1 Introduction to Conda

1.1 Reference

• Getting Started
• Managing environments
• Cheat Sheet
• Conda

1.2 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

1.3 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

. . .

1.3.1 Exercise

1.4 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

1.5 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

(py38)$ conda deactivate --help
(py38)$ conda deactivate

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

1.6 List Installed Packages

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

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

• in list --name base - base is the name of the environment
• in list python - only packages matching python string (regular expression) in the active environment (or base if no one active)

1.7 Search and Install Packages

Conda channels

Locations where packages are stored, e.g. default / main, conda-forge, bioconda, r

• search using the browser on anaconda.org

(py38)$ conda deactivate && conda deactivate
      $ conda search numpy=1.21

      $ conda install numpy=1.21.6 --name py38
      $ conda activate py38
(py38)$ conda install pandas="<1.5"

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

1.8 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

Note: In restoring to a revision the additional channels are needed explicitly.

1.9 Environment File - YAML Format

Environment File

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

YAML file: seaborn.yml

name: seaborn
channels:
  - defaults
dependencies:
  - seaborn=0.12.2

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

1.10 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.

1.10.1 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.

1.11 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

1.12 Removing environments - Solution

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

Note: You cannot remove the active environment!

1.13 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