)


/bin/zsh -lc "which jupyter"
jupyter not found
*************************************************** ❌ Terminated the network 📡 connection to [redacted] ***************************************************

For additional validation I ran: /bin/zsh -lc "$('/opt/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null) && conda activate env_conda && which jupyter" on the remote server and that worked and returned the path to the jupyter binary.

---

Here is the output of the command that we would expect to work if -c xxx was executed before conda activate.

> jupyter-forward phaestos --conda-env env_conda -c '$(/opt/miniconda3/bin/conda shell.zsh hook)'

*************************************************************************************** Authenticating ****************************************************************************************
Authenticating user (cmosig) from client (hiding) to remote host ([redacted])
✅ The client is authenticated successfully
********************************************************************************** Verifying shell location ***********************************************************************************
✅ Using shell: /bin/zsh
******************************************************************************** Running Jupyter sanity checks ********************************************************************************
mamba not found
⚠ Mamba check failed: Encountered a bad command exit code!

Command: '/bin/zsh -lc "which mamba"'

Exit code: 1

Stdout: already printed

Stderr: n/a (PTYs have no stderr)

/bin/zsh -lc "source activate env_conda && which jupyter"
zsh:source:1: no such file or directory: activate
❌ `source activate` failed. Trying next...
/bin/zsh -lc "conda activate env_conda && which jupyter"
zsh:1: command not found: conda
❌ `conda activate` failed. Trying next...
❌ Could not activate environment. Ensure Conda or Mamba is installed.
*************************************************** ❌ Terminated the network 📡 connection to [redacted] ***************************************************

[andreall]

Hi,
I am running into a similar issue. I am working on a local MacBook zsh shell and can successfully Jupyter-forward to several Linux machines. Now I am trying to connect into another iOS zsh machine and I get:

 **************************************** Authenticating ****************************************
Authenticating user (aliraloarca) from client (wilson.local) to remote host 
(dhcp56-169.dicca.unige.it)
✅ The client is authenticated successfully
*********************************** Verifying shell location ***********************************
✅ Using shell: /bin/zsh
******************************** Running jupyter sanity checks *********************************
/bin/zsh -lc "which jupyter"
jupyter not found
************* ❌ Terminated the network 📡 connection to dhcp56-169.dicca.unige.it *************

I have run /bin/zsh -lc "which jupyter" on the remote and get:

/opt/miniforge3/bin/jupyter

Which is correct I believe (I have the same in the other linux machines). I have added export PATH=/opt/miniforge3/bin:$PATH in the .zshrc file but it still doesn't work.

Any ideas?