Skip to content

Create the bbsig_pipeline virtual environment#

Warning

The information contained in this page is updated to mostly covers the packages needed to run the first three BBSIG pipelines included in v0.0.1 (i.e., ECG preprocessing, PPG preprocessing, HRV analysis). We will work on keeping the YAML file updated while we develop future pipelines using the same bbsig_pipeline environment.

Why a dedicated virtual environment?#

An environment is a directory that contains a self-isolated Python version and a specific collection of installed packages. This keeps dependencies required by different projects separate and avoids complications in your base environment.

To run the BBSIG pipelines, it is best to have a dedicated environment setup that guarantees the correct functioning of the packages. Following the steps below, you can create a bbsig_pipeline environment to start using our BBSIG preprocessing and analysis pipelines.

Note

If you are already familiar with conda and/or setting up virtual environments, you can jump directly to Sect. 3. Note that in the following instructions we have chosen to focus on conda, but you could also create your virtual environment using mamba or venv according to your preferences.

For now, the bbsig_pipeline environment is based on Python v3.11 and mainly includes the following packages:

How to create the bbsig_pipeline environment#

Follow these three steps to create the bbsig_pipeline environment on your local machine and start using our peripheral physiological analysis pipelines.

1. Install conda#

To install conda, we recommend using mini-forge, a minimal installer for Conda and Mamba specific to the conda-forge channel1. With mini-forge, the community-led “conda-forge” channel is pre-configured as the default channel to obtain packages, both in the base environment and in the creation of any further virtual environments. For more information on the installation of mini-forge on different Operating Systems, visit the mini-forge documentation.

2. Start conda#

Conda can be used with any terminal application: if you have installed conda using mini-forge, you can use their pre-configured Miniforge Prompt.

To verify that conda is installed correctly, in your terminal window of choice type and run: 

conda --version
This will show the version number that you have installed, such as conda 4.12.0. You can read more about managing conda here.

3. Create the bbsig_pipeline environment from YAML file#

In order to recreate the dedicated bbsig_pipeline virtual environment, you can use the bbsig_pipeline_environment.yml file provided here:

Download bbsig_pipeline_environment.yml

Use the terminal (e.g., Miniforge Prompt) to execute the following steps [inspired by the documentation here].

  1. Save the bbsig_pipeline_environment.yml file in your location of choice, then cd into that directory using the terminal, e.g. 
    cd /path/to/bbsig_pipeline_directory
  2. Create the environment from the bbsig_pipeline_environment.yml file by typing the following command in the terminal. The first line of the .yml file will set the new environment's name as bbsig_pipeline. It may take some time to download and extract all the required packages. 
    conda env create -f bbsig_pipeline_environment.yml
  3. Activate the newly created bbsig_pipeline environment: 
    conda activate bbsig_pipeline

Great, now your bbsig_pipeline environment is ready!#

  1. If you have installed conda using mini-forge, conda-forge should be already pre-configured as default channel to install packages (i.e., it avoids pulling packages from the Anaconda Distribution defaults channel). However, if you have installed conda using the Anaconda Distribution or Miniconda, we recommend adding the conda-forge channel as the highest priority channel (i.e., conda will first search the conda-forge channel before the defaults channel to install packages):

    conda config --add channels conda-forge
     ↩