I have a project set up in Pycharm, with an existing conda environment. My scripts work when run from within the console.
I would like to be able to run python -m path_to_my_script/script.py from any location, but I need conda activated. Conda recommends I do conda init but I'm worried it may change settings someplace and break things.
What does conda init do?
Strategy for Answering
Exactly what the conda init command does and its consequences are shell-specific. Instead of trying to cover all cases, let's walk through a case, noting along the way that one can replicate this analysis by substituting their shell of interest.
Case Study: conda init zsh
Let's look at zsh as the shell. This is a common shell (default for macOS 10.15+) and very close to bash. Plus, I don't already have it configured.
Probing the Command: Dry Run
Many Conda commands include some form of dry run functionality via a --dry-run, -d flag, which - combined with verbosity flags - enables seeing what this would do without doing them. For the init command, dry run alone will only tell us what files it would modify:
$ conda init -d zsh
no change /Users/mfansler/miniconda3/condabin/conda
no change /Users/mfansler/miniconda3/bin/conda
no change /Users/mfansler/miniconda3/bin/conda-env
no change /Users/mfansler/miniconda3/bin/activate
no change /Users/mfansler/miniconda3/bin/deactivate
no change /Users/mfansler/miniconda3/etc/profile.d/conda.sh
no change /Users/mfansler/miniconda3/etc/fish/conf.d/conda.fish
no change /Users/mfansler/miniconda3/shell/condabin/Conda.psm1
no change /Users/mfansler/miniconda3/shell/condabin/conda-hook.ps1
no change /Users/mfansler/miniconda3/lib/python3.7/site-packages/xontrib/conda.xsh
no change /Users/mfansler/miniconda3/etc/profile.d/conda.csh
modified /Users/mfansler/.zshrc
==> For changes to take effect, close and re-open your current shell. <==
Here we can see that it plans to target the user-level resources file for zsh, /Users/mfansler/.zshrc, but it doesn't tell us how it will modified it. Also, OMG! the UX here is awful, because it in no way reflects the fact that I used the -d flag. But don't worry: as long as the -d flag is there it won't actually change things.
Patch Preview
To see what exactly it will do, add a single verbosity flag (-v) to the command. This will give everything from the previous output, but will now shows us the diff it will use to patch (update) the .zshrc file.
$ conda init -dv zsh
/Users/mfansler/.zshrc
---
+++
## -0,0 +1,16 ##
+
+# >>> conda initialize >>>
+# !! Contents within this block are managed by 'conda init' !!
+__conda_setup="$('/Users/mfansler/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+ eval "$__conda_setup"
+else
+ if [ -f "/Users/mfansler/miniconda3/etc/profile.d/conda.sh" ]; then
+ . "/Users/mfansler/miniconda3/etc/profile.d/conda.sh"
+ else
+ export PATH="/Users/mfansler/miniconda3/bin:$PATH"
+ fi
+fi
+unset __conda_setup
+# <<< conda initialize <<<
+
# ...the rest is exactly as above
That is, the plan of action is to add these 16 lines to the .zshrc file. In this case, I don't have an existing .zshrc file, so it plans to add it at line 1. If the file had already existed, it would append these lines.
Interpreting the Shell Code
Let's overview this code, before focusing on the details. Essentially, this is a redundant sequence of attempts to set up some shell functionality. They are ordered from most to least functional.
What Conda Hopes To Do
The code
__conda_setup="$('/Users/mfansler/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
gets something from conda itself, storing the result to a string, and then evaluates that string if the command had a clean exit ($? -eq 0). The neat engineering here is that the subprocess (technically python -m conda) passes back a result that can be run within this current process (zsh), allowing it to define shell functions.
I'll dig deeper into what is going on here in a second.
Fallback 1: Hardcoded Shell Functions
If that strange internal command fails, the devs included a hardcoded version of some essential shell functions (specifically conda activate). This is in:
miniconda3/etc/profile.d/conda.sh
and they simply check the file exists and source it. Let's hit that last option, then we'll swing back to look at the functionality.
Fallback 2: The Last Resort
The absolute last resort is to literally violate the standing recommendation since Conda v4.4, which is to simply put the base environment's bin directory on PATH. In this case, there is no conda activate functionality; this only ensures that Conda is on your PATH.
Details: Shell Functionality
Coming back to the intended case, we can inspect exactly what it would evaluate by simply getting that string result:
$ conda shell.zsh hook
__add_sys_prefix_to_path() {
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then
SYSP=$(\dirname "${CONDA_EXE}")
else
SYSP=$(\dirname "${CONDA_EXE}")
SYSP=$(\dirname "${SYSP}")
fi
if [ -n "${WINDIR+x}" ]; then
PATH="${SYSP}/bin:${PATH}"
PATH="${SYSP}/Scripts:${PATH}"
PATH="${SYSP}/Library/bin:${PATH}"
PATH="${SYSP}/Library/usr/bin:${PATH}"
PATH="${SYSP}/Library/mingw-w64/bin:${PATH}"
PATH="${SYSP}:${PATH}"
else
PATH="${SYSP}/bin:${PATH}"
fi
\export PATH
}
__conda_exe() (
__add_sys_prefix_to_path
"$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 "$#")" || \return
\eval "$ask_conda"
__conda_hashr
}
__conda_reactivate() {
\local ask_conda
ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \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
I'm not going to walk through all this, but the main part is that instead of directly putting bin on PATH, it defines a shell function called conda and this serves as a wrapper for the condabin/conda entrypoint. This also defines a new functionality conda activate, which uses a shell function, __conda_activate(), behind the scenes. At the final step, it then activates the base environment.
Why do it this way?
This is engineered like this in order to be responsive to the configuration settings. Configuration options like auto_activate_base and change_ps1 affect how Conda manipulates the shell, and so that changes what functionality Conda includes in its shell functions.
Does Conda "Pollute the Environment"?
Not really. The main behavioral things like auto-activation and prompt modification can be disabled through configuration settings, so that conda init ultimately just adds the conda activate function to the shell, enabling clean switching between environments without ever having to manually manipulate PATH.
Your caution may be warranted. The conda init command adds Anaconda to the path on Linux or Mac (not recommended on Windows). Anaconda FAQ
You also need to prep for conda init by running source <path to conda>/bin/activate first.
You can run your script in your desired conda environment by specifying the python environment in the shebang statement in the first line of your code.
You can get that value by activating your desired environment and executing which python
(base) -> conda activate py39
(py39) -> which python
/home/user/anaconda3/envs/py39/bin/python
The shebang would be:
#!/home/user/anaconda3/env/py39/bin/python
On Mac and Linux, once you add the shebang you can chmod the file to be executable (e.g. chmod 700 myscript.py) and run from the command line directly. (I'm not a Windows user, so ymmv.)
(base) -> <path-to-script>/myscript.py
(Which now runs in shebang virtual environment instead of base.)
Related
on my windows system I've succesfully installed a virtual environment (python version is 3.9) using windows command prompt
python -m venv C:\my_path\my_venv
Always using windows command prompt, I'm able to activate the created venv via
C:\my_path\my_venv\Scripts\activate.bat
I am sure the venv is correctly activated since:
on the windows terminal, I see the command line is preceded by (my_venv)
if I activate python from the terminal (python) and run the following commands: import sys ; sys.path I can see, in the list of paths, the desired path [..., 'C:\\my_path\\my_venv\\lib\\site-packages\\win32\\lib', ...]
if I do stuff in the activated venv (like installing packages) everything works and is done inside the venv
To sum up, everything is fine so far.
I also have WSL2 (Ubuntu) and I'd like to activate the same venv using the Ubuntu terminal.
If, from the Ubuntu terminal, I activate the venv
source /mnt/c/my_path/my_venv/Scripts/activate
it seems to work since the command line is preceeded by (my_venv), but when I run python (python3 command) and then run import sys ; sys.path I see that the system is targeting the base Ubuntu python installation (version 3.8) and not the venv installation:
['', '/usr/lib/python38.zip', '/usr/lib/python3.8', '/usr/lib/python3.8/lib-dynload', '/usr/local/lib/python3.8/dist-packages', '/usr/lib/python3/dist-packages']
The venv is not really activated. Any suggestions to solve the issue?
If it can help, I add a couple of information.
If I try to create a venv directly using the Ubuntu terminal
python3 -m venv /mnt/c/my_path/my_venv_unix
and activate it via the Ubuntu terminal (source /mnt/c/my_path/my_venv_unix/bin/activate) everything works fine, but that's not what I want: I'd like to use WSL to activate a virtual environment created using windows command prompt, since on my machine I've a lot of venvs created with windows and I don't want to replicate them.
Following the script C:\my_path\my_venv\Scripts\activate (/mnt/c/my_path/my_venv/Scripts/activate using wsl folders naming) (I had to change the EOL from windows to Ubuntu, otherwise the command source /mnt/c/my_path/my_venv/Scripts/activate would not have worked)
# This file must be used with "source bin/activate" *from bash*
# you cannot run it directly
deactivate () {
# reset old environment variables
if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then
PATH="${_OLD_VIRTUAL_PATH:-}"
export PATH
unset _OLD_VIRTUAL_PATH
fi
if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then
PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}"
export PYTHONHOME
unset _OLD_VIRTUAL_PYTHONHOME
fi
# This should detect bash and zsh, which have a hash command that must
# be called to get it to forget past commands. Without forgetting
# past commands the $PATH changes we made may not be respected
if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
hash -r 2> /dev/null
fi
if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then
PS1="${_OLD_VIRTUAL_PS1:-}"
export PS1
unset _OLD_VIRTUAL_PS1
fi
unset VIRTUAL_ENV
if [ ! "${1:-}" = "nondestructive" ] ; then
# Self destruct!
unset -f deactivate
fi
}
# unset irrelevant variables
deactivate nondestructive
VIRTUAL_ENV="C:\my_path\my_venv"
export VIRTUAL_ENV
_OLD_VIRTUAL_PATH="$PATH"
PATH="$VIRTUAL_ENV/Scripts:$PATH"
export PATH
# unset PYTHONHOME if set
# this will fail if PYTHONHOME is set to the empty string (which is bad anyway)
# could use `if (set -u; : $PYTHONHOME) ;` in bash
if [ -n "${PYTHONHOME:-}" ] ; then
_OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}"
unset PYTHONHOME
fi
if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then
_OLD_VIRTUAL_PS1="${PS1:-}"
PS1="(.venv_ml_dl_gen_purpose) ${PS1:-}"
export PS1
fi
# This should detect bash and zsh, which have a hash command that must
# be called to get it to forget past commands. Without forgetting
# past commands the $PATH changes we made may not be respected
if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
hash -r 2> /dev/null
fi
Finally, here also the script /mnt/c/my_path/my_venv_unix/bin/activate
# This file must be used with "source bin/activate" *from bash*
# you cannot run it directly
deactivate () {
# reset old environment variables
if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then
PATH="${_OLD_VIRTUAL_PATH:-}"
export PATH
unset _OLD_VIRTUAL_PATH
fi
if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then
PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}"
export PYTHONHOME
unset _OLD_VIRTUAL_PYTHONHOME
fi
# This should detect bash and zsh, which have a hash command that must
# be called to get it to forget past commands. Without forgetting
# past commands the $PATH changes we made may not be respected
if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
hash -r
fi
if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then
PS1="${_OLD_VIRTUAL_PS1:-}"
export PS1
unset _OLD_VIRTUAL_PS1
fi
unset VIRTUAL_ENV
if [ ! "${1:-}" = "nondestructive" ] ; then
# Self destruct!
unset -f deactivate
fi
}
# unset irrelevant variables
deactivate nondestructive
VIRTUAL_ENV="/mnt/c/my_path/my_venv_unix"
export VIRTUAL_ENV
_OLD_VIRTUAL_PATH="$PATH"
PATH="$VIRTUAL_ENV/bin:$PATH"
export PATH
# unset PYTHONHOME if set
# this will fail if PYTHONHOME is set to the empty string (which is bad anyway)
# could use `if (set -u; : $PYTHONHOME) ;` in bash
if [ -n "${PYTHONHOME:-}" ] ; then
_OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}"
unset PYTHONHOME
fi
if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then
_OLD_VIRTUAL_PS1="${PS1:-}"
if [ "x(venv_unix) " != x ] ; then
PS1="(venv_unix) ${PS1:-}"
else
if [ "`basename \"$VIRTUAL_ENV\"`" = "__" ] ; then
# special case for Aspen magic directories
# see https://aspen.io/
PS1="[`basename \`dirname \"$VIRTUAL_ENV\"\``] $PS1"
else
PS1="(`basename \"$VIRTUAL_ENV\"`)$PS1"
fi
fi
export PS1
fi
# This should detect bash and zsh, which have a hash command that must
# be called to get it to forget past commands. Without forgetting
# past commands the $PATH changes we made may not be respected
if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
hash -r
fi
Thanks to anyone who wants to answer!
Short answer: It's highly recommended to use the Linux version of Python and tools when in WSL. You'll find a number of posts here on Stack Overflow related to this, but your question is different enough (regarding venv) that it deserves its own answer.
More Detail:
Also worth reading this question. In that case, the question was around a dual-boot system and whether or not the same venv could be shared between Windows and Linux.
I know it seems like things might be better on WSL, where you can run Windows .executables under Linux, but it really isn't for this particular case.
You've solved the first problem, in the difference in line endings, but the next problem that you are facing is the difference in the directory format. After sourcing activate, do an echo $PATH and you'll see that the Windows style C:\path\to\the\venv path has been prepended to your PATH. For WSL, that would need to be /mnt/c/path/to/the/venv.
That's not going to work.
Once you fix that (again, by editing activate), you are still trying to run python3. The venv executable is actually python.exe. Under WSL, you do have to specify the extension.
So if you:
Change the line-endings from CRLF to LF
Change the path style in activate from Windows to WSL2 format
Use the python.exe executable
Then you can at least launch the Windows Python version. Your import sys; sys.path will show the Windows paths.
That said, you are almost certainly going to run into additional problems that don't make it worth doing this. For instance, if a script assumes python or python3, or even pip; then those are going to fail because it needs to call, e.g., pip.exe.
Line endings and native code will also be a problem.
For these reasons (and likely more), it's highly recommended to use the Linux version of Python when in WSL.
I have a Mac (latest software update) with Pyenv and Anaconda. I manage packages with Homebrew and have installed Python 3 with it. When I echo $PATH I get the following:
/Library/Frameworks/Python.framework/Versions/3.8/bin:
\ /usr/local/bin:
\ /usr/bin:
\ /bin:
\ /usr/local/sbin:
\ /usr/sbin:
\ /sbin:
\ /Library/TeX/texbin:
\ /Users/luca/.pyenv/versions/anaconda3-2020.02/condabin:
\ /Users/luca/.pyenv/versions/3.8.5/bin:
\ /Users/luca/.pyenv/bin
I do not know what sets up /Library/Frameworks/Python.framework/Versions/3.8/bin: this directory is non-existent on my Mac. I had previously installed Python without Homebrew that is why the directory was created. I did remove that, but there is still something that exports that line in $PATH, but I cannot find it! Does someone have a guess? I did try and grep -r /* it, but that is too much of a search for my laptop to finish.
I set up in my .zshenv the code for initialising pyenv and conda. Of course, I did write PATH="/dir/to/conda/bin:$PATH" and the same for pyenv (see code below). I do not understand why, but they end up at the end of $PATH. Does someone know why? Is it because of eval "$(pyenv init -)" being evaluated before conda?
# >>> pyenv initialize
export PYENV_SHELL=$SHELL
export PATH="/Users/luca/.pyenv/bin:$PATH"
export PATH="/Users/luca/.pyenv/versions/3.8.5/bin:$PATH" #export Python 3.8 bin directory
if command -v pyenv 1>/dev/null 2>&1; then
eval "$(pyenv init -)"
fi
# <<< pyenv initialize <<<
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/Users/luca/.pyenv/versions/anaconda3-2020.02/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/Users/luca/.pyenv/versions/anaconda3-2020.02/etc/profile.d/conda.sh" ]; then
. "/Users/luca/.pyenv/versions/anaconda3-2020.02/etc/profile.d/conda.sh"
else
export PATH="/Users/luca/.pyenv/versions/anaconda3-2020.02/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
I have the exact same problem, and I could not find any other source on why the conda environment gets appended instead of prepended. I have added the following code to my .bash_profile (after conda initialisation) which flips the order of all path location. This is definitely a terrible practice, but it might be a quick fix for someone who is stuck on the same problem.
locations=($(echo $PATH | tr ":" "\n"))
path=""
for (( idx=${#locations[#]}-2 ; idx>=0 ; idx-- )) ; do
# Skip the last path location since this would put the general /Users/XXX/opt/anaconda3/condabin first
# To not do this change the -2 to -1
path="${path}:${locations[$idx]}"
done
path="${path:1}"
PATH=$path
export $PATH
As noted in the comment, I do not add the location "/Users/XXX/opt/anaconda3/condabin", since it would mess up my environment location, which is located second to last. Please examine your own path variable and decide accordingly.
EDIT: If anyone has a better solution, please let me know!
TL;DR
In macOS, if you place any code that modifies $PATH on macOS inside .zshenv, it will be overridden. You should put it in .zshrc or somewhere else which is then sourced by your .zshrc.
Complete explanation
As answered on Unix & Linux Stack Exchange, when zsh is sourced, files are read in the following order:
etc/zshenv/ -> $ZDOTDIR/.zshenv/ -> etc/zprofile/ -> $ZDOTDIR/.zprofile/ -> etc/zshrc/ -> $ZDOTDIR/.zshrc/ -> etc/zlogin/ -> $ZDOTDIR/.zlogin/
In macOS's /etc/zprofile, a script is sourced that overrides the $PATH according to the contents of these files:
/etc/paths
/etc/paths.d
/etc/manpaths
/etc/manpaths.d
So you should put not put any line that changes $PATH in your $ZDOTDIR/.zshenv, but rather in any file sourced after that (e.g. $ZDOTDIR/.zshrc). Do not edit files in /etc/!
I created a new Conda environment on an x86-64 Linux mainframe, using the command
conda create --name myenv --file somefile.txt --python=3.8.
I double checked my Python version in this environment using conda list, which returns
...
python 3.8.3 hcff3b4d_0
...
However, after activating this environment, Python 3 scripts doesn't run, and running which python reveals that the environment defaults to using the default system Python 2 interpreter:
$ which python
/usr/bin/python
My Efforts So Far
First, I added the line export PATH=$PATH:/home/miniconda3/envs/myenv/bin to my ~/.bashrc and ~/.profile files, to no effect. which python still returns /usr/bin/python.
I then checked my alias file to see if python is aliased to Python 2. But there is no entry in the alias file about python.
For your reference
my ~/.bashrc looks like this:
$ cat ~/.bashrc
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=
# User specific aliases and functions
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/home/miniconda3/etc/profile.d/conda.sh" ]; then
. "/home/miniconda3/etc/profile.d/conda.sh"
else
export PATH="/home/miniconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
alias julia="/home/julia-1.4.0/bin/julia"
export PATH=$PATH:/home/miniconda3/envs/myenv/bin
$ cat ~/.bash_profile
# .bash_profile
# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi
# User specific environment and startup programs
$ cat ~/.profile
export PATH=$PATH:/home/miniconda3/envs/myenv/bin
I think you need to add your env path to the front of the PATH variable so it will find python there first. The OS will look for a file or application in the PATH list, and use the first match that it finds.
Change
export PATH=$PATH:/home/qingyanz/miniconda3/envs/myenv/bin
to this:
export PATH=/home/qingyanz/miniconda3/envs/myenv/bin:$PATH
As an example, here are the settings on my conda environment:
(ds_tensorflow) C:\Users\me>which python
/c/Users/me/miniconda3/envs/ds_tensorflow/python
(ds_tensorflow) C:\Users\me>env | grep PATH
...
PATH=/c/Users/me/miniconda3/envs/ds_tensorflow:/mingw-w64/bin:/usr/bin:/bin:...
I have trouble using anaconda environment in Tmux. I am on OSX.
I first
tmux
Then activate the Conda env:
conda activate myenv
At this point when I conda info shows the correct active environment and correct location. But which python still points to the default /usr/bin/python.
In the .bash_profile I have these lines added by anaconda when installed. So I guess I need to add something to let the terminal find the right python path?
# added by Anaconda3 5.3.1 installer
# >>> conda init >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$(CONDA_REPORT_ERRORS=false '/Users/jiajunyang/anaconda3/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
\eval "$__conda_setup"
else
if [ -f "/Users/username/anaconda3/etc/profile.d/conda.sh" ]; then
. "/Users/username/anaconda3/etc/profile.d/conda.sh"
CONDA_CHANGEPS1=false conda activate base
else
\export PATH="/Users/username/anaconda3/bin:$PATH"
fi
fi
Thank you for your suggestion.
Below works for me on macOS 10.15 with zsh:
Add below line to your ~/.tmux.conf file
set -g default-command "/bin/zsh"
If you're using a shell other than zsh, I assume changing the path to the shell you're using will also work.
same here, mac 10.14, tmux 3.0a
solution is:
source /Users/mac/opt/anaconda3/etc/profile.d/conda.sh
[[ -z $TMUX ]] ∨ conda deactivate; conda activate base
add 2 lines in your .zshrc. Then
source ~/.zshrc
everything works fine now!!
I had the same issue. Finally I find that tmux will always call the profile for your shell, not just the rc. So if you are using bash like I do, it will call /etc/profile, which will have a call to path_helper.
In order to fix this, change /etc/profile to:
if [[ -z $TMUX ]] && [ -x /usr/libexec/path_helper ]; then
eval `/usr/libexec/path_helper -s`
fi
If you are using bash, also change any export PATH=$PATH:/foo in .bashrc to
if [[ -z $TMUX ]]; then
export PATH=$PATH:/foo
fi
then you restart the terminal(for example Iterm). Everything should be good!
My application is writen in python 3, and I work in a virtualenv. On my cluster, there is hdp (hortonworks) installed and some scripts require python 2. Those script have #!/usr/bin/env python in the header, but it links to my python 3 installation because my virtualenv is activated. How to solve this ? I can't modify hdp source for obvious reasons.
Modifying Your Virtualenv
If you want your virtualenv to always be ignored with a #!/usr/bin/env python shebang (but not with a #!/usr/bin/env python3 shebang), there's a big-hammer approach that prevents the python entry in the PATH added by the virtualenv from matching, but doesn't necessarily perform other cleanup:
rm "$VIRTUAL_ENV/bin/python"
...or a better-behaved alternative (assuming that you have a python2.7 in your PATH, and that it's what you want to use):
cat >"$VIRTUAL_ENV/bin/python" <<'EOF'
#!/usr/bin/env bash
path_prefix=$VIRTUAL_ENV/bin:
if [[ $PATH = $path_prefix* ]]; then
PATH=${PATH#$path_prefix}
fi
unset PYTHONHOME VIRTUAL_ENV
exec python2.7 "$#"
EOF
The below will assume you're looking for approaches with a bit more finesse.
Command-Specific Shell Wrapper
If you interact with Hortonworks through a frontend called hdp, consider the following a shell function, a wrapper for hdp that deactivates the virtualenv:
hdp() (
if [[ $VIRTUAL_ENV ]]; then
deactivate
fi
exec command hdp "$#"
)
Because this function is using parentheses instead of curly braces, it runs in a subshell -- a separate copy of the shell environment -- so when it runs deactivate, this doesn't impact your parent shell. This also means that the exec command causes the subshell to replace itself with the hdp command, rather than causing your parent shell to terminate.
Generic Shell Wrapper
If you want to be able to run other scripts with your virtualenv temporarily deactivated, consider instead:
# wv == "without virtualenv"
wv() (
if [[ $VIRTUAL_ENV ]]; then
deactivate
fi
exec "$#"
)
...such that wv foo will run foo with the virtualenv deactivated.