Installation

WL-align runs only on Python 3. The installation has the following dependencies:

• Numpy

• Scipy

If you are an Anaconda user, you may want to create a dedicated wlalign-env environment and populate it with the right dependencies, then install WL-align.

conda env create -n wlalign-env -f environment.yml
pip install wlalign

Alternatively, you can install the dependencies and WL-align all via pip.

pip install numpy
pip install scipy

pip install wlalign

To install WL-align directly from the source, clone this repository and run the standard local setup commands.

git clone https://gitlab.inria.fr/cobcom/wlalign.git
cd wlalign
pip install -U .

Check installation

To check that WL-align has been properly installed, try to import the wlalign module into a Python session and print the version as follows. If no error is raised, the installation has been successful.

>>> import wlalign
>>> print(wlalign.__version__)

For developers

If you are thinking about developing your own fork of WL-align, you may want to use the latest version in the devel branch of the repository and install it in editable mode.

git clone https://gitlab.inria.fr/cobcom/wlalign.git
cd WL-align
git checkout devel
pip install -e .

Tests

The package uses unittest as a testing suite. To run all the tests, execute the following command in the source’s root directory.

python -m unittest -v

Test coverage can be checked with coverage as follows.

coverage run -m unittest
coverage report -m

Documentation

The sources of the documentation are in the doc folder. The compilation requires the sphinx package and the theme to be installed.

pip install sphinx
pip install sphinx_rtd_theme

To compile the documentation, move to the doc folder and run make <format>, where the format can be html, latex or any other sphinx-compatible format. To get a local copy of the the html documentation, run the make html command.

cd doc
make clean  # deletes results of previous compilations
make html