12. Conda Environment¶
In this lesson, you’ll learn how to do the following:
Install and configure conda.
Create an environment in conda.
Handle environments in conda.
Work with cookiecutter
Note
This chapter contains detailed information to work with conda and e3. If you intend to work only with e3 environment, then this chapter can be skipped.
Conda¶
Conda is a Package, dependency and environment management for any language — Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN.
Conda is open-source and runs on Linux, MacOS and Windows. It allows to easily install packages and their dependencies in isolated environment. You can read more about conda concepts in the official user-guide.
Conda installation¶
To install conda, we’ll use the
Miniconda installer. The only
requirements to run the installation are bzip2 and wget.
$ mkdir -p ~/miniconda3
$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
$ bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
$ rm -rf ~/miniconda3/miniconda.sh
$ ~/miniconda3/bin/conda init bash
You can refer to the official documentation for more detailed information.
Conda update¶
The installer might not come with the latest available version of conda. After installation you should update conda:
$ conda update -y -c conda-forge -n base conda
To check the version of conda installed, run:
$ conda -V
conda 4.12.0
You need at least conda 4.7 to work with e3. Conda >=4.8 is recommended.
Conda configuration¶
If you don’t want conda to activate the base environment by default (and modify
your PATH), you should run:
$ conda config --set auto_activate_base false
All e3 packages are available on ESS
Artifactory. Artifactory includes mirrors for
anaconda-main and conda-forge channels. You should set artifactory as the
the default channel_alias. To work with e3, you have to use the
conda-e3-virtual channel:
$ conda config --set channel_alias https://artifactory.esss.lu.se/artifactory/api/conda
$ conda config --add channels conda-e3-virtual
$ conda config --remove channels defaults
Conda 4.7 introduced a new .conda package
format.
Artifactory 6.11.3 doesn’t support that format and it creates issues with remote
conda repository. See
RTFACT-19267. To use conda >=
4.7 with Artifactory you should force conda to only download .tar.bz2 packages
by setting the use_only_tar_bz2 boolean.
conda config --set use_only_tar_bz2 true
The previous commands created the following ~/.condarc file:
auto_activate_base: false
channel_alias: https://artifactory.esss.lu.se/artifactory/api/conda
channels:
- conda-e3-virtual
use_only_tar_bz2: true
You can modify the configuration by editing directly this file or using the
conda config command.
conda-build¶
conda-build is only required if you want to build conda packages locally. It’s not directly needed to work with e3.
Install conda-build in the base environment:
conda install -y -n base -c conda-forge conda-build
Note
The base environment shall be writeable by the current user to run this command.
Conda usage¶
How to create a new environment¶
To create an environment named “epics-7” with epics-base 7, run:
[iocuser@host:~]$ conda create -n epics-7 epics-base=7
How to activate an environment¶
Use the conda activate command followed by the environment name:
[iocuser@host:~]$ conda activate epics-7
How to deactivate an environment¶
Use conda deactivate:
(epics-7) [iocuser@host:~]$ conda deactivate
How to delete an environment¶
Use the conda env remove command:
[iocuser@host:~]$ conda env remove -n epics-7
How to export an environment¶
Use the conda env export command:
[iocuser@host:~]$ conda env export -n epics-7 > environment.yml
How to create an environment based on an environment file¶
Use the conda env create command:
[iocuser@host:~]$ conda env create -n epics-7 -f environment.yml
If you omit the -n parameter, the environment name will be taken from the
environment.yml file. The command will fail if the environment already
exists. You can to destroy it first by using --force.
Cookiecutter¶
Cookiecutter creates projects from templates. It’s used to easily create new e3 wrappers, recipes or IOCs for development. It’s not required to run e3.
Cookiecutter installation¶
Cookiecutter is a Python tool. It can be installed with pip. Note that you
should never run sudo pip install. This can override system packages.
Cookiecutter can be installed in different ways (pip install --user or using
pipx). As conda is installed, let’s use
it.
[iocuser@host:~]$ conda create -y -c conda-forge -n cookiecutter python=3 cookiecutter
Add an alias to your .bashrc:
[iocuser@host:~]$ echo "alias cookiecutter='~/miniconda/envs/cookiecutter/bin/cookiecutter'" >> ~/.bashrc
Reload the .bashrc file
[iocuser@host:~] source ~/.bashrc
You should be able to run cookiecutter:
[iocuser@host:~]$ cookiecutter --version
Cookiecutter 1.7.2 from /home/iocuser/miniconda/envs/cookiecutter/lib/python3.8/site-packages (Python 3.8)
Cookiecutter configuration¶
Create the file ~/.cookiecutterrc with your name:
default_context:
full_name: "Your Name"
This will override the variable full_name from any cookiecutter template with
your name. It will become the default value and avoid you having to enter it
every time you create a new project. Note that you could add to that file other
variables.
Add the following aliases to your .bashrc:
[iocuser@host:~]$ echo "alias e3-wrapper='cookiecutter git+https://gitlab.esss.lu.se/ics-cookiecutter/cookiecutter-e3-wrapper.git'" >> ~/.bashrc
[iocuser@host:~]$ echo "alias e3-recipe='cookiecutter git+https://gitlab.esss.lu.se/ics-cookiecutter/cookiecutter-e3-recipe.git'" >> ~/.bashrc
[iocuser@host:~]$ echo "alias e3-ioc='cookiecutter git+https://gitlab.esss.lu.se/ics-cookiecutter/cookiecutter-e3-ioc.git'" >> ~/.bashrc
To create a new e3 wrapper, recipe or IOC, just run e3-wrapper, e3-recipe or
e3-ioc.