A library for exploring persistent homology
Aleph is a C++ library for exploring and extending usages of persistent
homology. Its main
goal is to provide users with a versatile, simple-to-use implementation
that quickly permits building prototype applications.
Aleph is inspired by DIPHA andPHAT. In particular, Aleph
borrowed the idea of keeping the representation of a boundary matrix
separate from the implementation.
For more information, please read the original paper describingPHAT.
Since its inception in late 2016, Aleph has been used to support the
following papers:
Please refer to the list of
publications in the
documentation of Aleph for more details. The documentation covers how to
reproduce a subset of the results reported in the papers above.
If you want to contribute, please see the contribution
guidelines for more details.
Aleph contains numerous algorithms and helper classes that simplify
working with persistent homology. Here is a brief selection of the most
important ones:
Documentation of the main
features, including some tutorials, is available on GitHub. If you want
to delve into the code, the examples subdirectory is a good starting
point.
Aleph uses the MIT license. Please see the file LICENSE.md
in the main directory of the repository for more details.
CMake, preferably a recent version >= 3.2Boost dependencies for some of the data structures:Boost.FunctionalBoost.IteratorBoost.MultiIndexEigen3 for some auxiliary mathematicalFLANN for fast nearest-neighbour queriesHDF5 for parsing HDF5 input filespybind11 for building theRapidJSON for parsing JSON input filesTinyXML2 for parsingAleph is meant to be used as a header-only library on top of which you
can develop your own projects based on persistent homology. However,
Aleph ships with numerous unit tests, some example programs, and tools
required for my current research. For building them, please clone the
repository to some local directory on your computer. Running the
following commands within this directory should be sufficient in most
cases:
$ mkdir build$ cd build$ cmake ../$ make
It is advisable to test that Aleph works correctly on your system, so
you can run the unit tests with:
$ make test
Please submit any issues you may encounter.
For more information, including how to run tests, please refer to the
detailed build
instructions in the
documentation.
If you want to install Aleph from source, simply issue
$ make install
from the compilation directory. In general, this will require root
privileges, unless you change the CMAKE_INSTALL_PREFIX variable to
a local directory.
It is easier to install Aleph as a package. Currently, only packages
for Arch Linux are available. Use your favourite AUR helper tool for
installing Aleph:
$ pacaur -S aleph-git # pacaur (deprecated)$ trizen -S aleph-git # trizen$ yaourt -S aleph-git # yaourt
If you want to volunteer and submit a package for your favourite Linux
distribution, please take a look at issue #27
and add your comments.
If your build instructions are configured to build the Python bindings,
i.e. BUILD_PYTHON_BINDINGS follow these instructions to install them:
$ cd build/bindings/python/aleph$ python3 setup.py install
Note that this uses the old setuptools approach for installing the
package. A simpler installation based on pip is forthcoming.
For general discussion, questions, and comments, please contact the
principal developer and maintainer Bastian Rieck (bastian.rieck@bsse.ethz.ch).
The following people have contributed code to Aleph:
pybind11