Run the application

Simply run app.py in your IDE or use the terminal (python app.py by default).

Set up the IDE

We are using VS Code. To set it up, read this.

Installing the dependencies

The dependencies for this Python application are listed in requirements.txt. You need to install them by typing pip install -r requirements.txt. Please update this file whenever you import a new module during development.

For Mac Users and other Computers that use ARM64 architecture

You need to install the tkinterdnd2-universal package to ensure the functionality of the code. To set it up, read this post.

Required package versions for scVelo

The software uses scVelo for velocity computation and visualization. It requires certain versions of some packages. After installing the dependencies as listed above, make sure to run pip install --force-reinstall 'pandas==1.3.5' pip install --force-reinstall 'numpy==1.23.5' in this order. These are the versions that worked for us.

Additional trouble?

The file tests/package_versions.txt lists the package versions that worked for us. If a module is causing errors, try to reinstall it with the appropriate version.

Naming conventions

See here.

Documentation conventions

See here.