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diff --git a/python-pyfstat.spec b/python-pyfstat.spec new file mode 100644 index 0000000..ba9803e --- /dev/null +++ b/python-pyfstat.spec @@ -0,0 +1,1170 @@ +%global _empty_manifest_terminate_build 0 +Name: python-PyFstat +Version: 2.0.0 +Release: 1 +Summary: a python package for gravitational wave analysis with the F-statistic +License: MIT +URL: https://github.com/PyFstat/PyFstat +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/44/ab/611e5ca61fa940f8ec7067801bddd856ec65afc1a19eaff542a23bb3b552/PyFstat-2.0.0.tar.gz +BuildArch: noarch + +Requires: python3-attrs +Requires: python3-corner +Requires: python3-dill +Requires: python3-matplotlib +Requires: python3-numpy +Requires: python3-pathos +Requires: python3-ptemcee +Requires: python3-scipy +Requires: python3-tqdm +Requires: python3-versioneer +Requires: python3-lalsuite +Requires: python3-chainconsumer +Requires: python3-pre-commit +Requires: python3-sphinx +Requires: python3-sphinx-autodoc-defaultargs +Requires: python3-sphinx-autodoc-typehints +Requires: python3-sphinx-gallery +Requires: python3-sphinx-rtd-theme +Requires: python3-m2r2 +Requires: python3-mistune +Requires: python3-Pillow +Requires: python3-black +Requires: python3-flake8 +Requires: python3-flake8-docstrings +Requires: python3-flake8-executable +Requires: python3-flake8-isort +Requires: python3-isort +Requires: python3-pytest +Requires: python3-pytest-cov +Requires: python3-flaky +Requires: python3-nbmake +Requires: python3-wheel +Requires: python3-check-wheel-contents +Requires: python3-sphinx +Requires: python3-sphinx-autodoc-defaultargs +Requires: python3-sphinx-autodoc-typehints +Requires: python3-sphinx-gallery +Requires: python3-sphinx-rtd-theme +Requires: python3-m2r2 +Requires: python3-mistune +Requires: python3-Pillow +Requires: python3-pycuda +Requires: python3-black +Requires: python3-flake8 +Requires: python3-flake8-docstrings +Requires: python3-flake8-executable +Requires: python3-flake8-isort +Requires: python3-isort +Requires: python3-pytest +Requires: python3-pytest-cov +Requires: python3-flaky +Requires: python3-nbmake +Requires: python3-wheel +Requires: python3-check-wheel-contents + +%description +# 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](https://doi.org/10.7935/GT1W-FZ16). + +Getting started: +* This README provides information on +[installing](#installation), +[contributing](#contributors) to +and [citing](#citing-this-work) PyFstat. +* PyFstat usage and its API are documented at [pyfstat.readthedocs.io](https://pyfstat.readthedocs.io/). +* We also have a number of [tutorials](https://github.com/PyFstat/PyFstat/tree/master/examples/tutorials) and +[examples](https://github.com/PyFstat/PyFstat/tree/master/examples), demonstrating different use cases. +You can run them locally, or online as jupyter notebooks with +[binder](https://mybinder.org/v2/gh/PyFstat/PyFstat/master). +* The [project wiki](https://github.com/PyFstat/PyFstat/wiki) is mainly used for developer information. +* A [changelog](https://github.com/PyFstat/PyFstat/blob/master/CHANGELOG.md) +is also available. +* PyFstat >=2.0.0 requires a recent LALSuite (>=7.13) / lalpulsar (>=6.0) +including the [SFTv3 specification](https://dcc.ligo.org/T040164-v2/public). +If you need to work with older versions, the last PyFstat release supporting those was `1.19.1`. + +[](https://badge.fury.io/py/PyFstat) +[](https://anaconda.org/conda-forge/pyfstat) +[](https://doi.org/10.5281/zenodo.3967045) +[](https://ascl.net/2102.027) +[](https://doi.org/10.21105/joss.03000) +[](https://github.com/PyFstat/PyFstat/actions/workflows/docker-publish.yml) +[](https://mybinder.org/v2/gh/PyFstat/PyFstat/master) +[](https://github.com/PyFstat/PyFstat/actions/workflows/integration.yml) +[](https://codecov.io/gh/PyFstat/PyFstat) +[](https://pyfstat.readthedocs.io/en/latest/?badge=latest) +[](https://github.com/psf/black) + +## Installation + +PyFstat releases can be installed in a variety of ways, including +[`pip install` from PyPI](#pip-install-from-PyPi), +[conda](#conda-installation), +[Docker/Singularity images](#docker-container), +and [from source releases on Zenodo](#install-pyfstat-from-source-zenodo-or-git-clone). +Latest development versions can +[also be installed with pip](#pip-install-from-github) +or [from a local git clone](#install-pyfstat-from-source-zenodo-or-git-clone). + +If you don't have a recent `python` installation (`3.8+`) on your system, +then `Docker` or `conda` are the easiest paths. + +In either case, be sure to also check out the notes on +[dependencies](#dependencies) +and [citing this work](#citing-this-work). + +If you run into problems with ephemerides files, check the wiki page on +[ephemerides installation](https://github.com/PyFstat/PyFstat/wiki/ephemerides-installation). + +### pip install from PyPI + +PyPI releases are available from https://pypi.org/project/PyFstat/. + +A simple +``` +pip install pyfstat +``` +should give you the latest release version with all dependencies; +recent releases now also include a sufficient minimal set of ephemerides files. + +If you are not installing into a [venv](https://docs.python.org/3/library/venv.html) +or [conda environment](#conda-installation) +(you really should!), +on many systems you may need to use the `--user` flag. + +Note that the PyFstat installation will fail at the +LALSuite dependency stage +if your `pip` is too old (e.g. 18.1); to fix this, do +``` +pip install --upgrade pip setuptools +``` + +### conda installation + +See [this wiki page](https://github.com/PyFstat/PyFstat/wiki/conda-environments) +for further instructions on installing conda itself, +installing PyFstat into an existing environment, +or for .yml recipes to set up a PyFstat-specific environment +both for normal users and for developers. + +If getting PyFstat from conda-forge, it already includes the required ephemerides files. + +### Docker container + +Ready-to-use PyFstat containers are available at the [Packages](https://github.com/PyFstat/PyFstat/packages) +page. A GitHub account together with a personal access token is required. +[Go to the wiki page](https://github.com/PyFstat/PyFstat/wiki/Containers) +to learn how to pull them from the GitHub registry using `Docker` or `Singularity`. + +### 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 +``` + +This should pull in all dependencies in the same way as installing from PyPI, +and recent lalsuite dependencies will include ephemerides files too. + +### install PyFstat from source (Zenodo or git clone) + +You can download a source release tarball from [Zenodo](https://doi.org/10.5281/zenodo.3967045) +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. + +This should pull in all dependencies in the same way as installing from PyPI, +and recent lalsuite dependencies will include ephemerides files too. + +### Dependencies + +PyFstat uses the following external python modules, +which should all be pulled in automatically if you use `pip`: + +* [corner](https://pypi.python.org/pypi/corner/) +* [dill](https://pypi.python.org/pypi/dill) +* [lalsuite](https://pypi.org/project/lalsuite/) +* [matplotlib](https://matplotlib.org/) +* [numpy](https://www.numpy.org/) +* [pathos](https://pypi.python.org/pypi/pathos) +* [ptemcee](https://github.com/willvousden/ptemcee) +* [scipy](https://www.scipy.org/) +* [tqdm](https://pypi.python.org/pypi/tqdm) +* [versioneer](https://pypi.org/project/versioneer/) + +For a general introduction to installing modules, see +[here](https://docs.python.org/3/installing/index.html). + +NOTE: currently we have pinned to +`numpy<1.24.0` (due to an incompatibility with ptemcee). + +NOTE: We require a recent LALSuite (>=7.13) / lalpulsar (>=6.0). +If you need to work with older versions, +the last PyFstat release supporting those was `1.19.1`. + +### Optional dependencies + +PyFstat manages optional dependencies through setuptool's `extras_require`. + +Available sets of optional dependencies are: + +* `chainconsumer` ([Samreay/Chainconsumer](https://github.com/Samreay/ChainConsumer)): Required to run some optional +plotting methods and some of the [example scripts](./examples). +* `dev`: Collects `docs`, `style`, `test` and `wheel`. +* `docs`: Required dependencies to build the documentation. +* `pycuda` ([PyPI](https://pypi.org/project/pycuda/)): Required for the `tCWFstatMapVersion=pycuda` + option of the `TransientGridSearch` class. (Note: Installing `pycuda` requires a working + `nvcc` compiler in your path.) +* `style`: Includes the `flake8` linter ([flake8.pycqa](https://flake8.pycqa.org/en/latest)), + `black` style checker ([black.readthedocs](https://black.readthedocs.io)), + and `isort` for import ordering ([pycqa.github.io](https://pycqa.github.io/isort/)). + These checks are required to pass by the online integration pipeline. +* `test`: For running the test suite locally using [pytest](https://docs.pytest.org) and some of its addons + (`python -m pytest tests/`). +* `wheel`: Includes `wheel` and `check-wheel-contents`. + +Installation can be done by adding one or more of the aforementioned tags to the installation command. + +For example, installing PyFstat including `chainconsumer`, `pycuda` and `style` dependencies would look like +(mind the lack of whitespaces!) +``` +pip install pyfstat[chainconsumer,pycuda,style] +``` +This command accepts the "development mode" tag `-e`. + +Note that LALSuite is a default requirement, not an optional one, +but its installation from PyPI can be disabled +by setting the `NO_LALSUITE_FROM_PYPI` environment variable, +e.g. for a development install from a local git clone: +``` +NO_LALSUITE_FROM_PYPI=1 pip install -e . +``` +This can be useful to avoid duplication when in a conda environment +or installing LALSuite from source. + +### Using LALSuite built from source + +Instructions to use a custom local LALSuite installation can be found in [here on the wiki](https://github.com/PyFstat/PyFstat/wiki/Using-LALSuite-built-from-source). + +## 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](https://github.com/PyFstat/PyFstat/issues/new/choose) or +[pull request](https://github.com/PyFstat/PyFstat/compare). + +Here's what you need to know: +* As a developer, you should install directly from a git clone, + with either `pip install -e .[dev]` into some environment + or creating a development-enabled conda environment directly from the + `pyfstat-dev.yml` file + as explained on [this wiki page](https://github.com/PyFstat/PyFstat/wiki/conda-environments). + Please also run, just once after installing: + ``` + pre-commit install + ``` + + This sets up everything for automated code quality tests (see below) + to be checked for you at every commit. +* The github automated tests currently run on `python` [3.8,3.9,3.10,3.11] + and new PRs need to pass all these. +* You can also run the full test suite locally via `pytest tests/`, + or run individual tests as explained + [on this page](https://docs.pytest.org/en/6.2.x/usage.html#specifying-tests-selecting-tests). +* The automated test on github also runs + the [black](https://black.readthedocs.io) style checker, + the [flake8](https://flake8.pycqa.org/en/latest/) linter, + and the [isort](https://pycqa.github.io/isort/) import ordering helper. +* If you have installed the dev dependencies correctly via pip or conda, + and ran `pre-commit install` once, + then you're ready to let the `pre-commit` tool do all of this automatically for you + every time you do `git commit`. + For anything that would fail on the github integration tests, + it will then either automatically reformat your code to match our style + or print warnings for things to fix. + The first time it will take a while for setup, + later it should be faster. +* If for some reason you can't use `pre-commit`, + you can still manually run these tools before pushing changes / submitting PRs: + `isort .` to sort package imports, + `flake8 --count --statistics .` to find common coding errors and then fix them manually, + `black --check --diff .` to show the required style changes, or `black .` to automatically apply them. + +## 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](https://github.com/dfm/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: +* The recent JOSS (Journal of Open Source Software) paper summarising the package: +[Keitel, Tenorio, Ashton & Prix 2021](https://doi.org/10.21105/joss.03000) +([inspire:1842895](https://inspirehep.net/literature/1842895) +/ [ADS:2021arXiv210110915K](https://ui.adsabs.harvard.edu/abs/2021arXiv210110915K/)). +* The original paper introducing the package and the MCMC functionality: +[Ashton&Prix 2018](https://doi.org/10.1103/PhysRevD.97.103020) +([inspire:1655200](https://inspirehep.net/literature/1655200) +/ [ADS:2018PhRvD..97j3020A](https://ui.adsabs.harvard.edu/abs/2018PhRvD..97j3020A/)). +* The methods paper introducing a Bayes factor to evaluate the multi-stage follow-up: +[Tenorio, Keitel, Sintes 2021](https://doi.org/10.1103/PhysRevD.104.084012) +([inspire:1865975](https://inspirehep.net/literature/1865975) +/ [ADS:2021PhRvD.104h4012T](https://ui.adsabs.harvard.edu/abs/2021PhRvD.104h4012T/)) +* For transient searches: +[Keitel&Ashton 2018](https://doi.org/10.1088/1361-6382/aade34) +([inspire:1673205](https://inspirehep.net/literature/1673205) +/ [ADS:2018CQGra..35t5003K](https://ui.adsabs.harvard.edu/abs/2018CQGra..35t5003K/)). +* For glitch-robust searches: +[Ashton, Prix & Jones 2018](https://doi.org/10.1103/PhysRevD.98.063011) +([inspire:1672396](https://inspirehep.net/literature/1672396) +/ [ADS:2018PhRvD..98f3011A](https://ui.adsabs.harvard.edu/abs/2018PhRvD..98f3011A/) + +If you'd additionally like to cite the `PyFstat` package in general, +please refer to the [version-independent Zenodo listing](https://doi.org/10.5281/zenodo.3967045) +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](https://doi.org/10.5281/zenodo.3967045). + +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](https://doi.org/10.5281/zenodo.1243930) +and please amend the BibTeX entry accordingly. + + +PyFstat uses the [`ptemcee` sampler](https://github.com/willvousden/ptemcee), which can be +cited as +[Vousden, Far & Mandel 2015](https://doi.org/10.1093/mnras/stv2422) +([ADS:2016MNRAS.455.1919V](https://ui.adsabs.harvard.edu/abs/2016MNRAS.455.1919V/abstract)) +and [Foreman-Mackey, Hogg, Lang, and Goodman 2012](https://doi.org/10.1086/670067) +([2013PASP..125..306F](https://ui.adsabs.harvard.edu/abs/2013PASP..125..306F/abstract)). + +PyFstat also 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](https://git.ligo.org/lscsoft/lalsuite/#acknowledgment)) +and also [Wette 2020](https://doi.org/10.1016/j.softx.2020.100634) +([inspire:1837108](https://inspirehep.net/literature/1837108) +/ [ADS:2020SoftX..1200634W](https://ui.adsabs.harvard.edu/abs/2020SoftX..1200634W/)) +for the C-to-python [SWIG](http://www.swig.org) bindings. + + + + +%package -n python3-PyFstat +Summary: a python package for gravitational wave analysis with the F-statistic +Provides: python-PyFstat +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-PyFstat +# 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](https://doi.org/10.7935/GT1W-FZ16). + +Getting started: +* This README provides information on +[installing](#installation), +[contributing](#contributors) to +and [citing](#citing-this-work) PyFstat. +* PyFstat usage and its API are documented at [pyfstat.readthedocs.io](https://pyfstat.readthedocs.io/). +* We also have a number of [tutorials](https://github.com/PyFstat/PyFstat/tree/master/examples/tutorials) and +[examples](https://github.com/PyFstat/PyFstat/tree/master/examples), demonstrating different use cases. +You can run them locally, or online as jupyter notebooks with +[binder](https://mybinder.org/v2/gh/PyFstat/PyFstat/master). +* The [project wiki](https://github.com/PyFstat/PyFstat/wiki) is mainly used for developer information. +* A [changelog](https://github.com/PyFstat/PyFstat/blob/master/CHANGELOG.md) +is also available. +* PyFstat >=2.0.0 requires a recent LALSuite (>=7.13) / lalpulsar (>=6.0) +including the [SFTv3 specification](https://dcc.ligo.org/T040164-v2/public). +If you need to work with older versions, the last PyFstat release supporting those was `1.19.1`. + +[](https://badge.fury.io/py/PyFstat) +[](https://anaconda.org/conda-forge/pyfstat) +[](https://doi.org/10.5281/zenodo.3967045) +[](https://ascl.net/2102.027) +[](https://doi.org/10.21105/joss.03000) +[](https://github.com/PyFstat/PyFstat/actions/workflows/docker-publish.yml) +[](https://mybinder.org/v2/gh/PyFstat/PyFstat/master) +[](https://github.com/PyFstat/PyFstat/actions/workflows/integration.yml) +[](https://codecov.io/gh/PyFstat/PyFstat) +[](https://pyfstat.readthedocs.io/en/latest/?badge=latest) +[](https://github.com/psf/black) + +## Installation + +PyFstat releases can be installed in a variety of ways, including +[`pip install` from PyPI](#pip-install-from-PyPi), +[conda](#conda-installation), +[Docker/Singularity images](#docker-container), +and [from source releases on Zenodo](#install-pyfstat-from-source-zenodo-or-git-clone). +Latest development versions can +[also be installed with pip](#pip-install-from-github) +or [from a local git clone](#install-pyfstat-from-source-zenodo-or-git-clone). + +If you don't have a recent `python` installation (`3.8+`) on your system, +then `Docker` or `conda` are the easiest paths. + +In either case, be sure to also check out the notes on +[dependencies](#dependencies) +and [citing this work](#citing-this-work). + +If you run into problems with ephemerides files, check the wiki page on +[ephemerides installation](https://github.com/PyFstat/PyFstat/wiki/ephemerides-installation). + +### pip install from PyPI + +PyPI releases are available from https://pypi.org/project/PyFstat/. + +A simple +``` +pip install pyfstat +``` +should give you the latest release version with all dependencies; +recent releases now also include a sufficient minimal set of ephemerides files. + +If you are not installing into a [venv](https://docs.python.org/3/library/venv.html) +or [conda environment](#conda-installation) +(you really should!), +on many systems you may need to use the `--user` flag. + +Note that the PyFstat installation will fail at the +LALSuite dependency stage +if your `pip` is too old (e.g. 18.1); to fix this, do +``` +pip install --upgrade pip setuptools +``` + +### conda installation + +See [this wiki page](https://github.com/PyFstat/PyFstat/wiki/conda-environments) +for further instructions on installing conda itself, +installing PyFstat into an existing environment, +or for .yml recipes to set up a PyFstat-specific environment +both for normal users and for developers. + +If getting PyFstat from conda-forge, it already includes the required ephemerides files. + +### Docker container + +Ready-to-use PyFstat containers are available at the [Packages](https://github.com/PyFstat/PyFstat/packages) +page. A GitHub account together with a personal access token is required. +[Go to the wiki page](https://github.com/PyFstat/PyFstat/wiki/Containers) +to learn how to pull them from the GitHub registry using `Docker` or `Singularity`. + +### 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 +``` + +This should pull in all dependencies in the same way as installing from PyPI, +and recent lalsuite dependencies will include ephemerides files too. + +### install PyFstat from source (Zenodo or git clone) + +You can download a source release tarball from [Zenodo](https://doi.org/10.5281/zenodo.3967045) +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. + +This should pull in all dependencies in the same way as installing from PyPI, +and recent lalsuite dependencies will include ephemerides files too. + +### Dependencies + +PyFstat uses the following external python modules, +which should all be pulled in automatically if you use `pip`: + +* [corner](https://pypi.python.org/pypi/corner/) +* [dill](https://pypi.python.org/pypi/dill) +* [lalsuite](https://pypi.org/project/lalsuite/) +* [matplotlib](https://matplotlib.org/) +* [numpy](https://www.numpy.org/) +* [pathos](https://pypi.python.org/pypi/pathos) +* [ptemcee](https://github.com/willvousden/ptemcee) +* [scipy](https://www.scipy.org/) +* [tqdm](https://pypi.python.org/pypi/tqdm) +* [versioneer](https://pypi.org/project/versioneer/) + +For a general introduction to installing modules, see +[here](https://docs.python.org/3/installing/index.html). + +NOTE: currently we have pinned to +`numpy<1.24.0` (due to an incompatibility with ptemcee). + +NOTE: We require a recent LALSuite (>=7.13) / lalpulsar (>=6.0). +If you need to work with older versions, +the last PyFstat release supporting those was `1.19.1`. + +### Optional dependencies + +PyFstat manages optional dependencies through setuptool's `extras_require`. + +Available sets of optional dependencies are: + +* `chainconsumer` ([Samreay/Chainconsumer](https://github.com/Samreay/ChainConsumer)): Required to run some optional +plotting methods and some of the [example scripts](./examples). +* `dev`: Collects `docs`, `style`, `test` and `wheel`. +* `docs`: Required dependencies to build the documentation. +* `pycuda` ([PyPI](https://pypi.org/project/pycuda/)): Required for the `tCWFstatMapVersion=pycuda` + option of the `TransientGridSearch` class. (Note: Installing `pycuda` requires a working + `nvcc` compiler in your path.) +* `style`: Includes the `flake8` linter ([flake8.pycqa](https://flake8.pycqa.org/en/latest)), + `black` style checker ([black.readthedocs](https://black.readthedocs.io)), + and `isort` for import ordering ([pycqa.github.io](https://pycqa.github.io/isort/)). + These checks are required to pass by the online integration pipeline. +* `test`: For running the test suite locally using [pytest](https://docs.pytest.org) and some of its addons + (`python -m pytest tests/`). +* `wheel`: Includes `wheel` and `check-wheel-contents`. + +Installation can be done by adding one or more of the aforementioned tags to the installation command. + +For example, installing PyFstat including `chainconsumer`, `pycuda` and `style` dependencies would look like +(mind the lack of whitespaces!) +``` +pip install pyfstat[chainconsumer,pycuda,style] +``` +This command accepts the "development mode" tag `-e`. + +Note that LALSuite is a default requirement, not an optional one, +but its installation from PyPI can be disabled +by setting the `NO_LALSUITE_FROM_PYPI` environment variable, +e.g. for a development install from a local git clone: +``` +NO_LALSUITE_FROM_PYPI=1 pip install -e . +``` +This can be useful to avoid duplication when in a conda environment +or installing LALSuite from source. + +### Using LALSuite built from source + +Instructions to use a custom local LALSuite installation can be found in [here on the wiki](https://github.com/PyFstat/PyFstat/wiki/Using-LALSuite-built-from-source). + +## 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](https://github.com/PyFstat/PyFstat/issues/new/choose) or +[pull request](https://github.com/PyFstat/PyFstat/compare). + +Here's what you need to know: +* As a developer, you should install directly from a git clone, + with either `pip install -e .[dev]` into some environment + or creating a development-enabled conda environment directly from the + `pyfstat-dev.yml` file + as explained on [this wiki page](https://github.com/PyFstat/PyFstat/wiki/conda-environments). + Please also run, just once after installing: + ``` + pre-commit install + ``` + + This sets up everything for automated code quality tests (see below) + to be checked for you at every commit. +* The github automated tests currently run on `python` [3.8,3.9,3.10,3.11] + and new PRs need to pass all these. +* You can also run the full test suite locally via `pytest tests/`, + or run individual tests as explained + [on this page](https://docs.pytest.org/en/6.2.x/usage.html#specifying-tests-selecting-tests). +* The automated test on github also runs + the [black](https://black.readthedocs.io) style checker, + the [flake8](https://flake8.pycqa.org/en/latest/) linter, + and the [isort](https://pycqa.github.io/isort/) import ordering helper. +* If you have installed the dev dependencies correctly via pip or conda, + and ran `pre-commit install` once, + then you're ready to let the `pre-commit` tool do all of this automatically for you + every time you do `git commit`. + For anything that would fail on the github integration tests, + it will then either automatically reformat your code to match our style + or print warnings for things to fix. + The first time it will take a while for setup, + later it should be faster. +* If for some reason you can't use `pre-commit`, + you can still manually run these tools before pushing changes / submitting PRs: + `isort .` to sort package imports, + `flake8 --count --statistics .` to find common coding errors and then fix them manually, + `black --check --diff .` to show the required style changes, or `black .` to automatically apply them. + +## 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](https://github.com/dfm/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: +* The recent JOSS (Journal of Open Source Software) paper summarising the package: +[Keitel, Tenorio, Ashton & Prix 2021](https://doi.org/10.21105/joss.03000) +([inspire:1842895](https://inspirehep.net/literature/1842895) +/ [ADS:2021arXiv210110915K](https://ui.adsabs.harvard.edu/abs/2021arXiv210110915K/)). +* The original paper introducing the package and the MCMC functionality: +[Ashton&Prix 2018](https://doi.org/10.1103/PhysRevD.97.103020) +([inspire:1655200](https://inspirehep.net/literature/1655200) +/ [ADS:2018PhRvD..97j3020A](https://ui.adsabs.harvard.edu/abs/2018PhRvD..97j3020A/)). +* The methods paper introducing a Bayes factor to evaluate the multi-stage follow-up: +[Tenorio, Keitel, Sintes 2021](https://doi.org/10.1103/PhysRevD.104.084012) +([inspire:1865975](https://inspirehep.net/literature/1865975) +/ [ADS:2021PhRvD.104h4012T](https://ui.adsabs.harvard.edu/abs/2021PhRvD.104h4012T/)) +* For transient searches: +[Keitel&Ashton 2018](https://doi.org/10.1088/1361-6382/aade34) +([inspire:1673205](https://inspirehep.net/literature/1673205) +/ [ADS:2018CQGra..35t5003K](https://ui.adsabs.harvard.edu/abs/2018CQGra..35t5003K/)). +* For glitch-robust searches: +[Ashton, Prix & Jones 2018](https://doi.org/10.1103/PhysRevD.98.063011) +([inspire:1672396](https://inspirehep.net/literature/1672396) +/ [ADS:2018PhRvD..98f3011A](https://ui.adsabs.harvard.edu/abs/2018PhRvD..98f3011A/) + +If you'd additionally like to cite the `PyFstat` package in general, +please refer to the [version-independent Zenodo listing](https://doi.org/10.5281/zenodo.3967045) +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](https://doi.org/10.5281/zenodo.3967045). + +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](https://doi.org/10.5281/zenodo.1243930) +and please amend the BibTeX entry accordingly. + + +PyFstat uses the [`ptemcee` sampler](https://github.com/willvousden/ptemcee), which can be +cited as +[Vousden, Far & Mandel 2015](https://doi.org/10.1093/mnras/stv2422) +([ADS:2016MNRAS.455.1919V](https://ui.adsabs.harvard.edu/abs/2016MNRAS.455.1919V/abstract)) +and [Foreman-Mackey, Hogg, Lang, and Goodman 2012](https://doi.org/10.1086/670067) +([2013PASP..125..306F](https://ui.adsabs.harvard.edu/abs/2013PASP..125..306F/abstract)). + +PyFstat also 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](https://git.ligo.org/lscsoft/lalsuite/#acknowledgment)) +and also [Wette 2020](https://doi.org/10.1016/j.softx.2020.100634) +([inspire:1837108](https://inspirehep.net/literature/1837108) +/ [ADS:2020SoftX..1200634W](https://ui.adsabs.harvard.edu/abs/2020SoftX..1200634W/)) +for the C-to-python [SWIG](http://www.swig.org) bindings. + + + + +%package help +Summary: Development documents and examples for PyFstat +Provides: python3-PyFstat-doc +%description help +# 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](https://doi.org/10.7935/GT1W-FZ16). + +Getting started: +* This README provides information on +[installing](#installation), +[contributing](#contributors) to +and [citing](#citing-this-work) PyFstat. +* PyFstat usage and its API are documented at [pyfstat.readthedocs.io](https://pyfstat.readthedocs.io/). +* We also have a number of [tutorials](https://github.com/PyFstat/PyFstat/tree/master/examples/tutorials) and +[examples](https://github.com/PyFstat/PyFstat/tree/master/examples), demonstrating different use cases. +You can run them locally, or online as jupyter notebooks with +[binder](https://mybinder.org/v2/gh/PyFstat/PyFstat/master). +* The [project wiki](https://github.com/PyFstat/PyFstat/wiki) is mainly used for developer information. +* A [changelog](https://github.com/PyFstat/PyFstat/blob/master/CHANGELOG.md) +is also available. +* PyFstat >=2.0.0 requires a recent LALSuite (>=7.13) / lalpulsar (>=6.0) +including the [SFTv3 specification](https://dcc.ligo.org/T040164-v2/public). +If you need to work with older versions, the last PyFstat release supporting those was `1.19.1`. + +[](https://badge.fury.io/py/PyFstat) +[](https://anaconda.org/conda-forge/pyfstat) +[](https://doi.org/10.5281/zenodo.3967045) +[](https://ascl.net/2102.027) +[](https://doi.org/10.21105/joss.03000) +[](https://github.com/PyFstat/PyFstat/actions/workflows/docker-publish.yml) +[](https://mybinder.org/v2/gh/PyFstat/PyFstat/master) +[](https://github.com/PyFstat/PyFstat/actions/workflows/integration.yml) +[](https://codecov.io/gh/PyFstat/PyFstat) +[](https://pyfstat.readthedocs.io/en/latest/?badge=latest) +[](https://github.com/psf/black) + +## Installation + +PyFstat releases can be installed in a variety of ways, including +[`pip install` from PyPI](#pip-install-from-PyPi), +[conda](#conda-installation), +[Docker/Singularity images](#docker-container), +and [from source releases on Zenodo](#install-pyfstat-from-source-zenodo-or-git-clone). +Latest development versions can +[also be installed with pip](#pip-install-from-github) +or [from a local git clone](#install-pyfstat-from-source-zenodo-or-git-clone). + +If you don't have a recent `python` installation (`3.8+`) on your system, +then `Docker` or `conda` are the easiest paths. + +In either case, be sure to also check out the notes on +[dependencies](#dependencies) +and [citing this work](#citing-this-work). + +If you run into problems with ephemerides files, check the wiki page on +[ephemerides installation](https://github.com/PyFstat/PyFstat/wiki/ephemerides-installation). + +### pip install from PyPI + +PyPI releases are available from https://pypi.org/project/PyFstat/. + +A simple +``` +pip install pyfstat +``` +should give you the latest release version with all dependencies; +recent releases now also include a sufficient minimal set of ephemerides files. + +If you are not installing into a [venv](https://docs.python.org/3/library/venv.html) +or [conda environment](#conda-installation) +(you really should!), +on many systems you may need to use the `--user` flag. + +Note that the PyFstat installation will fail at the +LALSuite dependency stage +if your `pip` is too old (e.g. 18.1); to fix this, do +``` +pip install --upgrade pip setuptools +``` + +### conda installation + +See [this wiki page](https://github.com/PyFstat/PyFstat/wiki/conda-environments) +for further instructions on installing conda itself, +installing PyFstat into an existing environment, +or for .yml recipes to set up a PyFstat-specific environment +both for normal users and for developers. + +If getting PyFstat from conda-forge, it already includes the required ephemerides files. + +### Docker container + +Ready-to-use PyFstat containers are available at the [Packages](https://github.com/PyFstat/PyFstat/packages) +page. A GitHub account together with a personal access token is required. +[Go to the wiki page](https://github.com/PyFstat/PyFstat/wiki/Containers) +to learn how to pull them from the GitHub registry using `Docker` or `Singularity`. + +### 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 +``` + +This should pull in all dependencies in the same way as installing from PyPI, +and recent lalsuite dependencies will include ephemerides files too. + +### install PyFstat from source (Zenodo or git clone) + +You can download a source release tarball from [Zenodo](https://doi.org/10.5281/zenodo.3967045) +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. + +This should pull in all dependencies in the same way as installing from PyPI, +and recent lalsuite dependencies will include ephemerides files too. + +### Dependencies + +PyFstat uses the following external python modules, +which should all be pulled in automatically if you use `pip`: + +* [corner](https://pypi.python.org/pypi/corner/) +* [dill](https://pypi.python.org/pypi/dill) +* [lalsuite](https://pypi.org/project/lalsuite/) +* [matplotlib](https://matplotlib.org/) +* [numpy](https://www.numpy.org/) +* [pathos](https://pypi.python.org/pypi/pathos) +* [ptemcee](https://github.com/willvousden/ptemcee) +* [scipy](https://www.scipy.org/) +* [tqdm](https://pypi.python.org/pypi/tqdm) +* [versioneer](https://pypi.org/project/versioneer/) + +For a general introduction to installing modules, see +[here](https://docs.python.org/3/installing/index.html). + +NOTE: currently we have pinned to +`numpy<1.24.0` (due to an incompatibility with ptemcee). + +NOTE: We require a recent LALSuite (>=7.13) / lalpulsar (>=6.0). +If you need to work with older versions, +the last PyFstat release supporting those was `1.19.1`. + +### Optional dependencies + +PyFstat manages optional dependencies through setuptool's `extras_require`. + +Available sets of optional dependencies are: + +* `chainconsumer` ([Samreay/Chainconsumer](https://github.com/Samreay/ChainConsumer)): Required to run some optional +plotting methods and some of the [example scripts](./examples). +* `dev`: Collects `docs`, `style`, `test` and `wheel`. +* `docs`: Required dependencies to build the documentation. +* `pycuda` ([PyPI](https://pypi.org/project/pycuda/)): Required for the `tCWFstatMapVersion=pycuda` + option of the `TransientGridSearch` class. (Note: Installing `pycuda` requires a working + `nvcc` compiler in your path.) +* `style`: Includes the `flake8` linter ([flake8.pycqa](https://flake8.pycqa.org/en/latest)), + `black` style checker ([black.readthedocs](https://black.readthedocs.io)), + and `isort` for import ordering ([pycqa.github.io](https://pycqa.github.io/isort/)). + These checks are required to pass by the online integration pipeline. +* `test`: For running the test suite locally using [pytest](https://docs.pytest.org) and some of its addons + (`python -m pytest tests/`). +* `wheel`: Includes `wheel` and `check-wheel-contents`. + +Installation can be done by adding one or more of the aforementioned tags to the installation command. + +For example, installing PyFstat including `chainconsumer`, `pycuda` and `style` dependencies would look like +(mind the lack of whitespaces!) +``` +pip install pyfstat[chainconsumer,pycuda,style] +``` +This command accepts the "development mode" tag `-e`. + +Note that LALSuite is a default requirement, not an optional one, +but its installation from PyPI can be disabled +by setting the `NO_LALSUITE_FROM_PYPI` environment variable, +e.g. for a development install from a local git clone: +``` +NO_LALSUITE_FROM_PYPI=1 pip install -e . +``` +This can be useful to avoid duplication when in a conda environment +or installing LALSuite from source. + +### Using LALSuite built from source + +Instructions to use a custom local LALSuite installation can be found in [here on the wiki](https://github.com/PyFstat/PyFstat/wiki/Using-LALSuite-built-from-source). + +## 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](https://github.com/PyFstat/PyFstat/issues/new/choose) or +[pull request](https://github.com/PyFstat/PyFstat/compare). + +Here's what you need to know: +* As a developer, you should install directly from a git clone, + with either `pip install -e .[dev]` into some environment + or creating a development-enabled conda environment directly from the + `pyfstat-dev.yml` file + as explained on [this wiki page](https://github.com/PyFstat/PyFstat/wiki/conda-environments). + Please also run, just once after installing: + ``` + pre-commit install + ``` + + This sets up everything for automated code quality tests (see below) + to be checked for you at every commit. +* The github automated tests currently run on `python` [3.8,3.9,3.10,3.11] + and new PRs need to pass all these. +* You can also run the full test suite locally via `pytest tests/`, + or run individual tests as explained + [on this page](https://docs.pytest.org/en/6.2.x/usage.html#specifying-tests-selecting-tests). +* The automated test on github also runs + the [black](https://black.readthedocs.io) style checker, + the [flake8](https://flake8.pycqa.org/en/latest/) linter, + and the [isort](https://pycqa.github.io/isort/) import ordering helper. +* If you have installed the dev dependencies correctly via pip or conda, + and ran `pre-commit install` once, + then you're ready to let the `pre-commit` tool do all of this automatically for you + every time you do `git commit`. + For anything that would fail on the github integration tests, + it will then either automatically reformat your code to match our style + or print warnings for things to fix. + The first time it will take a while for setup, + later it should be faster. +* If for some reason you can't use `pre-commit`, + you can still manually run these tools before pushing changes / submitting PRs: + `isort .` to sort package imports, + `flake8 --count --statistics .` to find common coding errors and then fix them manually, + `black --check --diff .` to show the required style changes, or `black .` to automatically apply them. + +## 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](https://github.com/dfm/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: +* The recent JOSS (Journal of Open Source Software) paper summarising the package: +[Keitel, Tenorio, Ashton & Prix 2021](https://doi.org/10.21105/joss.03000) +([inspire:1842895](https://inspirehep.net/literature/1842895) +/ [ADS:2021arXiv210110915K](https://ui.adsabs.harvard.edu/abs/2021arXiv210110915K/)). +* The original paper introducing the package and the MCMC functionality: +[Ashton&Prix 2018](https://doi.org/10.1103/PhysRevD.97.103020) +([inspire:1655200](https://inspirehep.net/literature/1655200) +/ [ADS:2018PhRvD..97j3020A](https://ui.adsabs.harvard.edu/abs/2018PhRvD..97j3020A/)). +* The methods paper introducing a Bayes factor to evaluate the multi-stage follow-up: +[Tenorio, Keitel, Sintes 2021](https://doi.org/10.1103/PhysRevD.104.084012) +([inspire:1865975](https://inspirehep.net/literature/1865975) +/ [ADS:2021PhRvD.104h4012T](https://ui.adsabs.harvard.edu/abs/2021PhRvD.104h4012T/)) +* For transient searches: +[Keitel&Ashton 2018](https://doi.org/10.1088/1361-6382/aade34) +([inspire:1673205](https://inspirehep.net/literature/1673205) +/ [ADS:2018CQGra..35t5003K](https://ui.adsabs.harvard.edu/abs/2018CQGra..35t5003K/)). +* For glitch-robust searches: +[Ashton, Prix & Jones 2018](https://doi.org/10.1103/PhysRevD.98.063011) +([inspire:1672396](https://inspirehep.net/literature/1672396) +/ [ADS:2018PhRvD..98f3011A](https://ui.adsabs.harvard.edu/abs/2018PhRvD..98f3011A/) + +If you'd additionally like to cite the `PyFstat` package in general, +please refer to the [version-independent Zenodo listing](https://doi.org/10.5281/zenodo.3967045) +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](https://doi.org/10.5281/zenodo.3967045). + +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](https://doi.org/10.5281/zenodo.1243930) +and please amend the BibTeX entry accordingly. + + +PyFstat uses the [`ptemcee` sampler](https://github.com/willvousden/ptemcee), which can be +cited as +[Vousden, Far & Mandel 2015](https://doi.org/10.1093/mnras/stv2422) +([ADS:2016MNRAS.455.1919V](https://ui.adsabs.harvard.edu/abs/2016MNRAS.455.1919V/abstract)) +and [Foreman-Mackey, Hogg, Lang, and Goodman 2012](https://doi.org/10.1086/670067) +([2013PASP..125..306F](https://ui.adsabs.harvard.edu/abs/2013PASP..125..306F/abstract)). + +PyFstat also 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](https://git.ligo.org/lscsoft/lalsuite/#acknowledgment)) +and also [Wette 2020](https://doi.org/10.1016/j.softx.2020.100634) +([inspire:1837108](https://inspirehep.net/literature/1837108) +/ [ADS:2020SoftX..1200634W](https://ui.adsabs.harvard.edu/abs/2020SoftX..1200634W/)) +for the C-to-python [SWIG](http://www.swig.org) bindings. + + + + +%prep +%autosetup -n PyFstat-2.0.0 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-PyFstat -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Thu May 18 2023 Python_Bot <Python_Bot@openeuler.org> - 2.0.0-1 +- Package Spec generated |