/PyFstat

Primary LanguagePythonMIT LicenseMIT

PyFstat

This is a python package providing an interface to perform F-statistic based continuous gravitational wave (CW) searches, built on top of the LALSuite library.

Getting started:

PyPI version Conda version DOI Integration Tests Docker Documentation Status Binder

Installation

PyFstat releases can be installed in a variety of ways, including Docker/Singularity images, pip install from PyPi, conda and from source releases on Zenodo. Latest development versions can also be installed with pip or from a local git clone.

If you don't have a recent python installation (3.6+) on your system, then Docker or conda are the easiest paths.

In either case, be sure to also check out the notes on dependencies, ephemerides files and citing this work.

Docker container

Ready-to-use PyFstat containers are available at the Packages page. A GitHub account together with a personal access token is required. Go to the wiki page to learn how to pull them from the GitHub registry using Docker or Singularity.

conda installation

See this wiki page for installing conda itself and for a minimal .yml recipe to set up a PyFstat-specific environment.

To install into an existing conda environment, all you need to do is

conda install -c conda-forge pyfstat

If getting PyFstat from conda-forge, it already includes the required ephemerides files.

pip install from PyPi

PyPi releases are available from https://pypi.org/project/PyFstat/.

Note that the PyFstat installation will fail at the LALSuite dependency stage if your pip is too old (e.g. 18.1); to be on the safe side, before starting do

pip install --upgrade pip

Then, a simple

pip install pyfstat

should give you the latest release version with all dependencies.

If you are not installing into a venv or conda environment, on many systems you may need to use the --user flag.

Note that, if using pip, you need to install ephemerides files manually.

pip install from github

Development versions of PyFstat can also be easily installed by pointing pip directly to this git repository, which will give you the latest version of the master branch:

pip install git+https://github.com/PyFstat/PyFstat

or, if you have an ssh key installed in github:

pip install git+ssh://git@github.com/PyFstat/PyFstat

In this case, you also need to install ephemerides files manually.

install PyFstat from source (Zenodo or git clone)

You can download a source release tarball from Zenodo and extract to an arbitrary temporary directory. Alternatively, clone this repository:

git clone https://github.com/PyFstat/PyFstat.git

The module and associated scripts can be installed system wide (or to the currently active venv), assuming you are in the (extracted or cloned) source directory, via

python setup.py install

As a developer, alternatively

python setup.py develop

or

pip install -e /path/to/PyFstat

can be useful so you can directly see any changes you make in action. Alternatively (not recommended!), add the source directory directly to your python path.

To check that the installation was successful, run

python -c 'import pyfstat'

if no error message is output, then you have installed pyfstat. Note that the module will be installed to whichever python executable you call it from.

In this case, you also need to install ephemerides files manually.

Dependencies

PyFstat uses the following external python modules, which should all be pulled in automatically if you use pip:

In case the automatic install doesn't properly pull in all dependencies, to install all of these modules manually, you can also run

pip install -r /PATH/TO/THIS/DIRECTORY/requirements.txt

For a general introduction to installing modules, see here.

Optional dependencies:

  • pycuda, required for the tCWFstatMapVersion=pycuda option of the TransientGridSearch class. (Note: pip install pycuda requires a working nvcc compiler in your path.)
  • pytest for running the test suite locally (python -m pytest tests.py)
  • Developers are also highly encouraged to use the flake8 linter and black style checker locally, as these checks are required to pass by the online integration pipeline.
  • Some optional plotting methods depend on the additional package chainconsumer and some of the example scripts require this to run. For pip users, this is most conveniently installed by
pip install chainconsumer
  • If you prefer to make your own LALSuite installation from source, make sure it is swig-enabled and contains at least the lalpulsar and lalapps packages. A minimal configuration line to use would be e.g.:
./configure --prefix=${HOME}/lalsuite-install --disable-all-lal --enable-lalpulsar --enable-lalapps --enable-swig

Ephemerides installation

PyFstat requires paths to earth and sun ephemerides files in order to use the lalpulsar.ComputeFstat module and various lalapps tools.

If you have done pip install lalsuite (or it got pulled in automatically as a dependency), you need to manually download at least these two files:

(Other ephemerides versions exist, but these two files should be sufficient for most applications.) You then need to tell PyFstat where to find these files, by either setting an environment variable $LALPULSAR_DATADIR or by creating a ~/.pyfstat.conf file as described further below. If you are working with a virtual environment, you should be able to get a full working ephemerides installation with these commands:

mkdir -p $VIRTUAL_ENV/share/lalpulsar
wget https://git.ligo.org/lscsoft/lalsuite/raw/master/lalpulsar/lib/earth00-40-DE405.dat.gz -P $VIRTUAL_ENV/share/lalpulsar
wget https://git.ligo.org/lscsoft/lalsuite/raw/master/lalpulsar/lib/sun00-40-DE405.dat.gz -P $VIRTUAL_ENV/share/lalpulsar
echo 'export LALPULSAR_DATADIR=$VIRTUAL_ENV/share/lalpulsar' >> ${VIRTUAL_ENV}/bin/activate
deactivate
source path/to/venv/bin/activate

An executable version of this snippet is readily accessible by sourcing bin/get-and-export-ephemeris.sh. Mind that this script does not include an export command anywhere, so you will have to source it every time in order to properly set LALPULSAR_DATADIR variable.

If instead you have built and installed lalsuite from source, and set your path up properly through something like source $MYLALPATH/etc/lalsuite-user-env.sh, then the ephemerides path should be automatically picked up from the $LALPULSAR_DATADIR environment variable. Similarly, if you have installed lalsuite from conda-forge, it should come with ephemerides included and properly set up.

Alternatively, you can place a file ~/.pyfstat.conf into your home directory which looks like

earth_ephem = '/home/<USER>/lalsuite-install/share/lalpulsar/earth00-19-DE405.dat.gz'
sun_ephem = '/home/<USER>/lalsuite-install/share/lalpulsar/sun00-19-DE405.dat.gz'

Paths set in this way will take precedence over the environment variable.

Finally, you can manually specify ephemerides files when initialising each PyFstat search (as one of the arguments).

Contributing to PyFstat

This project is open to development, please feel free to contact us for advice or just jump in and submit an issue or pull request.

Here's what you need to know:

  • The github automated tests currently run on python [3.6,3.7,3.8] and new PRs need to pass all these.
  • The automated test also runs the black style checker and the flake8 linter. If at all possible, please run these two tools locally before pushing changes / submitting PRs: flake8 --count --statistics . to find common coding errors and then fix them manually, and then black --check --diff . to show the required style changes, or black . to automatically apply them.
  • bin/setup-dev-tools.sh gets your virtual environment ready for you. After making sure you are using a virtual environment (venv or conda), it installs black, flake8, pre-commit, pytest, wheel via pip and uses pre-commit to run the black and flake8 using a pre-commit hook. In this way, you will be prompted a warning whenever you forget to run black or flake8 before doing your commit 😉.

Contributors

Maintainers:

  • Greg Ashton
  • David Keitel

Active contributors:

  • Reinhard Prix
  • Rodrigo Tenorio

Other contributors:

  • Karl Wette
  • Sylvia Zhu
  • Dan Foreman-Mackey (pyfstat.gridcorner is based on DFM's corner.py)

Citing this work

If you use PyFstat in a publication we would appreciate if you cite both a release DOI for the software itself (see below) and one or more of the following scientific papers:

If you'd additionally like to cite the PyFstat package in general, please refer to the version-independent Zenodo listing or use directly the following BibTeX entry:

@misc{pyfstat,
  author       = {Ashton, Gregory and
                  Keitel, David and
                  Prix, Reinhard
                  and Tenorio, Rodrigo},
  title        = {PyFstat},
  month        = jul,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3967045},
  url          = {https://doi.org/10.5281/zenodo.3967045},
  note         = {\url{https://doi.org/10.5281/zenodo.3967045}}
}

You can also obtain DOIs for individual versioned releases (from 1.5.x upward) from the right sidebar at Zenodo.

Alternatively, if you've used PyFstat up to version 1.4.x in your works, the DOIs for those versions can be found from the sidebar at this older Zenodo record and please amend the BibTeX entry accordingly.

PyFstat makes generous use of functionality from the LALSuite library and it will usually be appropriate to also cite that project (see this recommended bibtex entry) and also Wette 2020 (inspire:1837108 / ADS:2020SoftX..1200634W) for the C-to-python SWIG bindings.