Pygamma-agreement

pygamma-agreement is an open-source package to measure Inter/Intra-annotator¹ agreement for sequences of annotations with the γ measure². It is written in Python3 and based mostly on NumPy, Numba and pyannote.core. For a full list of available functions, please refer to the package documentation.

Dependencies

The main dependencies of pygamma-agreement are NumPy, CVXPY, Numba and pyannote.core.

Optionally, to allow pygamma-agreement to display visual representations of our API's objects in Jupyter Notebooks, Matplotlib is needed.

pygamma-agreement is a Python 3 package and is currently tested for Python 3.7 to 3.11. pygamma-agreement does not work with Python 2.7.

Installation

pygamma-agreement can be easily installed using pip :

$ pip install pygamma-agreement

Pygamma-agreement uses the GNU Linear Programming Kit as its default Mixed Integer Programming solver (critical step of the gamma-agreement algorithm). Since it is quite slow, you can install the CBC solver and its official python API. To use those in pygamma-agreement, simply install them:

• Ubuntu/Debian : $ sudo apt install coinor-libcbc-dev
• Fedora : $ sudo yum install coin-or-Cbc-devel
• Arch Linux : $ sudo pacman -S coin-or-cbc
• Mac OS X :
  • $ brew tap coin-or-tools/coinor
  • $ brew install coin-or-tools/coinor/cbc pkg-config

then:

$ pip install "pygamma-agreement[CBC]"

If you have trouble during the two last steps, pygamma-agreement should work anyway, although significantly slower for larger input.

WARNING: A bug in GLPK causes the standard output to be polluted by non-deactivable messages. It is strongly advised to use the CBC solver.

Tests

The package comes with a unit-tests suite. To run it, first install the CBC solver, then the testing dependencies on your Python environment:

$ sudo apt install coinor-libcbc-dev
$ pip install "pygamma-agreement[testing]"

After that, tests are ready to be launched (they take ~2m on a recent laptop) :

$ pytest tests/

Documentation

The documentation for this package has been written using Sphinx. To build the documentation locally, run:

$ pip install "pygamma-agreement[docs]"
$ cd docs/
$ make html

After that, you can view the documentation by running

$ firefox build/html/index.html

Submitting and issue or contributing

Please read CONTRIBUTING.md before submitting and issue or writing some contribution to this package.

Citing Pygamma

If you're using pygamma in your work, please cite our package using the following bibtex entry:

@article{Titeux2021,
  doi = {10.21105/joss.02989},
  url = {https://doi.org/10.21105/joss.02989},
  year = {2021},
  publisher = {The Open Journal},
  volume = {6},
  number = {62},
  pages = {2989},
  author = {Hadrien Titeux and Rachid Riad},
  title = {pygamma-agreement: Gamma $\gamma$ measure for inter/intra-annotator agreement in Python},
  journal = {Journal of Open Source Software}
}

References