calling conda source activate from bash script
I'm trying to activate my conda env via a bash script. Even though the script runs fine and my PATH appears to be changed within the script, it's getting reset somehow after the script terminates. I can call source activate test from the cmd line and it works fine. An example along with output below.
script:
PycharmProjects/test » cat ./example.sh
echo "before calling source: $PATH"
source activate test
echo "after calling source: $PATH"
output:
./example.sh
before calling source: /Use rs/me/miniconda3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin
discarding /Users/me/miniconda3/bin from PATH
prepending /Users/me/miniconda3/envs/test/bin to PATH
after calling source: /Users/me/miniconda3/envs/test/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin`
but if I echo $PATH after the script finishes, you can see that the $PATH has not changed (i.e. no /Users/me/miniconda3/envs/test/bin):
PycharmProjects/test » echo $PATH /Users/me/miniconda3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin
Solution 1:
On more recent versions of conda (4.6+), I have noticed that the following works:
eval "$(conda shell.bash hook)"
conda activate <env-name>
Solution 2:
I have found the following to work on Mac OSX running a bash shell:
#!/bin/bash
source /Users/yourname/anaconda/bin/activate your_env
python --version # example way to see that your virtual env loaded as expected
Make sure you make the scripted executable with:
chmod +x yourscript.bash
Solution 3:
See the link below,
digitalocean-how-to-read-and-set-environmental-and-shell-variables-on-a-linux-vps
below is the snippet from the website,
This is because environmental variables are only passed to child processes. There isn't a built-in way of setting environmental variables of the parent shell. This is good in most cases and prevents programs from affecting the operating environment from which they were called.