diff options
Diffstat (limited to 'gnu/packages/astronomy.scm')
| -rw-r--r-- | gnu/packages/astronomy.scm | 207 |
1 files changed, 122 insertions, 85 deletions
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 5b9434fb33..e5c318c8bf 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -182,7 +182,7 @@ reused in several astronomical applications, such as @code{wsclean}, (define-public calceph (package (name "calceph") - (version "3.5.1") + (version "3.5.2") (source (origin (method url-fetch) @@ -190,7 +190,7 @@ 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 "078wn773pwf4pg9m0h0l00g4aq744pq1rb6kz6plgdpzp3hhpk1k")))) + (base32 "1rnjlaiii4j0agbj4k242p212bqqmqdqa0lni6c3bnhgfnrbjfp4")))) (build-system gnu-build-system) (native-inputs (list gfortran)) @@ -217,7 +217,7 @@ moment, supported SPICE files are: (define-public calcmysky (package (name "calcmysky") - (version "0.3.0") + (version "0.3.1") (source (origin (method git-fetch) @@ -226,7 +226,7 @@ moment, supported SPICE files are: (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1lgn937px4am0lggniwby1f1dl3v4l3iigq72rl9rlhx58zv4lj1")))) + (base32 "14jbaf9m9wig2bs7a531dvpmdkqpd09lmyvjvj1s0mhgh9g0x9m2")))) (build-system cmake-build-system) (arguments (list #:configure-flags @@ -531,13 +531,13 @@ mining in astronomy.") (define-public python-fitsio (package (name "python-fitsio") - (version "1.1.8") + (version "1.1.10") (source (origin (method url-fetch) (uri (pypi-uri "fitsio" version)) (sha256 - (base32 "1y80hgvlkjz1bijfyb2j03853yc1kc63yrf9ab7as31ad2r6kxb1")) + (base32 "0dv2vjj8qn3rq5sr99x5yjjch5h867c8q7zh73i67dzdsk7ix0jf")) (modules '((guix build utils))) (snippet ;; Remove the bundled cfitsio @@ -545,7 +545,7 @@ mining in astronomy.") (delete-file-recursively "cfitsio3490") (substitute* "MANIFEST.in" (("recursive-include cfitsio3490.*$\n") "")))))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments (list #:phases @@ -562,10 +562,16 @@ mining in astronomy.") (("self.system_fitsio_libdir = None") "pass") (("self.use_system_fitsio") "True") (("self.system_fitsio_includedir") includedir) - (("self.system_fitsio_libdir") libdir)))))))) - (inputs (list curl)) + (("self.system_fitsio_libdir") libdir))))) + (add-before 'check 'build-extensions + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (native-inputs + (list python-pytest)) + (inputs + (list curl cfitsio)) (propagated-inputs - (list python-numpy cfitsio)) + (list python-numpy)) (home-page "https://github.com/esheldon/fitsio") (synopsis "Python library to read from and write to FITS files") @@ -917,7 +923,7 @@ from Stark Labs.") (define-public sextractor (package (name "sextractor") - (version "2.25.0") + (version "2.28.0") (source (origin (method git-fetch) @@ -926,29 +932,33 @@ from Stark Labs.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0q69n3nyal57h3ik2xirwzrxzljrwy9ivwraxzv9566vi3n4z5mw")))) + (base32 "15v7brjiraj2rdyxiidcgb58b3dqzdd363j31cjrfqhd1wc8ii5j")))) (build-system gnu-build-system) ;; NOTE: (Sharlatan-20210124T103117+0000): Building with `atlas' is failing ;; due to missing shared library which required on configure phase. Switch ;; build to use `openblas' instead. It requires FFTW with single precision ;; `fftwf'. (arguments - `(#:configure-flags - (list - "--enable-openblas" - (string-append - "--with-openblas-libdir=" (assoc-ref %build-inputs "openblas") "/lib") - (string-append - "--with-openblas-incdir=" (assoc-ref %build-inputs "openblas") "/include") - (string-append - "--with-fftw-libdir=" (assoc-ref %build-inputs "fftw") "/lib") - (string-append - "--with-fftw-incdir=" (assoc-ref %build-inputs "fftw") "/include")))) + (list + #:configure-flags + #~(list + "--enable-openblas" + (string-append "--with-cfitsio-incdir=" + #$(this-package-input "cfitsio") "/include") + (string-append "--with-cfitsio-libdir=" + #$(this-package-input "cfitsio") "/lib") + (string-append "--with-fftw-incdir=" + #$(this-package-input "fftwf") "/include") + (string-append "--with-fftw-libdir=" + #$(this-package-input "fftwf") "/lib") + (string-append "--with-openblas-incdir=" + #$(this-package-input "openblas") "/include") + (string-append "--with-openblas-libdir=" + #$(this-package-input "openblas") "/lib")))) (native-inputs (list autoconf automake libtool)) (inputs - `(("openblas" ,openblas) - ("fftw" ,fftwf))) + (list cfitsio fftwf openblas)) (home-page "https://www.astromatic.net/software/sextractor") (synopsis "Extract catalogs of sources from astronomical images") (description @@ -998,7 +1008,7 @@ image formats.") (define-public splash (package (name "splash") - (version "3.7.2") + (version "3.8.2") (source (origin (method git-fetch) (uri (git-reference @@ -1006,7 +1016,7 @@ image formats.") (commit (string-append "v" version)))) (sha256 (base32 - "0nsm6rk0bi99xz7wclk0zy4bpqf0qcsdln5cdjb30lhpf37i2fpa")) + "0y6l135g0a3hvvh8w8sfdh1kfq2g0gbp0dgjhnmwid8bwwcjvw8v")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (arguments @@ -1343,13 +1353,13 @@ accurately in real time at any rate desired.") (define-public python-astropy (package (name "python-astropy") - (version "5.2.2") + (version "5.3.1") (source (origin (method url-fetch) (uri (pypi-uri "astropy" version)) (sha256 - (base32 "170ddflli35mvhf6pla7aizfw8a7ckq66g1mi1br99dx2r3y7ag6")) + (base32 "0x4dh7wx9sn1gy6sl2d54zsd24cgfjwrlk6kfrwpzzrmbsv22lwv")) (modules '((guix build utils))) (snippet '(begin @@ -1358,9 +1368,10 @@ accurately in real time at any rate desired.") (for-each delete-file-recursively '("ply" "configobj"))) ;; Remove cextern bundles. Check bundled versions against available ;; in Guix in the future update of astropy. + ;; Linking against an external cfitsio version has been removed, + ;; see https://github.com/astropy/astropy/pull/14311 (with-directory-excursion "cextern" - (for-each delete-file-recursively '("cfitsio" "expat" "wcslib"))) - #t)))) + (for-each delete-file-recursively '("expat" "wcslib"))))))) (build-system python-build-system) (arguments `(#:phases @@ -1427,7 +1438,7 @@ accurately in real time at any rate desired.") python-skyfield python-timezonefinder)) (inputs - (list cfitsio expat wcslib)) + (list expat wcslib)) (propagated-inputs (list python-configobj python-numpy @@ -1600,15 +1611,18 @@ Herschel.") (define-public python-ccdproc (package (name "python-ccdproc") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (pypi-uri "ccdproc" version)) (sha256 - (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1")))) + (base32 "186plgfhrj7wivs053y65jlv1x33y8ii31jdr2rm4s6pl0j7x29z")))) (build-system pyproject-build-system) - (native-inputs (list python-memory-profiler python-pytest-astropy)) + (native-inputs + (list python-memory-profiler + python-pytest-astropy + python-semantic-version)) (propagated-inputs (list python-astropy python-astroscrappy @@ -1626,7 +1640,7 @@ bad pixel tracking throughout the reduction process.") (define-public python-cdflib (package (name "python-cdflib") - (version "0.4.9") + (version "1.0.5") (source (origin (method git-fetch) ; no tests in pypi archive @@ -1635,7 +1649,7 @@ bad pixel tracking throughout the reduction process.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1k557najk7ln293zwyghnhw48ays3nqf9s94kibsc7r70c2q7p08")))) + (base32 "1pkda9gmpjhbqxl2jj5q9rjx77lv5c908mgf20lw3rz4nvfaa2wn")))) (build-system pyproject-build-system) (arguments (list #:phases @@ -1753,13 +1767,13 @@ Cesium.") (define-public python-drms (package (name "python-drms") - (version "0.6.3") + (version "0.6.4") (source (origin (method url-fetch) (uri (pypi-uri "drms" version)) (sha256 - (base32 "1b0w350y4wbgyy19zcf28xbb85mqq6gnhb6ppibbc4hbn2ixbcvj")))) + (base32 "0mkrmr55fgca441z7hvsyri6x9cjsh0sfas3hrj0k1k10k8vszbw")))) (build-system python-build-system) (arguments (list @@ -1914,23 +1928,29 @@ the easy construction of interactive matplotlib widget based animations.") (uri (pypi-uri "photutils" version)) (sha256 (base32 "1bq4ma402lpa5d6l85awlc23kasxf40nq8hgi3iyrilnfikan0jz")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:test-target "pytest" - #:phases - (modify-phases %standard-phases - ;; This file is opened in both install and check phases. - (add-before 'install 'writable-compiler - (lambda _ (make-file-writable "photutils/_compiler.c"))) - (add-before 'check 'writable-compiler - (lambda _ (make-file-writable "photutils/_compiler.c")))))) + (list + #:phases + #~(modify-phases %standard-phases + ;; This file is opened in both install and check phases. + (add-before 'install 'writable-compiler + (lambda _ (make-file-writable "photutils/_compiler.c"))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running + ;; the tests. If it's not build it fails with error: + ;; + ;; ModuleNotFoundError: No module named + ;; 'photutils.geometry.circular_overlap' + (make-file-writable "photutils/_compiler.c") + (invoke "python" "setup.py" "build_ext" "--inplace")))))) (propagated-inputs (list python-astropy python-numpy)) (native-inputs (list python-cython python-extension-helpers python-pytest-astropy - python-pytest-runner python-setuptools-scm)) (home-page "https://github.com/astropy/photutils") (synopsis "Source detection and photometry") @@ -2121,13 +2141,13 @@ Virtual observatory (VO) using Python.") (define-public python-reproject (package (name "python-reproject") - (version "0.10.0") + (version "0.11.0") (source (origin (method url-fetch) (uri (pypi-uri "reproject" version)) (sha256 - (base32 "1ha0a1ja7k09ysd05adffgsapfwzc6m6az34a0av2mhmlwy4zb1q")))) + (base32 "0p07qlqinb826m4n5b5invyfyv4z750sai2caqaf598mgj04l61p")))) (build-system pyproject-build-system) (arguments (list @@ -2150,21 +2170,26 @@ Virtual observatory (VO) using Python.") (lambda _ (setenv "HOME" (getcwd))))))) (propagated-inputs - (list python-astropy + (list python-asdf + python-astropy python-astropy-healpix + python-click + python-cloudpickle + python-dask + python-fsspec + python-gwcs python-numpy - python-scipy)) + python-pyvo + python-scipy + python-shapely + python-zarr)) (native-inputs - (list python-asdf - python-cython + (list python-cython python-extension-helpers - python-gwcs python-pytest-astropy - python-pyvo python-semantic-version python-pytest - python-setuptools-scm - python-shapely)) + python-setuptools-scm)) (home-page "https://reproject.readthedocs.io") (synopsis "Astronomical image reprojection in Python") (description @@ -2206,13 +2231,13 @@ orbits described in TLE files.") (define-public python-sunpy (package (name "python-sunpy") - (version "4.1.5") + (version "5.0.0") (source (origin (method url-fetch) (uri (pypi-uri "sunpy" version)) (sha256 - (base32 "1j5g0ivsrc5ji9s7jc3kcbi2injfs3y31pm3priycljwcsxspkpm")))) + (base32 "1w75yc8az86pwbf79h083j4kc2ycfk76ky5kzlmcwgp0ih23mhym")))) (build-system pyproject-build-system) (arguments (list @@ -2220,7 +2245,10 @@ orbits described in TLE files.") #~(list "-k" (string-append ;; XXX: Failed: DID NOT RAISE <class 'ModuleNotFoundError'> "not test_main_nonexisting_module" - " and not test_main_stdlib_module")) + " and not test_main_stdlib_module" + ;; XXX: packaging.version.InvalidVersion: Invalid version: 'unknown' + " and not test_read_cdf" + " and not test_read_empty_cdf")) #:phases #~(modify-phases %standard-phases (add-before 'install 'writable-compiler @@ -2466,13 +2494,13 @@ image processing functions: @code{xyxymatch}, @code{geomap}.") (define-public python-stcal (package (name "python-stcal") - (version "1.3.7") + (version "1.4.2") (source (origin (method url-fetch) (uri (pypi-uri "stcal" version)) (sha256 (base32 - "0yy0pwi3krvhxfby6nzgpgyz5il3sl1j29ihbk81dh9fdh3ys2n9")))) + "163vyqcd9qv2knf8jik8y449z7ljl2lvbd7im82bq61prgi3z2hj")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases @@ -2495,13 +2523,13 @@ image processing functions: @code{xyxymatch}, @code{geomap}.") (define-public python-stdatamodels (package (name "python-stdatamodels") - (version "1.5.0") + (version "1.7.1") (source (origin (method url-fetch) (uri (pypi-uri "stdatamodels" version)) (sha256 (base32 - "1lssz5mnkzgraqa9mdg1w39scsikymcp3zpmsjb146r0pqnwnpzw")))) + "0d7a27myl3xgri3z7yx26mr4dpqnlfhdh5i2ql2miwymi0mx3ij5")))) (build-system pyproject-build-system) (arguments (list @@ -2759,9 +2787,7 @@ standard astronomy libraries: (define-public libxisf (package (name "libxisf") - ;; TODO: v0.2.2 (current latest) failed to build on configure phase, issue - ;; was open directly with author as he hosts source on seflhosted gitea. - (version "0.2.1") + (version "0.2.8") (source (origin (method git-fetch) @@ -2770,7 +2796,7 @@ standard astronomy libraries: (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0fz9mmj1nz5v7hlr53q8na7khadfn1hm0d1gfpzzw3167bqpy2xv")))) + (base32 "1j2bg53hrr2yc55qa6549vcpj7qjnwmxjcdgc98w3ygnrjy7n7v0")))) (build-system cmake-build-system) (arguments (list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF"))) @@ -3216,26 +3242,32 @@ exposures and high-level data products (mosaics, extracted spectra, etc.).") (define-public python-pyerfa (package (name "python-pyerfa") - (version "2.0.0.1") + (version "2.0.0.3") (source (origin (method url-fetch) (uri (pypi-uri "pyerfa" version)) (sha256 - (base32 "0c6y1rm51kj8ahbr1vwbswck3ix77dc3zhc2fkg6w7iczrzn7m1g")) + (base32 "0f8zykzxjsiwv5ibdn5asla2ng2xl0xdkrcrrd61j31mb3xbnzyp")) (modules '((guix build utils))) (snippet - '(begin - ;; Remove bundled submodule library. - (delete-file-recursively "liberfa") - #t)))) - (build-system python-build-system) + #~(begin + ;; Remove bundled submodule library. + (delete-file-recursively "liberfa"))))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'build 'use-system-liberfa - (lambda _ - (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1")))))) + (list + ;; Disable only one failing test: + ;; AttributeError: __warningregistry__ + #:test-flags #~(list "-k" "not test_errwarn_reporting") + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'use-system-liberfa + (lambda _ + (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1"))) + (add-before 'check 'build-extensions + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace")))))) (native-inputs (list python-pytest-doctestplus python-pytest python-setuptools-scm)) (inputs @@ -3381,13 +3413,13 @@ datetime object.") (define-public python-synphot (package (name "python-synphot") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (pypi-uri "synphot" version)) (sha256 (base32 - "02pjp1bnbyq7zi1bxqv56nif4ijd8fscmnn9ldrs8yvgsbmgdvlc")))) + "10kcdg2gqmi1w2hsjx9hfizwbff3kll10s68hys13nzh4i8b7cc4")))) (build-system pyproject-build-system) (arguments (list @@ -3854,7 +3886,12 @@ pipelines.") (sha256 (base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb")))) (build-system pyproject-build-system) - (native-inputs (list python-astropy python-ccdproc python-pillow)) + (native-inputs + (list python-astropy + python-ccdproc + python-pillow + python-pytest + python-semantic-version)) (propagated-inputs (list python-bottleneck python-numpy |