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Setup

Installation

  1. Create a new environment using either conda (recommended) or venv and activate it

  2. Use UPOD's Cookiecutter for Data Science Projects and generate a new project template.

  3. Install the PyCellDyn package using pip with the following command:

pip install git+https://github.com/UPOD-datascience/pycelldyn

3.1 pip will try to install the required dependencies. However, for some reason sometimes the SSL certificate can't be confirmed and the installation throws an error:

Could not fetch URL https://pypi.python.org/simple/PACKAGENAME/: There was a problem confirming the ssl certificate: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:777) - skipping
Could not find a version that satisfies the requirement PACKAGENAME (from versions: XXX)

In that case, you need to install the missing packages one by one by hand with the following command:

pip install PACKAGENAME --trusted-host pypi.python.org --trusted-host files.pythonhosted.org --trusted-host pypi.org

That's it! You are done.