Installation

Note

Our tool could be installed on Linux with python3.7 or python3.8.

Pre-built installation (recommended)

pip install gefpy

Source installation

To install gefpy from source, you need:

HDF5 1.8.4 or newer with development headers
OpenCV 4.5 or newer with development headers
GEFTOOLS with development headers
A C compiler

On Unix platforms, you also need pkg-config unless you explicitly specify a path for HDF5 as described below.

You can specify build options for gefpy as environment variables when you build it from source:

git clone https://github.com/BGIResearch/gefpy.git
cd gefpy
export HDF5_DIR=/path/to/hdf5
export OpenCV_DIR=/path/to/opencv
export GEFTOOLS_DIR=/path/to/geftools
python setup.py install

The supported build options are:

To specify where to find HDF5, OpenCV, GEFTOOLS:

HDF5_DIR: a shortcut for common installations of HDF5, a directory with lib and include subdirectories containing compiled libraries and C headers.

OpenCV_DIR: a shortcut for common installations of OpenCV, a directory with lib and include subdirectories containing compiled libraries and C headers.

GEFTOOLS_DIR: a shortcut for common installations of geftools, a directory with lib and include subdirectories containing compiled libraries and C headers.

Source installation on OSX/MacOS

HDF5 and Python are most likely in your package manager (e.g. Homebrew, Macports, or Fink). Be sure to install the development headers, as sometimes they are not included in the main package.

XCode comes with a C compiler (clang), and your package manager will likely have other C compilers for you to install.

Source installation on Linux/Other Unix

HDF5 and Python are most likely in your package manager. A C compiler almost definitely is, usually there is some kind of metapackage to install the default build tools, e.g. build-essential, which should be sufficient for our needs. Make sure that that you have the development headers, as they are usually not installed by default. They can usually be found in python-dev or similar and libhdf5-dev or similar.

Source installation on Windows

Installing from source on Windows is a much more difficult prospect than installing from source on other OSs, as not only are you likely to need to compile HDF5 from source, everything must be built with the correct version of Visual Studio. Additional patches are also needed to HDF5 to get HDF5 and Python to work together.