mise removes $VIRTUAL_ENV in zsh/bash

[teaVeloper]

Describe the bug

When I am using zsh and 'initialize' mise (eval "$(mise activate zsh)") whenever I cd in or out of a folder with a .mise.toml or .tools-version file my $VIRTUAL_ENV varible is removed. It happens even on the 'eval' command as well.

I tried it with bash too, seems to do the same.

To Reproduce

my config files:
.mise.toml

[tools]
python = ['3.9', '3.10', '3.11']

~/.config/mise/config.toml

[tools]
python = ["3.10", "3.9", "3.11", "3.12"]
poetry = "1.6.1"
spark = "3.3.3"
java = "adoptopenjdk-11.0.16+8"
nodej = "20.6.0"
pipx = "1.6.0"

source any virtualenvironment
source path/to/venv/bin/activate

echo $VIRTUAL_ENV

path/to/venv

either have mise activated and be in a folder with the given .mise.toml:
cd ..
echo $VIRTUAL_ENV

``

or run:
eval "$(mise activate zsh)"
echo $VIRTUAL_ENV

``

while when I do
cd .. - now I am in a folder without .mise.toml
source path/to/venv/bin/activate
echo $VIRTUAL_ENV

path/to/venv

cd .. - again a folder without .mise.toml
echo $VIRTUAL_ENV

path/to/venv

A more detailed dump of me exploring is on the bottom.

Expected behavior
If not configured to automatically 'activate' or 'deactivate' virtual environments in 'python' to not touch the environment variable.
I guess $PATH modification in both cases is to be expected, as this is what 'mise' does when not using 'shims', maybe though, the modification should take into account if $VIRTUAL_ENV is set? (But I guess that would be more a feature request than this bug report?).

Maybe this is also intended behaviour, to not confuse having $VIRTUAL_ENV set, but pointing with $PATH to another python-interpreter?
The current behaviour definitely avoids somewhat problems for this case and if a the prompt shows the current virtual env by using the variable, at least one sees it immediately.
I would expect to still keep my sourced virtual env active, when traversing the file system.

mise doctor output

version: 2024.9.2 linux-x64 (2024-09-11)
activated: yes
shims_on_path: no

build_info: 
  Target: x86_64-unknown-linux-gnu
  Features: DEFAULT, NATIVE_TLS
  Built: Wed, 11 Sep 2024 23:13:29 +0000
  Rust Version: rustc 1.81.0 (eeb90cda1 2024-09-04) (Homebrew)
  Profile: release

shell: 
  /usr/bin/zsh
  zsh 5.8.1 (x86_64-ubuntu-linux-gnu)

dirs: 
  data: ~/.local/share/mise
  config: ~/.config/mise
  cache: ~/.cache/mise
  state: ~/.local/state/mise
  shims: ~/.local/share/mise/shims

config_files: 
  ~/.config/mise/config.toml
  ~/path/to/****/libraries/my-project/.mise.toml

backends: 
  cargo
  core
  go
  npm
  pipx
  spm
  ubi
  vfox

plugins: 
  poetry  https://github.com/mise-plugins/mise-poetry.git#431c335
  usage   https://github.com/jdx/mise-usage.git#fe3888a

toolset: 
  python@3.9.20         
  python@3.10.12        
  python@3.11.10        
  poetry@1.6.1          
  spark@3.3.3           (missing)
  java@adoptopenjdk-11.0.16+8  
  nodej@20.6.0          (missing)
  pipx@1.6.0            (missing)

env_vars: 
  MISE_SHELL=zsh

settings: 
  activate_aggressive = false
  all_compile = false
  always_keep_download = false
  always_keep_install = false
  asdf = true
  asdf_compat = false
  cargo_binstall = true
  color = true
  disable_default_shorthands = false
  disable_hints = []
  disable_tools = []
  experimental = false
  go_default_packages_file = "~/.default-go-packages"
  go_download_mirror = "https://dl.google.com/go"
  go_repo = "https://github.com/golang/go"
  go_set_gopath = false
  go_set_goroot = true
  go_skip_checksum = false
  http_timeout = 30
  jobs = 4
  legacy_version_file = true
  legacy_version_file_disable_tools = []
  libgit2 = true
  node_compile = false
  not_found_auto_install = true
  paranoid = false
  pipx_uvx = false
  plugin_autoupdate_last_check_duration = "7d"
  python_default_packages_file = "~/.default-python-packages"
  python_pyenv_repo = "https://github.com/pyenv/pyenv.git"
  raw = false
  trusted_config_paths = []
  quiet = false
  use_versions_host = true
  verbose = false
  vfox = false
  yes = false
  ci = false
  debug = false
  trace = false
  log_level = "info"
  python_venv_auto_create = false

  [status]
  missing_tools = "if_other_versions_installed"
  show_env = false
  show_tools = false

No warnings found
No problems found

Additional context
I tried it with an older version, there was the same behavior, then I updated mise and the behavior was still the same.
For comparison I started a bash to see if things are different there, and they are.

I tried with both .tools-versions and .mise.toml as config files locally.

Here a dump from my environment, with some censoring

mise was not initialized in this shell, to show it better:

# no mise initialized
❯ echo $PATH
/home/*****/.cache/antidote/https-COLON--SLASH--SLASH-github.51.al-SLASH-romkatv-SLASH-zsh-bench:/home/*****/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/home/linuxbrew/.linuxbrew/bin:/home/*****/.local/share/go/bin:/home/*****/.local/share/cargo/bin:/usr/local:/home/*****/.poetry/bin:/home/*****/.local/bin:/home/*****/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/*****/.rye/shims:/home/*****/.cargo/bin:/home/*****/.local/bin:/home/*****/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin:/bin:/home/*****/.fzf/bin

❯ which python
/home/*****/.rye/shims/python
# here I have ryes python version

❯ z html
# I jump into my project

~/path/to/****/libraries/my-project ****-***
❯ ls .mise.toml
.mise.toml

~/path/to/****/libraries/my-project ****-***
❯ source /home/*****/.local/share/virtualenvs/my-project/bin/activate

~/path/to/****/libraries/my-project ****-***
❯ which python
/home/*****/.local/share/virtualenvs/my-project/bin/python
# Now we have my venvs python

~/path/to/****/libraries/my-project ****-***
❯ echo $PATH
/home/*****/.local/share/virtualenvs/my-project/bin:/home/*****/.cache/antidote/https-COLON--SLASH--SLASH-github.51.al-SLASH-romkatv-SLASH-zsh-bench:/home/*****/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/home/linuxbrew/.linuxbrew/bin:/home/*****/.local/share/go/bin:/home/*****/.local/share/cargo/bin:/usr/local:/home/*****/.poetry/bin:/home/*****/.local/bin:/home/*****/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/*****/.rye/shims:/home/*****/.cargo/bin:/home/*****/.local/bin:/home/*****/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin:/bin:/home/*****/.fzf/bin

~/path/to/****/libraries/my-project ****-***
❯ echo $VIRTUAL_ENV
/home/*****/.local/share/virtualenvs/my-project
# The venv works

~/path/to/****/libraries/my-project ****-***
❯ cd ..

~/path/to/****/libraries
❯ ls .mise.toml
ls: cannot access '.mise.toml': No such file or directory

~/path/to/****/libraries
❯ echo $VIRTUAL_ENV
/home/*****/.local/share/virtualenvs/my-project
# Nothing changed by changing dir 

~/path/to/****/libraries
❯ eval "$(mise activate zsh)"
# Mise is activated

~/path/to/****/libraries 
❯ echo $VIRTUAL_ENV

# My venv is deleted

~/path/to/****/libraries
❯ echo $PATH       
/home/*****/.local/share/mise/installs/python/3.10/bin:/home/*****/.local/share/mise/installs/python/3.9/bin:/home/*****/.local/share/mise/installs/python/3.11/bin:/home/*****/.local/share/mise/installs/python/3.12/bin:/home/*****/.local/share/mise/installs/poetry/1.6.1/bin:/home/*****/.local/share/mise/installs/java/adoptopenjdk-11.0.16+8/bin:/home/*****/.local/share/virtualenvs/my-project/bin:/home/*****/.cache/antidote/https-COLON--SLASH--SLASH-github.51.al-SLASH-romkatv-SLASH-zsh-bench:/home/*****/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/home/linuxbrew/.linuxbrew/bin:/home/*****/.local/share/go/bin:/home/*****/.local/share/cargo/bin:/usr/local:/home/*****/.poetry/bin:/home/*****/.local/bin:/home/*****/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/*****/.rye/shims:/home/*****/.cargo/bin:/home/*****/.local/bin:/home/*****/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin:/bin:/home/*****/.fzf/bin
# My path is changed

~/path/to/****/libraries
❯ source /home/*****/.local/share/virtualenvs/my-project/bin/activate
# I activate my venv again


~/path/to/****/libraries
❯ echo $VIRTUAL_ENV
/home/*****/.local/share/virtualenvs/my-project

~/path/to/****/libraries
❯ cd -
~/path/to/****/libraries/my-project

~/path/to/****/libraries/my-project ****-***
❯ echo $VIRTUAL_ENV


# After changing dir, my virtual env is modified

~/path/to/****/libraries/my-project ****-***
❮ cd ..

~/path/to/****/libraries
❯ ls .mise.toml
ls: cannot access '.mise.toml': No such file or directory

# now I am in a folder with no mise config file
~/path/to/****/libraries
❯ source /home/*****/.local/share/virtualenvs/my-project/bin/activate


~/path/to/****/libraries
❯ echo $VIRTUAL_ENV
/home/*****/.local/share/virtualenvs/my-project

~/path/to/****/libraries
❮ cd ..

~/path/to/****
❯ ls .mise.toml
ls: cannot access '.mise.toml': No such file or directory

~/path/to/****
❯ echo $VIRTUAL_ENV
/home/*****/.local/share/virtualenvs/my-project

# Traversing the filesystem in between folders with no mise config file does not break venv