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* gnu/packages/astronomy.scm::(python-jplephem, python-pint-pulsar,
python-pysat, and python-sep-pjw): Sort variables alphabetically.

Change-Id: I22d3ecd9c6e7ecb91c6a98b1608c2715ba828e75
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Sharlatan Hellseher 2025-08-12 21:08:38 +01:00
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@ -4573,6 +4573,40 @@ observationally-derived galaxy merger catalogs.")
satellite.")
(license license:bsd-3)))
(define-public python-jplephem
(package
(name "python-jplephem")
(version "2.22")
(source
(origin
(method url-fetch)
(uri (pypi-uri "jplephem" version))
(sha256
(base32 "0b2rgb7pvwnl72pqjryf9c812mmdxr69fwiym7mnz05l2xrcr6hd"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "-m" "unittest" "discover" "-s" "test")))))))
(native-inputs
(list python-setuptools
python-wheel))
(propagated-inputs
(list python-numpy))
(home-page "https://github.com/brandon-rhodes/python-jplephem")
(synopsis "Python version of NASA DE4xx ephemerides")
(description
"@code{skyfield} computes positions for the stars, planets, and
satellites in orbit around the Earth. Its results should agree with the
positions generated by the United States Naval Observatory and their
Astronomical Almanac to within 0.0005 arcseconds (half a @emph{mas} or
milliarcsecond).")
(license license:expat)))
(define-public python-jwst
(package
(name "python-jwst")
@ -5325,6 +5359,131 @@ profiles. In particular, PetroFit includes tools for performing accurate
photometry, segmentations, Petrosian profiling, and Sérsic fitting.")
(license license:bsd-3)))
(define-public python-pint-pulsar
(package
(name "python-pint-pulsar")
(version "1.1.3")
(source
(origin
(method git-fetch) ; no tests data in the PyPI tarball
(uri (git-reference
(url "https://github.com/nanograv/PINT")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0n66z7v30q1981hx4q5vy3mibrh453gak8dd938038r5mwddya3f"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "-k" (string-join
;; Tests failing with assertion on not correct precision
;; or missing data files.
(list "not test_astropy_observatory"
"test_copy_wideband_fitter_object"
"test_IERS_B_builtin_agree_with_IERS_Auto_dX"
"test_astropy_observatory"
"test_time_construction_jds_exact[tdb]"
"test_copy_toa_object"
"test_copy_residuals"
"test_copy_fitter_object")
" and not ")
;; XXX: The most of the tests require additional data, select
;; files where they may run without it and check how to enable
;; more.
"tests/test_Galactic.py"
"tests/test_all_component_and_model_builder.py"
"tests/test_astrometry.py"
"tests/test_astropy_observatory.py"
"tests/test_astropy_times.py"
"tests/test_astropy_version.py"
"tests/test_binary_generic.py"
"tests/test_binconvert.py"
"tests/test_compare.py"
"tests/test_compare_model.py"
"tests/test_compare_model_ecl_vs_icrs.py"
"tests/test_convert_parfile.py"
"tests/test_copy.py"
"tests/test_covariance_matrix.py"
"tests/test_datafiles.py"
"tests/test_derived_quantities.py"
"tests/test_derivedparams.py"
"tests/test_dmxrange_add_sub.py"
"tests/test_erfautils.py"
"tests/test_eventstats.py"
"tests/test_funcpar.py"
"tests/test_kepler.py"
"tests/test_leapsec.py"
"tests/test_model_manual.py"
"tests/test_numpy.py"
"tests/test_observatory_envar.py"
"tests/test_observatory_metadata.py"
"tests/test_parfile.py"
"tests/test_parunits.py"
"tests/test_pb.py"
"tests/test_phase.py"
"tests/test_pickle.py"
"tests/test_plk_widget.py"
"tests/test_plot_utils.py"
"tests/test_plrednoise.py"
"tests/test_pmtransform_units.py"
"tests/test_precision.py"
"tests/test_prefix_param_inheritance.py"
"tests/test_priors.py"
"tests/test_process_parfile.py"
"tests/test_pulsar_mjd.py"
"tests/test_pulsar_position.py"
"tests/test_reduced_precision.py"
"tests/test_satobs.py"
"tests/test_t2binary2pint.py"
"tests/test_tcb2tdb.py"
"tests/test_templates.py"
"tests/test_variety_parfiles.py"
"tests/test_version.py")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'remove-deprecated-scripts
;; ImportError: cannot import name 'CompositeMCMCFitter' from
;; 'pint.mcmc_fitter'.
;;
;; Removed in 1.1.3: Broken fitter class `CompositeMCMCFitter`
;; (this fitter was added seemingly to deal with combined radio and
;; high-energy datasets, but has since been broken for a while.)
(lambda _
(substitute* "pyproject.toml"
(("event_optimize_multiple.*") "")))))))
(native-inputs
(list python-pytest
python-setuptools
python-versioneer
python-wheel))
(propagated-inputs
(list python-astropy
python-corner
python-emcee
python-jplephem
python-loguru
python-matplotlib
python-nestle
python-numdifftools
python-numpy
python-pyerfa
python-scipy
python-uncertainties))
(home-page "https://github.com/nanograv/PINT")
(synopsis "Software for high-precision pulsar timing")
(description
"PINT is not TEMPO3 - package providing a Pulsar Timing, written in
Python from scratch.
Features:
@itemize
@item a robust system to produce high-precision timing results that is
completely independent of TEMPO and Tempo2
@item a system that is easy to extend and modify due to a good design
and the use of a modern programming language, techniques, and libraries
@end itemize")
(license license:bsd-3)))
(define-public python-pixell
(package
(name "python-pixell")
@ -5588,6 +5747,63 @@ Features:
@end itemize")
(license license:expat)))
(define-public python-pysat
(package
(name "python-pysat")
(version "3.2.2")
(source
(origin
(method git-fetch) ; no tests data in the PyPI tarball
(uri (git-reference
(url "https://github.com/pysat/pysat")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0gm71zafigwc94s37wqyl86yjabpq6wx9izwxag74wg1ynhqyvf0"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "--durations=10" ; report 10 slowest tests
;; Tests require pysatSpaceWeather which is not packed yet.
"--ignore=pysat/tests/test_utils_files.py"
"-k" "not test_from_os")
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'pre-check
(lambda _
;; Do not run test coverage.
(substitute* "pyproject.toml"
((".*addopts.*cov.*") ""))
;; No such file or directory: '/homeless-shelter/.pysat'
(setenv "HOME" "/tmp")
(mkdir "pysatData")
(invoke "python" "-c"
"import pysat; pysat.params['data_dirs'] = 'pysatData'"))))))
(native-inputs
(list python-pytest
python-pytest-xdist
python-setuptools
python-wheel))
(propagated-inputs
(list python-dask
python-netcdf4
python-numpy
python-pandas
python-portalocker
python-scipy
python-toolz
python-xarray))
(home-page "https://github.com/pysat/pysat")
(synopsis "Supports science analysis across disparate data platforms")
(description
"The Python Satellite Data Analysis Toolkit (pysat) provides a simple and
flexible interface for robust data analysis from beginning to end - including
downloading, loading, cleaning, managing, processing, and analyzing
data. Pysat's plug-in design allows analysis support for any data, including
user provided data sets.")
(license license:bsd-3)))
(define-public python-pysiril
(package
(name "python-pysiril")
@ -5954,6 +6170,36 @@ observations from the Nancy Grace Roman Space Telescope.")
(list python-numpy))
(synopsis "Python library for Source Extraction and Photometry")))
(define-public python-sep-pjw
(package
(name "python-sep-pjw")
(version "1.3.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "sep_pjw" version))
(sha256
(base32 "0lhxfq1acc6qc8nszfdrpwq6dizaypz3b6frknfv5qm59mb488r0"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags #~(list "test.py")))
(native-inputs
(list python-cython
python-pytest
python-setuptools
python-setuptools-scm-next
python-wheel))
(propagated-inputs
(list python-numpy
python-sep))
(home-page "https://github.com/PJ-Watson/sep-pjw")
(synopsis "Alternative fork of SEP library")
(description
"This package provides an alternative maintained fork of SEP python
library with bug fixtures.")
(license (list license:expat license:lgpl3+ license:bsd-3))))
(define-public python-sirilic
(package
(name "python-sirilic")
@ -6391,40 +6637,6 @@ instruments.")
(license (list license:bsd-3 ; licenses/LICENSE.rst, same as python-astropy
license:expat)))) ; licenses/KOSMOS_LICENSE
(define-public python-jplephem
(package
(name "python-jplephem")
(version "2.22")
(source
(origin
(method url-fetch)
(uri (pypi-uri "jplephem" version))
(sha256
(base32 "0b2rgb7pvwnl72pqjryf9c812mmdxr69fwiym7mnz05l2xrcr6hd"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "-m" "unittest" "discover" "-s" "test")))))))
(native-inputs
(list python-setuptools
python-wheel))
(propagated-inputs
(list python-numpy))
(home-page "https://github.com/brandon-rhodes/python-jplephem")
(synopsis "Python version of NASA DE4xx ephemerides")
(description
"@code{skyfield} computes positions for the stars, planets, and
satellites in orbit around the Earth. Its results should agree with the
positions generated by the United States Naval Observatory and their
Astronomical Almanac to within 0.0005 arcseconds (half a @emph{mas} or
milliarcsecond).")
(license license:expat)))
(define-public python-photutils
(package
(name "python-photutils")
@ -7393,63 +7605,6 @@ astrophysical simulations supporting PKDGRAV/Gasoline, Gadget, Gadget4/Arepo,
N-Chilada and RAMSES AMR outputs.")
(license license:gpl3+)))
(define-public python-pysat
(package
(name "python-pysat")
(version "3.2.2")
(source
(origin
(method git-fetch) ; no tests data in the PyPI tarball
(uri (git-reference
(url "https://github.com/pysat/pysat")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0gm71zafigwc94s37wqyl86yjabpq6wx9izwxag74wg1ynhqyvf0"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "--durations=10" ; report 10 slowest tests
;; Tests require pysatSpaceWeather which is not packed yet.
"--ignore=pysat/tests/test_utils_files.py"
"-k" "not test_from_os")
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'pre-check
(lambda _
;; Do not run test coverage.
(substitute* "pyproject.toml"
((".*addopts.*cov.*") ""))
;; No such file or directory: '/homeless-shelter/.pysat'
(setenv "HOME" "/tmp")
(mkdir "pysatData")
(invoke "python" "-c"
"import pysat; pysat.params['data_dirs'] = 'pysatData'"))))))
(native-inputs
(list python-pytest
python-pytest-xdist
python-setuptools
python-wheel))
(propagated-inputs
(list python-dask
python-netcdf4
python-numpy
python-pandas
python-portalocker
python-scipy
python-toolz
python-xarray))
(home-page "https://github.com/pysat/pysat")
(synopsis "Supports science analysis across disparate data platforms")
(description
"The Python Satellite Data Analysis Toolkit (pysat) provides a simple and
flexible interface for robust data analysis from beginning to end - including
downloading, loading, cleaning, managing, processing, and analyzing
data. Pysat's plug-in design allows analysis support for any data, including
user provided data sets.")
(license license:bsd-3)))
(define-public python-pysiaf
(package
(name "python-pysiaf")
@ -7607,36 +7762,6 @@ well as ephemerides services
@end itemize")
(license license:bsd-3)))
(define-public python-sep-pjw
(package
(name "python-sep-pjw")
(version "1.3.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "sep_pjw" version))
(sha256
(base32 "0lhxfq1acc6qc8nszfdrpwq6dizaypz3b6frknfv5qm59mb488r0"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags #~(list "test.py")))
(native-inputs
(list python-cython
python-pytest
python-setuptools
python-setuptools-scm-next
python-wheel))
(propagated-inputs
(list python-numpy
python-sep))
(home-page "https://github.com/PJ-Watson/sep-pjw")
(synopsis "Alternative fork of SEP library")
(description
"This package provides an alternative maintained fork of SEP python
library with bug fixtures.")
(license (list license:expat license:lgpl3+ license:bsd-3))))
(define-public python-asdf-standard
(package
(name "python-asdf-standard")
@ -7779,131 +7904,6 @@ System (WCS) tags. Users should not need to install this directly; instead,
install an implementation package such as gwcs.")
(license license:bsd-3))))
(define-public python-pint-pulsar
(package
(name "python-pint-pulsar")
(version "1.1.3")
(source
(origin
(method git-fetch) ; no tests data in the PyPI tarball
(uri (git-reference
(url "https://github.com/nanograv/PINT")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0n66z7v30q1981hx4q5vy3mibrh453gak8dd938038r5mwddya3f"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "-k" (string-join
;; Tests failing with assertion on not correct precision
;; or missing data files.
(list "not test_astropy_observatory"
"test_copy_wideband_fitter_object"
"test_IERS_B_builtin_agree_with_IERS_Auto_dX"
"test_astropy_observatory"
"test_time_construction_jds_exact[tdb]"
"test_copy_toa_object"
"test_copy_residuals"
"test_copy_fitter_object")
" and not ")
;; XXX: The most of the tests require additional data, select
;; files where they may run without it and check how to enable
;; more.
"tests/test_Galactic.py"
"tests/test_all_component_and_model_builder.py"
"tests/test_astrometry.py"
"tests/test_astropy_observatory.py"
"tests/test_astropy_times.py"
"tests/test_astropy_version.py"
"tests/test_binary_generic.py"
"tests/test_binconvert.py"
"tests/test_compare.py"
"tests/test_compare_model.py"
"tests/test_compare_model_ecl_vs_icrs.py"
"tests/test_convert_parfile.py"
"tests/test_copy.py"
"tests/test_covariance_matrix.py"
"tests/test_datafiles.py"
"tests/test_derived_quantities.py"
"tests/test_derivedparams.py"
"tests/test_dmxrange_add_sub.py"
"tests/test_erfautils.py"
"tests/test_eventstats.py"
"tests/test_funcpar.py"
"tests/test_kepler.py"
"tests/test_leapsec.py"
"tests/test_model_manual.py"
"tests/test_numpy.py"
"tests/test_observatory_envar.py"
"tests/test_observatory_metadata.py"
"tests/test_parfile.py"
"tests/test_parunits.py"
"tests/test_pb.py"
"tests/test_phase.py"
"tests/test_pickle.py"
"tests/test_plk_widget.py"
"tests/test_plot_utils.py"
"tests/test_plrednoise.py"
"tests/test_pmtransform_units.py"
"tests/test_precision.py"
"tests/test_prefix_param_inheritance.py"
"tests/test_priors.py"
"tests/test_process_parfile.py"
"tests/test_pulsar_mjd.py"
"tests/test_pulsar_position.py"
"tests/test_reduced_precision.py"
"tests/test_satobs.py"
"tests/test_t2binary2pint.py"
"tests/test_tcb2tdb.py"
"tests/test_templates.py"
"tests/test_variety_parfiles.py"
"tests/test_version.py")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'remove-deprecated-scripts
;; ImportError: cannot import name 'CompositeMCMCFitter' from
;; 'pint.mcmc_fitter'.
;;
;; Removed in 1.1.3: Broken fitter class `CompositeMCMCFitter`
;; (this fitter was added seemingly to deal with combined radio and
;; high-energy datasets, but has since been broken for a while.)
(lambda _
(substitute* "pyproject.toml"
(("event_optimize_multiple.*") "")))))))
(native-inputs
(list python-pytest
python-setuptools
python-versioneer
python-wheel))
(propagated-inputs
(list python-astropy
python-corner
python-emcee
python-jplephem
python-loguru
python-matplotlib
python-nestle
python-numdifftools
python-numpy
python-pyerfa
python-scipy
python-uncertainties))
(home-page "https://github.com/nanograv/PINT")
(synopsis "Software for high-precision pulsar timing")
(description
"PINT is not TEMPO3 - package providing a Pulsar Timing, written in
Python from scratch.
Features:
@itemize
@item a robust system to produce high-precision timing results that is
completely independent of TEMPO and Tempo2
@item a system that is easy to extend and modify due to a good design
and the use of a modern programming language, techniques, and libraries
@end itemize")
(license license:bsd-3)))
(define-public python-rad
(package
(name "python-rad")