For documentation and tutorials, please see https://pennmem.github.io/ptsa_new/
Available on Linux, Mac, and Windows 64 bit:
conda install -c pennmem ptsa
To report a bug or a feature request please use https://github.com/pennmem/ptsa_new/issues.
Install dependencies:
conda install -y numpy scipy xarray swig traits
You will also need to install FFTW. To install FFTW with conda on Linux or Mac:
conda install -y -c conda-forge fftw
Alternatively, it can be installed with the system package manager on Linux (Debian-based command shown below):
sudo apt-get install libfftw3-dev
or on Mac using homebrew:
brew install fftw
To read EDF files, you will also need to install pybind11:
conda install -y -c conda-forge pybind11
Install PTSA:
python setup.py install
If you encounter problems installing, some environment variables may need to be
set, particularly if you installed FFTW with conda. If your anaconda
distribution is installed in $HOME/anaconda3 and the environment name is
ptsa, set the CPATH and the LD_LIBRARY_PATH as follows:
export CPATH=$HOME/anaconda3/envs/ptsa/include
export LD_LIBRARY_PATH=$HOME/anaconda3/envs/ptsa/lib
To run the PTSA test suite locally, first set up a testing environment:
conda env create -f environment.yml
source activate ptsa
and then build build the extension modules and run the test suite:
python setup.py develop
pytest tests/
The shell script run_tests will also run the test suite, assuming the environment is configured.
To skip tests that depend on Rhino the NO_RHINO environment variable must be set:
export NO_RHINO=TRUE
When running tests which require rhino access, the path to the root rhino directory is guessed based on common mount points.
If you don't already have it installed, you'll need to install the conda build tool:
conda install conda-build
Update the version number in conda.recipe/meta.yaml.
Build packages with:
conda build conda.recipe
To allow uploads you need to install anaconda-client:
conda install anaconda-client
After that installing anaconda-client you need to to provide your anaconda.io login credentials:
anaconda login
At this point you will be ready to upload newly built conda PTSA packages. After the build is successfully completed you go to the directory where package tarballs have been generated and type:
anaconda upload --user pennmem ./ptsa-*.tar.bz2
Hint: conda packages will be most likely generated in <conda installation dir>/conda-bld/<architecture_folder>
where <architecture folder> denotes name of the arget architecture for which conda package was build. e.g. on 64-bit
Windows the architecture folder will be called win-64 (hence conda packages will be generated in
<conda installation dir>/conda-bld/win-64
You'll want to install Microsoft Visual Studio 2015 (or newer) community edition
in order to compile extensions. For environment variables to be setup correctly,
use the "Developer Command Prompt for VS20xy" which can be found for example
in Start->All Programs->Visual Studio 2015->Visual Studio Tools.
PTSA is licensed under the GNU GPL version 3.
This repository also includes: