notebook problems with running conda envs

[KoSv]

Issue Type: Bug
Related: #13071
install python extenstion
open a .ipynb file
set the conda env
on run:

Command failed: . activate myenv && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python /home//.vscode/extensions/ms-python.python-2020.9.111407/pythonFiles/pyvsc-run-isolated.py /home//.vscode/extensions/ms-python.python-2020.9.111407/pythonFiles/printEnvVariables.py bash: activate: Datei oder Verzeichnis nicht gefunden

Extension version: 2020.9.111407
VS Code version: Code 1.49.2 (e5e9e69aed6e1984f7499b7af85b3d05f9a6883a, 2020-09-24T16:26:09.944Z)
OS version: Linux x64 5.8.11-arch1-1

System Info

Item	Value
CPUs	Intel(R) Core(TM) i5-5300U CPU @ 2.30GHz (4 x 2294)
GPU Status	2d_canvas: enabled flash_3d: enabled flash_stage3d: enabled flash_stage3d_baseline: enabled gpu_compositing: enabled multiple_raster_threads: enabled_on oop_rasterization: disabled_off opengl: enabled_on protected_video_decode: unavailable_off rasterization: disabled_software skia_renderer: enabled_on video_decode: unavailable_off vulkan: disabled_off webgl: enabled webgl2: enabled
Load (avg)	1, 1, 1
Memory (System)	7.48GB (2.81GB free)
Process Argv	--no-sandbox --unity-launch --crash-reporter-id 1b09f273-3ad9-4d17-b97b-06cad50c25cb
Screen Reader	no
VM	0%
DESKTOP_SESSION	xfce
XDG_CURRENT_DESKTOP	XFCE
XDG_SESSION_DESKTOP	undefined
XDG_SESSION_TYPE	x11

[karthiknadig]

This occurs due to some limitation we have with the VS Code terminals and conda. Here is a workaround for this:

1. Turn off auto activation. To do this, disable these two settings, ideally only for the project you are working on:
   
2. Exit VS Code.
3. Open Anaconda Prompt, navigate to your project.
4. Activate the environment that you want.
5. Run code . or code project.code-workspace to launch VS Code.

This will give you an activated environment, and the extension will not have to try and activate every time a terminal is created.

[KoSv]

This occurs due to some limitation we have with the VS Code terminals and conda. Here is a workaround for this:

1. Turn off auto activation. To do this, disable these two settings, ideally only for the project you are working on:
   
2. Exit VS Code.
3. Open Anaconda Prompt, navigate to your project.
4. Activate the environment that you want.
5. Run code . or code project.code-workspace to launch VS Code.

This will give you an activated environment, and the extension will not have to try and activate every time a terminal is created.

thanks, but this doesn't work for me.
getting the same error.

[karrtikr]

@KoSv Thanks for trying it out? Can you try running the command in the error in bash terminal and see if it works for you? I assume you're on Unix.

. activate myenv && echo 'e8b39361-0157-4923-80e1-22d70d46dee6' && python /home//.vscode/extensions/ms-python.python-2020.9.111407/pythonFiles/pyvsc-run-isolated.py /home//.vscode/extensions/ms-python.python-2020.9.111407/pythonFiles/printEnvVariables.py

The error Datei oder Verzeichnis nicht gefunden in German translates to File or directory not found, I'm not sure which file this is referring to.

[KoSv]

@karrtikr sure. here I've replace my username with <USER>
instead of "." I've added "conda". otherwise I got error bash: activate: Datei oder Verzeichnis nicht gefunden or File or directory not found

{"SHELL": "/bin/bash", "SESSION_MANAGER": "local/Arch:@/tmp/.ICE-unix/813,unix/Arch:/tmp/.ICE-unix/813", "WINDOWID": "79692942", "COLORTERM": "truecolor", "XDG_CONFIG_DIRS": "/etc/xdg", "XDG_MENU_PREFIX": "xfce-", "CONDA_EXE": "/opt/miniconda3/bin/conda", "_CE_M": "", "rvm_prefix": "/home/<USER>", "SSH_AUTH_SOCK": "/tmp/ssh-t9rwvNxoaFwX/agent.962", "MY_RUBY_HOME": "/home/<USER>/.rvm/rubies/ruby-2.6.3", "DESKTOP_SESSION": "xfce", "SSH_AGENT_PID": "963", "DPAT_PASSWORD": "pass", "GTK_MODULES": "canberra-gtk-module:canberra-gtk-module", "XDG_SEAT": "seat0", "RUBY_VERSION": "ruby-2.6.3", "PWD": "/home/<USER>", "LOGNAME": "<USER>", "XDG_SESSION_TYPE": "x11", "CONDA_PREFIX": "/home/<USER>/.conda/envs/myenv", "rvm_version": "1.29.9 (latest)", "XAUTHORITY": "/home/<USER>/.Xauthority", "MOTD_SHOWN": "pam", "HOME": "/home/<USER>", "LANG": "de_DE.UTF-8", "XDG_CURRENT_DESKTOP": "XFCE", "DPAT_USER": "[email protected]", "VTE_VERSION": "6200", "CONDA_PROMPT_MODIFIER": "(myenv) ", "NVM_DIR": "/home/<USER>/.nvm", "rvm_bin_path": "/home/<USER>/.rvm/bin", "GEM_PATH": "/home/<USER>/.rvm/gems/ruby-2.6.3:/home/<USER>/.rvm/gems/ruby-2.6.3@global", "GEM_HOME": "/home/<USER>/.rvm/gems/ruby-2.6.3", "XDG_SESSION_CLASS": "user", "TERM": "xterm-256color", "_CE_CONDA": "", "USER": "<USER>", "CONDA_SHLVL": "1", "DISPLAY": ":0.0", "SHLVL": "1", "NVM_CD_FLAGS": "", "XDG_VTNR": "7", "XDG_SESSION_ID": "1", "CONDA_PYTHON_EXE": "/opt/miniconda3/bin/python", "MOZ_PLUGIN_PATH": "/usr/lib/mozilla/plugins", "XDG_RUNTIME_DIR": "/run/user/1000", "PS1": "(myenv) \\u@\\h \\W/$(parse_git_branch)$ ", "CONDA_DEFAULT_ENV": "myenv", "XDG_DATA_DIRS": "/usr/local/share:/usr/share", "PATH": "/home/<USER>/.conda/envs/myenv/bin:/home/<USER>/.nvm/versions/node/v10.16.3/bin:/opt/miniconda3/condabin:/home/<USER>/.rvm/gems/ruby-2.6.3/bin:/home/<USER>/.rvm/gems/ruby-2.6.3@global/bin:/home/<USER>/.rvm/rubies/ruby-2.6.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/home/<USER>/.rvm/bin:/home/<USER>/.rvm/bin", "DBUS_SESSION_BUS_ADDRESS": "unix:path=/run/user/1000/bus", "NVM_BIN": "/home/<USER>/.nvm/versions/node/v10.16.3/bin", "MAIL": "/var/mail/<USER>", "IRBRC": "/home/<USER>/.rvm/rubies/ruby-2.6.3/.irbrc", "rvm_path": "/home/<USER>/.rvm", "_": "/home/<USER>/.conda/envs/myenv/bin/python"}

[karrtikr]

Thanks that helps, looks like the activation command failed for you. conda activate is the best way to do this on new versions of conda, but source activate should also work provided that it's done in the right directory - and . activate is a shorthand for that.

I think it might be that you don't have the conda bin directory in PATH, and so bash can't find the activate script. Can you please run the following which prints environment variables before activation?

python /home//.vscode/extensions/ms-python.python-2020.9.111407/pythonFiles/pyvsc-run-isolated.py /home//.vscode/extensions/ms-python.python-2020.9.111407/pythonFiles/printEnvVariables.py

I'm particularly interested in PATH, and if it has condabin directory on PATH.

[KoSv]

aha..
there it is:
"PATH": "/home/USER/.nvm/versions/node/v10.16.3/bin:/opt/miniconda3/condabin:/home/USER/.rvm/gems/ruby-2.6.3/bin:/home/USER/.rvm/gems/ruby-2.6.3@global/bin:/home/USER/.rvm/rubies/ruby-2.6.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/home/USER/.rvm/bin:/home/USER/.rvm/bin"

so it has condabin in there. but when I run source activate myenv I get the File or directory not found error. So my conda is not properly installed? But with conda insead ot source I have no problems..

[karrtikr]

Yes, it should work with both, source should also be able to find the activation script given it's in PATH. So I would think you have a corrupt install.

[karrtikr]

Actually it's the bin directory that contains the activation script, not condabin, so can you try adding /opt/miniconda3/bin to PATH (or wherever the bin directory is) and see if it works?

[KoSv]

OK it works now!
Thank you very much!
I've added the folowing line to my .bashrc file:
export PATH="/opt/miniconda3/bin:$PATH"
After that:

source ~/.bashrc

..
But when I source deactivate I get a DeprecationWarning that I should use conda instead of .
So that you know ;)
Greetings!

[karrtikr]

Awesome