1 Introduction to Conda

1.1 Reference

• Getting Started
• Managing environments
• Cheat Sheet
• Conda

1.2 Installing conda

For evaluation purposes

The default Anaconda installation is only recommended for evaluation or testing purposes!

• Download Anaconda distribution / Miniconda
• Follow the installation instructions for your OS
• Verify your installation

In production

Due to Anaconda Terms of Service, the use of alternative, community-supported channels is recommended in production

• Miniforge is the preferred conda-forge installer
• Follow Miniforge installation instructions for your OS
• To use the default Anaconda / Miniconda distributions in production, make sure to add the following to the .condarc file:

. . .

channel_priority: strict
channels:
- conda-forge

1.3 Starting conda

Command Line Interface

• Linux: open a terminal
• macOS: press command + Space and search Terminal
• Windows: search anaconda and select Anaconda Prompt or Anaconda Powershell Prompt

$ conda deactivate

1.4 Version, Info and Help

conda Environment

A directory that contains specific installed packages (system libraries, python/R modules, …).

base Environment

The default environment that you have when installing conda.

$ conda --version

$ conda --help

$ conda info

. . .

1.4.1 Exercise

1.5 Create / Clone and List all Envs

$ conda create --name py38 python=3.8

$ conda create --name py38-clone --clone py38

$ conda env list

• in --name py38 - py38 is the name of the environment
• in python=3.8 - python package version 3.8 is installed in the new environment
• in --clone py38 - py38 is the name of the cloned existing environment
• conda env list - is equivalent with conda info --env

1.6 Activate and Deactivate Env

Check Python version on:

1. the system,
2. the base env, and
3. the new py38 env.

      $ python --version

      $ conda activate 
(base)$ python --version

(base)$ conda activate py38
(py38)$ python --version

• in conda activate - the default (base) environment is activated
• in conda activate py38 - py38 is the name of the environment

1.7 List Installed Packages

(py38)$ conda list
(py38)$ conda list --name base

(py38)$ conda list python
(py38)$ conda list ^lib

• in list --name base - base is the name of the environment
• in list python - only packages matching python string (regular expression) are listed
• in list ^lib - only packages starting with lib string (regular expression) are listed

1.8 Search and Install Packages

Conda channels

• Locations where packages are stored, e.g. conda-forge, bioconda, r
• [default / main → not recommended!]
• search packages on conda-forge using the browser

(py38)$ conda search numpy=1.21
(py38)$ conda install numpy=1.21.6

(py38)$ conda install pandas="<1.5"

• in install pandas="<1.5" - the quotes are mandatory
• more about Installing with conda

1.9 Update Packages and Revisions

(py38)$ conda update pandas
(py38)$ conda update --all

(py38)$ conda list --revisions
(py38)$ conda install --revision 2
(py38)$ conda list --revisions

• in update ... pandas - update pandas to the latest compatible version
• in update --all - update all packages
• in list --revisions - list history of changes
• in install --revision 2 - restore to revision 2

1.10 Environment File - YAML Format

Environment File

A YAML file that contains all information to create an environment.

YAML file: seaborn.yml

name: seaborn
# important: do not use 'defaults', but always include 'nodefaults'
  - conda-forge
  - nodefaults

dependencies:
  - seaborn=0.12.2

Note: seaborn is is a Python data visualization library based on matplotlib.

1.11 Environment File to Environment and back

 (py38)$ conda env create --file seaborn.yml
 (py38)$ conda activate seaborn

(seaborn)$ conda env export
(seaborn)$ conda env export --no-builds
(seaborn)$ conda env export --from-history
(seaborn)$ conda env export --no-builds > seaborn_export.yaml
(seaborn)$ conda env create --file seaborn_export.yaml --name seaborn_export

• in env export - all installed packages are exported (in yaml format)
• in env export --no-builds - the build specification is removed
• in env export --from-history - all packages that you explicitly asked for
• platform information is not exported

Note: The build specification is generally platform dependent.

Note: The packages might not be available on all platforms.

. . .

1.11.1 Identical Environments

Spec File

A text file that contains all information to create an identical environment.

(seaborn)$ conda list --explicit 

(seaborn)$ conda list --explicit > seaborn_spec_file.txt
(seaborn)$ conda create --name seaborn_explicit --file seaborn_spec_file.txt

• in conda create --file seaborn_spec_file.txt - conda does not check the platform nor the dependencies
• platform information is exported

Warning: Use the spec file on a similar platform.

1.12 Removing environments

Finally, try yourself to remove some or all of the environments that we just created.

Hint: Have a look at the documentation for the conda env command: conda env --help

1.13 Removing environments - Solution

(seaborn)$ conda activate base
(base)$ conda env remove --name seaborn

Note: You cannot remove the active environment!

1.14 What Did We Learn?

• we can create new environments
• we can install and update packages, from desired channels and asking for a specific version
• once we are happy with the environment we can create an environment file that allows us to reproduce the desired environment
• for long-term preservation we can export the environment in a new file and list explicitly the installed packages