@@ 4319,6 4319,39 @@ cache. It is possible to download the full background cache to your local
machine.")
(license license:bsd-3)))
+(define-public python-jwst-reffiles
+ (package
+ (name "python-jwst-reffiles")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "jwst_reffiles" version))
+ (sha256
+ (base32 "1dlw955cw49qczdmimglmlcbal8vd3wbv5j48ckllvjgd59pwr3s"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; One test fails with error: FileNotFoundError: [Errno 2] No such file
+ ;; or directory.
+ #:test-flags #~(list "-k" "not test_calib_prep_steps")))
+ (native-inputs
+ (list python-pytest))
+ (propagated-inputs
+ (list python-astropy
+ python-jwst
+ python-matplotlib
+ python-numpy
+ python-scipy))
+ (home-page "https://github.com/spacetelescope/jwst_reffiles")
+ (synopsis "Tool for JWST's CRDS-formatted reference files creation")
+ (description
+ "This package provides a tool to create @acronym{Calibration References
+Data System,CRDS}-formatted reference files for @acronym{James Webb Space
+Telescope,JWST} from a set of input dark current files and a set of flat field
+files.")
+ (license license:bsd-3)))
+
(define-public python-libstempo
(package
(name "python-libstempo")
@@ 4573,6 4606,74 @@ perform MCMC fitting of radiative models to X-ray, GeV, and TeV spectra using
Carlo.")
(license license:bsd-3)))
+(define-public python-ndcube
+ (package
+ (name "python-ndcube")
+ (version "2.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ndcube" version))
+ (sha256
+ (base32 "0hf261l36jxmd0r8sh2vyxaapv8gcdmnnv82k0hqvq6wh1qp5ksv"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "--numprocesses" (number->string (parallel-job-count))
+ "-k" (string-append
+ ;; Break cycle: python-ndcube -> python-specutils ->
+ ;; python-ndcube, see
+ ;; <https://github.com/sunpy/ndcube/issues/733>.
+ "not test_rebin_specutils"
+ ;; Introduced with astropy 6.1.3, see
+ ;; <https://github.com/sunpy/ndcube/issues/758>.
+ " and not test_2d[celestial_2d_ape14_wcs]"
+ " and not test_2d[celestial_2d_fitswcs]"))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'break-cycle
+ (lambda _
+ (substitute* "ndcube/tests/test_ndcube.py"
+ (("from specutils import Spectrum1D") ""))))
+ (add-before 'check 'set-home-env
+ (lambda _
+ ;; Tests require HOME to be set.
+ ;; Permission denied: '/homeless-shelter'
+ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs
+ (list python-astropy
+ python-gwcs
+ python-matplotlib
+ python-mpl-animators
+ python-numpy
+ python-reproject))
+ (native-inputs
+ (list python-dask
+ python-pytest
+ python-pytest-astropy
+ python-pytest-mpl
+ ;; python-pytest-memray ; not packaged yet
+ python-pytest-xdist
+ python-scipy
+ python-setuptools
+ python-setuptools-scm-next
+ python-sunpy-minimal
+ python-wheel))
+ (home-page "https://docs.sunpy.org/projects/ndcube/")
+ (synopsis "Multi-dimensional contiguous and non-contiguous coordinate aware arrays")
+ (description
+ "@code{ndcube} is a package for manipulating, inspecting and visualizing
+multi-dimensional contiguous and non-contiguous coordinate-aware data arrays.
+
+It combines data, uncertainties, units, metadata, masking, and coordinate
+transformations into classes with unified slicing and generic coordinate
+transformations and plotting/animation capabilities. It is designed to handle
+data of any number of dimensions and axis types (e.g. spatial, temporal,
+spectral, etc.) whose relationship between the array elements and the real world
+can be described by @acronym{WCS, World Coordinate System} translations.")
+ (license license:bsd-2)))
+
(define-public python-petrofit
(package
(name "python-petrofit")
@@ 4733,6 4834,61 @@ position-frequency slice.")
(list python-setuptools
python-wheel)))))
+(define-public python-pyregion
+ (package
+ (name "python-pyregion")
+ (version "2.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pyregion" version))
+ (sha256
+ (base32 "09a98v3zk1vdjns1q64al58mapr4cns3nlnyi6b26wqi888qfjg8"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; setup.py was removed in b26ec4fe88e29447dc8391fcdef7082a4f7876ce
+ ;; TODO: Check how to implement it in python-build-system.
+ (add-after 'unpack 'create-setup.py
+ (lambda _
+ (call-with-output-file "setup.py"
+ (lambda (port)
+ (format port "from setuptools import setup
+from extension_helpers import get_extensions
+setup(ext_modules=get_extensions())")))))
+ (add-before 'check 'build-extensions
+ (lambda _
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+ (propagated-inputs
+ (list python-astropy
+ python-numpy
+ python-pyparsing))
+ (native-inputs
+ (list python-cython
+ python-extension-helpers
+ python-pytest
+ python-pytest-astropy
+ python-pytest-astropy-header
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
+ (home-page "https://github.com/astropy/pyregion")
+ (synopsis "Python parser for ds9 region files")
+ (description
+ "@code{pyregion} is a python module to parse ds9 region files. It also
+supports ciao region files.
+Features:
+@itemize
+@item ds9 and ciao region files.
+@item (physical, WCS) coordinate conversion to the image coordinate.
+@item convert regions to matplotlib patches.
+@item convert regions to spatial filter (i.e., generate mask images)
+@end itemize")
+ (license license:expat)))
+
(define-public python-pysiril
(package
(name "python-pysiril")
@@ 4897,6 5053,50 @@ export the simulated X-ray events to other software packages to simulate the
end products of specific X-ray observatories.")
(license license:bsd-3)))
+(define-public python-radiospectra
+ (package
+ (name "python-radiospectra")
+ (version "0.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "radiospectra" version))
+ (sha256
+ (base32 "14p4hp9yncyjsrbys0yjq7jbj0n9wf0x5sy67kilqrw14d1xvzch"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "--numprocesses" (number->string (parallel-job-count)))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'set-home-env
+ (lambda _
+ ;; Tests require HOME to be set.
+ ;; Permission denied: '/homeless-shelter'
+ (setenv "HOME" "/tmp"))))))
+ (native-inputs
+ (list python-pytest
+ python-pytest-astropy
+ python-pytest-doctestplus
+ python-pytest-xdist
+ python-setuptools
+ python-setuptools-scm
+ python-sunpy-soar
+ python-wheel))
+ (propagated-inputs
+ (list python-cdflib
+ python-matplotlib
+ python-numpy
+ python-scipy
+ python-sunpy))
+ (home-page "https://docs.sunpy.org/projects/radiospectra")
+ (synopsis "Support for radio spectra on solar physics")
+ (description
+ "@code{radiospectra} provides support for some type of radio spectra in
+solar physics.")
+ (license license:bsd-2)))
+
(define-public python-regularizepsf
(package
(name "python-regularizepsf")
@@ 4929,6 5129,34 @@ end products of specific X-ray observatories.")
PSF} describing how the optical system spreads light from sources.")
(license license:expat)))
+(define-public python-sep
+ (package/inherit libsep
+ (name "python-sep")
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags #~(list "test.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "pyproject.toml"
+ ;; numpy = "^1.26.4"
+ (("1.26.4") "1.26.2"))))
+ (add-after 'unpack 'set-version
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
+ #$(package-version this-package)))))))
+ (native-inputs
+ (list python-cython
+ python-pytest
+ python-setuptools
+ python-setuptools-scm-next
+ python-wheel))
+ (propagated-inputs
+ (list python-numpy))
+ (synopsis "Python library for Source Extraction and Photometry")))
+
(define-public python-sirilic
(package
(name "python-sirilic")
@@ 5339,39 5567,6 @@ Astronomical Almanac to within 0.0005 arcseconds (half a @emph{mas} or
milliarcsecond).")
(license license:expat)))
-(define-public python-jwst-reffiles
- (package
- (name "python-jwst-reffiles")
- (version "1.0.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "jwst_reffiles" version))
- (sha256
- (base32 "1dlw955cw49qczdmimglmlcbal8vd3wbv5j48ckllvjgd59pwr3s"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- ;; One test fails with error: FileNotFoundError: [Errno 2] No such file
- ;; or directory.
- #:test-flags #~(list "-k" "not test_calib_prep_steps")))
- (native-inputs
- (list python-pytest))
- (propagated-inputs
- (list python-astropy
- python-jwst
- python-matplotlib
- python-numpy
- python-scipy))
- (home-page "https://github.com/spacetelescope/jwst_reffiles")
- (synopsis "Tool for JWST's CRDS-formatted reference files creation")
- (description
- "This package provides a tool to create @acronym{Calibration References
-Data System,CRDS}-formatted reference files for @acronym{James Webb Space
-Telescope,JWST} from a set of input dark current files and a set of flat field
-files.")
- (license license:bsd-3)))
-
(define-public python-kanon
(package
(name "python-kanon")
@@ 5455,74 5650,6 @@ astronomical tables
@end itemize")
(license license:bsd-3)))
-(define-public python-ndcube
- (package
- (name "python-ndcube")
- (version "2.3.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "ndcube" version))
- (sha256
- (base32 "0hf261l36jxmd0r8sh2vyxaapv8gcdmnnv82k0hqvq6wh1qp5ksv"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- #~(list "--numprocesses" (number->string (parallel-job-count))
- "-k" (string-append
- ;; Break cycle: python-ndcube -> python-specutils ->
- ;; python-ndcube, see
- ;; <https://github.com/sunpy/ndcube/issues/733>.
- "not test_rebin_specutils"
- ;; Introduced with astropy 6.1.3, see
- ;; <https://github.com/sunpy/ndcube/issues/758>.
- " and not test_2d[celestial_2d_ape14_wcs]"
- " and not test_2d[celestial_2d_fitswcs]"))
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'break-cycle
- (lambda _
- (substitute* "ndcube/tests/test_ndcube.py"
- (("from specutils import Spectrum1D") ""))))
- (add-before 'check 'set-home-env
- (lambda _
- ;; Tests require HOME to be set.
- ;; Permission denied: '/homeless-shelter'
- (setenv "HOME" "/tmp"))))))
- (propagated-inputs
- (list python-astropy
- python-gwcs
- python-matplotlib
- python-mpl-animators
- python-numpy
- python-reproject))
- (native-inputs
- (list python-dask
- python-pytest
- python-pytest-astropy
- python-pytest-mpl
- ;; python-pytest-memray ; not packaged yet
- python-pytest-xdist
- python-scipy
- python-setuptools
- python-setuptools-scm-next
- python-sunpy-minimal
- python-wheel))
- (home-page "https://docs.sunpy.org/projects/ndcube/")
- (synopsis "Multi-dimensional contiguous and non-contiguous coordinate aware arrays")
- (description
- "@code{ndcube} is a package for manipulating, inspecting and visualizing
-multi-dimensional contiguous and non-contiguous coordinate-aware data arrays.
-
-It combines data, uncertainties, units, metadata, masking, and coordinate
-transformations into classes with unified slicing and generic coordinate
-transformations and plotting/animation capabilities. It is designed to handle
-data of any number of dimensions and axis types (e.g. spatial, temporal,
-spectral, etc.) whose relationship between the array elements and the real world
-can be described by @acronym{WCS, World Coordinate System} translations.")
- (license license:bsd-2)))
-
(define-public python-photutils
(package
(name "python-photutils")
@@ 6452,61 6579,6 @@ astrophysical simulations supporting PKDGRAV/Gasoline, Gadget, Gadget4/Arepo,
N-Chilada and RAMSES AMR outputs.")
(license license:gpl3+)))
-(define-public python-pyregion
- (package
- (name "python-pyregion")
- (version "2.3.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "pyregion" version))
- (sha256
- (base32 "09a98v3zk1vdjns1q64al58mapr4cns3nlnyi6b26wqi888qfjg8"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- ;; setup.py was removed in b26ec4fe88e29447dc8391fcdef7082a4f7876ce
- ;; TODO: Check how to implement it in python-build-system.
- (add-after 'unpack 'create-setup.py
- (lambda _
- (call-with-output-file "setup.py"
- (lambda (port)
- (format port "from setuptools import setup
-from extension_helpers import get_extensions
-setup(ext_modules=get_extensions())")))))
- (add-before 'check 'build-extensions
- (lambda _
- ;; Cython extensions have to be built before running the tests.
- (invoke "python" "setup.py" "build_ext" "--inplace"))))))
- (propagated-inputs
- (list python-astropy
- python-numpy
- python-pyparsing))
- (native-inputs
- (list python-cython
- python-extension-helpers
- python-pytest
- python-pytest-astropy
- python-pytest-astropy-header
- python-setuptools
- python-setuptools-scm
- python-wheel))
- (home-page "https://github.com/astropy/pyregion")
- (synopsis "Python parser for ds9 region files")
- (description
- "@code{pyregion} is a python module to parse ds9 region files. It also
-supports ciao region files.
-Features:
-@itemize
-@item ds9 and ciao region files.
-@item (physical, WCS) coordinate conversion to the image coordinate.
-@item convert regions to matplotlib patches.
-@item convert regions to spatial filter (i.e., generate mask images)
-@end itemize")
- (license license:expat)))
-
(define-public python-pysat
(package
(name "python-pysat")
@@ 6721,34 6793,6 @@ well as ephemerides services
@end itemize")
(license license:bsd-3)))
-(define-public python-sep
- (package/inherit libsep
- (name "python-sep")
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags #~(list "test.py")
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "pyproject.toml"
- ;; numpy = "^1.26.4"
- (("1.26.4") "1.26.2"))))
- (add-after 'unpack 'set-version
- (lambda _
- (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
- #$(package-version this-package)))))))
- (native-inputs
- (list python-cython
- python-pytest
- python-setuptools
- python-setuptools-scm-next
- python-wheel))
- (propagated-inputs
- (list python-numpy))
- (synopsis "Python library for Source Extraction and Photometry")))
-
(define-public python-sep-pjw
(package
(name "python-sep-pjw")
@@ 7186,50 7230,6 @@ channels
@end itemize")
(license license:bsd-3)))
-(define-public python-radiospectra
- (package
- (name "python-radiospectra")
- (version "0.6.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "radiospectra" version))
- (sha256
- (base32 "14p4hp9yncyjsrbys0yjq7jbj0n9wf0x5sy67kilqrw14d1xvzch"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- #~(list "--numprocesses" (number->string (parallel-job-count)))
- #:phases
- #~(modify-phases %standard-phases
- (add-before 'check 'set-home-env
- (lambda _
- ;; Tests require HOME to be set.
- ;; Permission denied: '/homeless-shelter'
- (setenv "HOME" "/tmp"))))))
- (native-inputs
- (list python-pytest
- python-pytest-astropy
- python-pytest-doctestplus
- python-pytest-xdist
- python-setuptools
- python-setuptools-scm
- python-sunpy-soar
- python-wheel))
- (propagated-inputs
- (list python-cdflib
- python-matplotlib
- python-numpy
- python-scipy
- python-sunpy))
- (home-page "https://docs.sunpy.org/projects/radiospectra")
- (synopsis "Support for radio spectra on solar physics")
- (description
- "@code{radiospectra} provides support for some type of radio spectra in
-solar physics.")
- (license license:bsd-2)))
-
(define-public python-regions
(package
(name "python-regions")