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bug#42920: conda 4.8.3 on guix cannot activate environments

From: Hugo Buddelmeijer
Subject: bug#42920: conda 4.8.3 on guix cannot activate environments
Date: Thu, 20 Aug 2020 18:39:05 +0200

Hi Ricardo,

On Wed, 19 Aug 2020 at 12:07, Ricardo Wurmus <rekado@elephly.net> wrote:

> The conda 4.8.3 package on guix does not seem to work as expected.

Thanks for letting me know.  The upgrade took a long time and required
quite a bit of patching.

Thanks for doing this hard work! It is much appreciated, I don't think I would have started experimenting with guix without your head start.
> But activating it does not work properly:
> hugo@alex ~$ conda activate testenv
> CommandNotFoundError: Your shell has not been properly configured to use
> 'conda activate'.
> To initialize your shell, run
>     $ conda init <SHELL_NAME>

This is very unfortunate, but perhaps we can work around this.
Initially I noticed that almost none of the Conda features worked
without “conda init”, so I decided to run “conda init” as part of the
build.  This installs a whole bunch of shell initialization files into
the prefix directory, which — I assume — are meant to be evaluated when
the shell starts.

So I suspect that you can get around this by manually sourcing the
appropriate shell init files.  Which of these need to be sourced
probably depends on your current shell.

That indeed kinda works. `conda init bash` adds this to `.bashrc` (apparently before asking for the sudo password):

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
    if [ -f "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/conda.sh" ]; then
        . "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/conda.sh"
        export PATH="/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin:$PATH"
unset __conda_setup
# <<< conda initialize <<<

And running this will indeed allow an environment to be activated. The `testenv3` environment contains only Python:

hugo@alex ~$ which python
which: no python in (/run/setuid-programs:/home/hugo/.config/guix/current/bin:/home/hugo/.guix-profile/bin:/run/current-system/profile/bin:/run/current-system/profile/sbin)
hugo@alex ~$ source .bashrc
(base) conda activate testenv3
(testenv3) which python
(testenv3) python
-bash: /home/hugo/.conda/envs/testenv3/bin/python: No such file or directory
(testenv3) readelf --all $(which python) | grep interpreter
      [Requesting program interpreter: /lib64/ld-linux-x86-64.so.2]

So there are three problems:

1. The PATHS in .bashrc should be to ~/.guix-profile/etc/profile.d/, not to /gnu/store directly. This is trivial to fix manually.

2. The prompt is not set correctly, as in, what should happen is that the current conda environment is added to the prompt. Instead, the prompt is replaced entirely by the environment. This shouldn't be too hard to fix manually though.

3. The installed software does not have the proper interpreter set. This can probably be fixed with patchelf, but now I'm wondering whether this is the right approach, because that would be necessary for all packages installed through conda. (Or is there a way to do that automatically? Apparently just symlinking ld-linux-x86.so.2 into (from?) /lib64 also works, but that feels like a very un-guixy hack.)

Sidenote, FWIW, there are also some problems with some of the scripts installed in /gnu/store:

hugo@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda
-bash: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/python: bad interpreter: No such file or directory
hugo@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line 3: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-real: Permission denied
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line 3: exec: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-real: cannot execute: Permission denied

It seems not necessary to actually use these scripts though.

Ultimately it would be nice if all conda packages would be available in guix directly (as guix packages, removing the need for conda), but that is going to take a while. The above workarounds are probably sufficient to get something going until then.

Once we settle on a good way to approach this, where should we document this? As in, if we want users to ignore the complaints from conda and instead put something in their .bashrc manually, then that information should be discoverable somehow.

> FWIW, maybe it would be simpler to create a micromamba package than a conda
> package:
> https://github.com/TheSnakePit/mamba

Why not both?

Maybe I'll give it a shot. (micro)mamba is still a bit unstable it seems, but it might be a good fit for guix.


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