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diff --git a/python-pyuvdata.spec b/python-pyuvdata.spec new file mode 100644 index 0000000..cd7965d --- /dev/null +++ b/python-pyuvdata.spec @@ -0,0 +1,931 @@ +%global _empty_manifest_terminate_build 0 +Name: python-pyuvdata +Version: 2.3.2 +Release: 1 +Summary: an interface for astronomical interferometeric datasets in python +License: BSD +URL: https://github.com/RadioAstronomySoftwareGroup/pyuvdata +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/d2/b1/284acc6752b9b2f1eadddd469f384a0385610cb78379097b78567215558f/pyuvdata-2.3.2.tar.gz + +Requires: python3-astropy +Requires: python3-h5py +Requires: python3-numpy +Requires: python3-pyerfa +Requires: python3-scipy +Requires: python3-setuptools-scm +Requires: python3-astroquery +Requires: python3-casacore +Requires: python3-pyyaml +Requires: python3-hdf5plugin +Requires: python3-astropy-healpix +Requires: python3-lunarsky +Requires: python3-novas +Requires: python3-novas-de405 +Requires: python3-astroquery +Requires: python3-casacore +Requires: python3-pyyaml +Requires: python3-astroquery +Requires: python3-casacore +Requires: python3-pyyaml +Requires: python3-hdf5plugin +Requires: python3-astropy-healpix +Requires: python3-lunarsky +Requires: python3-novas +Requires: python3-novas-de405 +Requires: python3-pytest +Requires: python3-pytest-xdist +Requires: python3-pytest-cases +Requires: python3-pytest-cov +Requires: python3-cython +Requires: python3-coverage +Requires: python3-pre-commit +Requires: python3-sphinx +Requires: python3-pypandoc +Requires: python3-sphinx +Requires: python3-pypandoc +Requires: python3-hdf5plugin +Requires: python3-astropy-healpix +Requires: python3-lunarsky +Requires: python3-novas +Requires: python3-novas-de405 +Requires: python3-astroquery +Requires: python3-casacore +Requires: python3-pyyaml +Requires: python3-hdf5plugin +Requires: python3-astropy-healpix +Requires: python3-lunarsky +Requires: python3-novas +Requires: python3-novas-de405 +Requires: python3-pytest +Requires: python3-pytest-xdist +Requires: python3-pytest-cases +Requires: python3-pytest-cov +Requires: python3-cython +Requires: python3-coverage +Requires: python3-pre-commit + +%description +# pyuvdata + +[](https://circleci.com/gh/RadioAstronomySoftwareGroup/pyuvdata?branch=main) +[](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/actions) +[](https://codecov.io/gh/RadioAstronomySoftwareGroup/pyuvdata) +[](https://doi.org/10.21105/joss.00140) + +pyuvdata defines a pythonic interface to interferometric data sets. +Currently pyuvdata supports reading and writing of miriad, uvfits, CASA measurement sets +and uvh5 files and reading of FHD +([Fast Holographic Deconvolution](https://github.com/EoRImaging/FHD)) visibility save files, SMA Mir files and MWA correlator FITS files. + +API documentation and a tutorial is hosted on [ReadTheDocs](https://pyuvdata.readthedocs.io). + +# Motivation +The main goals are: + +1. To provide a high quality, well documented path to convert between data formats +2. Support the direct use of datasets from python with minimal software +3. Provide precise data definition via both human readable code and high quality online documentation + +# Package Details +pyuvdata has four major user classes: + +* UVData: supports interferometric data (visibilities) and associated metadata +* UVCal: supports interferometric calibration solutions (antenna-based) and +associated metadata (Note that this is a fairly new object, consider it to be a beta version) +* UVBeam: supports primary beams (E-field or power) and associated metadata +(Note that this is a fairly new object, consider it to be a beta version) +* UVFlag: A class to handle the manipulation and combination of flags for data sets. +Also can convert raw data quality metrics into flags using thresholding. +(This object is very new and experimental. Consider it to be a beta version) + +## UVData File standard notes +* miriad has been thoroughly tested with aipy-style miriad files and minimally +tested with ATCA files +* uvfits conforms to AIPS memo 117 (as of March 2020). It is tested against +FHD, CASA, and AIPS. However AIPS is limited to <80 antennas and CASA uvfits +import does not seem to support >255 antennas. Users with data sets containing > 255 +antennas should use the measurement set writer instead. +* CASA measurement sets, primarily conforming to [CASA Memo 229](https://casa.nrao.edu/Memos/229.html), with some elements taken from the proposed v3.0 format documented in [CASA Memo 264](https://casacore.github.io/casacore-notes/264.html). Measurement sets are tested against +VLA and MWA data sets, (the latter filled via cotter), with some manual verification +haven been performed against ALMA and SMA data sets, the latter filled using the `importuvfits` task of CASA. +tested against ALMA-filled datasets and with SMA datasets +* uvh5 is an HDF5-based file format defined by the HERA collaboration, +details in the [uvh5 memo](docs/references/uvh5_memo.pdf). Note that this is a +somewhat new format, so it may evolve a bit +but we will strive to make future versions backwards compatible with the current format. +It is probably not compatible with other interferometric HDF5 files defined by other groups. +* FHD (read-only support, tested against MWA and PAPER data) +* MIR (read-only support, though experimental write functions are available, tested against SMA data) +* MWA correlator FITS files (read-only support, tested against Cotter outputs and FHD) + +## UVCal file formats +* calfits: a new format defined in pyuvdata, details in the [calfits_memo](docs/references/calfits_memo.pdf). +Note that this format was recently defined and may change in coming versions, +based on user needs. Consider it to be a beta version, but we will strive to +make future versions backwards compatible with the current format. +* FHD calibration files (read-only support) + +## UVBeam file formats +* regularly gridded fits for both E-field and power beams +* non-standard HEALPix fits for both E-field and power beams (in an ImageHDU +rather than a binary table to support frequency, polarization and E-field vector axes) +* read support for CST beam text files, with a defined yaml file format for +metadata, details here: [cst settings file](docs/cst_settings_yaml.rst) + +## Under Development +* UVCal: object and calfits file format (beta version) +* UVBeam: object and beamfits file format (beta version) +* UVFlag: object and HDF5 file format. (beta version) +* Mir: object (part of UVData class) (beta version) +* MirParser: object and python interface for MIR file format (beta version) + +## Known Issues and Planned Improvements +* UVBeam: support phased-array antenna beams (e.g. MWA beams). +* UVFlag: Adding requires a high level knowledge of individual objects. (see [issue #653](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues/653)) + +For details see the [issue log](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues). + +## Community Guidelines +Contributions to this package to add new file formats or address any of the +issues in the [issue log](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues) +are very welcome, as are bug reports and feature requests. +Please see our [guide on contributing](.github/CONTRIBUTING.md) + +# Telescopes +pyuvdata has been used with data from the following telescopes. If you use it on +data from a telescope we don't have listed here please let us know how it went +via an issue! We would like to make pyuvdata generally useful to the community for +as many telescopes as possible. + +* MWA +* HERA +* PAPER +* LWA +* ALMA +* VLA +* ATCA +* SMA + +# Versioning +We use a `generation.major.minor` version number format. We use the `generation` +number for very significant improvements or major rewrites, the `major` number +to indicate substantial package changes (intended to be released every 3-4 months) +and the `minor` number to release smaller incremental updates (intended to be +released approximately monthly and which usually do not include breaking API +changes). We do our best to provide a significant period (usually 2 major +generations) of deprecation warnings for all breaking changes to the API. +We track all changes in our [changelog](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/CHANGELOG.md). + +# History +pyuvdata was originally developed in the low frequency 21cm community to support +the development of and interchange of data between calibration and foreground +subtraction pipelines. Particular focus has been paid to supporting drift and +phased array modes. + +# Citation +Please cite pyuvdata by citing our JOSS paper: + +Hazelton et al, (2017), pyuvdata: an interface for astronomical interferometeric +datasets in python, Journal of Open Source Software, 2(10), 140, doi:10.21105/joss.00140 + +[ADS Link](https://ui.adsabs.harvard.edu/abs/2017JOSS....2..140H); +[Bibtex entry](http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2017JOSS....2..140H&data_type=BIBTEX&db_key=GEN&nocookieset=1) + +# Installation +Simple installation via conda is available for users, developers should follow +the directions under [Developer Installation](#developer-installation) below. + +For simple installation, the latest stable version is available via conda +(preferred: ```conda install -c conda-forge pyuvdata```) or pip (```pip install pyuvdata```). + +There are some optional dependencies that are required for specific functionality, +which will not be installed automatically by conda or pip. +See [Dependencies](#dependencies) for details on installing optional dependencies. + +Note that as of v2.2, `pyuvdata` is only supported on python 3.7+. + +## Dependencies + +Required: + +* astropy >= 5.0.4 +* h5py >= 3.1 +* numpy >= 1.20 +* pyerfa >= 2.0 +* scipy >= 1.5 +* setuptools_scm <7.0|>=7.0.3 + +Optional: + +* astropy-healpix >= 0.6 (for working with beams in HEALPix formats) +* astroquery >= 0.4.4 (for enabling phasing to ephemeris objects using JPL-Horizons) +* hdf5plugin >= 3.1.0 (for enabling bitshuffle and other hdf5 compression filters in uvh5 files) +* lunarsky >=0.2.1 (for working with simulated datasets for lunar telescopes) +* novas and novas_de405 (for using the NOVAS library for astrometry) +* python-casacore >= 3.3.1 (for working with CASA measurement sets) +* pyyaml >= 5.1 (for working with settings files for CST beam files) + + +The numpy and astropy versions are important, so make sure these are up to date. + +We suggest using conda to install all the dependencies. If you want to install +python-casacore and astropy-healpix, you'll need to add conda-forge as a channel +(```conda config --add channels conda-forge```). + +If you do not want to use conda, the packages are also available on PyPI +(python-casacore may require more effort, see details for that package below). +You can install the optional dependencies via pip by specifying an option +when you install pyuvdata, as in ```pip install pyuvdata[healpix]``` +which will install all the required packages for using the HEALPix functionality +in pyuvdata. The options that can be passed in this way are: +[`astroquery`, `casa`, `cst`, `hdf5_compression`, `healpix`, `lunar`, `novas`, `all`, `test`, +`doc`, `dev`]. The first set (`astroquery`, `casa`, `cst`, `hdf5_compression`, +`healpix`, `lunar`, `novas`) enable various specific functionality while `all` will install all +optional dependencies. The last three (`test`, `doc`, `dev`) may be useful for developers +of pyuvdata. + +### Installing python-casacore +python-casacore requires the casacore c++ libraries. It can be installed easily +using conda (```python-casacore``` on conda-forge). + +If you do not want to use conda, the casacore c++ libraries are available for +ubuntu through the [kern suite](http://kernsuite.info/). On OSX, casacore is +available through the [ska-sa brew tap](https://github.com/ska-sa/homebrew-tap). +The python-casacore library (with manual install instructions) is available at +https://github.com/casacore/python-casacore + +## Developer Installation +Clone the repository using +```git clone https://github.com/RadioAstronomySoftwareGroup/pyuvdata.git``` + +Navigate into the pyuvdata directory and run `pip install .` +(note that `python setup.py install` does not work). +Note that this will attempt to automatically install any missing dependencies. +If you use anaconda or another package manager you might prefer to first install +the dependencies as described in [Dependencies](#dependencies). + +To install without dependencies, run `pip install --no-deps .` + +To compile the binary extension modules such that you can successfully run +`import pyuvdata` from the top-level directory of your Git checkout, run: +```python setup.py build_ext --inplace``` + +If you want to do development on pyuvdata, in addition to the other dependencies +you will need the following packages: + +* pytest >= 6.2 +* pytest-cases >= 3.6.9 +* pytest-cov +* cython >=0.23 (This is necessary for coverage reporting of cython extensions) +* coverage +* pre-commit +* sphinx +* pypandoc + +One other package, pytest-xdist, is not required, but can be used to speed up running +the test suite by running tests in parallel. To use it call pytest with the +```-n auto``` option. + +One way to ensure you have all the needed packages is to use the included +`environment.yaml` file to create a new environment that will +contain all the optional dependencies along with dependencies required for +testing and development (```conda env create -f environment.yaml```). +Alternatively, you can specify `test`, `doc`, or `dev` when installing pyuvdata +(as in `pip install pyuvdata[dev]`) to install the packages needed for testing +(including coverage and linting) and documentation development; +`dev` includes everything in `test` and `doc`. + +To use pre-commit to prevent committing code that does not follow our style, you'll +need to run `pre-commit install` in the top level `pyuvdata` directory. + +## Tests +Uses the `pytest` package to execute test suite. +From the source pyuvdata directory run ```pytest``` or ```python -m pytest```. + +Testing of `UVFlag` module requires the `pytest-cases` plug-in. + +# API +The primary interface to data from python is via the UVData object. It provides +import functionality from all supported file formats (UVFITS, Miriad, UVH5, FHD, +CASA measurement sets, SMA Mir, MWA correlator FITS) and export to UVFITS, Miriad, +CASA measurement sets and UVH5 formats and can +be interacted with directly. Similarly, the primary calibration, beam, and flag +interfaces are via the UVCal, UVBeam, and UVflag objects. The attributes of the UVData, +UVCal, UVBeam, and UVFlag objects are described in the UVData Parameters, UVCal Parameters, +UVBeam Parameters and UVFlag Parameters pages on [ReadTheDocs](https://pyuvdata.readthedocs.io). + + +# Maintainers +pyuvdata is maintained by the RASG Managers, which currently include: + + - Adam Beardsley (Winona State University) + - Bryna Hazelton (University of Washington) + - Daniel Jacobs (Arizona State University) + - Matt Kolopanis (Arizona State University) + - Paul La Plante (University of Nevada, Las Vegas) + - Jonathan Pober (Brown University) + +Please use the channels discussed in the [guide on contributing](.github/CONTRIBUTING.md) +for code-related discussions. You can contact us privately if needed at +[rasgmanagers@gmail.com](mailto:rasgmanagers@gmail.com). + +# Acknowledgments + +Support for pyuvdata was provided by NSF awards #1835421 and #1835120. + + +%package -n python3-pyuvdata +Summary: an interface for astronomical interferometeric datasets in python +Provides: python-pyuvdata +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +BuildRequires: python3-cffi +BuildRequires: gcc +BuildRequires: gdb +%description -n python3-pyuvdata +# pyuvdata + +[](https://circleci.com/gh/RadioAstronomySoftwareGroup/pyuvdata?branch=main) +[](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/actions) +[](https://codecov.io/gh/RadioAstronomySoftwareGroup/pyuvdata) +[](https://doi.org/10.21105/joss.00140) + +pyuvdata defines a pythonic interface to interferometric data sets. +Currently pyuvdata supports reading and writing of miriad, uvfits, CASA measurement sets +and uvh5 files and reading of FHD +([Fast Holographic Deconvolution](https://github.com/EoRImaging/FHD)) visibility save files, SMA Mir files and MWA correlator FITS files. + +API documentation and a tutorial is hosted on [ReadTheDocs](https://pyuvdata.readthedocs.io). + +# Motivation +The main goals are: + +1. To provide a high quality, well documented path to convert between data formats +2. Support the direct use of datasets from python with minimal software +3. Provide precise data definition via both human readable code and high quality online documentation + +# Package Details +pyuvdata has four major user classes: + +* UVData: supports interferometric data (visibilities) and associated metadata +* UVCal: supports interferometric calibration solutions (antenna-based) and +associated metadata (Note that this is a fairly new object, consider it to be a beta version) +* UVBeam: supports primary beams (E-field or power) and associated metadata +(Note that this is a fairly new object, consider it to be a beta version) +* UVFlag: A class to handle the manipulation and combination of flags for data sets. +Also can convert raw data quality metrics into flags using thresholding. +(This object is very new and experimental. Consider it to be a beta version) + +## UVData File standard notes +* miriad has been thoroughly tested with aipy-style miriad files and minimally +tested with ATCA files +* uvfits conforms to AIPS memo 117 (as of March 2020). It is tested against +FHD, CASA, and AIPS. However AIPS is limited to <80 antennas and CASA uvfits +import does not seem to support >255 antennas. Users with data sets containing > 255 +antennas should use the measurement set writer instead. +* CASA measurement sets, primarily conforming to [CASA Memo 229](https://casa.nrao.edu/Memos/229.html), with some elements taken from the proposed v3.0 format documented in [CASA Memo 264](https://casacore.github.io/casacore-notes/264.html). Measurement sets are tested against +VLA and MWA data sets, (the latter filled via cotter), with some manual verification +haven been performed against ALMA and SMA data sets, the latter filled using the `importuvfits` task of CASA. +tested against ALMA-filled datasets and with SMA datasets +* uvh5 is an HDF5-based file format defined by the HERA collaboration, +details in the [uvh5 memo](docs/references/uvh5_memo.pdf). Note that this is a +somewhat new format, so it may evolve a bit +but we will strive to make future versions backwards compatible with the current format. +It is probably not compatible with other interferometric HDF5 files defined by other groups. +* FHD (read-only support, tested against MWA and PAPER data) +* MIR (read-only support, though experimental write functions are available, tested against SMA data) +* MWA correlator FITS files (read-only support, tested against Cotter outputs and FHD) + +## UVCal file formats +* calfits: a new format defined in pyuvdata, details in the [calfits_memo](docs/references/calfits_memo.pdf). +Note that this format was recently defined and may change in coming versions, +based on user needs. Consider it to be a beta version, but we will strive to +make future versions backwards compatible with the current format. +* FHD calibration files (read-only support) + +## UVBeam file formats +* regularly gridded fits for both E-field and power beams +* non-standard HEALPix fits for both E-field and power beams (in an ImageHDU +rather than a binary table to support frequency, polarization and E-field vector axes) +* read support for CST beam text files, with a defined yaml file format for +metadata, details here: [cst settings file](docs/cst_settings_yaml.rst) + +## Under Development +* UVCal: object and calfits file format (beta version) +* UVBeam: object and beamfits file format (beta version) +* UVFlag: object and HDF5 file format. (beta version) +* Mir: object (part of UVData class) (beta version) +* MirParser: object and python interface for MIR file format (beta version) + +## Known Issues and Planned Improvements +* UVBeam: support phased-array antenna beams (e.g. MWA beams). +* UVFlag: Adding requires a high level knowledge of individual objects. (see [issue #653](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues/653)) + +For details see the [issue log](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues). + +## Community Guidelines +Contributions to this package to add new file formats or address any of the +issues in the [issue log](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues) +are very welcome, as are bug reports and feature requests. +Please see our [guide on contributing](.github/CONTRIBUTING.md) + +# Telescopes +pyuvdata has been used with data from the following telescopes. If you use it on +data from a telescope we don't have listed here please let us know how it went +via an issue! We would like to make pyuvdata generally useful to the community for +as many telescopes as possible. + +* MWA +* HERA +* PAPER +* LWA +* ALMA +* VLA +* ATCA +* SMA + +# Versioning +We use a `generation.major.minor` version number format. We use the `generation` +number for very significant improvements or major rewrites, the `major` number +to indicate substantial package changes (intended to be released every 3-4 months) +and the `minor` number to release smaller incremental updates (intended to be +released approximately monthly and which usually do not include breaking API +changes). We do our best to provide a significant period (usually 2 major +generations) of deprecation warnings for all breaking changes to the API. +We track all changes in our [changelog](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/CHANGELOG.md). + +# History +pyuvdata was originally developed in the low frequency 21cm community to support +the development of and interchange of data between calibration and foreground +subtraction pipelines. Particular focus has been paid to supporting drift and +phased array modes. + +# Citation +Please cite pyuvdata by citing our JOSS paper: + +Hazelton et al, (2017), pyuvdata: an interface for astronomical interferometeric +datasets in python, Journal of Open Source Software, 2(10), 140, doi:10.21105/joss.00140 + +[ADS Link](https://ui.adsabs.harvard.edu/abs/2017JOSS....2..140H); +[Bibtex entry](http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2017JOSS....2..140H&data_type=BIBTEX&db_key=GEN&nocookieset=1) + +# Installation +Simple installation via conda is available for users, developers should follow +the directions under [Developer Installation](#developer-installation) below. + +For simple installation, the latest stable version is available via conda +(preferred: ```conda install -c conda-forge pyuvdata```) or pip (```pip install pyuvdata```). + +There are some optional dependencies that are required for specific functionality, +which will not be installed automatically by conda or pip. +See [Dependencies](#dependencies) for details on installing optional dependencies. + +Note that as of v2.2, `pyuvdata` is only supported on python 3.7+. + +## Dependencies + +Required: + +* astropy >= 5.0.4 +* h5py >= 3.1 +* numpy >= 1.20 +* pyerfa >= 2.0 +* scipy >= 1.5 +* setuptools_scm <7.0|>=7.0.3 + +Optional: + +* astropy-healpix >= 0.6 (for working with beams in HEALPix formats) +* astroquery >= 0.4.4 (for enabling phasing to ephemeris objects using JPL-Horizons) +* hdf5plugin >= 3.1.0 (for enabling bitshuffle and other hdf5 compression filters in uvh5 files) +* lunarsky >=0.2.1 (for working with simulated datasets for lunar telescopes) +* novas and novas_de405 (for using the NOVAS library for astrometry) +* python-casacore >= 3.3.1 (for working with CASA measurement sets) +* pyyaml >= 5.1 (for working with settings files for CST beam files) + + +The numpy and astropy versions are important, so make sure these are up to date. + +We suggest using conda to install all the dependencies. If you want to install +python-casacore and astropy-healpix, you'll need to add conda-forge as a channel +(```conda config --add channels conda-forge```). + +If you do not want to use conda, the packages are also available on PyPI +(python-casacore may require more effort, see details for that package below). +You can install the optional dependencies via pip by specifying an option +when you install pyuvdata, as in ```pip install pyuvdata[healpix]``` +which will install all the required packages for using the HEALPix functionality +in pyuvdata. The options that can be passed in this way are: +[`astroquery`, `casa`, `cst`, `hdf5_compression`, `healpix`, `lunar`, `novas`, `all`, `test`, +`doc`, `dev`]. The first set (`astroquery`, `casa`, `cst`, `hdf5_compression`, +`healpix`, `lunar`, `novas`) enable various specific functionality while `all` will install all +optional dependencies. The last three (`test`, `doc`, `dev`) may be useful for developers +of pyuvdata. + +### Installing python-casacore +python-casacore requires the casacore c++ libraries. It can be installed easily +using conda (```python-casacore``` on conda-forge). + +If you do not want to use conda, the casacore c++ libraries are available for +ubuntu through the [kern suite](http://kernsuite.info/). On OSX, casacore is +available through the [ska-sa brew tap](https://github.com/ska-sa/homebrew-tap). +The python-casacore library (with manual install instructions) is available at +https://github.com/casacore/python-casacore + +## Developer Installation +Clone the repository using +```git clone https://github.com/RadioAstronomySoftwareGroup/pyuvdata.git``` + +Navigate into the pyuvdata directory and run `pip install .` +(note that `python setup.py install` does not work). +Note that this will attempt to automatically install any missing dependencies. +If you use anaconda or another package manager you might prefer to first install +the dependencies as described in [Dependencies](#dependencies). + +To install without dependencies, run `pip install --no-deps .` + +To compile the binary extension modules such that you can successfully run +`import pyuvdata` from the top-level directory of your Git checkout, run: +```python setup.py build_ext --inplace``` + +If you want to do development on pyuvdata, in addition to the other dependencies +you will need the following packages: + +* pytest >= 6.2 +* pytest-cases >= 3.6.9 +* pytest-cov +* cython >=0.23 (This is necessary for coverage reporting of cython extensions) +* coverage +* pre-commit +* sphinx +* pypandoc + +One other package, pytest-xdist, is not required, but can be used to speed up running +the test suite by running tests in parallel. To use it call pytest with the +```-n auto``` option. + +One way to ensure you have all the needed packages is to use the included +`environment.yaml` file to create a new environment that will +contain all the optional dependencies along with dependencies required for +testing and development (```conda env create -f environment.yaml```). +Alternatively, you can specify `test`, `doc`, or `dev` when installing pyuvdata +(as in `pip install pyuvdata[dev]`) to install the packages needed for testing +(including coverage and linting) and documentation development; +`dev` includes everything in `test` and `doc`. + +To use pre-commit to prevent committing code that does not follow our style, you'll +need to run `pre-commit install` in the top level `pyuvdata` directory. + +## Tests +Uses the `pytest` package to execute test suite. +From the source pyuvdata directory run ```pytest``` or ```python -m pytest```. + +Testing of `UVFlag` module requires the `pytest-cases` plug-in. + +# API +The primary interface to data from python is via the UVData object. It provides +import functionality from all supported file formats (UVFITS, Miriad, UVH5, FHD, +CASA measurement sets, SMA Mir, MWA correlator FITS) and export to UVFITS, Miriad, +CASA measurement sets and UVH5 formats and can +be interacted with directly. Similarly, the primary calibration, beam, and flag +interfaces are via the UVCal, UVBeam, and UVflag objects. The attributes of the UVData, +UVCal, UVBeam, and UVFlag objects are described in the UVData Parameters, UVCal Parameters, +UVBeam Parameters and UVFlag Parameters pages on [ReadTheDocs](https://pyuvdata.readthedocs.io). + + +# Maintainers +pyuvdata is maintained by the RASG Managers, which currently include: + + - Adam Beardsley (Winona State University) + - Bryna Hazelton (University of Washington) + - Daniel Jacobs (Arizona State University) + - Matt Kolopanis (Arizona State University) + - Paul La Plante (University of Nevada, Las Vegas) + - Jonathan Pober (Brown University) + +Please use the channels discussed in the [guide on contributing](.github/CONTRIBUTING.md) +for code-related discussions. You can contact us privately if needed at +[rasgmanagers@gmail.com](mailto:rasgmanagers@gmail.com). + +# Acknowledgments + +Support for pyuvdata was provided by NSF awards #1835421 and #1835120. + + +%package help +Summary: Development documents and examples for pyuvdata +Provides: python3-pyuvdata-doc +%description help +# pyuvdata + +[](https://circleci.com/gh/RadioAstronomySoftwareGroup/pyuvdata?branch=main) +[](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/actions) +[](https://codecov.io/gh/RadioAstronomySoftwareGroup/pyuvdata) +[](https://doi.org/10.21105/joss.00140) + +pyuvdata defines a pythonic interface to interferometric data sets. +Currently pyuvdata supports reading and writing of miriad, uvfits, CASA measurement sets +and uvh5 files and reading of FHD +([Fast Holographic Deconvolution](https://github.com/EoRImaging/FHD)) visibility save files, SMA Mir files and MWA correlator FITS files. + +API documentation and a tutorial is hosted on [ReadTheDocs](https://pyuvdata.readthedocs.io). + +# Motivation +The main goals are: + +1. To provide a high quality, well documented path to convert between data formats +2. Support the direct use of datasets from python with minimal software +3. Provide precise data definition via both human readable code and high quality online documentation + +# Package Details +pyuvdata has four major user classes: + +* UVData: supports interferometric data (visibilities) and associated metadata +* UVCal: supports interferometric calibration solutions (antenna-based) and +associated metadata (Note that this is a fairly new object, consider it to be a beta version) +* UVBeam: supports primary beams (E-field or power) and associated metadata +(Note that this is a fairly new object, consider it to be a beta version) +* UVFlag: A class to handle the manipulation and combination of flags for data sets. +Also can convert raw data quality metrics into flags using thresholding. +(This object is very new and experimental. Consider it to be a beta version) + +## UVData File standard notes +* miriad has been thoroughly tested with aipy-style miriad files and minimally +tested with ATCA files +* uvfits conforms to AIPS memo 117 (as of March 2020). It is tested against +FHD, CASA, and AIPS. However AIPS is limited to <80 antennas and CASA uvfits +import does not seem to support >255 antennas. Users with data sets containing > 255 +antennas should use the measurement set writer instead. +* CASA measurement sets, primarily conforming to [CASA Memo 229](https://casa.nrao.edu/Memos/229.html), with some elements taken from the proposed v3.0 format documented in [CASA Memo 264](https://casacore.github.io/casacore-notes/264.html). Measurement sets are tested against +VLA and MWA data sets, (the latter filled via cotter), with some manual verification +haven been performed against ALMA and SMA data sets, the latter filled using the `importuvfits` task of CASA. +tested against ALMA-filled datasets and with SMA datasets +* uvh5 is an HDF5-based file format defined by the HERA collaboration, +details in the [uvh5 memo](docs/references/uvh5_memo.pdf). Note that this is a +somewhat new format, so it may evolve a bit +but we will strive to make future versions backwards compatible with the current format. +It is probably not compatible with other interferometric HDF5 files defined by other groups. +* FHD (read-only support, tested against MWA and PAPER data) +* MIR (read-only support, though experimental write functions are available, tested against SMA data) +* MWA correlator FITS files (read-only support, tested against Cotter outputs and FHD) + +## UVCal file formats +* calfits: a new format defined in pyuvdata, details in the [calfits_memo](docs/references/calfits_memo.pdf). +Note that this format was recently defined and may change in coming versions, +based on user needs. Consider it to be a beta version, but we will strive to +make future versions backwards compatible with the current format. +* FHD calibration files (read-only support) + +## UVBeam file formats +* regularly gridded fits for both E-field and power beams +* non-standard HEALPix fits for both E-field and power beams (in an ImageHDU +rather than a binary table to support frequency, polarization and E-field vector axes) +* read support for CST beam text files, with a defined yaml file format for +metadata, details here: [cst settings file](docs/cst_settings_yaml.rst) + +## Under Development +* UVCal: object and calfits file format (beta version) +* UVBeam: object and beamfits file format (beta version) +* UVFlag: object and HDF5 file format. (beta version) +* Mir: object (part of UVData class) (beta version) +* MirParser: object and python interface for MIR file format (beta version) + +## Known Issues and Planned Improvements +* UVBeam: support phased-array antenna beams (e.g. MWA beams). +* UVFlag: Adding requires a high level knowledge of individual objects. (see [issue #653](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues/653)) + +For details see the [issue log](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues). + +## Community Guidelines +Contributions to this package to add new file formats or address any of the +issues in the [issue log](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues) +are very welcome, as are bug reports and feature requests. +Please see our [guide on contributing](.github/CONTRIBUTING.md) + +# Telescopes +pyuvdata has been used with data from the following telescopes. If you use it on +data from a telescope we don't have listed here please let us know how it went +via an issue! We would like to make pyuvdata generally useful to the community for +as many telescopes as possible. + +* MWA +* HERA +* PAPER +* LWA +* ALMA +* VLA +* ATCA +* SMA + +# Versioning +We use a `generation.major.minor` version number format. We use the `generation` +number for very significant improvements or major rewrites, the `major` number +to indicate substantial package changes (intended to be released every 3-4 months) +and the `minor` number to release smaller incremental updates (intended to be +released approximately monthly and which usually do not include breaking API +changes). We do our best to provide a significant period (usually 2 major +generations) of deprecation warnings for all breaking changes to the API. +We track all changes in our [changelog](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/CHANGELOG.md). + +# History +pyuvdata was originally developed in the low frequency 21cm community to support +the development of and interchange of data between calibration and foreground +subtraction pipelines. Particular focus has been paid to supporting drift and +phased array modes. + +# Citation +Please cite pyuvdata by citing our JOSS paper: + +Hazelton et al, (2017), pyuvdata: an interface for astronomical interferometeric +datasets in python, Journal of Open Source Software, 2(10), 140, doi:10.21105/joss.00140 + +[ADS Link](https://ui.adsabs.harvard.edu/abs/2017JOSS....2..140H); +[Bibtex entry](http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2017JOSS....2..140H&data_type=BIBTEX&db_key=GEN&nocookieset=1) + +# Installation +Simple installation via conda is available for users, developers should follow +the directions under [Developer Installation](#developer-installation) below. + +For simple installation, the latest stable version is available via conda +(preferred: ```conda install -c conda-forge pyuvdata```) or pip (```pip install pyuvdata```). + +There are some optional dependencies that are required for specific functionality, +which will not be installed automatically by conda or pip. +See [Dependencies](#dependencies) for details on installing optional dependencies. + +Note that as of v2.2, `pyuvdata` is only supported on python 3.7+. + +## Dependencies + +Required: + +* astropy >= 5.0.4 +* h5py >= 3.1 +* numpy >= 1.20 +* pyerfa >= 2.0 +* scipy >= 1.5 +* setuptools_scm <7.0|>=7.0.3 + +Optional: + +* astropy-healpix >= 0.6 (for working with beams in HEALPix formats) +* astroquery >= 0.4.4 (for enabling phasing to ephemeris objects using JPL-Horizons) +* hdf5plugin >= 3.1.0 (for enabling bitshuffle and other hdf5 compression filters in uvh5 files) +* lunarsky >=0.2.1 (for working with simulated datasets for lunar telescopes) +* novas and novas_de405 (for using the NOVAS library for astrometry) +* python-casacore >= 3.3.1 (for working with CASA measurement sets) +* pyyaml >= 5.1 (for working with settings files for CST beam files) + + +The numpy and astropy versions are important, so make sure these are up to date. + +We suggest using conda to install all the dependencies. If you want to install +python-casacore and astropy-healpix, you'll need to add conda-forge as a channel +(```conda config --add channels conda-forge```). + +If you do not want to use conda, the packages are also available on PyPI +(python-casacore may require more effort, see details for that package below). +You can install the optional dependencies via pip by specifying an option +when you install pyuvdata, as in ```pip install pyuvdata[healpix]``` +which will install all the required packages for using the HEALPix functionality +in pyuvdata. The options that can be passed in this way are: +[`astroquery`, `casa`, `cst`, `hdf5_compression`, `healpix`, `lunar`, `novas`, `all`, `test`, +`doc`, `dev`]. The first set (`astroquery`, `casa`, `cst`, `hdf5_compression`, +`healpix`, `lunar`, `novas`) enable various specific functionality while `all` will install all +optional dependencies. The last three (`test`, `doc`, `dev`) may be useful for developers +of pyuvdata. + +### Installing python-casacore +python-casacore requires the casacore c++ libraries. It can be installed easily +using conda (```python-casacore``` on conda-forge). + +If you do not want to use conda, the casacore c++ libraries are available for +ubuntu through the [kern suite](http://kernsuite.info/). On OSX, casacore is +available through the [ska-sa brew tap](https://github.com/ska-sa/homebrew-tap). +The python-casacore library (with manual install instructions) is available at +https://github.com/casacore/python-casacore + +## Developer Installation +Clone the repository using +```git clone https://github.com/RadioAstronomySoftwareGroup/pyuvdata.git``` + +Navigate into the pyuvdata directory and run `pip install .` +(note that `python setup.py install` does not work). +Note that this will attempt to automatically install any missing dependencies. +If you use anaconda or another package manager you might prefer to first install +the dependencies as described in [Dependencies](#dependencies). + +To install without dependencies, run `pip install --no-deps .` + +To compile the binary extension modules such that you can successfully run +`import pyuvdata` from the top-level directory of your Git checkout, run: +```python setup.py build_ext --inplace``` + +If you want to do development on pyuvdata, in addition to the other dependencies +you will need the following packages: + +* pytest >= 6.2 +* pytest-cases >= 3.6.9 +* pytest-cov +* cython >=0.23 (This is necessary for coverage reporting of cython extensions) +* coverage +* pre-commit +* sphinx +* pypandoc + +One other package, pytest-xdist, is not required, but can be used to speed up running +the test suite by running tests in parallel. To use it call pytest with the +```-n auto``` option. + +One way to ensure you have all the needed packages is to use the included +`environment.yaml` file to create a new environment that will +contain all the optional dependencies along with dependencies required for +testing and development (```conda env create -f environment.yaml```). +Alternatively, you can specify `test`, `doc`, or `dev` when installing pyuvdata +(as in `pip install pyuvdata[dev]`) to install the packages needed for testing +(including coverage and linting) and documentation development; +`dev` includes everything in `test` and `doc`. + +To use pre-commit to prevent committing code that does not follow our style, you'll +need to run `pre-commit install` in the top level `pyuvdata` directory. + +## Tests +Uses the `pytest` package to execute test suite. +From the source pyuvdata directory run ```pytest``` or ```python -m pytest```. + +Testing of `UVFlag` module requires the `pytest-cases` plug-in. + +# API +The primary interface to data from python is via the UVData object. It provides +import functionality from all supported file formats (UVFITS, Miriad, UVH5, FHD, +CASA measurement sets, SMA Mir, MWA correlator FITS) and export to UVFITS, Miriad, +CASA measurement sets and UVH5 formats and can +be interacted with directly. Similarly, the primary calibration, beam, and flag +interfaces are via the UVCal, UVBeam, and UVflag objects. The attributes of the UVData, +UVCal, UVBeam, and UVFlag objects are described in the UVData Parameters, UVCal Parameters, +UVBeam Parameters and UVFlag Parameters pages on [ReadTheDocs](https://pyuvdata.readthedocs.io). + + +# Maintainers +pyuvdata is maintained by the RASG Managers, which currently include: + + - Adam Beardsley (Winona State University) + - Bryna Hazelton (University of Washington) + - Daniel Jacobs (Arizona State University) + - Matt Kolopanis (Arizona State University) + - Paul La Plante (University of Nevada, Las Vegas) + - Jonathan Pober (Brown University) + +Please use the channels discussed in the [guide on contributing](.github/CONTRIBUTING.md) +for code-related discussions. You can contact us privately if needed at +[rasgmanagers@gmail.com](mailto:rasgmanagers@gmail.com). + +# Acknowledgments + +Support for pyuvdata was provided by NSF awards #1835421 and #1835120. + + +%prep +%autosetup -n pyuvdata-2.3.2 + +%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-pyuvdata -f filelist.lst +%dir %{python3_sitearch}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Thu May 18 2023 Python_Bot <Python_Bot@openeuler.org> - 2.3.2-1 +- Package Spec generated |