I am hoping to run a simple shell script to ease the management around some conda environments. Activating conda environments via conda activate in a linux os works fine in the shell but is problematic within a shell script. Could someone point me into the right direction as to why this is happening?
Example to repeat the issue:
# default conda env
$ conda info | egrep "conda version|active environment"
active environment : base
conda version : 4.6.9
# activate new env to prove that it works
$ conda activate scratch
$ conda info | egrep "conda version|active environment"
active environment : scratch
conda version : 4.6.9
# revert back to my original conda env
$ conda activate base
$ cat shell_script.sh
#!/bin/bash
conda activate scratch
# run shell script - this will produce an error even though it succeeded above
$ ./shell_script.sh
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'.
I use 'source command' to run the shell script, it works:
source shell_script.sh
The error message is rather helpful - it's telling you that conda is not properly set up from within the subshell that your script is running in. To be able to use conda within a script, you will need to (as the error message says) run conda init bash (or whatever your shell is) first. The behaviour of conda and how it's set up depends on your conda version, but the reason for the version 4.4+ behaviour is that conda is dependent on certain environment variables that are normally set up by the conda shell itself. Most importantly, this changelog entry explains why your conda activate and deactivate commands no longer behave as you expect in versions 4.4 and above.
For more discussion of this, see the official conda issue on GitHub.
Edit: Some more research tells me that the conda init function mentioned in the error message is actually a new v4.6.0 feature that allows a quick environment setup so that you can use conda activate instead of the old source activate. However, the reason why this works is that it adds/changes several environment variables of your current shell and also makes changes to your RC file (e.g.: .bashrc), and RC file changes are never picked up in the current shell - only in newly created shells. (Unless of course you source .bashrc again). In fact, conda init --help says as much:
IMPORTANT: After running conda init, most shells will need to be closed and restarted for changes to take effect
However, you've clearly already run conda init, because you are able to use conda activate interactively. In fact, if you open up your .bashrc, you should be able to see a few lines added by conda teaching your shell where to look for conda commands. The problem with your script, though, lies in the fact that the .bashrc is not sourced by the subshell that runs shell scripts (see this answer for more info). This means that even though your non-login interactive shell sees the conda commands, your non-interactive script subshells won't - no matter how many times you call conda init.
This leads to a conjecture (I don't have conda on Linux myself, so I can't test it) that by running your script like so:
bash -i shell_script.sh
you should see conda activate work correctly. Why? -i is a bash flag that tells the shell you're starting to run in interactive mode, which means it will automatically source your .bashrc. This should be enough to enable you to use conda within your script as if you were using it normally.
Quick solution for bash: prepend the following init script into your Bash scripts.
eval "$(command conda 'shell.bash' 'hook' 2> /dev/null)"
Done.
For other shells, check the init conf of your shell, copy the following content within the shell conf and prepend it into your scripts.
# >>> conda initialize >>>
...
# <<< conda initialize <<<
You can also use
conda init --all --dry-run --verbose
to get the init script you need in your scripts.
Explanation
This is related with the introduction of conda init in conda 4.6.
Quote from conda 4.6 release log
Conda 4.4 allowed “conda activate envname”. The problem was that setting up your shell to use this new feature was not always straightforward. Conda 4.6 adds extensive initialization support so that more shells than ever before can use the new “conda activate” command. For more information, read the output from “conda init –help”
After conda init is introduced in conda 4.6, conda only expose command
conda into the PATH but not all the binaries from "base". And environment switch is unified by conda activate env-name and conda deactivate on all platforms.
But to make these new commands work, you have to do an additional initialization with conda init.
The problem is that your script file is run in a sub-shell, and conda is not initialized in this sub-shell.
References
Conda 4.6 Release
Unix shell initialization
Shell startup scripts
Using conda activate or source activate in shell scripts does not always work and can throw errors like this. An easy work around it to place source ~/miniconda3/etc/profile.d/conda.sh above any conda activate command in the script:
source ~/miniconda3/etc/profile.d/conda.sh # Or path to where your conda is
conda activate some-conda-environment
This is the solution that has worked for me and will also work if sharing scripts. This also gets around having to use conda init as on some clusters I have worked with the system is initialised but conda activate still won't work in a shell script.
if you want to use the shell script to run the other python file in the other conda env, just run the other file via the following command.
os.system('conda run -n <env_name> python <path_to_other_script>')
What is the problem with simply doing something like this in your shell:
source /opt/conda/etc/profile.d/conda.sh
(The conda init is still marked as Experimental, and thus not sure if it is a good idea to use it yet).
I also had the exact same error when trying to activate conda env from C++ or Python file. I solved it by bypassing the conda activate statement and using the absolute path of the specific conda env.
For me, I set up an environment called "testenv" using conda.
I searched all python environments using
whereis python | grep 'miniconda'
It returned a list of python environments. Then I ran my_python_file.py using the following command.
~/miniconda3/envs/testenv/bin/python3.8 my_python_file.py
You can do the same thing on windows too but looking up for python and conda python environments is a bit different.
This answer from Github worked for me (I'm using Ubuntu so it's not for Windows only):
eval "$(conda shell.bash hook)"
conda activate my_env
I just followed a similar solution like the one from hong-xu
So to run a shell command that calls the script with arguments and using a specific conda environment:
from a jupyter cell, goes like this :
p1 = <some-value>
run = f"conda run -n {<env-name>} python {<script-name>.py} \
--parameter_1={p1}"
!{run}
I didn't find any of the above scripts useful. These are fine if you want to run conda in non-interactive mode, but I'd like to run it in interactive mode. If I run:
conda activate my_environment
in a bash script it just runs in the script.
I found that creating an alias in .bashrc is all that is required to change directory to a particular project I'm working on, and set up the correct conda environment for me. So I included in .bashrc:
alias my_environment="cd ~/subdirectory/my_project && conda activate my_environment"
and then:
source ~/.bashrc
Then I can just type at the command line:
my_environment
to change to the correct project and correct environment everytime I want to work on a different project.
This answer is similar to #Lamma answer. This worked for me ->
(1) I defined several variables; the conda activate function, environments directory and environment
conda_activate=~/anaconda3/bin/activate
conda_envs_dir=~/anaconda3/envs
conda_env=<env name>
(2) I source conda activate with the environment
source ${conda_activate} ${conda_envs_dir}/${conda_env}
(3) then you can run your python script
python <path to script.py>
This bypasses the conda init requirement. my .bashrc already was initialized and sourcing the .bashrc file didn't work for me. #Lamma's answer worked for me as well as the above code.
The problem is that when you run the bash script, a new (linux) shell environment is created that was not initialized properly. If your intention is to activate a conda environment, and then run python through the script, you can properly initialize the created shell
environment as discussed in the accepted solution.
If however you want to have the conda environment active after you finish this script, then this will not work because the conda environment has changed on the new shell and you exit that shell when you finish the script. Think of this as running bash, then conda activate... then running exit to exit that bash... More details in How to execute script in the current shell on Linux?:
TL;DR:
Add the line #!/bin/bash as the first line of the script
Type the command source shell_script.sh or . shell_script.sh
Note: . in bash is equivalent to source in bash.
$ conda activate scratch
or
$ source activate scratch
#open terminal or CMD as administrator
$ cd <path Anaconda3 install>\Scripts
$ activate
$ cd ..
$ conda activate scratch
I am trying to resolve this issue and trying to get it work. What are all the steps of the solution? I really don't know what to do on my Mac terminal
-bash: emacs.profile: command not found
What are you trying to accomplish? If you're trying to open a file named .profile with emacs you'll want to add a space between the command emacs and the file .profile:
$ emacs .profile
If you are typing emacs.profile you will get an error because you are mixing together the command emacs and the file you are trying to edit: .profile. Therefore the solution would be to add a space between them like someone suggested: $ emacs .profile.
On the other hand, if you are typing emacs .profile and you are still getting: -bash: emacs: command not found, this means that you haven't installed emacs yet and your system doesn't recognize that instruction.
Emacs is a very popular text editor and is widely used by technical users, but it is not installed by default.
Solution 1:
If you want to edit a file (in this case ~/.profile) you don't need emacs to do so, you could just use a normal text editor or a pre-installed text editor using your terminal like:
$ vi ~/.profile or $ nano ~/.profile
(Guide to use Vi/Vim text editors) (Guide to use Nano).
Solution 2:
If you want to install emacs to edit that file, you can do so using brew:
$ brew update
$ brew install emacs
And after that you can use:
$ emacs ~/.profile
You can find other ways to install emacs here.
Important Note:
One important thing to consider in this example, is that if you are trying to edit the .profile file (i.e. to set an exported environment variable) you should know that the name of the .profile file might vary from one Mac system to another. The name of this profile configuration file depends on the shell of your system, if you are using bash the name of this profile will be .bashrc or .bash_profile.
Before editing your profile file make sure what is the name of the profile file you are trying to edit. To do so, you can use:
$ cd $HOME
to go to the Home folder and then use:
$ ls -al
to see hidden files (These files starting with . are hidden files). You will find the profile file of your system there.
I'm having trouble with installing Flutter on ubuntu.
Attached is an image of my terminal with the steps I've followed, and the files associated with the flutter directory.
I've followed the steps shown on https://flutter.io/docs/get-started/install/linux and also tried to install with git clone.
https://i.stack.imgur.com/ltmNd.png
I think your problem is in the pwd part of the export command.
Replace the single quotes in 'pwd' with Backtick/back quote (``) like this
export PATH="$PATH:`pwd`/flutter/bin"
EDITED
Above command will just work until you close the terminal.
To make the change permanent you have to edit the .bashrc (or .zshrc, etc), using a text editor like vim, gedit or nano and place the same command at the end of the file.
vim ~/.bashrc or nano ~/.bashrc
Add the next line at the end of the file
# Add flutter to the path
export PATH="$PATH:`pwd`/flutter/bin"
Restart your terminal and verify that your PATH was set correctly with the echo $PATH command
Good luck!!
I am using Linux 18.04 version.
first, add the flutter path in .bash_profile as
export PATH="$PATH:(''flutter path)/flutter/bin"
I have this problem.run the following command in the terminal
source '(flutter path)'.bash_profile'
I installed Anaconda on macOS. It installed successfully, but when I ran the command in terminal it does not recognize the command conda. On my initial search, I found out I have look if the environment variable is set in .bash_profile. As the following picture shows the path is all set, but I can not still run the command.
You are not using bash but zsh as your current shell.
zsh does not source .bash_profile - instead, it sources the .zprofile file for its initialization.
So, just copy the export PATH=... line to the .zprofile file (create it if it does not exist). Logout and login, and it should work.
I have installed the Anaconda for Mac, but there is something wrong with me:
when I type the commandwhich conda or which ipython, I get conda not found and ipython not find
Then I find this command export PATH=~/anaconda/bin:"$PATH" works for me. It solves the problem above, but everytime I rerun the terminal the problem is still there, I have to type it again.
so I want to find a way to solve the problem fundamentally
I have tried to add it into the ~/.bashrc, ~/.profile, ~/.bash_profile, but these don't work for me.
Try this in .bash_profile
export PATH="$HOME/anaconda/bin:$PATH"
Then try launching a new terminal and running:
echo $PATH
The output should start with /anaconda/bin:
If that still doesn't work... A work around might be to invoke bash after running terminal i.e. type "bash". Which should cause bash to launch with .bash_profile
I run on MacOs Catalina 10.15 and this did the trick for me:
shell is zsh !
$ source /Users/myprofilename/anaconda3/bin/activate
then
$ conda init zsh
the new anaconda documentation also highlights this:
Make sure you're not using ZShell or another form of a shell. If the case you'd have to add the path to your respective shell file, e.g .zshrc.
sudo xed /etc/environment
after open this archive add :/home/youruser/anaconda3/bin
If you're using ZShell follow the steps below:
In your terminal type open ~/.zshrc
Add the following to the file export PATH=/opt/homebrew/bin:$PATH
Save your file and then run the following command source ~/.zshrc
Please note that the homebrew path on Apple silicon is /opt/homebrew/bin