Micromamba >v1.4.5 broken with cygwin

[0xbe7a]

Troubleshooting docs

• My problem is not solved in the Troubleshooting docs

How did you install Mamba?

Micromamba

Search tried in issue tracker

yes

Latest version of Mamba

• My problem is not solved with the latest version

Tried in Conda?

Not applicable

Describe your issue

I'm using micromamba with cygwin. My .bash_profile looks like

# >>> mamba initialize >>>
# !! Contents within this block are managed by 'mamba init' !!
export MAMBA_EXE='/cygdrive/c/Users/USER/.bin/micromamba.exe';
export MAMBA_ROOT_PREFIX='/cygdrive/c/Users/USER/micromamba_prefix';
eval "$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX")"
# <<< mamba initialize <<<

With micromamba <=1.4.5 shell hook --shell bash checked if !hook_source_path().empty() and if true just emitted the file shell hook without substituting $MAMBA_EXE. Only if hook_source_path() was empty would get_hook_contents be used to emit the shell hook. Crucially get_hook_contents replaced $MAMBA_EXE with the path to the binary on its own. However, this produces a broken config, as the replaced path is in windows format which cant be opened by cygwins bash. PR #2631 changed the behavior of shell hook so that get_hook_contents is always used which breaks my cygwin config.

I'm not really sure how to tackle this problem, but i think a --no-replace option for shell hook would solve my issue.

mamba info / micromamba info

No response

Logs

No response

environment.yml

No response

~/.condarc

No response

[jonashaag]

I think we should use the equivalent of cygpath -u for get_hook_contents in bash

[jonashaag]

I wonder why this hasn't been found in the tests.

[AntoinePrv]

Thank you for reporting @0xbe7a

If I understand correctly, the issue can be solved by using /unix/like/paths?
More precisely changing the format here?
I think it is safe to make it always unix-like when using unix shells.

[0xbe7a]

Yes, i think the assumption should hold in general and would solve my issue!

[AntoinePrv]

@0xbe7a could you try #2685 locally?

[0xbe7a]

I can't build micromamba in the enterprise environment im in. I could test out the artifacts from the CI builds, however the CI Build micromamba - win-64 is failing

[AntoinePrv]

I could test out the artifacts from the CI builds, however the CI Build micromamba - win-64 is failing

That should be a temporary VCPKG issue 🤞

[pavelzw]

That should be a temporary VCPKG issue 🤞

Let's hope microsoft/vcpkg#32600 is fixed soon 😅

[0xbe7a]

The PR still replaces the $MAMBA_EXE with a path in windows format

~ $ micromamba shell hook --shell=bash micromamba_prefix/

# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause

__mamba_exe() (
    "C:\Users\USER\micromamba.exe" "${@}"
)

After discovering more issues with cygwins cygdrive i abandonned cygwin for gits bash.exe. gits bash.exe can handle paths in windows format so micromamba 1.4.9 works.

[jonashaag]

I'll reopen because it's not fixed.

[goyalyashpal]

as this is related with unix shells on windows, saying just for recrods; that micromamba 1.4.9 works fine with msys2 3.4.7.x86_64.

[vickunwu]

as this is related with unix shells on windows, saying just for recrods; that micromamba 1.4.9 works fine with msys2 3.4.7.x86_64.

@goyalyashpal Hello friend. I'm using msys2 with zsh as shell(not Git Bash) but I cannot get micromamba working. Could you please give me some instructions about the details of how to make it run? Appreciate it a lot.

[goyalyashpal]

I'm using msys2 with zsh as shell(not Git Bash) but I cannot get micromamba working

hi! i may have helped, but i don't have enough information. read here: https://tinyurl.com/stack-checklist/ and here: http://catb.org/~esr/faqs/smart-questions.html#beprecise

[vickunwu]

I'm using msys2 with zsh as shell(not Git Bash) but I cannot get micromamba working

hi! i may have helped, but i don't have enough information. read here: https://tinyurl.com/stack-checklist/

@goyalyashpal
I've managed to get the micromamba auto completion works by modifying the following line in my rc file:
eval "$("$MAMBA_EXE" shell hook --shell ${SHELL##*/} --root-prefix "$MAMBA_ROOT_PREFIX" | sed "s#$(cygpath -w $MAMBA_EXE|sed 's|\\|\\\\|g')#$MAMBA_EXE#g")"

The reason I did this is that msys2 do not recognize windows path (e.g. 'C:\micromamba\micromamba.exe') that called in the shell hook.

But when I tried to activate a certain env, here's the output:

(eval):.:7: no such file or directory: C:\Users\vickunwu\scoop\persist\micromamba\mamba\envs\whisperx\etc\conda\activate.d\openssl_activate.sh^M

I guess it's the same issue but this time I'm not able to do hacks anymore as it's controlled by the program.

[goyalyashpal]

micromamba auto completion works
I tried to activate a certain env, here's the output:

$ micromamba activate 
critical libmamba Shell not initialized

'micromamba' is running as a subprocess and can't modify the parent shell. 
Thus you must initialize your shell before using activate and deactivate.  

To initialize the current bash shell, run:
    $ eval "$(micromamba shell hook --shell bash)"
and then activate or deactivate with:
    $ micromamba activate
To automatically initialize all future (bash) shells, run:
    $ micromamba shell init --shell bash --root-prefix=~/micromamba        
If your shell was already initialized, reinitialize your shell with:       
    $ micromamba shell reinit --shell bash
Otherwise, this may be an issue. In the meantime you can run commands. See:
    $ micromamba run --help

Supported shells are {bash, zsh, csh, xonsh, cmd.exe, powershell, fish}.   

$ eval "$(micromamba shell hook --shell bash)"

$ micromamba activate 
warning  libmamba 'root_prefix' set with default value: C:\Users\...\micromamba
(base) 
$

sed 's|\\|\\\\|g'

why not use forward slashes?

[vickunwu]

@goyalyashpal

why not use forward slashes?

I'm not clear about where should I use forward slashes. I think '' should be processed as it's an escape character.

Here's my output of executing eval "$(micromamba shell hook -s bash)"

eval "$(micromamba shell hook -s bash)"
zsh: parse error near `^M'

I'm using msys_shell.cmd to spawn a mingw64 session in Windows terminal. Does this make a difference?

I think the output is a CRLF/LF issue. However, as the shell hook contains lines like \return, I cannot just tr -d '\r' or sed 's/\r//g'.

I've tried dos2unix but it still messes the shell hook.

[goyalyashpal]

msys_shell.cmd to spawn a mingw64 session in Windows terminal

that script is no longer required as there are dedicated .exe launchers now.

but i launch the bash session directly from konsole or wezterm terminal. konsole allows picking default shell in its settings - i picked bash there.

i have faint memory that there probably were some problems on invoking from cmd, but can't say for sure

---

also, have u tried invoking activation command from bash?

[goyalyashpal]

scoop\persist\micromamba\mamba\envs

i installed micromamba directly - without using scoop. just guessing here - that as scoop is windows only, and u seemed to be facing errors in that direction - so, maybe try direct install of micromamba too.

https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html#umamba-install

[vickunwu]

also, have u tried invoking activation command from bash?

I tried bash this time, and it works on both launcher and cmd without any problem. I guess that's a zsh issue.
Thanks for your kind assistance!

---

I'm sad to say that I use Msys2 mainly because it's native support for zsh. Otherwise, I would rather use Git Bash as it seems to have less compatibility issues.

Maybe I should open another issue.

[ThomasMarwitzQC]

@0xbe7a and I discovered a quick fix that you can use as long as this is not fixed and you don't want to abandon Cygwin:

# >>> mamba initialize >>>
# !! Contents within this block are managed by 'mamba init' !!
export MAMBA_EXE='/cygdrive/c/Users/thomas/.bin/micromamba';
export MAMBA_ROOT_PREFIX='/cygdrive/c/Users/thomas/micromamba_prefix';
eval "$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX")"
# <<< mamba initialize <<<

__mamba_exe() (
    "${MAMBA_EXE}" "${@}"
)

micromamba activate base