diff options
Diffstat (limited to 'gnu/packages/astronomy.scm')
| -rw-r--r-- | gnu/packages/astronomy.scm | 596 |
1 files changed, 594 insertions, 2 deletions
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 964e72642c..cdb6750f09 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -651,7 +651,7 @@ astronomical image-processing packages like Drizzle, Swarp or SExtractor.") (define-public gnuastro (package (name "gnuastro") - (version "0.19") + (version "0.20") (source (origin (method url-fetch) @@ -659,7 +659,7 @@ astronomical image-processing packages like Drizzle, Swarp or SExtractor.") version ".tar.lz")) (sha256 (base32 - "192q3i4zlfmwfcchlf9lnpfgys9dssh7npr5qx0gzn3d2fri0xbz")))) + "05bkad0xbax9k0m2g2507mdmjg2109sfg72dsx16f44yj55llh2n")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--disable-static"))) @@ -1355,6 +1355,38 @@ be as fast as possible so some of the readability has been sacrificed, specifically in the C code.") (license license:bsd-3))) +(define-public python-bayesicfitting + (package + (name "python-bayesicfitting") + (version "3.1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dokester/BayesicFitting") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "07y9dr9wxhxrvhk0jjakhbyrgal60i92m7z7q14fp12k8x0gl69l")))) + (build-system python-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "unittest" "discover" + "test"))))))) + (propagated-inputs (list python-astropy python-future python-matplotlib + python-numpy python-scipy)) + (home-page "https://www.bayesicfitting.nl") + (synopsis "Python Toolbox for Astronimical Bayesian fitting") + (description + "The BayesicFitting package is a python version of the the fitter classes +in @acronym{HCSS, Herschel Common Science System}. HCSS was the all +encompassing software system for the operations and analysis of the ESA satelite +Herschel.") + (license license:gpl3+))) + (define-public python-ccdproc (package (name "python-ccdproc") @@ -1425,6 +1457,58 @@ attempting to maintain ISTP compliance @end itemize") (license license:expat))) +(define-public python-crds + (package + (name "python-crds") + (version "11.17.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "crds" version)) + (sha256 + (base32 + "0sdz1k4hrgrc2jwihp9ns7lx23kcz7f90c222q7aaqf9g3vvpqlr")))) + (build-system pyproject-build-system) + (arguments + (list + ;; XXX: Tests require Internet access to https://hst-crds.stsci.edu and + ;; additional test data. See: + ;; https://github.com/spacetelescope/crds/blob/master/setup_test_cache + #:tests? #f)) + (propagated-inputs (list python-asdf + python-astropy + python-boto3 + python-filelock + python-lxml + python-numpy + python-parsley + python-pysynphot + python-roman-datamodels + python-stsynphot + python-requests)) + (native-inputs (list python-flake8 + python-ipython + python-lockfile + python-mock + python-nose + python-pylint + python-pytest + python-semantic-version + python-setuptools-scm)) + (home-page "https://hst-crds.stsci.edu") + (synopsis "Calibration Reference Data System for HST and JWST") + (description + "CRDS is a package used for working with astronomical reference files for +the HST and JWST telescopes. CRDS is useful for performing various operations +on reference files or reference file assignment rules. CRDS is used to assign, +check, and compare reference files and rules, and also to predict those datasets +which should potentially be reprocessed due to changes in reference files or +assignment rules. CRDS has versioned rules which define the assignment of +references for each type and instrument configuration. CRDS has web sites +corresponding to each project (http://hst-crds.stsci.edu or +https://jwst-crds.stsci.edu/) which record information about reference files and +provide related services.") + (license license:bsd-3))) + (define-public python-czml3 (package (name "python-czml3") @@ -1493,6 +1577,53 @@ JSOC (@url{http://jsoc.stanford.edu/}) DRMS server by default, but can also be used with local NetDRMS sites.") (license license:bsd-2))) +(define-public python-drizzle + (package + (name "python-drizzle") + (version "1.13.7") + (source (origin + (method git-fetch) ;PyPi doesn't have the test data sets + (uri (git-reference + (url "https://github.com/spacetelescope/drizzle") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0x591d9gjasds91fvwcf37bhxp5nra28g0vq5zkykczpc70ywiy8")))) + (build-system pyproject-build-system) + (arguments + (list + ;; XXX: 2 of 26 tests failed with AssertionError, disable them for now. + ;; Consider mention it in upstream. + #:test-flags #~(list "-k" + (string-append "not test_square_with_point" + " and not test_square_with_grid")) + #:phases #~(modify-phases %standard-phases + (add-before 'build 'set-env-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" + #$version))) + (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)) + (native-inputs (list python-coverage python-flake8 python-pytest + python-pytest-cov python-setuptools-scm)) + (home-page "https://github.com/spacetelescope/drizzle") + (synopsis + "Astronomical tool for combining dithered images into a single image") + (description + "The drizzle library is a Python package for combining dithered images into +a single image. This library is derived from code used in DrizzlePac. Like +DrizzlePac, most of the code is implemented in the C language. The biggest +change from DrizzlePac is that this code passes an array that maps the input to +output image into the C code, while the DrizzlePac code computes the mapping by +using a Python callback. Switching to using an array allowed the code to be +greatly simplified.") + (license license:bsd-3))) + (define-public python-ephem (package (name "python-ephem") @@ -2045,6 +2176,211 @@ spherical polygons that represent arbitrary regions of the sky.") ;; QD_LIBRARY_LICENSE.rst for bandeled QD source (license license:bsd-3))) +(define-public python-stsci-image + (package + (name "python-stsci-image") + (version "2.3.5") + (source (origin + (method url-fetch) + (uri (pypi-uri "stsci.image" version)) + (sha256 + (base32 + "1vnp4256nbdvapa69cmm80sjz11ygxa49abr9nbvssj6nyyp5icb")))) + (build-system pyproject-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (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-numpy python-scipy)) + (native-inputs (list python-pytest python-setuptools-scm)) + (home-page "https://github.com/spacetelescope/stsci.image") + (synopsis "Image array manipulation functions") + (description + "This package provides Python modules of @acronym{STScI, Space Telescope +Science Institute} image array manipulation functions.") + (license license:bsd-3))) + +(define-public python-stsci-imagestats + (package + (name "python-stsci-imagestats") + (version "1.6.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "stsci.imagestats" version)) + (sha256 + (base32 + "14457izlbnks84dyza75ib3nvx2w8nhlqm9vc1zb7hbhknb5gjvw")))) + (build-system python-build-system) + (arguments + (list #:tests? #f)) ;No tests + (propagated-inputs (list python-numpy)) + (native-inputs (list python-setuptools-scm)) + (home-page "https://stsciimagestats.readthedocs.io/en/latest/") + (synopsis "Compute sigma-clipped statistics on data arrays") + (description + "@code{stsci.imagestats} is a package designed to compute various +statistics on image data using sigma-clipping iterations. It is designed to +replicate core behaviour of the IRAF's +@url{http://stsdas.stsci.edu/cgi-bin/gethelp.cgi?imstatistics, imstatistics +task}.") + (license license:bsd-3))) + +(define-public python-stsci-stimage + (package + (name "python-stsci-stimage") + (version "0.2.6") + (source (origin + (method url-fetch) + (uri (pypi-uri "stsci.stimage" version)) + (sha256 + (base32 + "0i7xby1gaiplvbqqv8a4f4cw1is8fwj89mix1z3bqrykqi3n24g0")))) + (build-system pyproject-build-system) + (arguments + (list + ;; XXX: Fix failing tests. There are errors to load test files. + #:tests? #f)) + (propagated-inputs (list python-numpy)) + (native-inputs (list python-codecov python-pytest python-pytest-cov + python-setuptools-scm)) + (home-page "https://stscistimage.readthedocs.io/en/latest/") + (synopsis "STScI image processing") + (description "This package provides an astronomical Python package with +image processing functions: @code{xyxymatch}, @code{geomap}.") + (license license:bsd-3))) + +(define-public python-stcal + (package + (name "python-stcal") + (version "1.3.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "stcal" version)) + (sha256 + (base32 + "0yy0pwi3krvhxfby6nzgpgyz5il3sl1j29ihbk81dh9fdh3ys2n9")))) + (build-system pyproject-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + ;; XXX: Can't detect opencv-python version. The input + ;; opencv might not set the version correctly. + (delete 'sanity-check)))) + (propagated-inputs (list opencv ;Provides OpenCV-Python + python-astropy python-numpy python-scipy)) + (native-inputs (list python-psutil + python-pytest + python-pytest-cov + python-pytest-doctestplus + python-pytest-openfiles + python-setuptools-scm)) + (home-page "https://github.com/spacetelescope/stcal") + (synopsis "STScI tools and algorithms used in calibration pipelines") + (description "STScI tools and algorithms used in calibration pipelines.") + (license license:bsd-3))) + +(define-public python-stdatamodels + (package + (name "python-stdatamodels") + (version "1.5.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "stdatamodels" version)) + (sha256 + (base32 + "1lssz5mnkzgraqa9mdg1w39scsikymcp3zpmsjb146r0pqnwnpzw")))) + (build-system pyproject-build-system) + (arguments + (list + ;; Disable tests requiring access to CRDS servers to download ~500MiB + ;; of data. + #:test-flags #~(list "-k" "not test_crds_selectors_vs_datamodel") + #:phases #~(modify-phases %standard-phases + (add-before 'check 'set-home + (lambda _ + (setenv "HOME" "/tmp")))))) + (propagated-inputs (list python-asdf + python-asdf-astropy + python-astropy + python-jsonschema + python-numpy + python-psutil)) + (native-inputs (list python-crds + python-pytest + python-pytest-doctestplus + python-pytest-openfiles + python-scipy + python-semantic-version + python-setuptools-scm)) + (home-page "https://github.com/spacetelescope/stdatamodels") + (synopsis + "Core support for DataModel classes used in calibration pipelines") + (description + "Provides DataModel, which is the base class for data models implemented in +the @acronym{JWST, James Webb Space Telescope} and @acronym{Roman, Nancy Grace +Roman Space Telescope} calibration software.") + (license license:bsd-3))) + +(define-public python-stpipe + (package + (name "python-stpipe") + (version "0.5.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "stpipe" version)) + (sha256 + (base32 + "17gnwzhl10vbg059lfprdyci19dlh3whkmb9rl7z25wr593rnvcp")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-asdf python-astropy python-crds + python-semantic-version python-stdatamodels)) + (native-inputs (list python-pytest python-pytest-doctestplus + python-pytest-openfiles python-setuptools-scm)) + (home-page "https://github.com/spacetelescope/stpipe") + (synopsis "Framework for calibration pipeline software") + (description + "This package provides base classes and command-line tools for +implementing calibration pipeline software.") + ;; LICENSE Association of Universities for Research in Astronomy (AURA) + (license license:bsd-3))) + +(define-public python-stsynphot + (package + (name "python-stsynphot") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "stsynphot" version)) + (sha256 + (base32 + "0qkdh47j84v7fzri7bmi1jcmggdqq0a8byamfm73d8mbz86v8sn4")))) + (build-system pyproject-build-system) + (arguments + (list + ;; XXX: Tests fails on missing file, it might need to be downloaded, + ;; disable them for now. astropy.utils.exceptions.AstropyUserWarning: + ;; Failed to load Vega spectrum from + ;; /grp/redcat/trds/calspec/alpha_lyr_stis_010.fits; + #:tests? #f)) + (propagated-inputs (list python-astropy + python-beautifulsoup4 + python-matplotlib + python-numpy + python-scipy + python-synphot)) + (native-inputs (list python-pytest python-pytest-astropy + python-pytest-astropy-header python-setuptools-scm)) + (home-page "https://github.com/spacetelescope/stsynphot_refactor") + (synopsis "Synthetic photometry using Astropy for HST and JWST") + (description + "This package provides a replacement for IRAF STSDAS SYNPHOT and ASTROLIB +PYSYNPHOT, utilizing Astropy covering instrument specific portions of the old +packages for HST.") + (license license:bsd-3))) + (define-public libnova (package (name "libnova") @@ -2590,6 +2926,73 @@ Moon position, etc.") JPL ephemerides use to predict raw (x,y,z) planetary positions.") (license license:expat))) +(define-public python-jwst + (package + (name "python-jwst") + (version "1.10.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "jwst" version)) + (sha256 + (base32 + "1lmfyw2y7c84rs9xqavah9aidj478ijiiijlz6fag11xqn1vs98y")))) + (build-system pyproject-build-system) + (arguments + (list + ;; XXX: Tests require access to https://jwst-crds-pub.stsci.edu server for + ;; getting data sets. + #:tests? #f + #:phases #~(modify-phases %standard-phases + ;; NOTE: (Sharlatan-20230529T113448+0100): opencv-python's + ;; version can't be detected, it could the way it's packed in + ;; Guix. Review failing sanity check with more efforts, + ;; disable for now to make package buildable. + (delete 'sanity-check)))) + ;; opencv provides OpenCV-Python which is Listed as install requirement. + (propagated-inputs (list opencv + python-asdf + python-asdf-astropy + python-astropy + python-bayesicfitting + python-crds + python-drizzle + python-gwcs + python-jsonschema + python-numpy + python-photutils + python-poppy + python-psutil + python-pyparsing + python-requests + python-scikit-image + python-scipy + python-spherical-geometry + python-stcal + python-stdatamodels + python-stpipe + python-stsci-image + python-stsci-imagestats + python-tweakwcs + python-wiimatch)) + (native-inputs (list python-codecov + python-colorama + python-flake8 + python-pytest + python-pytest-cov + python-pytest-doctestplus + python-pytest-openfiles + python-requests-mock + python-setuptools-scm)) + (home-page "https://jwst-pipeline.readthedocs.io/en/latest/") + (synopsis + "Python library for science observations from the James Webb Space Telescope") + (description + "This package provides an access to the JWST Science Calibration Pipeline +processes data from all JWST instruments and observing modes by applying various +science corrections sequentially, producing both fully-calibrated individual +exposures and high-level data products (mosaics, extracted spectra, etc.).") + (license license:bsd-3))) + (define-public python-pyerfa (package (name "python-pyerfa") @@ -2687,6 +3090,38 @@ astrophysical simulations supporting PKDGRAV/Gasoline, Gadget, Gadget4/Arepo, N-Chilada and RAMSES AMR outputs.") (license license:gpl3+))) +(define-public python-pysynphot + (package + (name "python-pysynphot") + (version "2.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "pysynphot" version)) + (sha256 + (base32 + "1rr29m63bnj47f6gvbvg3pm1296x14ad29c6qd0sdj4f4ilrzhj5")))) + (build-system pyproject-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-before 'check 'set-env-data-path + (lambda _ + (setenv "PYSYN_CDBS" + (string-append #$output "/crds"))))))) + (native-inputs (list python-pytest python-pytest-remotedata + python-setuptools-scm)) + (propagated-inputs (list python-astropy python-beautifulsoup4 python-numpy + python-pytest-astropy-header python-six)) + (home-page "https://github.com/spacetelescope/pysynphot") + (synopsis "Python Synthetic Photometry Utilities") + (description + "Astrolib PySynphot (hereafter referred to only as pysynphot) is an +object-oriented replacement for STSDAS SYNPHOT synthetic photometry package in +IRAF. @code{pysynphot} simulates photometric data and spectra as they are +observed with the Hubble Space Telescope (HST). Passbands for standard +photometric systems are available, and users can incorporate their own filters, +spectra, and data.") + (license license:bsd-3))) + (define-public python-sep (package (inherit libsep) @@ -2723,6 +3158,67 @@ Takes a WGS84 (GPS) latitude/longitude as input as well as an UTC or local datetime object.") (license license:lgpl3+))) +(define-public python-synphot + (package + (name "python-synphot") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "synphot" version)) + (sha256 + (base32 + "02pjp1bnbyq7zi1bxqv56nif4ijd8fscmnn9ldrs8yvgsbmgdvlc")))) + (build-system pyproject-build-system) + (arguments + (list + ;; XXX: Test needs more love to pass. + ;; ERROR collecting synphot/tests/test_utils.py + #:tests? #f)) + (propagated-inputs (list python-astropy python-numpy python-scipy)) + (native-inputs (list python-pytest python-pytest-astropy + python-setuptools-scm)) + (home-page "https://github.com/spacetelescope/synphot_refactor") + (synopsis "Synthetic photometry using Astropy") + (description + "This package provides a replacement for IRAF STSDAS SYNPHOT and ASTROLIB +PYSYNPHOT, utilizing Astropy and covering the non-instrument specific portions +of the old packages.") + (license license:bsd-3))) + +(define-public python-tweakwcs + (package + (name "python-tweakwcs") + (version "0.8.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "tweakwcs" version)) + (sha256 + (base32 + "1500w737n9vf5hv16xkybk4shl7g4wfzb2ji9mc4vgzj41gkrwl4")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-astropy + python-gwcs + python-numpy + python-packaging + python-spherical-geometry + python-stsci-imagestats + python-stsci-stimage)) + (native-inputs (list python-codecov + python-pytest + python-pytest-cov + python-scipy + python-semantic-version + python-setuptools-scm)) + (home-page "https://tweakwcs.readthedocs.io/en/latest/") + (synopsis + "Algorithms for matching and aligning catalogs and for tweaking the WCS") + (description + "@code{tweakwcs} is a package that provides core algorithms for computing +and applying corrections to @code{WCS} objects such as to minimize mismatch +between image and reference catalogs. Currently only aligning images with +@code{FITS WCS} and @code{JWST gWCS} are supported.") + (license license:bsd-3))) + (define-public python-asdf (package (name "python-asdf") @@ -3050,6 +3546,79 @@ the entire transformation pipeline from input coordinates (detector by default) to world coordinates.") (license license:bsd-3))) +(define-public python-rad + (package + (name "python-rad") + (version "0.15.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "rad" version)) + (sha256 + (base32 + "0j51pkywxdaqrfz162rdsywlvx1mbb2h0gi5framvhf25i1im7mb")))) + (build-system pyproject-build-system) + (arguments + (list #:test-flags #~(list "-k" "not remote_data"))) + (native-inputs (list python-astropy + python-pytest + python-pytest-doctestplus + python-pytest-openfiles + python-semantic-version + python-setuptools-scm)) + (propagated-inputs (list python-asdf python-asdf-astropy)) + (home-page "https://github.com/spacetelescope/rad") + (synopsis "Roman Attribute Dictionary") + (description + "@acronym{RAD, The Roman Attribute Dictionary} is package which defines +schemas for the Nancy Grace Roman Space Telescope shared attributes for +processing and archive. These schemas are schemas for the ASDF file file +format, which are used by ASDF to serialize and deserialize data for the Nancy +Grace Roman Space Telescope.") + (license license:bsd-3))) + +(define-public python-roman-datamodels + (package + (name "python-roman-datamodels") + (version "0.15.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "roman_datamodels" version)) + (sha256 + (base32 + "0frhm1cqqd8934yizhm4fy78y38q2w9ncm4rv1n74hfypkyis4ap")))) + (build-system pyproject-build-system) + (arguments + ;; XXX: Check how to make all tests enabled, probably some more inner + ;; input chain needs to be upgraded, keep them disabled to make the build + ;; green. + (list #:test-flags #~(list "-k" + (string-append "not test_will_validate" + " and not test_will_strict_validate" + " and not test_nuke_validation")))) + (propagated-inputs (list python-asdf + python-asdf-astropy + python-asdf-standard + python-astropy + python-gwcs + python-numpy + python-psutil + python-rad)) + (native-inputs (list python-pytest python-pytest-doctestplus + python-pytest-openfiles python-semantic-version + python-setuptools-scm)) + (home-page "https://github.com/spacetelescope/roman_datamodels") + (synopsis "Roman Datamodels Support") + (description + "This package provides a Python package of Roman Datamodels for the +calibration pipelines started with the @acronym{JWST, James Webb Space +Telescope} calibration pipelines. The goal for the JWST pipelines was motivated +primarily by the need to support FITS data files, specifically with isolating +the details of where metadata and data were located in the FITS file from the +representation of the same items within the Python code. That is not a concern +for Roman since FITS format data files will not be used by the Roman calibration +pipelines.") + (license license:bsd-3))) + (define-public python-astroalign (package (name "python-astroalign") @@ -3102,3 +3671,26 @@ astronomical images, especially when there is no WCS information available.") "Skyfield computes positions for the stars, planets, and satellites in orbit around the Earth.") (license license:expat))) + +(define-public python-wiimatch + (package + (name "python-wiimatch") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "wiimatch" version)) + (sha256 + (base32 + "0x6p5z6a2cqinckwlpinjxagvmswl149s1jn6ihmdxk4k0h8rrz0")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-scipy)) + (native-inputs (list python-codecov python-pytest python-pytest-cov + python-pytest-doctestplus python-setuptools-scm)) + (home-page "https://github.com/spacetelescope/wiimatch") + (synopsis + "Optimal matching of weighted N-dimensional image intensity data") + (description + "@code{wiimatch} is a package that provides core computational algorithms +for optimal @code{matching} of weighted N-dimensional image intensity data +using (multivariate) polynomials.") + (license license:bsd-3))) |