conda.sh at different location

[eleanorjboyd]

from @robertwinkler-research in microsoft/vscode-python#25291 (comment)

Also, for bash, when specifying "python-envs.terminal.autoActivationType": "shellStartup",
terminal output:
. /usr/etc/profile.d/conda.sh && conda activate epiatl-downstr
bash: /usr/etc/profile.d/conda.sh: No such file or directory

My conda.sh is not in this location and I am not sure where to specify its location. I would be grateful for any tips.

[karthiknadig]

@robertwinkler-research Can you share what you have in ~/.bashrc for conda and vscode. You can hide the other parts if it has private information. Just need to see what conda and vscode added there.

[robertwinkler-research]

Hello, I guess this one was my bad. My bashrc (below) did have a wrong conda path, though I'm not sure why. When I edited to the correct path this works now.

(epiatl-downstr) [RWinkler@cpu1 epigenetics_atlas]$ cat ~/.bashrc
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

# User specific environment
if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]]
then
    PATH="$HOME/.local/bin:$HOME/bin:$PATH"
fi
export PATH

# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=

# User specific aliases and functions
if [ -d ~/.bashrc.d ]; then
        for rc in ~/.bashrc.d/*; do
                if [ -f "$rc" ]; then
                        . "$rc"
                fi
        done
fi

unset rc
export SINGULARITY_TMPDIR=/home/cache/work_winkler_cpu1/
# VSCode conditional R paths
export R_PATH="/home/RWinkler/.conda/envs/epiatl-downstr/bin/R"
export RADIAN_PATH="/home/RWinkler/.conda/envs/epiatl-downstr/bin/radian"
export R_PROFILE_USER=~/.Rprofile

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/usr/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/usr/etc/profile.d/conda.sh" ]; then
        . "/usr/etc/profile.d/conda.sh"
    else
        export PATH="/usr/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

[robertwinkler-research]

Update: I was wrong, even after updating to the correct path in the conda init block, it still does not work. I realize editing the path will make no diference anyways as it uses the hook first.

Problem:

(base) [RWinkler@cpu1 epigenetics_atlas]$ . /usr/etc/profile.d/conda.sh && conda activate epiatl-downstr
bash: /usr/etc/profile.d/conda.sh: No such file or directory

When setting python.condaPath to my conda.sh:

(base) [RWinkler@cpu1 epigenetics_atlas]$ . /usr/lib/python3.9/site-packages/conda/shell/etc/etc/profile.d/conda.sh && conda activate epicompare_env
bash: /usr/lib/python3.9/site-packages/conda/shell/etc/etc/profile.d/conda.sh: No such file or directory

Notice the added /etc, how strange.
Setting python.condaPath to /usr/lib/python3.9/site-packages/conda/shell/profile.d/conda.sh (which does not exist, I removed the etc/), works. Fixed..

(base) [RWinkler@cpu1 epigenetics_atlas]$ . /usr/lib/python3.9/site-packages/conda/shell/etc/profile.d/conda.sh && conda activate epiatl-downstr
(epiatl-downstr) [RWinkler@cpu1 epigenetics_atlas]$ 

I think ultimately this is an error my admin made with how system wide conda is set up (I'm remote on an HPC), I do not understand it. Just weird that it worked before python environments extension began being used. Also setting condaPath seems to have some weird behaviour. Sorry I don't understand well how environment activation works in vscode.

[eleanorjboyd]

Hi @robertwinkler-research! Thank you for all the info and your investigation this really helps.

To give some background that might help, for conda there are two steps which need to be taken to get to the goal of an activated environment:

1. sourcing conda (in your case the conda.sh script) this is a shell hook that makes conda activate work in your shell
2. activate a specific conda environment conda activate name_of_env

For the first step, there are a few ways you can achieve this:
A. if you run conda init in the shell you are using it will make an edit to your shell profile file and handle the sourcing (that is the code you see in between the # >>> conda initialize >>> tags in your bashrc. This will be permanent as long as that code is in your shell profile and will apply to just that shell.
B. running the shell hook to source conda (in your case the conda.sh script) in a specific terminal instance. This will ONLY impact your currently open shell and does not last.

Given the two paths to achieve step 1, we attempt to determine if we need to source conda when a user creates a new terminal or if we can just do step 2 and activate it. We do this right now by checking the conda path you have to see if its absolute or just says conda (which we either find or if you have python.condaPath it is set to this value).

The problem you are facing, where /etc/ is added is very confusing.python.condaPath is supposed to link to the executable not the sourcing script so maybe try changing that and see if it helps.

On my side, I need to determine two things.
A. Can we improve our logic so that sourcing is not attempted in your case given that conda is already sourced via your bashrc?
B. Why did we find the wrong sourcing file . /usr/etc/profile.d/conda.sh that doesn't exist instead of the correct one /usr/lib/python3.9/site-packages/conda/shell/etc/profile.d/conda.sh

Sorry for the verbose explanation and let me know if you have questions. I am going to investigate those two issues on my end and circle back. Thanks

[eleanorjboyd]

Writing down the questions has helped on my end and I have begun investigating:

It seems like your conda might have been installed via pip install conda which is abnormal but valid. The extension is finding the wrong sourcing file path because it does not look in the right place but instead attempts to concat the path to support a different installation location. I will need to add support to search in the place your conda is located. Thanks for helping me find this!

[eleanorjboyd]

Hello again! This is connected to a larger problem we were having with Conda activation which I did a rewrite of to fit with our new architecture but use prioritization like that for the old method. Can you try it again and let me know the status and the logs now that the improved version is out?

If you install the new pre-release of the python-environments extension and reload your window, you will have the new code. From there give it a try and if it doesn’t work, here are the steps to get me the necessary information for me to fix it. I have added extensive logging to hopefully make it easier:

1. use developer: set log level command to set your log level to trace
2. reload your window
3. copy all the logs out of your python-environments extension output channel. (if you do not feel comfortable posting this I can share my email so you can reach out to me specifically or you can sanitize your logs)
4. include what you expect to happen- so I can see where it went down the wrong path.

Again, thank you so much and I hope the rewrite will be a step up from the previous implementation. Thank you

[github-actions]

Because we have not heard back with the information we requested, we are closing this issue for now. If you are able to provide the info later on, then we will be happy to re-open this issue to pick up where we left off.

Happy Coding!