diff options
Diffstat (limited to 'gnu/packages/astronomy.scm')
| -rw-r--r-- | gnu/packages/astronomy.scm | 1515 |
1 files changed, 1112 insertions, 403 deletions
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index da15283ef3..bde29f7990 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -12,6 +12,8 @@ ;;; Copyright © 2023 Iliya Tikhonenko <tikhonenko@mpe.mpg.de> ;;; Copyright © 2023 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2023 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2024 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2024 Andy Tai <lichengtai@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -157,8 +159,8 @@ randomly altered. (license license:gpl3))) (define-public aocommon - (let ((commit "7329a075271edab8f6264db649e81e62b2b6ae5e") - (revision "1")) + (let ((commit "9272ea36693a7ce7aa3524a9e212a60a509c3b8a") + (revision "2")) (package (name "aocommon") (version (git-version "0.0.0" revision commit)) @@ -169,7 +171,7 @@ randomly altered. (url "https://gitlab.com/aroffringa/aocommon") (commit commit))) (sha256 - (base32 "0qcfax6pbzs0yigy0x8xibrkk539wm2pbvjsb4lh50fybir02nix")) + (base32 "0klcrrlkc4sjpr83m2gnwb65lg798rydyvrlpangf7np1qg4zbk5")) (file-name (git-file-name name version)))) (build-system copy-build-system) (arguments @@ -186,7 +188,7 @@ reused in several astronomical applications, such as @code{wsclean}, (define-public calceph (package (name "calceph") - (version "3.5.3") + (version "3.5.5") (source (origin (method url-fetch) @@ -194,7 +196,7 @@ reused in several astronomical applications, such as @code{wsclean}, "https://www.imcce.fr/content/medias/recherche/equipes/asd/calceph/calceph-" version ".tar.gz")) (sha256 - (base32 "12apl806h8qx1kq74malq3828jqapwfi27cn05pvvxfiq7gfpllx")))) + (base32 "1jiaqyir2qcxzjlhk7f9fhrf6snjsiwxznvzdl996xr6m4lzbb7p")))) (build-system gnu-build-system) (native-inputs (list gfortran)) @@ -221,7 +223,7 @@ moment, supported SPICE files are: (define-public calcmysky (package (name "calcmysky") - (version "0.3.1") + (version "0.3.2") (source (origin (method git-fetch) @@ -230,7 +232,7 @@ moment, supported SPICE files are: (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "14jbaf9m9wig2bs7a531dvpmdkqpd09lmyvjvj1s0mhgh9g0x9m2")))) + (base32 "1kybjlddrm8x4x5y82qczi6z1d2riv6zcfjzrh7pzg2vwj89izh0")))) (build-system cmake-build-system) (arguments (list #:configure-flags @@ -278,7 +280,7 @@ rendering of the atmosphere model and examine its properties. (define-public aoflagger (package (name "aoflagger") - (version "3.2.0") + (version "3.4.0") (source (origin (method git-fetch) @@ -286,16 +288,15 @@ rendering of the atmosphere model and examine its properties. (url "https://gitlab.com/aroffringa/aoflagger") (commit (string-append "v" version)))) (sha256 - (base32 "1dcbfrbiybhpbypna2xhddx1wk7yifh38ha2r6p5rzsikzwlsin1")) + (base32 "0dxmcy04cayhs4s2z41wls1dnmg9hkffvlqcmc660idqziffvv1g")) (patches (search-patches "aoflagger-use-system-provided-pybind11.patch")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments (list - ;; XXX: Tests require external files download from + ;; Tests require external files download from ;; https://www.astron.nl/citt/ci_data/aoflagger/ - ;; FIXME: runtest is not found #:tests? #f #:configure-flags #~(list (string-append "-DCASACORE_ROOT_DIR=" @@ -452,7 +453,7 @@ with namespaces, exception handling, and member template functions.") (define-public cfitsio (package (name "cfitsio") - (version "4.2.0") + (version "4.3.1") (source (origin (method url-fetch) @@ -460,7 +461,7 @@ with namespaces, exception handling, and member template functions.") "https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/" "cfitsio-" version ".tar.gz")) (sha256 - (base32 "128qsv2q0f0g714ahlsixiikvvbwxi9bg9q9pcr5cd3f7wdkv9gb")))) + (base32 "1gk2a07ypmc8rcngakcarprznq7hi3xr9szfv3hy2yv80ppci9s7")))) (build-system gnu-build-system) (arguments (list @@ -504,6 +505,13 @@ in FITS files.") (sha256 (base32 "0ph9jhv4q4i4z6nkqr6hjw9148kdlnayxsn83qgv5dqn0h3nc9r8")))) (build-system pyproject-build-system) + (arguments + (list + ;; FIXME: https://github.com/aplpy/aplpy/issues/492 + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (delete 'sanity-check)))) (propagated-inputs (list python-astropy python-matplotlib @@ -561,7 +569,13 @@ Main features: (arguments (list #:test-flags - '(list "--ignore-glob=examples/*") + '(list "--ignore-glob=examples/*" + ;; Disable tests which are not compatible with Astropy 6.0.0, see + ;; <https://github.com/astroML/astroML/issues/273>. + "--ignore=astroML/density_estimation/tests/test_bayesian_blocks.py" + "--ignore=astroML/density_estimation/tests/test_bayesian_blocks.py" + "--ignore=astroML/density_estimation/tests/test_hist_binwidth.py" + "--ignore=astroML/density_estimation/tests/test_hist_binwidth.py") #:phases '(modify-phases %standard-phases (add-after 'unpack 'patch-build-system @@ -572,6 +586,17 @@ Main features: ;; Do not test examples (("testspaths = astroML doc examples") "testspaths = astroML")))) + (add-after 'unpack 'matplotlib-compatibility + (lambda _ + (substitute* "astroML/plotting/tools.py" + (("^( *)ax.(lines|patches|tables|artists|images).clear.*" _ indent type) + (string-append indent "for art in ax." type ":\n" + indent " art.remove()\n"))))) + ;; See commit e1c779de1f0ce4cb499dbda6c23d14f76b98e430 + (add-after 'unpack 'scipy-compatibility + (lambda _ + (substitute* "astroML/dimensionality/iterative_pca.py" + (("sym_pos=True") "assume_a=\"pos\"")))) (add-before 'check 'pre-check ;; Some tests need this (lambda _ @@ -681,6 +706,63 @@ CFITSIO library. Among other things, it can series in Python.") (license license:bsd-2))) +(define-public python-ginga + (package + (name "python-ginga") + (version "5.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ginga" version)) + (sha256 + (base32 "1kydi6qqsscgsa55fa2za35vr5j8xjn09lfbnb5ajr8yxdgm4n3y")))) + (build-system pyproject-build-system) + (propagated-inputs + (list ;;python-exifread ; optional, not packed yet in Guix + python-astropy + python-astroquery + python-dateutil + python-magic + python-matplotlib + python-fitsio + python-numpy + python-photutils + python-pillow + python-qtpy + python-scipy)) + (native-inputs + (list python-attrs + python-docutils + python-pytest-astropy + python-semantic-version + python-tornado)) + (home-page "https://ejeschke.github.io/ginga/") + (synopsis "Scientific image viewer and toolkit for FITS files") + (description "Ginga is a toolkit designed for building viewers for +scientific image data in Python, visualizing 2D pixel data in numpy arrays. It +can view astronomical data such as contained in files based on the +FITS (Flexible Image Transport System) file format. It is written and is +maintained by software engineers at the National Astronomical Observatory of +Japan (NAOJ), the Space Telescope Science Institute (STScI), and other +contributing entities. + +The Ginga toolkit centers around an image display object which supports zooming +and panning, color and intensity mapping, a choice of several automatic cut +levels algorithms and canvases for plotting scalable geometric forms. In +addition to this widget, a general purpose \"reference\" FITS viewer is +provided, based on a plugin framework. A fairly complete set of standard plugins +are provided for features that we expect from a modern FITS viewer: panning and +zooming windows, star catalog access, cuts, star pick/FWHM, thumbnails, etc.") +(license license:bsd-3))) + +(define-public ginga-qt5 + (package/inherit python-ginga + (name "ginga-qt5") + (inputs + (modify-inputs (package-inputs python-ginga) + (prepend python-pyqt))) + (synopsis "Qt5 image viewer build based on python-ginga library"))) + (define-public qfits (package (name "qfits") @@ -758,14 +840,14 @@ corrections.") (define-public wcslib (package (name "wcslib") - (version "8.1") + (version "8.2.2") (source (origin (method url-fetch) (uri (string-append "https://www.atnf.csiro.au/people/mcalabre/WCS/" "wcslib-" version ".tar.bz2")) (sha256 - (base32 "17hjnkwn2rd5d9krw2n637q4y8ma4nzk2i55zzn8l2yimdpkxwib")) + (base32 "0cvqppjf7gk0f3rs9cc46h5fffv2l8ylrb234r9fbx0px0525632")) (snippet #~(begin (use-modules (guix build utils)) (delete-file-recursively "C/flexed"))))) @@ -938,7 +1020,7 @@ different kinds of input files.") (define-public gnuastro (package (name "gnuastro") - (version "0.21") + (version "0.22") (source (origin (method url-fetch) @@ -946,7 +1028,7 @@ different kinds of input files.") version ".tar.lz")) (sha256 (base32 - "1zyk764pmfrsfj45gnc3qp4z1zfmgrv7kcsji2bxfzvs9inzzq4c")))) + "15rljx1mx9dyvni17qpj7y9gv086cvmjf9f5j34m1pbiyn989fqz")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--disable-static"))) @@ -970,7 +1052,7 @@ programs for the manipulation and analysis of astronomical data.") (define-public phd2 (package (name "phd2") - (version "2.6.11") + (version "2.6.13") (source (origin (method git-fetch) @@ -979,7 +1061,7 @@ programs for the manipulation and analysis of astronomical data.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0n87xsv9gzrwk1ygws4vw397ffq40xybp5b3c3bd5kcmff0avaw9")) + (base32 "0shr50ngi7dliijy8fxrd1c4hzkm4vp4m0a4m0d9gvrx56vzyx0s")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-26))) @@ -1082,7 +1164,7 @@ crowded star fields.") (define-public siril (package (name "siril") - (version "1.2.0") + (version "1.2.1") (source (origin (method git-fetch) (uri (git-reference @@ -1090,7 +1172,7 @@ crowded star fields.") (commit version))) (sha256 (base32 - "0ss1m9w4cz1752vp5738057nzmqc6k7fc9pi6kr9cwgspi1haall")) + "1lc6ga1n18br43rlj8qmg23chfniyvjz3vx73km6sv171z4c2fwy")) (file-name (git-file-name name version)))) (build-system meson-build-system) (native-inputs (list cmake git glib libconfig pkg-config)) @@ -1121,7 +1203,7 @@ image formats.") (define-public splash (package (name "splash") - (version "3.9.0") + (version "3.10.3") (source (origin (method git-fetch) (uri (git-reference @@ -1129,7 +1211,7 @@ image formats.") (commit (string-append "v" version)))) (sha256 (base32 - "19r5j4jrxhp3gf865ns59vvfnn5a303dqgmb8y2kgcsx26fci1hs")) + "077s9if7fmccvhsbp0dhvyqcil46vpbgdm1y6qn6h34r8lfqj9z6")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (arguments @@ -1216,57 +1298,56 @@ astronomical fields. SkyMaker is part of the (base32 "0rz29v33n0x0k40hv3v79ym5ylch1v0pbph4i21809gz2al5p7dq")))) (build-system gnu-build-system) (arguments - `(#:make-flags - (list - (string-append - "SKRY_INCLUDE_PATH=" (assoc-ref %build-inputs "libskry") "/include") - (string-append - "SKRY_LIB_PATH=-L" (assoc-ref %build-inputs "libskry") "/lib") - (string-append - "LIBAV_INCLUDE_PATH=" (assoc-ref %build-inputs "ffmpeg") "/include")) - #:phases - (modify-phases %standard-phases - ;; no configure and tests are provided - (delete 'configure) - (delete 'check) - (add-after 'unpack 'fix-paths - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "src/main.cpp" - (("\"\\.\\.\", \"lang\"") - "\"../share/stackistry\", \"lang\"")) - (substitute* "src/utils.cpp" - (("\"\\.\\.\", \"icons\"") - "\"../share/stackistry\", \"icons\"")) - #t)) - (replace 'install - ;; The Makefile lacks an ‘install’ target. - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (icons (string-append out "/share/stackistry/icons")) - (lang (string-append out "/share/stackistry/lang"))) - (copy-recursively "bin" bin) - (copy-recursively "icons" icons) - (copy-recursively "lang" lang)) - #t))))) + (list + #:tests? #f ; No test target + #:make-flags + #~(list + (string-append + "SKRY_INCLUDE_PATH=" #$(this-package-input "libskry") "/include") + (string-append + "SKRY_LIB_PATH=-L" #$(this-package-input "libskry") "/lib") + (string-append + "LIBAV_INCLUDE_PATH=" #$(this-package-input "ffmpeg") "/include")) + #:phases + #~(modify-phases %standard-phases + ;; no configure and tests are provided + (delete 'configure) + (add-after 'unpack 'fix-paths + (lambda _ + (substitute* "src/main.cpp" + (("\"\\.\\.\", \"lang\"") + "\"../share/stackistry\", \"lang\"")) + (substitute* "src/utils.cpp" + (("\"\\.\\.\", \"icons\"") + "\"../share/stackistry\", \"icons\"")))) + (replace 'install + ;; The Makefile lacks an ‘install’ target. + (lambda _ + (let* ((out #$output) + (bin (string-append out "/bin")) + (icons (string-append out "/share/stackistry/icons")) + (lang (string-append out "/share/stackistry/lang"))) + (copy-recursively "bin" bin) + (copy-recursively "icons" icons) + (copy-recursively "lang" lang))))))) (native-inputs (list pkg-config)) - (inputs - (list gtkmm-3 libskry ffmpeg-4)) - (home-page "https://github.com/GreatAttractor/stackistry") - (synopsis "Astronomical lucky imaging/image stacking tool") - (description - "Stackistry implements the lucky imaging principle of astronomical + (inputs + (list gtkmm-3 libskry ffmpeg-4)) + (home-page "https://github.com/GreatAttractor/stackistry") + (synopsis "Astronomical lucky imaging/image stacking tool") + (description + "Stackistry implements the lucky imaging principle of astronomical imaging: creating a high-quality still image out of a series of many (possibly thousands) low quality ones (blurred, deformed, noisy). The resulting image stack typically requires post-processing, including sharpening (e.g. via deconvolution). Such post-processing is not performed by Stackistry.") - (license license:gpl3+))) + (license license:gpl3+))) (define-public stellarium (package (name "stellarium") - (version "23.3") + (version "23.4") (source (origin (method git-fetch) @@ -1275,7 +1356,7 @@ deconvolution). Such post-processing is not performed by Stackistry.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "15kl8kn5fmmppbm93w5ki7lpjn09lhyhn245v3jc335xifcwd2vd")))) + (base32 "11l3lql3cxj7s7q7n74qd4rhbjy374b4c0lpm0dr8s85mfrq6fmc")))) (build-system cmake-build-system) ;; TODO: Complete documentation build and split into dedicated outputs. (arguments @@ -1301,6 +1382,7 @@ deconvolution). Such post-processing is not performed by Stackistry.") gpsd indi libnova + nlopt openssl qtbase-5 qtcharts @@ -1466,13 +1548,13 @@ accurately in real time at any rate desired.") (define-public python-astropy (package (name "python-astropy") - (version "5.3.4") + (version "6.0.0") (source (origin (method url-fetch) (uri (pypi-uri "astropy" version)) (sha256 - (base32 "1n7iwvjari4xv37094cpiapmjhhm57b04hi4r40wqb5czbigg46l")) + (base32 "1nbpqx7ibm8zsyyy17y5rmfjamwz6mv0sy4drlisap9hald81k83")) (modules '((guix build utils))) (snippet '(begin @@ -1487,64 +1569,69 @@ accurately in real time at any rate desired.") (for-each delete-file-recursively '("expat" "wcslib"))))))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'preparations - (lambda _ - ;; Use our own libraries in place of bundles. - (setenv "ASTROPY_USE_SYSTEM_ALL" "1") - ;; Some tests require a writable home. - (setenv "HOME" "/tmp") - ;; Relax xfail tests. - (substitute* "setup.cfg" - (("xfail_strict = true") "xfail_strict = false")) - ;; Replace all references to external ply. - (let ((ply-files '("coordinates/angle_formats.py" - "utils/parsing.py"))) - (with-directory-excursion "astropy" - (map (lambda (file) - (substitute* file (("astropy.extern.ply") - "ply"))) - ply-files))) - ;; Replace reference to external configobj. - (with-directory-excursion "astropy/config" - (substitute* "configuration.py" - (("from astropy.extern.configobj ") ""))))) - ;; This file is opened in both install and check phases. - (add-before 'install 'writable-compiler - (lambda _ (make-file-writable "astropy/_compiler.c"))) - (add-before 'check 'writable-compiler - (lambda _ (make-file-writable "astropy/_compiler.c"))) - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - ;; Extensions have to be rebuilt before running the tests. - (invoke "python" "setup.py" "build_ext" "--inplace") - (invoke "python" "-m" "pytest" "--pyargs" "astropy" - ;; Skip tests that need remote data. - "-k" (string-append - "not remote_data" - ;; XXX: Check why this tests failing. - " and not test_ignore_sigint" - " and not test_parquet_filter" - ;; See https://github.com/astropy/astropy/issues/15537 - " and not test_pvstar")))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'preparations + (lambda _ + ;; Use our own libraries in place of bundles. + (setenv "ASTROPY_USE_SYSTEM_ALL" "1") + ;; Relax xfail tests. + (substitute* "pyproject.toml" + (("xfail_strict = true") "xfail_strict = false")) + ;; Replace reference to external ply. + (substitute* "astropy/utils/parsing.py" + (("astropy.extern.ply") "ply")) + ;; Replace reference to external configobj. + (substitute* "astropy/config/configuration.py" + (("from astropy.extern.configobj ") "")))) + ;; This file is opened in both install and check phases. + (add-before 'install 'writable-compiler + (lambda _ + (make-file-writable "astropy/_compiler.c"))) + (add-before 'check 'prepare-test-environment + (lambda _ + ;; Some tests require a writable home. + (setenv "HOME" "/tmp") + (make-file-writable "astropy/_compiler.c") + ;; Extensions have to be rebuilt before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace" + "-j" (number->string (parallel-job-count))))) + ;; TODO: The swap to pyproject-build-system introduced all tests + ;; failed due to pytest could not load conftest.py, find out how + ;; to resolve it and migrate completely to pyproject-build-system. + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "--pyargs" "astropy" + ;; with -n : 133.00s + ;; without -n : 326.14s + "-n" (number->string (parallel-job-count)) + "-k" (string-append + ;; Skip tests that need remote data. + "not remote_data" + ;; E astropy.samp.errors.SAMPProxyError: + ;; <SAMPProxyError 1: 'Timeout expired!'> + " and not test_main" + ;; E ModuleNotFoundError: No module named 'wofz' + " and not test_pickle_functional")))))))) (native-inputs (list pkg-config python-colorlog python-coverage - python-cython + python-cython-3 python-extension-helpers python-h5py python-ipython python-jplephem + python-matplotlib python-objgraph python-pandas python-pyarrow python-pytest python-pytest-astropy python-pytest-astropy-header + python-pytest-mpl python-pytest-xdist python-scikit-image python-scipy @@ -1555,7 +1642,8 @@ accurately in real time at any rate desired.") (inputs (list expat wcslib)) (propagated-inputs - (list python-configobj + (list python-astropy-iers-data + python-configobj python-numpy python-packaging python-ply @@ -1572,13 +1660,13 @@ astronomy and astrophysics.") (define-public python-astropy-healpix (package (name "python-astropy-healpix") - (version "1.0.0") + (version "1.0.2") (source (origin (method url-fetch) (uri (pypi-uri "astropy_healpix" version)) (sha256 - (base32 "18zfmdv0vs0yawirq8c2mpjxx7bvy66z0rlcyc1n6s0fl5ifz0pl")))) + (base32 "0fij80ws16xzbph8z9v27w54dnc3vry8fk9p3mvxrglnjgnscvq5")))) (build-system pyproject-build-system) (arguments (list @@ -1604,37 +1692,164 @@ astronomy and astrophysics.") (description "This package provides HEALPix to the Astropy project.") (license license:bsd-3))) +(define-public python-astropy-iers-data + (package + (name "python-astropy-iers-data") + ;; In case of changing the source method git-fetch, consider to check the + ;; tag as it's not following the PyPI version, see + ;; <https://github.com/astropy/astropy-iers-data/issues/17>. + (version "0.2024.3.18.0.29.47") + (source + (origin + (method url-fetch) + (uri (pypi-uri "astropy-iers-data" version)) + (sha256 + (base32 "1mf03iqw09rp6d8hbby33f4jwfjan9gkb1z7xqsjr2jpj7zwpn3y")))) + (build-system pyproject-build-system) + (arguments + (list + ;; Dependencies cycle wit python-astropy, see + ;; <https://github.com/astropy/astropy-iers-data/issues/21>. + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-env-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))) + (native-inputs + (list python-hypothesis + python-pytest + python-pytest-remotedata + python-setuptools-scm)) + (home-page "https://docs.astropy.org/en/latest/utils/iers.html") + (synopsis "IERS Earth Rotation and Leap Second tables for the astropy core package") + (description + "The @code{iers} package provides access to the tables provided by the +@acronym{International Earth Rotation and Reference Systems, IERS} service, in +particular the +@url{https://www.iers.org/IERS/EN/DataProducts/EarthOrientationData/eop.html, +Earth Orientation data} allowing interpolation of published UT1-UTC and polar +motion values for given times. The UT1-UTC values are used in +@url{https://docs.astropy.org/en/latest/time/index.html#astropy-time, Time and +Dates (astropy.time)} to provide UT1 values, and the polar motions are used in +@code{astropy.coordinates} to determine Earth orientation for +celestial-to-terrestrial coordinate transformations.") + (license license:bsd-3))) + +(define-public python-astroplan + (package + (name "python-astroplan") + (version "0.9.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "astroplan" version)) + (sha256 + (base32 "0jrgii0f11ckxvywinr9kcsljxnpnkh7hv5638wxwcb1iyjmx36r")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "astroplan/tests" + "-k" (string-append + ;; Test requiring newer python-pytz + "not test_timezone" + ;; Disable tests requiring remote data. + " and not test_FixedTarget_from_name" + " and not test_altitude_constraint" + " and not test_at_night_basic" + " and not test_caches_shapes" + " and not test_compare_airmass_constraint_and_observer" + " and not test_compare_altitude_constraint_and_observer" + " and not test_docs_example" + " and not test_eclipses" + " and not test_eq_observer" + " and not test_event_observable" + " and not test_galactic_plane_separation" + " and not test_get_skycoord" + " and not test_hash_observer" + " and not test_is_night" + " and not test_local_time_constraint_hawaii_tz" + " and not test_local_time_constraint_utc" + " and not test_moon_illumination" + " and not test_moon_separation" + " and not test_observability_table" + " and not test_observer_lon_lat_el" + " and not test_regression_airmass_141" + " and not test_regression_shapes" + " and not test_sun_separation" + " and not test_tonight") + "--ignore=astroplan/tests/test_scheduling.py") + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'prepare-test-environment + (lambda _ + (setenv "HOME" "/tmp") + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs + (list python-astropy + python-astroquery + python-matplotlib + python-numpy + python-pytz + python-six)) + (native-inputs + (list python-pytest-astropy + python-pytest-mpl + python-setuptools-scm)) + (home-page "https://github.com/astropy/astroplan") + (synopsis "Observation planning package for astronomers") + (description + "This package provides a flexible toolbox for observation planning and +scheduling. When complete, the goal is to be easy for Python beginners and new +observers to to pick up, but powerful enough for observatories preparing nightly +and long-term schedules. + +Features: +@itemize +@item calculate rise/set/meridian transit times, alt/az positions for targets at +observatories anywhere on Earth +@item built-in plotting convenience functions for standard observation planning +plots (airmass, parallactic angle, sky maps) +@item determining observability of sets of targets given an arbitrary set of +constraints (i.e., altitude, airmass, moon separation/illumination, etc.) +@end itemize") + (license license:bsd-3))) + (define-public python-astroquery (package (name "python-astroquery") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) (uri (pypi-uri "astroquery" version)) (sha256 - (base32 "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h")))) + (base32 "1jbyfhqk74wsdjxzqi0hcrgc7ha4q8cyjx96nv6w9bjg1b5vlzq4")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--pyargs" "astroquery" - "-m" "not remote_data") + "-m" "not remote_data" + ;; Some tests failed with parallel run, see + ;; <https://github.com/astropy/astroquery/issues/2968>. + ;; "-n" "auto" + "-k" (string-append + ;; Failed: DID NOT RAISE <class + ;; 'astropy.utils.exceptions.AstropyDeprecationWarning'> + "not test_raises_deprecation_warning")) #:phases #~(modify-phases %standard-phases - (add-before 'check 'prepare-test-environment - (lambda _ - (setenv "HOME" (getcwd)) ; some tests need a writable home - ;; To solve pytest/conftest issue. Pytest tries to load all - ;; files with word 'test' in them. - ;; - ;; ImportError while loading conftest ... - ;; _pytest.pathlib.ImportPathMismatchError: ... - ;; - (call-with-output-file "pytest.ini" - (lambda (port) - (format port "[pytest] -python_files = test_*.py")))))))) + (replace 'check + (lambda* (#:key tests? test-flags #:allow-other-keys) + (when tests? + ;; Some tests require write access to $HOME. + (setenv "HOME" "/tmp") + ;; Step out of the source directory to avoid interference; + ;; we want to run the installed code with extensions etc. + (with-directory-excursion "/tmp" + (apply invoke "pytest" "-v" test-flags)))))))) (propagated-inputs (list python-astropy python-beautifulsoup4 @@ -1795,22 +2010,19 @@ bad pixel tracking throughout the reduction process.") (define-public python-cdflib (package (name "python-cdflib") - (version "1.2.3") + (version "1.2.6") (source (origin - (method git-fetch) ; no tests in pypi archive + (method git-fetch) ; no tests in PyPI release (uri (git-reference (url "https://github.com/MAVENSDC/cdflib") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0vpgcbc9pmx0qqfia1frnwq3jkgfp8y3ikqdnzs5bs1sr13p9p3w")))) + (base32 "1wxr35sqsdqzf85xyjh1v8hmwwiyv4cn0lr7q8l1kkngfywq5l2r")))) (build-system pyproject-build-system) (arguments - ;; Disable shaky test. - ;; See https://github.com/MAVENSDC/cdflib/issues/234 - (list #:test-flags #~(list "-k" "not test_compute_cdfepoch16") - #:phases + (list #:phases #~(modify-phases %standard-phases (add-before 'build 'set-env-version (lambda _ @@ -1844,16 +2056,41 @@ attempting to maintain ISTP compliance @end itemize") (license license:expat))) +(define-public python-cmyt + (package + (name "python-cmyt") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cmyt" version)) + (sha256 + (base32 "1zabmckr1z637pfqqvlkj0asfqqvx2x92163dby8x0c8yiqgdvjb")))) + (build-system pyproject-build-system) + (native-inputs + (list python-colorspacious python-pytest python-pytest-mpl)) + (propagated-inputs + (list python-matplotlib python-numpy)) + (home-page "https://yt-project.org/") + (synopsis "Matplotlib colormaps from the yt project") + (description + "This package provides a range of colormaps designed for scientific +use with Matplotlib. It includes perceptually uniform sequential colormaps such +as @code{abre}, @code{dusk}, @code{kepl}, and @code{octarine}, as well as +monochromatic sequential colormaps like @code{blue}, @code{green}, and +@code{red}, and others (@code{algae}, @code{pastel}, and @code{xray}).") + (license license:bsd-3))) + (define-public python-crds (package (name "python-crds") - (version "11.17.9") + (version "11.17.19") (source (origin (method url-fetch) (uri (pypi-uri "crds" version)) (sha256 (base32 - "0ha7ibs5lmqs9pcr546jyxzgrmx1xyqps7fsp220rvlsbsisdgm0")))) + "1x48yw6jnz7dw0myc86ds0qaki6v1anqaihd5qzrxwrrl61kyp6x")))) (build-system pyproject-build-system) (arguments (list @@ -1885,14 +2122,14 @@ attempting to maintain ISTP compliance (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.") +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 @url{http://hst-crds.stsci.edu} or +@url{https://jwst-crds.stsci.edu/} which record information about reference +files and provide related services.") (license license:bsd-3))) (define-public python-czml3 @@ -1929,13 +2166,13 @@ Cesium.") (define-public python-drms (package (name "python-drms") - (version "0.6.4") + (version "0.7.1") (source (origin (method url-fetch) (uri (pypi-uri "drms" version)) (sha256 - (base32 "0mkrmr55fgca441z7hvsyri6x9cjsh0sfas3hrj0k1k10k8vszbw")))) + (base32 "01q00zwpbhik9lgbc42z6q791ybxc41rxgrj04fpcfkl3hcl0nyr")))) (build-system pyproject-build-system) (native-inputs (list python-astropy @@ -1955,7 +2192,7 @@ used with local NetDRMS sites.") (define-public python-drizzle (package (name "python-drizzle") - (version "1.14.3") + (version "1.15.1") (source (origin (method git-fetch) ;PyPi doesn't have the test data sets @@ -1964,7 +2201,7 @@ used with local NetDRMS sites.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "04gncwg76yivcaq7rwgsw5k8w4h3c4wcrjcamb53h0d5s820z7dl")))) + (base32 "14l3d3bx73r7cxhcl1cfh1q088qh5wq5pz5fs9dx7w79kp8mp6pg")))) (build-system pyproject-build-system) (arguments (list @@ -1980,7 +2217,7 @@ used with local NetDRMS sites.") (propagated-inputs (list python-astropy python-numpy)) (native-inputs - (list python-flake8 python-pytest python-setuptools-scm)) + (list python-pytest python-setuptools-scm)) (home-page "https://github.com/spacetelescope/drizzle") (synopsis "Astronomical tool for combining dithered images into a single image") @@ -1994,6 +2231,28 @@ 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-dust-extinction + (package + (name "python-dust-extinction") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "dust_extinction" version)) + (sha256 + (base32 "14zy6kyrfi4ash7qg1k3im1zzgr2r7rnaggzk0ar3jlfmsii743k")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-astropy python-scipy)) + (native-inputs + (list python-pytest-astropy)) + (home-page "http://dust-extinction.readthedocs.io/") + (synopsis "Interstellar Dust Extinction Models") + (description + "This package provides astronomical interstellar dust extinction curves +implemented using the astropy.modeling framework.") + (license license:bsd-3))) + (define-public python-ephem (package (name "python-ephem") @@ -2017,21 +2276,49 @@ for a table giving the position of a planet, asteroid, or comet for a series of dates.") (license license:expat))) +(define-public python-extinction + (package + (name "python-extinction") + (version "0.4.6") + (source + (origin + (method git-fetch) ; No tests in PyPI + (uri (git-reference + (url "https://github.com/kbarbary/extinction") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1adxq926jd469mxm6llvsljgf2jqb06905h61i9qzc7m2yrm4wga")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags #~(list "test.py"))) + (native-inputs (list python-cython python-pytest)) + (propagated-inputs (list python-numpy)) + (home-page "http://github.com/kbarbary/extinction") + (synopsis "Fast interstellar dust extinction laws") + (description + "This package provides a cython-optimized implementations of empirical dust +exitinction laws found in the literature.") + (license license:expat))) + (define-public python-hvpy (package (name "python-hvpy") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "hvpy" version)) (sha256 - (base32 "0r0asyflz2sw9zn5vgs138nh81m0rbwbakmrncbc1ghdr3g6jahv")))) + (base32 "0bly1bgp0axxhzzf5imqsgmms41z8cxbjahxsibvb55dk94gwig6")))) (build-system pyproject-build-system) (arguments (list #:tests? #f)) ; Requires HTTP(S) access to api.beta.helioviewer.org - (propagated-inputs (list python-pydantic python-requests)) - (native-inputs (list python-pytest python-pytest-astropy)) + (propagated-inputs + (list python-pydantic-2 python-pydantic-settings python-requests)) + (native-inputs + (list python-pytest python-pytest-astropy)) (home-page "https://helioviewer.org/") (synopsis "Helioviewer Python API Wrapper") (description "@code{hvpy} is a Python API wrapper around the formal @@ -2041,13 +2328,13 @@ of dates.") (define-public python-mpl-animators (package (name "python-mpl-animators") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (pypi-uri "mpl_animators" version)) (sha256 - (base32 "12kjmj7rn3pk9ly82h5s5hn0kl3kxkr7bgkz9zr9k59pir8z1r8b")))) + (base32 "078dshs383ny182dac0spg7z0iilcwa0fnwv1vizsr6p1d3ar98b")))) (build-system pyproject-build-system) (native-inputs (list python-pytest @@ -2064,19 +2351,70 @@ of dates.") the easy construction of interactive matplotlib widget based animations.") (license license:bsd-3))) +(define-public python-ndcube + (package + (name "python-ndcube") + (version "2.2.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ndcube" version)) + (sha256 + (base32 "1b3vbnm438j5jb48vilp145lq137fbrg1l4845rc55mz2p025x34")))) + (build-system pyproject-build-system) + (arguments + (list + #: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")))))) + (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-scipy + python-setuptools-scm + python-sunpy)) + (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") - (version "1.9.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (pypi-uri "photutils" version)) (sha256 - (base32 "0gjvrmcb10lyqx3h9521zqskqngd5xcp3l9h2b02mk1p7q54mzdy")))) + (base32 "148zhdxhlcgj6dxyzaz78bzxw1q44qa9q9sfdqbfbla0s0w2jaay")))) (build-system pyproject-build-system) (arguments (list + #:test-flags + #~(list "-n" "auto") #:phases #~(modify-phases %standard-phases ;; This file is opened in both install and check phases. @@ -2092,11 +2430,23 @@ the easy construction of interactive matplotlib widget based animations.") (make-file-writable "photutils/_compiler.c") (invoke "python" "setup.py" "build_ext" "--inplace")))))) (propagated-inputs - (list python-astropy python-numpy)) + (list python-astropy + python-bottleneck + python-gwcs + python-matplotlib + python-numpy + python-rasterio + python-scikit-image + python-scikit-learn + python-scipy + python-shapely + python-tqdm)) (native-inputs (list python-cython python-extension-helpers python-pytest-astropy + python-pytest-xdist + python-semantic-version python-setuptools-scm)) (home-page "https://github.com/astropy/photutils") (synopsis "Source detection and photometry") @@ -2104,6 +2454,9 @@ the easy construction of interactive matplotlib widget based animations.") of astronomical sources.") (license license:bsd-3))) +;; XXX: The project is archived, maintained fork is available see +;; <https://github.com/poliastro/poliastro/issues/1640>. +;; Maintained fork <https://github.com/pleiszenburg/hapsira>. (define-public python-poliastro (package (name "python-poliastro") @@ -2130,9 +2483,28 @@ of astronomical sources.") " and not test_czml_custom_packet" " and not test_czml_ground_station" " and not test_czml_groundtrack" - " and not test_czml_preamble")) + " and not test_czml_preamble" + ;; This fails with "ufunc 'isfinite' not + ;; supported for the input types" + " and not test_porkchop_plotting")) #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "pyproject.toml" + (("5.0,<6") "5.0,<7")))) + (add-after 'unpack 'matplotlib-compatibility + (lambda _ + (substitute* "src/poliastro/plotting/static.py" + (("import numpy as np.*" m) + (string-append m "\ +import itertools\n")) + (("( +)self._ax = ax.*" m indent) + (string-append m indent + "\ +self.colors = itertools.cycle(plt.rcParams[\"axes.prop_cycle\"].by_key()[\"color\"])\n")) + (("color = next\\(self._ax._get_lines.prop_cycler\\)\\[\"color\"\\]") + "color = next(self.colors)")))) ;; NOTE: Tests take about 7-10 minutes to pass. (add-before 'check 'prepare-test-environment (lambda _ @@ -2185,6 +2557,10 @@ Low-Earth Orbit (LEO).") (base32 "0s8rb61q8dz66s8d3qg44kb6bb5gi40zl41ik9wyccgb4kyf3brp")))) (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "-n" "auto"))) (propagated-inputs ;; XXX: With python-synphot (marked as optional) package added to the list ;; it tries to download from remote host during tests and fails. Overall @@ -2199,8 +2575,10 @@ Low-Earth Orbit (LEO).") python-pandas python-pytest python-pytest-astropy - python-sphinx - python-setuptools-scm)) + python-pytest-xdist + python-scikit-image + python-setuptools-scm + python-sphinx)) (home-page "https://poppy-optics.readthedocs.io/") (synopsis "Physical Optics Propagation in Python") (description @@ -2244,18 +2622,18 @@ interest, and which require portability between platforms or ease of scripting." (define-public python-pyvo (package (name "python-pyvo") - (version "1.4.2") + (version "1.5.1") (source (origin (method url-fetch) (uri (pypi-uri "pyvo" version)) (sha256 - (base32 "1jwmgpavw80mf9sigfz5p2cqh6vz5mvm11ziqmdp5zdccn42kzk6")))) + (base32 "0cm6agaf1gvc5bi95wx6a70ngj9vn95rx78fs59vlrmpww7q2807")))) (build-system pyproject-build-system) (native-inputs (list python-pytest-astropy python-requests-mock python-setuptools-scm)) (propagated-inputs - (list python-astropy python-mimeparse python-pillow python-requests)) + (list python-astropy python-pillow python-requests)) (home-page "https://github.com/astropy/pyvo") (synopsis "Access Virtual Observatory data and services") (description @@ -2266,36 +2644,43 @@ Virtual observatory (VO) using Python.") (define-public python-regions (package (name "python-regions") - (version "0.7") + (version "0.8") (source (origin (method url-fetch) (uri (pypi-uri "regions" version)) (sha256 - (base32 "08wsg9kxnki5pz8gdp81bq06jdmsip382fl02rvnr96cvzr7wf3m")))) - (build-system python-build-system) + (base32 "09401pz7926zlci7cznd78hmv9947f6jxyy2afqdqc1xaccpzcq2")))) + (build-system pyproject-build-system) (arguments - `(#:test-target "pytest" - #:phases - (modify-phases %standard-phases - ;; This doctest requires online data. - (add-after 'unpack 'delete-doctest - (lambda _ (delete-file "docs/masks.rst"))) - ;; This file is opened in both install and check phases. - (add-before 'install 'writable-compiler - (lambda _ (make-file-writable "regions/_compiler.c"))) - (add-before 'check 'writable-compiler - (lambda _ (make-file-writable "regions/_compiler.c"))) - (add-before 'check 'writable-home - (lambda _ (setenv "HOME" (getcwd))))))) + (list + #:test-flags + #~(list "-n" "auto") + #:phases + #~(modify-phases %standard-phases + ;; This file is opened in both install and check phases. + ;; XXX: Check if it is still required. + (add-before 'install 'writable-compiler + (lambda _ (make-file-writable "regions/_compiler.c"))) + (add-before 'check 'prepare-test-environment + (lambda _ + (setenv "HOME" "/tmp") + (make-file-writable "regions/_compiler.c") + (invoke "python" "setup.py" "build_ext" "--inplace")))))) (propagated-inputs - (list python-astropy python-numpy)) + (list python-astropy + python-h5py + python-matplotlib + python-numpy + python-scipy + python-shapely)) (native-inputs (list python-cython python-extension-helpers python-pytest-arraydiff python-pytest-astropy python-pytest-runner + python-pytest-xdist python-setuptools-scm)) (home-page "https://github.com/astropy/regions") (synopsis "Package for region handling") @@ -2305,13 +2690,13 @@ Virtual observatory (VO) using Python.") (define-public python-reproject (package (name "python-reproject") - (version "0.12.0") + (version "0.13.0") (source (origin (method url-fetch) (uri (pypi-uri "reproject" version)) (sha256 - (base32 "1cjdfv7wd4c0ia63vqakxf9w8hd5dfz6jzi520scd37rliy1xgld")))) + (base32 "1qkjbx8xsawhi1gjzqimais3crvkwgbzy1pr51x6anjjln88rgll")))) (build-system pyproject-build-system) (arguments (list @@ -2398,31 +2783,45 @@ orbits described in TLE files.") (define-public python-sunpy (package (name "python-sunpy") - (version "5.0.1") + (version "5.1.1") (source (origin (method url-fetch) (uri (pypi-uri "sunpy" version)) (sha256 - (base32 "1r4phc91k527kvpa2jd1d417x97wqyrm3ydayr9hshwz1k5v5ngf")))) + (base32 "07rfdj4v29kcb718sgjfsagazvnl11r01ciqjvazr5x3yadfqrwk")))) (build-system pyproject-build-system) (arguments (list #:test-flags - #~(list "-k" (string-append - ;; XXX: Failed: DID NOT RAISE <class 'ModuleNotFoundError'> - ;; It struggles to find python-opencsv package info with - ;; 'importlib.metadata' - "not test_main_nonexisting_module" - " and not test_main_stdlib_module")) + #~(list + "-n" "auto" + "-k" (string-append + ;; XXX: Failed: DID NOT RAISE <class 'ModuleNotFoundError'> + ;; It struggles to find python-opencsv package info with + ;; 'importlib.metadata' + "not test_main_nonexisting_module" + " and not test_main_stdlib_module") + ;; Requries SpicePy not packed in Guix yet. + "--ignore=sunpy/coordinates/tests/test_spice.py") #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.cfg" + ;; It's already updated in master branch, but not released yet. + ;; drms>=0.6.1,<0.7.0 + (("0.7.0") "0.7.2")))) (add-before 'install 'writable-compiler (lambda _ (make-file-writable "sunpy/_compiler.c"))) (add-before 'check 'prepare-test-environment (lambda _ - (setenv "HOME" "/tmp")))))) + (setenv "HOME" "/tmp") + (call-with-output-file "pytest.ini" + (lambda (port) + (format port "[pytest] +python_files = test_*.py")))))))) (native-inputs (list opencv ; For tests, includes OpenCV-Python python-aiohttp @@ -2459,6 +2858,7 @@ orbits described in TLE files.") python-scikit-image python-scipy python-semantic-version + ;; python-spiceypy ; Not packed yet in Guix, long jorney. python-sqlalchemy python-tqdm python-zeep)) @@ -2469,6 +2869,50 @@ orbits described in TLE files.") SolarSoft data analysis environment.") (license license:bsd-2))) +(define-public python-sunpy-soar + (package + (name "python-sunpy-soar") + (version "1.10") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sunpy-soar" version)) + (sha256 + (base32 "0pb7dr06n20hdhlqf8npb4j1qb5034cgwqi3iciqdi1wxyy5pjc6")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; Disabe tests requireing network access. + #~(list "-k" (string-append + "not test_search" + " and not test_search_low_latency" + " and not test_insitu_search" + " and not test_no_results" + " and not test_no_instrument" + " and not test_download_path" + " and not test_search_soop" + " and not test_when_soar_provider_passed" + " and not test_when_sdac_provider_passed" + " and not test_when_wrong_provider_passed")) + #: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")))))) + (propagated-inputs + (list python-sunpy)) + (native-inputs + (list python-pytest)) + (home-page "https://docs.sunpy.org/projects/soar") + (synopsis "Solar Orbiter Archive plugin for SunPy") + (description + "This package provides a @code{sunpy} FIDO plugin for accessing data in the +@acronym{Solar Orbiter Archive, SOAR}.") + (license license:bsd-2))) + (define-public python-astral (package (name "python-astral") @@ -2533,17 +2977,25 @@ elevation, solar azimuth, rahukaalam, and the phases of the moon.") (define-public python-spectral-cube (package (name "python-spectral-cube") - (version "0.6.3") + (version "0.6.5") (source (origin (method url-fetch) (uri (pypi-uri "spectral-cube" version)) (sha256 - (base32 "10q76rsgf9w4j7y68mfa870bpxf06m6kqvivj4340jmgnsrfy1zg")))) + (base32 "0cqxgmk46gv2qa2kls8fph105lgwbwf13hvizh6w85mzgypyp740")))) (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "-n" "auto"))) (propagated-inputs (list python-astropy - python-aplpy + ;; XXX: Currently failing in upstream as it's optional silent + ;; until a new version is released, see: + ;; <https://github.com/aplpy/aplpy/issues/492>. + ;; + ;; python-aplpy python-casa-formats-io python-dask python-distributed @@ -2563,6 +3015,7 @@ elevation, solar azimuth, rahukaalam, and the phases of the moon.") ;; in [noviz] option. ;; python-pvextractor python-pytest-astropy + python-pytest-xdist python-regions python-semantic-version python-setuptools-scm)) @@ -2584,12 +3037,59 @@ of axis order, spatial projections, and spectral units that exist in the wild. @end itemize") (license license:bsd-3))) +(define-public python-specutils + (package + (name "python-specutils") + (version "1.13.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "specutils" version)) + (sha256 + (base32 "0cfsigvsa0i7z2nq9ci9gxccp074kqsgr01xi2npk8xf7cjisrfq")))) + (build-system pyproject-build-system) + (arguments + (list + ;; Disabling test requiring access to download + ;; <https://datacenter.iers.org/data/9/finals2000A.all>. + ;; XXX: Check if test data may be packed as standalone package. + #:test-flags #~(list "-k" "not test_create_spectral_axis") + #: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")))))) + (propagated-inputs + (list ;; python-stdatamodels ; cycle with python-synphot, optional. + python-asdf + python-asdf-astropy + python-gwcs + python-ndcube + python-numpy + python-scipy)) + (native-inputs + (list python-matplotlib + python-pytest-astropy + python-semantic-version + python-setuptools-scm + python-spectral-cube)) + (home-page "https://specutils.readthedocs.io/") + (synopsis "Package for spectroscopic astronomical data") + (description + "@code{specutils} is a Python package for representing, loading, manipulating, +and analyzing astronomical spectroscopic data. The generic data containers and +accompanying modules provide a toolbox that the astronomical community can use +to build more domain-specific packages. For more details about the underlying +principles, +see @url{https://github.com/astropy/astropy-APEs/blob/main/APE13.rst, APE13}.") + (license license:bsd-3))) + (define-public python-spherical-geometry (package (name "python-spherical-geometry") - ;; XXX: Can't be updated to the latest see: - ;; https://github.com/spacetelescope/spherical_geometry/issues/227 - (version "1.2.22") + (version "1.3.1") (source (origin (method git-fetch) @@ -2598,7 +3098,7 @@ of axis order, spatial projections, and spectral units that exist in the wild. (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0kzcncqir4v7nhk9lxj9gxr32p3krkaqa58y2i4kksgxxy24qw4z")))) + (base32 "172f81h42jq6mv3gpx497z2nkhkx11w4pzmcqljcicri2zqj1m6g")))) (build-system pyproject-build-system) (arguments (list @@ -2612,18 +3112,23 @@ of axis order, spatial projections, and spectral units that exist in the wild. (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) ;; Use our own libraries in place of bundles. (setenv "USE_SYSTEM_QD" "1"))) - (add-before 'check 'build-extensions + (add-before 'check 'prepare-test-environment (lambda _ - (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (invoke "python" "setup.py" "build_ext" "--inplace") + (call-with-output-file "pytest.ini" + (lambda (port) + (format port "[pytest] +python_files = test_*.py")))))))) (native-inputs (list python-pytest + python-pytest-astropy-header python-setuptools-scm)) (inputs (list qd)) (propagated-inputs (list python-astropy python-numpy)) - (home-page "https://github.com/spacetelescope/tweakwcs") + (home-page "https://github.com/spacetelescope/spherical_geometry") (synopsis "Python astronimical package for handling spherical polygons") (description "The @code{spherical_geometry} library is a Python package for handling @@ -2663,18 +3168,24 @@ Science Institute} image array manipulation functions.") (define-public python-stsci-imagestats (package (name "python-stsci-imagestats") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (pypi-uri "stsci.imagestats" version)) (sha256 (base32 - "14457izlbnks84dyza75ib3nvx2w8nhlqm9vc1zb7hbhknb5gjvw")))) + "01jqqrhcna0ghin48bbcza57d12371ny4l4pqws89irwdhd8xr0r")))) (build-system pyproject-build-system) (arguments - (list #:tests? #f)) ;No tests + (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)) - (native-inputs (list python-setuptools-scm)) + (native-inputs (list python-pytest python-setuptools-scm)) (home-page "https://stsciimagestats.readthedocs.io/en/latest/") (synopsis "Compute sigma-clipped statistics on data arrays") (description @@ -2724,37 +3235,43 @@ image processing functions: @code{xyxymatch}, @code{geomap}.") (define-public python-stcal (package (name "python-stcal") - (version "1.4.4") + (version "1.6.1") (source (origin (method url-fetch) (uri (pypi-uri "stcal" version)) (sha256 - (base32 "031ldihdmsdrwz4wl49bfk2bxmzbp1i3kidrw46xz936765zmnc0")))) + (base32 "1rwvzjpidz0sfp52mqgs25599hbvxyc4gdc1yk0kdm8aynhdwi82")))) (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) + (add-before 'build 'silent-check-for-opencv + (lambda _ + ;; XXX: Can't detect opencv-python version. The input opencv + ;; might not set the version correctly. + (substitute* "pyproject.toml" + ((".*opencv-python-headless.*") "")))) (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 opencv ;Provides OpenCV-Python + python-asdf python-astropy + python-gwcs python-numpy python-scipy)) (native-inputs - (list python-cython + (list python-cython-3 python-psutil python-pytest python-pytest-cov python-pytest-doctestplus python-pytest-openfiles + python-semantic-version python-setuptools-scm)) (home-page "https://github.com/spacetelescope/stcal") (synopsis "STScI tools and algorithms used in calibration pipelines") @@ -2764,19 +3281,21 @@ image processing functions: @code{xyxymatch}, @code{geomap}.") (define-public python-stdatamodels (package (name "python-stdatamodels") - (version "1.8.3") + (version "1.10.0") (source (origin (method url-fetch) (uri (pypi-uri "stdatamodels" version)) (sha256 - (base32 "0265xa9nrp6qp1z7v9kmnd3c8jc0dad2vzin657clk3rrsj2qll5")))) + (base32 "00zc7z3f2fjvmms2h7176wnzjb025v0aasc6fiib9055sk34bc94")))) (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") + #:test-flags + #~(list "-n" "auto" + ;; Disable tests requiring access to CRDS servers to download + ;; ~500MiB of data. + "-k" "not test_crds_selectors_vs_datamodel") #:phases #~(modify-phases %standard-phases (add-before 'check 'set-home @@ -2792,6 +3311,7 @@ image processing functions: @code{xyxymatch}, @code{geomap}.") (list python-crds python-pytest python-pytest-doctestplus + python-pytest-xdist python-scipy python-semantic-version python-setuptools-scm)) @@ -2834,13 +3354,13 @@ implementing calibration pipeline software.") (define-public python-stsynphot (package (name "python-stsynphot") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (pypi-uri "stsynphot" version)) (sha256 (base32 - "0qkdh47j84v7fzri7bmi1jcmggdqq0a8byamfm73d8mbz86v8sn4")))) + "15m3vy39mc7rh1mrxs8d2bs0bx5vv632m6wg8n15fqjzhadqy7j5")))) (build-system pyproject-build-system) (arguments (list @@ -2855,8 +3375,11 @@ implementing calibration pipeline software.") python-numpy python-scipy python-synphot)) - (native-inputs (list python-pytest python-pytest-astropy - python-pytest-astropy-header python-setuptools-scm)) + (native-inputs (list python-pytest + python-pytest-astropy + python-pytest-astropy-header + python-semantic-version + python-setuptools-scm)) (home-page "https://github.com/spacetelescope/stsynphot_refactor") (synopsis "Synthetic photometry using Astropy for HST and JWST") (description @@ -2870,24 +3393,24 @@ packages for HST.") (name "libnova") (version "0.16") (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://git.code.sf.net/p/libnova/libnova.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0icwylwkixihzni0kgl0j8dx3qhqvym6zv2hkw2dy6v9zvysrb1b")))) + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.code.sf.net/p/libnova/libnova.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0icwylwkixihzni0kgl0j8dx3qhqvym6zv2hkw2dy6v9zvysrb1b")))) (build-system gnu-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-git-version - (lambda _ - (substitute* "./git-version-gen" - (("/bin/sh") (which "sh"))) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-git-version + (lambda _ + (substitute* "./git-version-gen" + (("/bin/sh") (which "sh")))))))) (native-inputs (list autoconf automake libtool)) (synopsis "Celestial mechanics, astrometry and astrodynamics library") @@ -2984,7 +3507,7 @@ low quality ones") (define-public libpasastro (package (name "libpasastro") - (version "1.4.1") + (version "1.4.2") (source (origin (method git-fetch) @@ -2993,25 +3516,32 @@ low quality ones") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1h92p9ph3zi4w8krny1azd9wgwna2nf07ims983jcky1chkfm0is")))) + (base32 "1na3gyb3nzb5gdgccs1653j2gnz6w3v1mqzhyhkx3yqw8bs3q5x0")))) (build-system gnu-build-system) (arguments - `(#:tests? #f - #:make-flags - (list - ,(match (or (%current-target-system) (%current-system)) - ((or "aarch64-linux" "armhf-linux" "i686-linux" "x86_64-linux") - "OS_TARGET=linux") - (_ #f)) - ,(match (or (%current-target-system) (%current-system)) - ("i686-linux" "CPU_TARGET=i386") - ("x86_64-linux" "CPU_TARGET=x86_64") - ((or "armhf-linux" "aarch64-linux") "CPU_TARGET=armv7l") - (_ #f)) - (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:phases - (modify-phases %standard-phases - (delete 'configure)))) + (list + #:tests? #f ; no tests provided + #:make-flags + #~(list + ;; Keep OS detection for the case when Hurd would be suitable to try. + #$@(if (target-linux?) '("OS_TARGET=linux") '()) + ;; Enable buildtime CPU detection where supported, + ;; and set a suitable CPU target variable. + #$@(match (or (%current-target-system) + (%current-system)) + ("i686-linux" + '("CPU_TARGET=i386")) + ("x86_64-linux" + '("CPU_TARGET=x86_64")) + ;; There is no a case for RISCV in upstream, attempt to treat it + ;; as ARM. + ((or "armhf-linux" "aarch64-linux" "riscv64") + '("CPU_TARGET=armv7l")) + (_ '())) + (string-append "PREFIX=" #$output)) + #:phases + #~(modify-phases %standard-phases + (delete 'configure)))) (home-page "https://github.com/pchev/libpasastro") (synopsis "Interface to astronomy library for use from Pascal program") (description @@ -3023,13 +3553,13 @@ standard astronomy libraries: @item @code{libpasplan404.so}: Interface with Plan404 to compute planets position. @item @code{libpaswcs.so}: Interface with libwcs to work with FITS WCS. @item @code{libpasspice.so}: To work with NAIF/SPICE kernel. -@end itemize\n") +@end itemize") (license license:gpl2+))) (define-public libxisf (package (name "libxisf") - (version "0.2.10") + (version "0.2.11") (source (origin (method git-fetch) @@ -3038,7 +3568,7 @@ standard astronomy libraries: (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0q5qipn8887yhrk9pmi4fksxxmqas3w2aw2p194yhzkjapxk2k9h")))) + (base32 "02lnlsdg7f6pbcfk9amzh2k42wsb19d97yp2jq122lzivx9inwn1")))) (build-system cmake-build-system) (arguments (list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF"))) @@ -3145,6 +3675,8 @@ Mercator, Mollweide, Peters, polyconic, orthographic and rectangular.") (license license:gpl2+))) (define-public gpredict + ;; The latest tag, 2.3, has no major difference with 2.2.1 and is dated for + ;; 2018. Additionally, there is some activity on the master branch. (package (name "gpredict") (version "2.2.1") @@ -3171,14 +3703,32 @@ Mercator, Mollweide, Peters, polyconic, orthographic and rectangular.") (list gettext-minimal intltool pkg-config)) (inputs (list curl glib goocanvas gtk+)) - (home-page "http://gpredict.oz9aec.net/index.php") + (home-page "https://oz9aec.dk/gpredict/") (synopsis "Satellite tracking and orbit prediction application") (description "Gpredict is a real-time satellite tracking and orbit prediction application. It can track a large number of satellites and display their position and other data in lists, tables, maps, and polar plots (radar view). Gpredict can also predict the time of future passes for a satellite, and -provide you with detailed information about each pass.") +provide you with detailed information about each pass. + +Some core features of Gpredict include: + +@itemize +@item Tracking of a large number of satellites only limited by the physical +memory and processing power of the computer +@item Display the tracking data in lists, maps, polar plots and any +combination of these +@item Have many modules open at the same either in a notebook or in their own +windows. The modules can also run in full-screen mode +@item You can use many ground stations +@item Predict upcoming passes +@item Gpredict can run in real-time, simulated real-time (fast forward and +backward), and manual time control +@item Detailed information both the real time and non-real time modes +@item Doppler tuning of radios via Hamlib rigctld +@item Antenna rotator control via Hamlib rotctld +@end itemize") (license license:gpl2+))) (define-public sgp4 @@ -3256,7 +3806,7 @@ floating-point (no compression, LZW- or ZIP-compressed), FITS 8-bit, 16-bit, (define-public indi-2.0 (package (name "indi") - (version "2.0.4") + (version "2.0.6") (source (origin (method git-fetch) @@ -3265,7 +3815,7 @@ floating-point (no compression, LZW- or ZIP-compressed), FITS 8-bit, 16-bit, (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1pp72bqxrvdij47fqfrnyxwqw1w8prxvs1igjsazcw8ncbrdbbjc")))) + (base32 "0j1yr8wz6q6xi4dskv3yyhm0valsyfhcw1n8xpfgzbzbdzc8biyw")))) (build-system cmake-build-system) (arguments ;; TODO: fix failing tests on aarch64-system. @@ -3394,13 +3944,13 @@ Moon position, etc.") (define-public python-jplephem (package (name "python-jplephem") - (version "2.20") + (version "2.21") (source (origin (method url-fetch) (uri (pypi-uri "jplephem" version)) (sha256 - (base32 "1yp1l3n07849411099f976ps0pyv8jk8k5l9da9nhv54ir86v65v")))) + (base32 "0mcdhb22vwbyavcnkcwchj0cxnxsvaw5563v464ipwlm0rhln69l")))) (build-system pyproject-build-system) (arguments (list @@ -3425,13 +3975,13 @@ milliarcsecond).") (define-public python-jwst (package (name "python-jwst") - (version "1.12.5") + (version "1.13.4") (source (origin (method url-fetch) (uri (pypi-uri "jwst" version)) (sha256 (base32 - "0blrl00lz1snhcnr7j59nh05rnpqxdnfp8hhgagkr50h85q4smrn")))) + "0n5cfjayg15kf5p6pns7k2zfcldqz1464ndbldgzanc33fp9wnfz")))) (build-system pyproject-build-system) (arguments (list @@ -3538,7 +4088,7 @@ functions, so that they can be called with scalar or array inputs.") (define-public python-pynbody (package (name "python-pynbody") - (version "1.4.2") + (version "1.6.0") (source (origin (method git-fetch) ;PyPi doesn't have not prebuit version. @@ -3547,7 +4097,7 @@ functions, so that they can be called with scalar or array inputs.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1lwjs8vf3pc4a64c93fa5k6r276g1c60722swns2r10ig1s4wk0a")) + (base32 "00isg6nsqzgjqpkczwvrcmj3ndzav3bfzla0a72b44cgdj20wyv8")) (modules '((guix build utils))) (snippet ;; Symlink goes to not existing directory. @@ -3562,6 +4112,8 @@ functions, so that they can be called with scalar or array inputs.") ;; https://github.com/pynbody/pynbody/blob/ \ ;; f4bd482dc47532831b3ec115c7cb07149d61bfc5/ \ ;; .github/workflows/build-test.yaml#L41 + ;; See <https://github.com/pynbody/pynbody/issues/778> + "--ignore=tests/copy_on_access_test.py" "--ignore=tests/gravity_test.py" "--ignore=tests/adaptahop_test.py" "--ignore=tests/ahf_halos_test.py" @@ -3583,7 +4135,20 @@ functions, so that they can be called with scalar or array inputs.") "--ignore=tests/sph_smooth_test.py" "--ignore=tests/subfind_test.py" "--ignore=tests/subfindhdf_gadget4_test.py" - "--ignore=tests/tipsy_test.py") + "--ignore=tests/tipsy_test.py" + "-k" + (string-append + "not test_div_curl_smoothing" + " and not test_float_kd" + " and not test_kd_delete" + " and not test_kd_issue_88" + " and not test_kdtree_from_existing_kdtree" + " and not test_kdtree_shared_mem" + " and not test_neighbour_list" + " and not test_particles_in_sphere" + " and not test_periodic_smoothing" + " and not test_smooth" + " and not test_smooth_WendlandC2")) #:phases #~(modify-phases %standard-phases (add-before 'build 'set-compiler @@ -3647,36 +4212,54 @@ Features: (license license:expat))) (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 + ;; XXX: 2.0.0 was released in 2021 there are a lot of changes since that + ;; time and it failed to build with python-astropy 6.0.0, use the latest + ;; upstream commit for now. + (let ((commit "54e9e2a624910c4d177ca70f8e9fb8110c8fae5b") + (revision "0")) + (package + (name "python-pysynphot") + (version (git-version "2.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/spacetelescope/pysynphot") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09sivpfqilk86zp8k5wmrs4g48m4kypn34jcy95y5h4ygbn5zbzy")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" "2.0.0"))) + (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))) + (license license:bsd-3)))) (define-public python-sep (package @@ -3696,34 +4279,34 @@ spectra, and data.") (define-public python-suntime (package (name "python-suntime") - (version "1.2.5") - (source (origin - (method url-fetch) - (uri (pypi-uri "suntime" version)) - (sha256 - (base32 - "0ja64w293wjx76q3z18ikx4rdihwkbj6pnjpbs82ycyyzhfnbpz4")))) - (build-system python-build-system) - (propagated-inputs (list python-dateutil)) + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "suntime" version)) + (sha256 + (base32 "1kyd1r6zcs0jmh5gq74adrnb1h7dfr1mzjq4k4vbngfiga8gfd28")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-dateutil)) (home-page "https://github.com/SatAgro/suntime") (synopsis "Sunset and sunrise time calculation python library") (description - "Python library doing sunrise and sunset time calculation. - -Takes a WGS84 (GPS) latitude/longitude as input as well as an UTC or local -datetime object.") + "Python library doing sunrise and sunset time calculation. 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 "1.2.1") - (source (origin - (method url-fetch) - (uri (pypi-uri "synphot" version)) - (sha256 - (base32 - "10kcdg2gqmi1w2hsjx9hfizwbff3kll10s68hys13nzh4i8b7cc4")))) + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "synphot" version)) + (sha256 + (base32 "0a54bfrx9aar66040324sw9qdjz5lg67y28sjsxhyv9h3gppc7c0")))) (build-system pyproject-build-system) (arguments (list @@ -3742,9 +4325,17 @@ datetime object.") (lambda (port) (format port "[pytest] python_files = test_*.py")))))))) - (propagated-inputs (list python-astropy python-numpy python-scipy)) - (native-inputs (list python-pytest python-pytest-astropy - python-setuptools-scm)) + (propagated-inputs + (list python-astropy + python-dust-extinction + python-numpy + python-scipy + python-specutils )) + (native-inputs + (list python-pytest + python-pytest-astropy + python-semantic-version + python-setuptools-scm)) (home-page "https://github.com/spacetelescope/synphot_refactor") (synopsis "Synthetic photometry using Astropy") (description @@ -3756,13 +4347,13 @@ of the old packages.") (define-public python-tweakwcs (package (name "python-tweakwcs") - (version "0.8.3") + (version "0.8.6") (source (origin (method url-fetch) (uri (pypi-uri "tweakwcs" version)) (sha256 (base32 - "09bd8b77rpn641cwmkhcyzx43xkx3va83wdcb47wcqqa7qgx9f1m")))) + "1j75i02xzd36gp7pf6gks6nmp4ivi9cbphya4l69py5p62iaab99")))) (build-system pyproject-build-system) (propagated-inputs (list python-astropy python-gwcs @@ -3787,17 +4378,29 @@ 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-3.0 +(define-public python-asdf (package (name "python-asdf") - (version "3.0.1") + (version "3.1.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf" version)) (sha256 - (base32 "1jsk7b4mx04l0a08j832vnl309dba3gjnha9mbd61dzs9ridrfna")))) + (base32 "0fa6y3gmqc0y3nz0h68vq3a84pvx6gc5zp33wg8a4n9b4kipm464")))) (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "-n" "auto" "-p" "no:legacypath") + #:phases + #~(modify-phases %standard-phases + ;; ImportError: Error importing plugin " no:legacypath": No module + ;; named ' no:legacypath' + (add-before 'check 'fix-tests-setup + (lambda _ + (substitute* "pyproject.toml" + ((".*:legacypath.*") ""))))))) (native-inputs (list python-fsspec python-packaging @@ -3805,6 +4408,7 @@ between image and reference catalogs. Currently only aligning images with python-pytest python-pytest-doctestplus python-pytest-remotedata + python-pytest-xdist python-semantic-version python-setuptools-scm)) (propagated-inputs @@ -3825,56 +4429,71 @@ interchange format for scientific data. This package contains the Python implementation of the ASDF Standard.") (license license:bsd-3))) -(define-public python-asdf-2.15 - (package - (inherit python-asdf-3.0) - (version "2.15.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "asdf" version)) - (sha256 - (base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8")))) - (arguments - (list #:test-flags - #~(list "-k" (string-append - "not test_overwrite" - " and not test_tagging_scalars" - " and not test_info_command" - " and not test_array_inline_threshold_recursive")))) - (native-inputs - (modify-inputs (package-native-inputs python-asdf-3.0) - (prepend python-astropy python-pytest-openfiles))) - (propagated-inputs - (modify-inputs (package-propagated-inputs python-asdf-3.0) - (prepend python-jsonschema python-importlib-resources))))) - -(define-public python-asdf - ;; Default version of ASDF.. - python-asdf-2.15) +(define-public python-asdf-compression + ;; TODO: No release, change to tag when it's ready. + (let ((commit "57cc7e76fb4163be3e99fb740b36b5ec5ae96e49") + (revision "0")) + (package + (name "python-asdf-compression") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/asdf-format/asdf-compression") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1g6iiyls950k66dmd0pbqqdvz74kksc4j191n0ik6fhjnkiwifgs")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" "0.0.1")))))) + (native-inputs + (list python-numpy + python-pytest + python-semantic-version + python-setuptools-scm)) + (propagated-inputs + (list python-asdf + python-blosc + python-lz4 + python-zstandard)) + (home-page "https://github.com/asdf-format/asdf-fits-schemas") + (synopsis "ASDF extension to support various compression algorithms") + (description + "This package includes a plugin for the Python library ASDF to add +support for reading and writing various compression algorithms including: +@url{https://www.blosc.org/python-blosc/reference.html,Blosc}, +@url{https://python-lz4.readthedocs.io/en/stable/lz4.frame.html,LZ4 Frame}, +@url{http://facebook.github.io/zstd/,Zstandard}.") + (license license:bsd-3)))) (define-public python-asdf-standard (package (name "python-asdf-standard") - (version "1.0.3") + (version "1.1.1") (source (origin (method url-fetch) (uri (pypi-uri "asdf_standard" version)) (sha256 (base32 - "0i7xdjwn5prg2hcnf1zhw57mszc68jjr5sv4rimpzcg7f2dgzn5g")))) + "00k1fzc8y8j0ar1chq0nqyfw8bgkkjgrkm32ibn0kz2vn715nlq1")))) (build-system pyproject-build-system) (arguments - (list #:phases #~(modify-phases %standard-phases - (add-before 'check 'remove-blocking-tests - (lambda _ - ;; Remove tests require python-asdf where - ;; python-asdf require python-asdf-standard, - ;; break circular dependencies. - (for-each delete-file - (list "tests/test_manifests.py" - "tests/test_integration.py"))))))) + (list + #:test-flags + ;; Remove tests requiring python-asdf where python-asdf requires + ;; python-asdf-standard, break circular dependencies. + #~(list "--ignore=tests/test_asdf_schema.py" + "--ignore=tests/test_integration.py" + "--ignore=tests/test_manifests.py" + "--ignore=tests/test_yaml_schema.py"))) (native-inputs (list python-astropy python-jsonschema python-pypa-build @@ -3897,13 +4516,13 @@ up-front for extensibility.") (define python-asdf-transform-schemas (package (name "python-asdf-transform-schemas") - (version "0.3.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf_transform_schemas" version)) (sha256 - (base32 "1midgn575970p5cnsh9y6bz77fjr392b5nfxb3z0id6c49xzzwhc")))) + (base32 "0as6dcf9dmxjh24gwdmqwbbrk56fhgsmzwi7af4llwvm4mw4rkw2")))) (build-system pyproject-build-system) (arguments ;; Dependency cycle with python-asdf @@ -3921,16 +4540,23 @@ package such as asdf-astropy.") (define python-asdf-coordinates-schemas (package (name "python-asdf-coordinates-schemas") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf_coordinates_schemas" version)) (sha256 - (base32 "1x6mipg76c6qldq8s2p2wpsq0cpr9b5krp62xskljdz1f84abyg3")))) + (base32 "0kk0rlzv0kkcw6fiwvps4n0x05867xc9hxyyzica31zcvhan12y9")))) (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "-n" "auto"))) (native-inputs - (list python-pytest python-semantic-version python-setuptools-scm)) + (list python-pytest + python-pytest-xdist + python-semantic-version + python-setuptools-scm)) (propagated-inputs (list python-asdf)) (home-page "https://github.com/asdf-format/asdf-coordinates-schemas") @@ -3942,8 +4568,8 @@ install an implementation package such as asdf-astropy.") (define python-asdf-fits-schemas ;; TODO: No release, change to tag when it's ready. - (let ((commit "572bb370d777f3a325b25c1af9d76e1b7d27dcea") - (revision "0")) + (let ((commit "d1b5e7a12a49fe61d43855045bab106be34cd252") + (revision "1")) (package (name "python-asdf-fits-schemas") (version (git-version "0.0.1" revision commit)) @@ -3956,7 +4582,7 @@ install an implementation package such as asdf-astropy.") (file-name (git-file-name name version)) (sha256 (base32 - "1yqnzd0gcrdfl0jqm8m8kz5fd36i8lgh7xkglmp1chsi1cc6mkz2")))) + "1h2xbk9c9l2959i3sdnwviv3z0hp1f0lba2vz9hpzgcm46qadqp8")))) (build-system pyproject-build-system) (arguments (list @@ -3977,8 +4603,8 @@ install an implementation package such as asdf-astropy.") (define python-asdf-time-schemas ;; TODO: No release, change to tag when it's ready. - (let ((commit "e9174083d9cfd3c6f7ded9eeb360d99ccb8d9d18") - (revision "2")) + (let ((commit "a3062066ee70f1b934f7339d1ce96a5c5f61f055") + (revision "3")) (package (name "python-asdf-time-schemas") (version (git-version "0.0.1" revision commit)) @@ -3991,7 +4617,7 @@ install an implementation package such as asdf-astropy.") (file-name (git-file-name name version)) (sha256 (base32 - "1i40hcxp8sds2zq939fwczjlshfqb9r9pnzy3a44c3wqdbwhcbdb")))) + "1i8lm2d18r6fadsch52dxc2zp1swkfa8w40s03albn7p290n4a97")))) (build-system pyproject-build-system) (arguments (list @@ -4015,14 +4641,14 @@ install an implementation package such as asdf-astropy.") (define python-asdf-unit-schemas (package (name "python-asdf-unit-schemas") - (version "0.1.0") + (version "0.2.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf_unit_schemas" version)) (sha256 (base32 - "16grpx3a9h0v1wirp0zqrfsxm867v5c0xyr98pylzziy45kqvds2")))) + "0h24gvm1wip4gh3fw5ki8kwnvcy8gw6b6pajw3i1zvriamdw95fr")))) (build-system pyproject-build-system) (arguments ;; Dependency cycle with python-asdf @@ -4034,21 +4660,49 @@ install an implementation package such as asdf-astropy.") (description "This package provides ASDF schemas for validating unit tags.") (license license:bsd-3))) +(define-public python-asdf-zarr + (package + (name "python-asdf-zarr") + (version "0.0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asdf_zarr" version)) + (sha256 + (base32 "0ax7c9xarh6fi2yxm1z2p90mc3d57q23a7wc8av30xg8ririrl4s")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-asdf python-fsspec python-zarr)) + (native-inputs + (list python-pytest python-semantic-version python-setuptools-scm)) + (home-page "https://github.com/asdf-format/asdf-zarr") + (synopsis "Asdf extension to support Zarr arrays") + (description + "This package includes an extension for the Python library asdf to add +support for reading and writing chunked +@url{https://zarr.readthedocs.io/en/stable/,Zarr} arrays, a file storage +format for chunked, compressed, N-dimensional arrays based on an open-source +specification.") + (license license:bsd-3))) + (define-public python-asdf-astropy (package (name "python-asdf-astropy") - (version "0.4.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf-astropy" version)) (sha256 - (base32 "1difb2y1hlalbhrw8znwmmc0vzgg44zfsay98lpllb7y0536fas6")))) + (base32 "0cxwknkjkgiavwmsz3vzk88c3spdi1cj4kwp62hgj92g2mh5k0zh")))) (build-system pyproject-build-system) (arguments - (list #:phases #~(modify-phases %standard-phases - (add-before 'check 'set-home-env - (lambda _ (setenv "HOME" "/tmp")))))) + (list + #:test-flags + #~(list "-n" "auto") + #:phases #~(modify-phases %standard-phases + (add-before 'check 'set-home-env + (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs (list python-coverage python-h5py @@ -4074,18 +4728,27 @@ Astropy objects.") (define python-asdf-wcs-schemas (package (name "python-asdf-wcs-schemas") - (version "0.1.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf_wcs_schemas" version)) (sha256 - (base32 "0khyab9mnf2lv755as8kwhk3lqqpd3f4291ny3b9yp3ik86fzhz1")))) + (base32 "1d08ng890xc1ilf3y1hrimx09x990wvg9g18n0ijwvpilnw49fy0")))) (build-system pyproject-build-system) + (arguments + (list + #:test-flags #~(list "tests"))) (native-inputs - (list python-pytest python-setuptools-scm python-semantic-version)) + (list python-asdf + python-pytest + python-pytest-openfiles + python-semantic-version + python-setuptools-scm)) (propagated-inputs - (list python-asdf)) + (list python-asdf-coordinates-schemas + python-asdf-standard + python-asdf-transform-schemas)) (home-page "https://github.com/asdf-format/asdf-wcs-schemas") (synopsis "ASDF WCS Schemas") (description @@ -4097,13 +4760,13 @@ install an implementation package such as gwcs.") (define-public python-gwcs (package (name "python-gwcs") - (version "0.19.0") + (version "0.21.0") (source (origin (method url-fetch) (uri (pypi-uri "gwcs" version)) (sha256 - (base32 "1f3h41aq4nwcl6k80jb9s8shn2mhvz32mx9qhcm1xmcqrflqyf52")))) + (base32 "1fn5l4v236bl7xqi1is40c2q57dji8by98iwqcndfnmjwqf7zllc")))) (build-system pyproject-build-system) (native-inputs (list python-jsonschema @@ -4135,20 +4798,23 @@ default) to world coordinates.") (define-public python-rad (package (name "python-rad") - (version "0.18.0") + (version "0.19.0") (source (origin (method url-fetch) (uri (pypi-uri "rad" version)) (sha256 (base32 - "1wgnbhldgq0j55yzg33y11vd5k5nzwckiccxywvmq518qh19pky5")))) + "0cp3nrv1vq3g61zx6dq36vdlxd5i8g52vg4hwpxakmwvqvc8p3gd")))) (build-system pyproject-build-system) (arguments (list - ;; XXX: Tests introduce dependencies cycle, breaking it by disable them. + ;; Ignore tests requiring python-crds to break cycle: ;; python-rad -> python-roman-datamodels -> python-crds -> python-rad - #:tests? #f)) - (native-inputs (list python-semantic-version python-setuptools-scm)) + #:test-flags #~(list "--ignore=tests/test_schemas.py"))) + (native-inputs + (list python-pytest + 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") @@ -4163,13 +4829,13 @@ Grace Roman Space Telescope.") (define-public python-radio-beam (package (name "python-radio-beam") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (pypi-uri "radio-beam" version)) (sha256 - (base32 "19c6gmm1wvyp5nn1yfbzl428rkysdq273j2yaarxpivv7cwj7qjk")))) + (base32 "0dg6vqdhmzh47awdkkcbf455gw6if2qwxyhcqbq2dkhbwsx680gc")))) (build-system pyproject-build-system) (propagated-inputs (list python-astropy @@ -4194,19 +4860,58 @@ channels @end itemize") (license license:bsd-3))) +(define-public python-radiospectra + (package + (name "python-radiospectra") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "radiospectra" version)) + (sha256 + (base32 "0nw71a7i875lfwbwhpc80nvwalb7iq3fynfkbngx6f6jb3v10dgs")))) + (build-system pyproject-build-system) + (arguments + (list + #: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")))))) + (propagated-inputs + (list python-cdflib + python-matplotlib + python-numpy + python-scipy + python-sunpy)) + (native-inputs + (list python-pytest-astropy + python-setuptools-scm + python-sunpy-soar)) + (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-roman-datamodels (package (name "python-roman-datamodels") - (version "0.18.0") + (version "0.19.0") (source (origin (method url-fetch) (uri (pypi-uri "roman_datamodels" version)) (sha256 (base32 - "0crlmd99p2nyqmrbykdqqng7v8zb4sibm8j9aqrq3ppak3r3r7q1")))) + "1ym06rj637fq9gxncdrn3phplk5djrzdwqghszis0di1dvsrif4j")))) (build-system pyproject-build-system) (arguments (list + #:test-flags + #~(list "-n" "auto") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'set-env @@ -4223,6 +4928,7 @@ channels (native-inputs (list python-pytest python-pytest-doctestplus python-pytest-env + python-pytest-xdist python-semantic-version python-setuptools-scm)) (home-page "https://github.com/spacetelescope/roman_datamodels") @@ -4275,20 +4981,23 @@ astronomical images, especially when there is no WCS information available.") (define-public python-skyfield (package (name "python-skyfield") - (version "1.46") + (version "1.48") (source (origin (method url-fetch) (uri (pypi-uri "skyfield" version)) (sha256 - (base32 "1r4kpsh1pa4h3diyxy3gyapp0rykfjdqmn5w348a2ck2qkdlx997")))) + (base32 "1qaz0k0lkni3y423r66mkvj99bx08qa9xgqp3cs2df70cmdz30cb")))) (build-system python-build-system) (arguments - ;; NOTE: (Sharlatan-20210207T163305+0000): tests depend on custom test - ;; framework https://github.com/brandon-rhodes/assay + ;; XXX: Tests depend on custom test framework + ;; https://github.com/brandon-rhodes/assay `(#:tests? #f)) - (inputs - (list python-certifi python-jplephem python-numpy python-sgp4)) + (propagated-inputs + (list python-certifi + python-jplephem + python-numpy + python-sgp4)) (home-page "https://rhodesmill.org/skyfield/") (synopsis "Astronomy for Python") (description |