PTSA

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For documentation and tutorials, please see https://pennmem.github.io/ptsa/

Install via conda

Available on Linux, Mac, and Windows 64 bit:

.. code-block:: shell-session

conda install -c pennmem -c conda-forge ptsa

Report bug or feature request

To report a bug or a feature request please use https://github.com/pennmem/ptsa/issues.

Build from source

Install dependencies:

.. code-block:: shell-session

conda install -y numpy scipy xarray swig traits

You will also need to install FFTW. To install FFTW with conda on Linux or Mac:

.. code-block:: shell-session

conda install -y -c pennmem fftw

Alternatively, it can be installed with the system package manager on Linux (Debian-based command shown below):

.. code-block:: shell-session

sudo apt-get install libfftw3-dev

or on Mac using homebrew:

.. code-block:: shell-session

brew install fftw

To read EDF__ files, you will also need to install pybind11:

.. code-block:: shell-session

conda install -y -c conda-forge pybind11

__ http://www.edfplus.info/

Install PTSA:

.. code-block:: shell-session

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:

.. code-block:: shell-session

export CPATH=$HOME/anaconda3/envs/ptsa/include
export LD_LIBRARY_PATH=$HOME/anaconda3/envs/ptsa/lib

Running Tests

To run the PTSA test suite locally, first set up a testing environment:

.. code-block:: shell-session

conda env create -f environment.yml
source activate ptsa

and then build build the extension modules and run the test suite:

.. code-block:: shell-session

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:

.. code-block:: shell-session

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.

Building conda packages

See separte HOW_TO_RELEASE.md document! Alternatively, this repository is now set up to deploy automatically on tagged commits.

License

PTSA is licensed under the GNU GPL version 3.

This repository also includes:

• FFTW_ (GPL license)
• EDFLib_ (BSD license)

.. _FFTW: http://fftw.org/ .. _EDFLib: https://www.teuniz.net/edflib/