diff --git a/README.md b/README.md index e3af04ae..aff1d6f9 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,45 @@ [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1003173.svg)](https://doi.org/10.5281/zenodo.1003173) # StructureAnalysis + +This package provides tools for statistical analysis of the structure of a plant. + +> warning:: +> This package in under development, even the master branch is broken + +## Install + +### Dependencies +We recommand to use python virtual environments to install the package (conda is a good choice, especialy since conda-only packages are required as dependencies). + +Required dependencies available from `conda-forge` channel are : +- boost +- scons +- openalea.deploy +- openalea.sconsx +- nose (for tests, only via pip install) + +### Doing the development install +To install the package for developments, you can use the `multisetup.py` script. It will use the `Multisetup` from `openalea.deploy` to compile `stat_tools` and `sequence_analysis` packages. + +```bash +python multisetup.py develop +``` + +However, compilation can be a bit long and you may want to install using parallel compilation. To do so, you can use the following sequence (compilation with 4 cores, but you can adapt to your ressources): + +```bash +cd stat_tools +scons -j4 +pip install -e . +cd ../sequence_analysis +scons -j4 +pip install -e . +cd .. +``` + +### After-install issues +Observed only on OSX (so far), you may need to extend your `LD_LIBRARY_PATH` environment variable to include the path of your newly built libraries: +``` +export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/your/conda/env/:/path/to/StructureAnalysis/stat_tool/:/path/to/StructureAnalysis/sequence_analysis/ +``` \ No newline at end of file