bug#42920: conda 4.8.3 on guix cannot activate environments

bug#42920: conda 4.8.3 on guix cannot activate environments

[Hugo Buddelmeijer]

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Dear Ricardo et al.,

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

Conda info:

hugo@alex ~$ which conda
/home/hugo/.guix-profile/bin/conda
hugo@alex ~$ realpath $(which conda)
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda
hugo@alex ~$ conda -V
conda 4.8.3


Creating an environment works fine:

hugo@alex ~$ conda create -n testenv -y
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/hugo/.conda/envs/testenv

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate testenv
#
# To deactivate an active environment, use
#
#     $ conda deactivate


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>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running
'conda init'.


Unfortunately, conda init does not work well, because it needs root access:

hugo@alex ~$ conda init bash --dry-run
no change
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda
modified
 /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda
modified
 /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda-env
modified
 /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate
modified
 /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/deactivate
no change
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/conda.sh
no change
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/fish/conf.d/conda.fish
no change
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/shell/condabin/Conda.psm1
no change
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/shell/condabin/conda-hook.ps1
no change
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/lib/python3.8/site-packages/xontrib/conda.xsh
no change
/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/conda.csh
modified      /home/hugo/.bashrc

==> For changes to take effect, close and re-open your current shell. <==


The last change of the conda package seems to be 638ef1e81d8 from August 13.

This is my first week with guix, so I'm not even sure where to begin to
debug this.

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

Cheers,
Hugo

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bug#42920: conda 4.8.3 on guix cannot activate environments

[Ricardo Wurmus]

Hi Hugo,

> 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.

> 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.

> Unfortunately, conda init does not work well, because it needs root
> access: […]

Yeah, it’s a terrible design decision on the part of the Conda
developers.  Luckily you won’t need any of that because we already
installed all these files at build time.

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

Why not both?

-- 
Ricardo

bug#42920: conda 4.8.3 on guix cannot activate environments

[Hugo Buddelmeijer]

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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"
else
    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"
    else
        export
PATH="/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin:$PATH"
    fi
fi
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)
(testenv3) which python
/home/hugo/.conda/envs/testenv3/bin/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.

Cheers,
Hugo

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bug#42920: conda 4.8.3 on guix cannot activate environments

[Ricardo Wurmus]

Hugo Buddelmeijer <hugo@buddelmeijer.nl> writes:

> 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.

Perhaps we can replace these locations with
${GUIX_PROFILE:-/gnu/store/…} just as we do in our generated etc/profile
file.

> 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.

Weird!  Is this something Conda does wrong because it assumes too much
about the existing prompt?

> 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.)

There’s nothing we can do about this in a general fashion.  Creating a
link from /lib64/ld-linux-x86-64.so.2 to the loader in the glibc package
is indeed what is necessary on Guix System.  If you don’t like to do
this manually, you can use the extra-special-file service.

> 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.

Would be good to fix them, though.  The activate script may just need a
chmod.  Obviously, the bin/python thing is dead wrong — I must have
missed that instance of prefix confusion that litters the Conda code
base.

> 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.

We shouldn’t need to document this at all; we should patch Conda to do
mostly the right thing.  This involves limiting “conda init” to
user-level changes.

-- 
Ricardo

bug#42920: conda 4.8.3 on guix cannot activate environments

[Hugo Buddelmeijer]

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Just sharing a bit of more info about why the conda prompt breaks.

On Fri, 21 Aug 2020 at 05:52, Ricardo Wurmus <rekado@elephly.net> wrote:

>
> Hugo Buddelmeijer <hugo@buddelmeijer.nl> writes:
>
> > 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.
>
> Weird!  Is this something Conda does wrong because it assumes too much
> about the existing prompt?
>

This is what happens, reducing the files to the essence:

1) .bashrc runs

__conda_setup="$('/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda'
'shell.bash' 'hook' 2> /dev/null)"
eval "$__conda_setup"

2) __conda_setup runs

__conda_activate() {
    ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix
"$cmd" "$@")" || \return $?
    \eval "$ask_conda"
}
conda activate base

3) ask_conda will contain the new PS1 definition. The command ran to create
ask_conda  is

PS1="\u@\h \w\$"
"/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda"
shell.posix "activate" "base"

4) conda runs

#!/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash
export PYTHONPATH="/gnu/store....."
exec -a "$0"
"/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.conda-real"
"$@"

5) .conda.real generates the prompt in Python:

from conda.cli import main
sys.exit(main())

6) .conda.real outputs
PS1='(base) '
export PATH='...

The problem with the prompt arises from step 4), because 'conda' has bash
as interpreter, and "non-interactive bashes go out of their way to unset
PS1":
https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1
https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html

So .conda.real never gets the PS1 variable and it disappears.

I don't really understand why there is a bash function, a conda bash script
and a .conda-real python script.

My local miniconda 4.8.3 installation on an Ubuntu machine (in my home
directory) does not have a ".conda-real": "conda" directly is the Python
script, so everything works.

Maybe more later.

Hugo



> --
> Ricardo
>

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bug#42920: conda 4.8.3 on guix cannot activate environments

[Ricardo Wurmus]

Hi Hugo,

> The problem with the prompt arises from step 4), because 'conda' has bash
> as interpreter, and "non-interactive bashes go out of their way to unset
> PS1":
> https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1
> https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html

Good sleuthing!

> So .conda.real never gets the PS1 variable and it disappears.
>
> I don't really understand why there is a bash function, a conda bash script
> and a .conda-real python script.

That’s because we wrap application to ensure that they run with expected
environment variables.  By default this wrapper is implemented as a Bash
script, but we also have “wrap-script”, which turns scripts using “#” as
a comment character into polyglottal Guile scripts, setting variables
with Guile and then reexecuting themselves with the actual interpreter.

Not sure if that would help here.

(There also have been reports about “wrap-script” being buggy, but I
don’t recall any details.)

-- 
Ricardo

bug#42920: conda 4.8.3 on guix cannot activate environments

[Hugo Buddelmeijer]

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Hi Ricardo,

On Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <rekado@elephly.net> wrote:

>
> > The problem with the prompt arises from step 4), because 'conda' has bash
> > as interpreter, and "non-interactive bashes go out of their way to unset
> > PS1":
> >
> https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1
> > https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html
>
> Good sleuthing!
>
> > So .conda.real never gets the PS1 variable and it disappears.


I did some more experiments, and forcing the wrapper script to start in
interactive mode solves the problem.

`conda init` adds some things to `.bashrc`, in particular it `eval`s the
output from `conda shell.bash hook`, which creates the `conda` bash
function (and associated functions).

The output from `conda shell.bash hook` seems to be based on
`/etc/profile.d/conda.sh`:
https://github.com/conda/conda/blob/master/conda/shell/etc/profile.d/conda.sh
As in, it prefixes some environment variables and appends the activation of
the base environment.

Now if we replace all 5 occurances of
"$CONDA_EXE" $_CE_M $_CE_CONDA
in that file with
bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA
then everything works as expected.

The -i is to enable interactive mode, preventing PS1 from being eaten.
--norc is necessary to not source .bashrc.
There are two occurences of "$CONDA_EXE" that should not be replaced, hence
adding the CE variables.

Would editing files like that be possible in a guix package script?

It seems that it is only a simple sed replace on a single file. It is a bit
hackish, because it adds knowledge to the package that a) there is a
wrapper script and b) it is in bash.

I have only experimented with it by copying the output off `conda
shell.bash hook` to a file in my home directory and editing that. Maybe I
can try to update the package too.

Other options:
- Use some other sh than bash, one that does not eat PS1, (e.g. dash) as
wrapper script. I just verified that *all* wrappers on my machine are bash.
However, some are using bash-minimal, so that means that there is a choice,
so maybe switching shells is possible?
- Somehow let conda work with another variable than PS1. Seems more
complicated.

Then what is left is updating `conda init` such that
- it doesn't complain when it cannot edit files
- it only uses paths in ~/.guix-profile
but this is not essential to get conda to work.

Cheers,
Hugo

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bug#42920: conda 4.8.3 on guix cannot activate environments

[Hugo Buddelmeijer]

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Hi Ricardo et al.,

I've not yet looked into updating the conda package, but want to add a
small thing to the bug report, so it can easily be found.

Lines in the sourced conda.sh script like the one below won't work anymore
once the conda executable is wrapped in the guix shell script, because PS1
is eaten by the wrapper:

    "$CONDA_EXE" $_CE_M $_CE_CONDA

It is necessary to explicitly call bash in interactive mode to have PS1
available:

    bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA

However, that will add every executed line to the .bash_history file,
including very long "export PYTHONPATH" lines. This can be avoided by
explicitly setting the history file to nothing:

    HISTFILE= bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA

Cheers,
Hugo


On Tue, 25 Aug 2020 at 17:03, Hugo Buddelmeijer <hugo@buddelmeijer.nl>
wrote:

> Hi Ricardo,
>
> On Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <rekado@elephly.net> wrote:
>
>>
>> > The problem with the prompt arises from step 4), because 'conda' has
>> bash
>> > as interpreter, and "non-interactive bashes go out of their way to unset
>> > PS1":
>> >
>> https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1
>> > https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html
>>
>> Good sleuthing!
>>
>> > So .conda.real never gets the PS1 variable and it disappears.
>
>
> I did some more experiments, and forcing the wrapper script to start in
> interactive mode solves the problem.
>
> `conda init` adds some things to `.bashrc`, in particular it `eval`s the
> output from `conda shell.bash hook`, which creates the `conda` bash
> function (and associated functions).
>
> The output from `conda shell.bash hook` seems to be based on
> `/etc/profile.d/conda.sh`:
>
> https://github.com/conda/conda/blob/master/conda/shell/etc/profile.d/conda.sh
> As in, it prefixes some environment variables and appends the activation
> of the base environment.
>
> Now if we replace all 5 occurances of
> "$CONDA_EXE" $_CE_M $_CE_CONDA
> in that file with
> bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA
> then everything works as expected.
>
> The -i is to enable interactive mode, preventing PS1 from being eaten.
> --norc is necessary to not source .bashrc.
> There are two occurences of "$CONDA_EXE" that should not be replaced,
> hence adding the CE variables.
>
> Would editing files like that be possible in a guix package script?
>
> It seems that it is only a simple sed replace on a single file. It is a
> bit hackish, because it adds knowledge to the package that a) there is a
> wrapper script and b) it is in bash.
>
> I have only experimented with it by copying the output off `conda
> shell.bash hook` to a file in my home directory and editing that. Maybe I
> can try to update the package too.
>
> Other options:
> - Use some other sh than bash, one that does not eat PS1, (e.g. dash) as
> wrapper script. I just verified that *all* wrappers on my machine are bash.
> However, some are using bash-minimal, so that means that there is a choice,
> so maybe switching shells is possible?
> - Somehow let conda work with another variable than PS1. Seems more
> complicated.
>
> Then what is left is updating `conda init` such that
> - it doesn't complain when it cannot edit files
> - it only uses paths in ~/.guix-profile
> but this is not essential to get conda to work.
>
> Cheers,
> Hugo
>
>

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bug#42920: conda 4.8.3 on guix cannot activate environments

[Ricardo Wurmus]

We have since upgraded to 4.10.3, but the problems still persist. 
Conda still asks users to run “conda init”, which attempts to run 
“sudo” to modify root-owned files.  It’s a big mess.

Any ideas?

-- 
Ricardo

bug#42920: conda 4.8.3 on guix cannot activate environments

[zimoun]

Hi Ricardo,

On Wed, 18 Aug 2021 at 12:07, Ricardo Wurmus <rekado@elephly.net> wrote:
> We have since upgraded to 4.10.3, but the problems still persist. Conda still
> asks users to run “conda init”, which attempts to run “sudo” to modify
> root-owned files.  It’s a big mess.

What is the point to have Conda installed by Guix?


Cheers,
simon

bug#42920: conda 4.8.3 on guix cannot activate environments

[Ricardo Wurmus]

zimoun <zimon.toutoune@gmail.com> writes:

> On Wed, 18 Aug 2021 at 12:07, Ricardo Wurmus <rekado@elephly.net> wrote:
>> We have since upgraded to 4.10.3, but the problems still persist. Conda still
>> asks users to run “conda init”, which attempts to run “sudo” to modify
>> root-owned files.  It’s a big mess.
>
> What is the point to have Conda installed by Guix?

Convenience.

-- 
Ricardo

bug#42920: conda 4.8.3 on guix cannot activate environments

[Dominic Martinez]

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>> On Wed, 18 Aug 2021 at 12:07, Ricardo Wurmus 
>> <rekado@elephly.net> wrote:
>>> We have since upgraded to 4.10.3, but the problems still 
>>> persist. Conda still
>>> asks users to run “conda init”, which attempts to run “sudo” 
>>> to modify
>>> root-owned files.  It’s a big mess.

I don't think conda init will ever work on Guix, and it seems out 
of scope to try and prevent Conda from prompting users to do 
that. I was able to get conda working with the following steps:

1. Expose the glibc interpreter so that conda python can function
#+begin_src scheme
(extra-special-file "/lib64/ld-linux-x86-64.so.2"
                       (file-append glibc 
                       "/lib/ld-linux-x86-64.so.2"))
#+end_src
2. Source the conda environment variables. I do this both in my 
profile (through home-shell-profile-service-type) and through my 
rc file for interactive shells, as I think I remember having 
problems not sourcing it in both.
#+begin_src scheme
(define-public (home-profile-service script)
  "Creates a service that sources a home profile.d script provided 
  by a package."
  (simple-service 'profile.d-service
                  home-shell-profile-service-type
                  `(,(plain-file
                      (string-append script "-profile")
                      (string-append "source 
                      ~/.guix-home/profile/etc/profile.d/" script 
                      ".sh")))))

(home-profile-service "conda")
#+end_src

#+begin_src shell
source ~/.guix-home/profile/etc/profile.d/conda.sh
#+end_src

I agree that this setup is not ideal, but I think that guix home 
has the promise of fixing a lot of these issues with home 
services! Hopefully in the near future we'll be able to turn these 
fixed into services for users.

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bug#42920: conda 4.8.3 on guix cannot activate environments

[Ricardo Wurmus]

Dominic Martinez <dom@dominicm.dev> writes:

> [[PGP Signed Part:Undecided]]
>
>>> On Wed, 18 Aug 2021 at 12:07, Ricardo Wurmus 
>>> <rekado@elephly.net> wrote:
>>>> We have since upgraded to 4.10.3, but the problems still 
>>>> persist. Conda still
>>>> asks users to run “conda init”, which attempts to run “sudo” 
>>>> to modify
>>>> root-owned files.  It’s a big mess.
>
> I don't think conda init will ever work on Guix

Why?  It used to work just fine IIRC.  The fact that it tries to write
to root-owned files is arguably a bug in Conda.

-- 
Ricardo