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Development Environment Setup

Instructions to setup the (local) Python development environment.

Virtual Environment using venv

The venv module provides support for creating lightweight “virtual environments” with their own site directories, optionally isolated from system site directories. Each virtual environment has its own Python binary (which matches the version of the binary that was used to create this environment) and can have its own independent set of installed Python packages in its site directories.

Note: The venv module is part of the Python Standard Library, so no further installation is required.

The following 3 steps are required to setup a new virtual environment using venv:

  1. Create the environment:

    python -m venv </path/to/new/virtual/environment>

  2. Activate the environment:

    source </path/to/new/virtual/environment/bin/activate>

  3. Install the Required Package (using the requirements.txt file):

    pip install -r requirements.txt

  4. (Optional) Create new Jupyter notebook Kernel

To avoid re-installing the entire Jupyter stack into the new environment, it is possible to add a new Jupyter Kernel to be used in notebooks with the "default" Jupyter.

To do so, please make sure that the ipykernel package is installed in the new Python environment:

pip install ipykernel  ## this should be the default pip

Then, execute the following command:

python -m ipykernel install --user --prefix /path/to/new/virtual/environment --display-name "Python 3 (DL Biomed)"

Further information here

Setting up conda environment

If you are using Anaconda Python distribution, it is possible to re-create the virtual (conda) environment using the export .yml (YAML) file:

conda env create -f dl-biomed.yml

This will create a new Conda environment named dl-torch with all the required packages.

To activate the environment:

conda activate dl-biomed
(Optional) Create new Jupyter notebook Kernel

To avoid re-installing the entire Jupyter stack into the new environment, it is possible to add a new Jupyter Kernel to be used in notebooks with the "default" Jupyter.

To do so, please make sure that the ipykernel package is installed in the new conda environment:

conda install ipykernel

Then, still remaining in the new conda environment, execute the following command:

python -m ipykernel install --user --name dl-torch --display-name "Python 3.7 (DL Biomed)"

Further information here