This installation route installs all necessary software – including the prerequisite services PostgreSQL and RabbitMQ – into a Conda environment.

First we install the prerequisite services + AiiDA (core)

conda create -n aiida -c conda-forge aiida-core aiida-core.services

conda activate aiida

reentry scan

Then we need to initialize a database storage area on disk.

initdb -D mylocal_db

This database cluster may contain a collection of databases (one per profile) that is managed by a single running server process. We start this process with:

pg_ctl -D mylocal_db -l logfile start

Then, start the RabbitMQ server:

rabbitmq-server -detached

Finally, start the AiiDA daemon(s) [example below starts 2 of them]:

verdi daemon start 2

Shut-down services

After finishing with your aiida session, particularly if switching between profiles, you may wish to power down the services:

verdi daemon stop

pg_ctl stop

Deactivate base autoload

It is possible that conda will set things up so that the default "base" environment is loaded upon logging into the computer. If you wish to disable that option, you can run [1]:

conda config --set auto_activate_base false

The first time you run it, it'll create a ./condarc in your home directory with that setting to override the default.

List environments

$ conda env list

# conda environments:
#
myenv                 /home/username/miniconda/envs/myenv
snowflakes            /home/username/miniconda/envs/snowflakes
bunnies               /home/username/miniconda/envs/bunnies

List packages in environment

$ conda list -n myenv

# packages in environment at /home/framirez/miniconda3/envs/aiida-tutorial:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             4.5                       1_gnu  
alabaster                 0.7.12                   pypi_0    pypi
anyio                     3.2.0                    pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
argon2-cffi               20.1.0                   pypi_0    pypi
async-generator           1.10                     pypi_0    pypi
attrs                     21.2.0                   pypi_0    pypi
(...)

You can just run conda list to show the ones in the currently loaded environment.

Install pip in environment

$ conda install -n myenv pip

We recommend that you:

• Use pip only after conda: Install as many requirements as possible with conda then use pip. Pip should be run with --upgrade-strategy only-if-needed (the default). Do not use pip with the --user argument, avoid all users installs

• Use conda environments for isolation: Create a conda environment to isolate any changes pip makes. Environments take up little space thanks to hard links. Care should be taken to avoid running pip in the root environment.

• Recreate the environment if changes are needed: Once pip has been used, conda will be unaware of the changes. To install additional conda packages, it is best to recreate the environment.

• Store conda and pip requirements in text files: Package requirements can be passed to conda via the --file argument. Pip accepts a list of Python packages with -r or --requirements. Conda env will export or create environments based on a file with conda and pip requirements.

Removing environments

$ conda env remove --name myenv

Sources

[1] https://stackoverflow.com/questions/54429210/how-do-i-prevent-conda-from-activating-the-base-environment-by-default [2] https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#viewing-a-list-of-your-environments

Older information

$ conda deactivate
$ conda env remove -n ENV_NAME

# Alternative
$ conda remove --name myenv --all 

# Check
$ conda info --envs

https://conda.io/projects/conda/en/latest/user-guide/getting-started.html

Where to set activation and deactivation env variables

cd $CONDA_PREFIX
mkdir -p ./etc/conda/activate.d
mkdir -p ./etc/conda/deactivate.d
touch ./etc/conda/activate.d/env_vars.sh
touch ./etc/conda/deactivate.d/env_vars.sh

How to set them in ./etc/conda/activate.d/env_vars.sh:

#!/bin/sh

export MY_KEY='secret-key-value'
export MY_FILE=/path/to/my/file/

How to unset them in ./etc/conda/deactivate.d/env_vars.sh:

#!/bin/sh

unset MY_KEY
unset MY_FILE

Export environment:

$ conda env export > environment.yml

# Import
$ conda env create -f environment.yml

Set during creation or in multiple steps:

conda create -n myenv scipy=0.15.0
# EQUIVALENT
conda create -n myenv python
conda install -n myenv scipy=0.15.0

Others...

conda create -n myenv python=3.4 scipy

conda create -n myenv python=3.4
conda install -n myenv scipy

https://docs.conda.io/projects/conda/en/4.6.1/user-guide/index.html