Scan

This repository contains the python 3 package SCAN, implementing the machine learning technique Reservoir Computing (RC) and related methods.

SCAN: Software for Complex system Analysis via Networks.

License

The SCAN software is provided under the MIT License.

Installation

Prerequisites

• Git
• Python 3.8+
• Pip or Conda (the latter typically via Miniforge)

The Basics

First, clone the scan repository to a folder of your choice.

Once you have done this, enter the cloned folder, and tell git who you are:

git config user.name "Lastname, Firstname"
git config user.email "[email protected]"

From here, follow either the conda or pip installation instructions below. If you don't know which one to choose, install miniforge as conda distribution and then follow the conda installation instructions.

Installation using Conda

Create a new python 3.9 environment named scan and install the scan package requirements as well as the packages used for further development:

conda create --name scan python=3.9 --file requirements.txt --file requirements_dev.txt

On some systems, mostly Windows, the above may fail due to no MPI being installed. In that case, use the no_mpi requirements file. You will miss out on some features and performance, but as MPI is optional, you'll still be able to use the package:

conda create --name scan python=3.9 --file requirements_no_mpi.txt --file requirements_dev.txt

Notably, if you are not intersted in changing the package or running its tests, you can also install the minimal requirements necessary to install scan via:

conda create --name scan python=3.9 --file requirements.txt

or

conda create --name scan python=3.9 --file requirements_no_mpi.txt

respectively. This is not recommended as running the tests is the only reasonable way to know if the package actually does what it's supposed to.

Now activate the conda environment

conda activate scan

and install the package in editable mode:

pip install -e .

Finally, run the unit tests to see if everything is working as intended:

pytest

If no errors pop up, you have installed the scan package successfully.

Installation using Pip

If you are using pip, it is still highly recommended to not change your system python and instead create a virtual environment using a tool of your choice to install scan in. Pyenv with the pyenv-virtualenv plugin are recommended, but exchangeable.

Once you have activated said virtual environment, install the requirements using:

pip install -r requirements.txt -r requirements_dev.txt

Similarly to the conda installation instruction above, the requirements files can be adjusted if your system doesn't have MPI installed:

pip install -r requirements_no_mpi.txt -r requirements_dev.txt

or you don't want to edit the package and run its tests:

pip install -r requirements.txt

or both:

pip install -r requirements_no_mpi.txt

Now, install the package in editable mode:

pip install -e .

and run the unit tests to see if everything is working as intended:

pytest

If no errors pop up, you have installed the scan package successfully.

Push and Merge Request Steps

Before any push or merge request do the following from inside the scan repository main folder within an active development environment. following:

1. Use black and isort the format the code:

   black . && isort .
   

2. Run mypy to check for type hint coverage and type related problems:

   mypy
   

3. Run the testing suite in your active environment to check for bugs and code coverage:

   pytest --cov-report term-missing --cov=scan tests/
   

4. Run the testing suite in all tox-conda environments:

   tox --develop -c tox-conda.ini