miniconda on Windows has newline issues when run from msys2 zsh

### Checklist

- [X] I added a descriptive title
- [X] I searched open reports and couldn't find a duplicate

### What happened?

I installed miniconda3 on a fresh Windows machine, which has msys2. In the installer, I selected not to add miniconda to $PATH. In my user environment (in the registry) I add the necessary dirs (`~/miniconda3` and `~/miniconda3/Scripts`) to $PATH. 
In my `.zshrc` I try to set up miniconda like this:
```
 eval $($HOME/miniconda3/Scripts/conda shell.zsh hook)
```
but that fails because of `\r` (CR) characters in the output of `cygpath` and the conda exe. 
As a workaround, I put the output of the `shell.zsh hook` command into a tmp shell script and added 4 calls to `|tr -d '\r'`, i.e. remove the extraneous CRs. Now that script works to set up conda in my msys zsh; I can activate, deactivate, and use python.

I'm not sure where to patch miniconda itself, but here is my modified script. See the `tr` calls. I think you could add these always without issue on other systems (Mac, Linux) as long as they can find `tr`.

```zsh
export CONDA_EXE="$(cygpath 'C:\Users\garyo\miniconda3\Scripts\conda.exe' | tr -d '\r')"
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE="$(cygpath 'C:\Users\garyo\miniconda3\python.exe' | tr -d '\r')"

# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
__conda_exe() (
    "$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
)

__conda_hashr() {
    if [ -n "${ZSH_VERSION:+x}" ]; then
        \rehash
    elif [ -n "${POSH_VERSION:+x}" ]; then
        :  # pass
    else
        \hash -r
    fi
}

__conda_activate() {
    if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
        # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
        # after conda updated to >= 4.4. See issue #6173.
        PS1="$CONDA_PS1_BACKUP"
        \unset CONDA_PS1_BACKUP
    fi
    \local ask_conda
    ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@" | tr -d '\r')" || \return
    \eval "$ask_conda"
    __conda_hashr
}

__conda_reactivate() {
    \local ask_conda
    ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate | tr -d '\r')" || \return
    \eval "$ask_conda"
    __conda_hashr
}

conda() {
    \local cmd="${1-__missing__}"
    case "$cmd" in
        activate|deactivate)
            __conda_activate "$@"
            ;;
        install|update|upgrade|remove|uninstall)
            __conda_exe "$@" || \return
            __conda_reactivate
            ;;
        *)
            __conda_exe "$@"
            ;;
    esac
}

if [ -z "${CONDA_SHLVL+x}" ]; then
    \export CONDA_SHLVL=0
    # In dev-mode CONDA_EXE is python.exe and on Windows
    # it is in a different relative location to condabin.
    if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
        PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
    else
        PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
    fi
    \export PATH

    # We're not allowing PS1 to be unbound. It must at least be set.
    # However, we're not exporting it, which can cause problems when starting a second shell
    # via a first shell (i.e. starting zsh from bash).
    if [ -z "${PS1+x}" ]; then
        PS1=
    fi
fi

conda activate base
```

### Conda Info

```shell
active environment : None
            shell level : 0
       user config file : C:\Users\garyo\.condarc
 populated config files :
          conda version : 23.10.0
    conda-build version : not installed
         python version : 3.11.5.final.0
       virtual packages : __archspec=1=x86_64
                          __win=0=0
       base environment : C:\Users\garyo\miniconda3  (writable)
      conda av data dir : C:\Users\garyo\miniconda3\etc\conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\Users\garyo\miniconda3\pkgs
                          C:\Users\garyo\.conda\pkgs
                          C:\Users\garyo\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\garyo\miniconda3\envs
                          C:\Users\garyo\.conda\envs
                          C:\Users\garyo\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/23.10.0 requests/2.31.0 CPython/3.11.5 Windows/10 Windows/10.0.22631 solver/libmamba conda-libmamba-solver/23.11.1 libmambapy/1.5.3
          administrator : False
             netrc file : None
           offline mode : False
```


### Conda Config

```shell
--nothing here--
```


### Conda list

```shell
# packages in environment at C:\Users\garyo\miniconda3:
#
# Name                    Version                   Build  Channel
archspec                  0.2.1              pyhd3eb1b0_0    defaults
boltons                   23.0.0          py311haa95532_0    defaults
brotli-python             1.0.9           py311hd77b12b_7    defaults
bzip2                     1.0.8                he774522_0    defaults
ca-certificates           2023.08.22           haa95532_0    defaults
certifi                   2023.7.22       py311haa95532_0    defaults
cffi                      1.15.1          py311h2bbff1b_3    defaults
charset-normalizer        2.0.4              pyhd3eb1b0_0    defaults
colorama                  0.4.6           py311haa95532_0    defaults
conda                     23.10.0         py311haa95532_0    defaults
conda-content-trust       0.2.0           py311haa95532_0    defaults
conda-libmamba-solver     23.11.1         py311haa95532_0    defaults
conda-package-handling    2.2.0           py311haa95532_0    defaults
conda-package-streaming   0.9.0           py311haa95532_0    defaults
console_shortcut_miniconda 0.1.1                haa95532_1    defaults
cryptography              41.0.3          py311h89fc84f_0    defaults
fmt                       9.1.0                h6d14046_0    defaults
idna                      3.4             py311haa95532_0    defaults
jsonpatch                 1.32               pyhd3eb1b0_0    defaults
jsonpointer               2.1                pyhd3eb1b0_0    defaults
libarchive                3.6.2                hb62f4d4_2    defaults
libcurl                   8.1.1                h86230a5_0    defaults
libffi                    3.4.4                hd77b12b_0    defaults
libiconv                  1.16                 h2bbff1b_2    defaults
libmamba                  1.5.3                hcd6fe79_0    defaults
libmambapy                1.5.3           py311h77c03ed_0    defaults
libsolv                   0.7.24               h23ce68f_0    defaults
libssh2                   1.10.0               he2ea4bf_2    defaults
libxml2                   2.10.4               h0ad7f3c_1    defaults
lz4-c                     1.9.4                h2bbff1b_0    defaults
menuinst                  1.4.19          py311h59b6b97_1    defaults
openssl                   3.0.12               h2bbff1b_0    defaults
packaging                 23.1            py311haa95532_0    defaults
pcre2                     10.42                h0ff8eda_0    defaults
pip                       23.3            py311haa95532_0    defaults
pluggy                    1.0.0           py311haa95532_1    defaults
powershell_shortcut_miniconda 0.0.1                haa95532_1    defaults
pybind11-abi              4                    hd3eb1b0_1    defaults
pycosat                   0.6.6           py311h2bbff1b_0    defaults
pycparser                 2.21               pyhd3eb1b0_0    defaults
pyopenssl                 23.2.0          py311haa95532_0    defaults
pysocks                   1.7.1           py311haa95532_0    defaults
python                    3.11.5               he1021f5_0    defaults
reproc                    14.2.4               hd77b12b_1    defaults
reproc-cpp                14.2.4               hd77b12b_1    defaults
requests                  2.31.0          py311haa95532_0    defaults
ruamel.yaml               0.17.21         py311h2bbff1b_0    defaults
setuptools                68.0.0          py311haa95532_0    defaults
sqlite                    3.41.2               h2bbff1b_0    defaults
tk                        8.6.12               h2bbff1b_0    defaults
tqdm                      4.65.0          py311h746a85d_0    defaults
truststore                0.8.0           py311haa95532_0    defaults
tzdata                    2023c                h04d1e81_0    defaults
urllib3                   1.26.18         py311haa95532_0    defaults
vc                        14.2                 h21ff451_1    defaults
vs2015_runtime            14.27.29016          h5e58377_2    defaults
wheel                     0.41.2          py311haa95532_0    defaults
win_inet_pton             1.1.0           py311haa95532_0    defaults
xz                        5.4.2                h8cc25b3_0    defaults
yaml-cpp                  0.8.0                hd77b12b_0    defaults
zlib                      1.2.13               h8cc25b3_0    defaults
zstandard                 0.19.0          py311h2bbff1b_0    defaults
zstd                      1.5.5                hd43e919_0    defaults
```


### Additional Context

Windows 11 Home, msys2 in `c:/msys64`

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

miniconda on Windows has newline issues when run from msys2 zsh #13391

Checklist

What happened?

Conda Info

Conda Config

Conda list

Additional Context

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

miniconda on Windows has newline issues when run from msys2 zsh #13391

Description

Checklist

What happened?

Conda Info

Conda Config

Conda list

Additional Context

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions