Migrating from Anaconda¶

The University of Vienna does not have a license for the official anaconda.inc repositories and employees shall not use these. There are alternatives that are used most of the time anyways.

to Micromamba/Mamba/Miniforge¶

To migrate from Anacondo to Micromamba follow the steps below.

1. Export the installed Packages into a yml

conda env export -n <env-name> > <env-name>.yml

Make sure your yml doesn't use the defaults channel but conda-forge instead

name: test
channels:
- pkgs/main   # replace with conda-forge
dependencies:
- ...

Open the yml file you just created and remove the channel default. Add the channel conda-forge. Using both at the same time can lead to problems with the environment.

2. Create the new environment from the yml file

# using micromamba, available on all IMGW servers
micromamba create -n <env-name> --file <env-name>.yml

# or using mamba
mamba env create -n my_new_env -f environment.yml

Remember that you should also remove the conda part in your ~.bashrc file. e.g.:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/path/to/conda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/path/to/conda/etc/profile.d/conda.sh" ]; then
        . "/path/to/conda/etc/profile.d/conda.sh"
    else
        export PATH="/path/to/conda/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

Remove this! You can add the micromamba shell init if you wish by running: micromamba shell init

to venv¶

1. Export the packages into a requirements.txt:

# activate conda environment or use -n or -p options.
conda list -n <env_name> -p <env_path> --export > requirements.txt

2. Run the following command to create a new virtual environment:

python -m venv <env-name>

Activate the virtual environment

<env-name>\Scripts\activate

Now that your virtual environment is active, you can install the packages from your Conda environment.

pip install -r requirements.txt

finished.