mcfly 3.1.0

The goal of mcfly is to ease the use of deep learning technology for time series classification. The advantage of deep learning is that it can handle raw data directly, without the need to compute signal features. Deep learning does not require expert domain knowledge about the data, and has been shown to be competitive with conventional machine learning techniques. As an example, you can apply mcfly on accelerometer data for activity classification, as shown in the tutorial.

If you use mcfly in your research, please cite the following software paper:

D. van Kuppevelt, C. Meijer, F. Huber, A. van der Ploeg, S. Georgievska, V.T. van Hees. Mcfly: Automated deep learning on time series. SoftwareX, Volume 12, 2020. doi: 10.1016/j.softx.2020.100548

Installation

Prerequisites:

• Python 3.6, 3.7 or 3.8
• pip
• Tensorflow 2.0, if pip errors that it can't find it for your python/pip version

Installing all dependencies in separate conda environment:

conda env create -f environment.yml

# activate this new environment
source activate mcfly

To install the package, run in the project directory:

pip install .

Installing on Windows

When installing on Windows, there are a few things to take into consideration. The preferred (in other words: easiest) way to install Keras and mcfly is as follows:

• Use Anaconda
• Install numpy and scipy through the conda package manager (and not with pip)
• To install mcfly, run pip install mcfly in the cmd prompt.
• Loading and saving models can give problems on Windows, see https://github.com/NLeSC/mcfly-tutorial/issues/17

Visualization

We build a tool to visualize the configuration and performance of the models. The tool can be found on http://nlesc.github.io/mcfly/. To run the model visualization on your own computer, cd to the html directory and start up a python web server:

python -m http.server 8888 &

Navigate to http://localhost:8888/ in your browser to open the visualization. For a more elaborate description of the visualization see user manual.

User documentation

User and code documentation.

Contributing

You are welcome to contribute to the code via pull requests. Please have a look at the NLeSC guide for guidelines about software development.

We use numpy-style docstrings for code documentation.

Necessary steps for making a new release

• Check citation.cff using general DOI for all version (option: create file via 'cffinit')
• Create .zenodo.json file from CITATION.cff (using cffconvert)
  cffconvert --validate
cffconvert --ignore-suspect-keys --outputformat zenodo --outfile .zenodo.json
• Set new version number in mcfly/_version.py
• Edit Changelog (based on commits in https://github.com/NLeSC/mcfly/compare/v1.0.1...master)
• Create Github release
• Upload to pypi:
  python setup.py sdist bdist_wheel
python -m twine upload --repository-url https://upload.pypi.org/legacy/ dist/*
  (or python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/* to test first)
• Check doi on zenodo
• If the visualization has changed, deploy it to github pages:

git subtree push --prefix html origin gh-pages

Licensing

Source code and data of mcfly are licensed under the Apache License, version 2.0.