Installation#
Stable release#
Python#
To install abess on Python, you can simply get the stable version with:
$ pip install abess
If you don't have pip installed, this Python installation guide can guide you through the process.
Latest version#
This page gives instructions on how to build and install abess from the
source code. If the instructions do not help for you, please feel free
to ask questions by opening an
issue.
First of all, clone our the latest github project by Git to your device:
$ git clone https://github.com/abess-team/abess.git
$ cd abess
Next, there have different processing depend on the programming langulage you prefer.
Python#
Before installing abess from source, some compiling tools should be installed
first, which may be a little different in different platforms:
cmake: control the software compilation process. Make sure it has been added into PATH, which means it can be called on the command line like
cmake --version.pybind11: create Python bindings of existing C++ code. If you want to install from PyPI, please use
pip install "pybind11[global]".For Linux and MacOS user, please download and install GCC.
For Windows user, please download Microsoft C++ Build Tools, and then install the "Desktop development with C++" module inside.
After that, we can manually install abess by conducting command:
$ cd ./python
$ pip install .
or
$ cd ./python
$ python setup.py install --user
If it finishes with Finished processing dependencies for abess, the
installation is successful.
Alternatively, if you would like to develop abess, install abess in editable mode
(it is very convenient for development):
$ cd ./python
$ pip install -e .
or
$ cd ./python
$ python setup.py develop --user
Note that some may meet "Permission denied" problem like this issue
when installing with pip install -e .. There are three solutions:
1. run the command as administrator;
2. feel free to use python setup.py develop --user instead;
3. try to edit setup.py like here (not recommend).
R#
To install the development version, some dependencies need to be installed.
Before installing abess, some dependencies should be installed
first, which may be a little different in different platforms:
Linux:
$ sudo apt install autoconf(for Ubuntu, other Linux systems are similar);Windows: install Rtools.
MacOS:
$ brew install autoconf.
Then, you need to install R library dependencies Rcpp and RcppEigen via conducting install.packages(c("Rcpp", "RcppEigen")) in R console.
After installing dependencies, run the following code in terminal/bash:
cd R-package
autoreconf
R CMD INSTALL .
If it finishes with * DONE (abess), the installation is successful.
Dependencies#
C++#
Our core C++ code is based on some dependencies:
Eigen (version 3.3.4): a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
Spectra (version 1.0.0): a header-only C++ library for large scale eigenvalue problems.
They would be automatically included while installing the abess
packages.
OpenMP#
To support OpenMP parallelism in Cpp, the dependence for OpenMP should be install. Actually, many compliers and tools have supported and you can check here.
What is more, if you receive a warning like “Unknown option ‘-fopenmp’” while installing abess, it means that OpenMP has not been enabled. Without OpenMP, abess only use a single CPU core, leading to suboptimal learning speed.
To enable OpenMP:
In Windows, Visual C++ or many other C++ compliers can support OpenMP API, but you may need to enable it manually in additional features (based on the complier you use).
In Linux, the dependence would be supported if GCC is installed (version 4.2+).
In MacOS, the dependence can be installed by:
$ brew install llvm $ brew install libomp
Python#
Some basic Python
packages
are required for abess. Actually, they can be found on
abess/python/setup.py and automatically installed during the
installation.
pybind11: seamless operability between C++11 and Python
numpy: the fundamental package for array computing with Python.
scipy: work with NumPy arrays, and provides many user-friendly and efficient numerical routines.
scikit-learn: a Python module for machine learning built on top of SciPy.
pandas: support data manipulation and input.
Furthermore, if you want to develop the Python packages, some additional packages should be installed:
pytest: simple powerful testing with Python.
lifelines: support testing for survival analysis.
Sphinx: develop the Python documentation.
sphinx-rtd-theme: “Read the Docs” theme for Sphinx.
sphinix-gallery: develop the gallery of Python examples.
R#
The R version should be 3.1.0 and newer in order to support C++11. abess
R package relies on limited R packages dependencies:
Furthermore, if you would to develop the R package, it would be better to additionally install: