pennmem / ptsa

PTSA - Python Time Series Analysis

PTSA

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

Install via conda

Available on Linux, Mac, and Windows 64 bit:

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:

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 pennmem 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

Running Tests

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.

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)