python - Anaconda: Permanently include external packages (like in PYTHONPATH)

53
votes

I know how to install packages in Anaconda using conda install and also how to install packages that are on PyPi which is described in the manual.

But how can I permanently include packages/folders into the PYTHONPATH of an Anaconda environment so that code that I am currently working on can be imported and is still available after a reboot?

My current approach is to use sys:

import sys
sys.path.append(r'/path/to/my/package')

which is not really convenient.

Any hints?

Thanks in advance!

4
pythonanaconda
I don't understand what "permanently include packages/folders in Anaconda e.g. with code that I am currently working on" means, do you mean a) conda and pip are not locally installing them into the right conda environment (in which case do conda activate/deactivate until you get to the right Python environment, you may have several in conda), or b) you want to manually bundle third-party packages with your package(? sounds like a terrible idea, just define package dependencies). What does "permanently" mean, on which machine? - smci
I just want to be code that I am working on to be available/importable within a specific environment even after reboot. So I have specified the question above. Actually, I found different solutions for my problem which I have provided below. But let me know if there are others ways and I'll add them! - Cord Kaldemeyer

4 Answers

101
votes

I found two answers to my question in the Anaconda forum:

1.) Put the modules into into site-packages, i.e. the directory $HOME/path/to/anaconda/lib/pythonX.X/site-packages which is always on sys.path. This should also work by creating a symbolic link.

2.) Add a .pth file to the directory $HOME/path/to/anaconda/lib/pythonX.X/site-packages. This can be named anything (it just must end with .pth). A .pth file is just a newline-separated listing of the full path-names of directories that will be added to your path on Python startup.

Alternatively, if you only want to link to a particular conda environment then add the .pth file to ~/anaconda3/envs/{NAME_OF_ENVIRONMENT}/lib/pythonX.X/site-packages/

Both work straightforward and I went for the second option as it is more flexible.

*** UPDATE:

3.) Use conda develop i. e. conda-develop /path/to/module/ to add the module which creates a .pth file as described under option 2.).

4.) Create a setup.py in the folder of your package and install it using pip install -e /path/to/package which is the cleanest option from my point of view because you can also see all installations using pip list. Note that the option -e allows to edit the package code. See here for more information.

Thanks anyway!

9
votes

I'm able to include local modules using the following: 

conda-develop /path/to/module/

I hope it helps.

1
votes

Just to add to Cord Kaldemeyer's answer above, for the 2nd option. If you only want to link to a particular conda environment then add the .pth file to ~/anaconda3/envs/{NAME_OF_ENVIRONMENT}/lib/pythonX.X/site-packages/

1
votes

The way I do this, which I believe is the most native to conda, is by creating env_vars.sh files in my environment, as per the official documentation here.

For macOS and Linux users, the steps are as follows:

  1. Go to your environment folder (e.g. /miniconda1/env/env_name). $CONDA_PREFIX is the environemnt variable for your environment path.

    cd $CONDA_PREFIX

  2. Create the activate.d and deactivate.d directories.

    mkdir -p ./etc/conda/activate.d
mkdir -p ./etc/conda/deactivate.d

  3. Inside the each respective directory, create one env_vars.sh file. The one in the activate.d directory will set (or export) your environment variables when you conda activate your environment. The file in the deactivate.d directory will serve to unset the environment variables when you conda deactivate your environment.

    touch ./etc/conda/activate.d/env_vars.sh
touch ./etc/conda/deactivate.d/env_vars.sh

  4. First edit the $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh to export the desired environment variables.

    #!/bin/sh

export VAR_A='some-thing-here'
export VAR_B=/path/to/my/file/

  5. Afterwards, open to edit the $CONDA_PREFIX/etc/conda/deactivate/env_vars.sh, in order to unset the env variables when you conda deactivate like so:

    #!/bin/sh

unset VAR_A
unset VAR_B

Again, the source of my description comes straight from the conda docs here.