Installation¶
It is highly recommended to install the project into a new virtual environment.
Python Requirements¶
The project is only available for Python 3.7. The main reason for this restriction is an external dependency ANTsPy that does not provide many precompiled wheels on PyPI.
External Dependencies¶
Some of the functionalities of atlalign
depend on the
TensorFlow implementation of the Learned Perceptual Image Patch Similarity.
Unfortunately, the
package is not available on PyPI and must be installed manually as follows.
pip install git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf
You can now move on to installing the actual atlalign package!
Installation from PyPI¶
The atlalign
package can be easily installed from PyPI.
pip install atlalign
Installation from source¶
As an alternative to installing from PyPI, if you want to try the latest version you can also install from source.
pip install git+https://github.com/BlueBrain/atlas_alignment#egg=atlalign
Development installation¶
For development installation one needs additional dependencies grouped in extras_requires
in the
following way:
dev - pytest + plugins, flake8, pydocstyle, tox
docs - sphinx
git clone https://github.com/BlueBrain/atlas_alignment
cd atlas_alignment
pip install -e .[dev,docs]
Generating documentation¶
To generate the documentation make sure you have dependencies from extras_requires
- docs
.
cd docs
make clean && make html
One can view the docs by opening docs/_build/html/index.html
in a browser.