diff options
Diffstat (limited to 'gnu/packages/astronomy.scm')
| -rw-r--r-- | gnu/packages/astronomy.scm | 781 |
1 files changed, 659 insertions, 122 deletions
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 16752367be..4c963c9c91 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -42,6 +42,7 @@ #:use-module (gnu packages bison) #:use-module (gnu packages boost) #:use-module (gnu packages build-tools) + #:use-module (gnu packages c) #:use-module (gnu packages certs) #:use-module (gnu packages check) #:use-module (gnu packages cmake) @@ -51,6 +52,7 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) + #:use-module (gnu packages freedesktop) #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages gettext) @@ -353,7 +355,7 @@ moment, supported SPICE files are: (define-public calcmysky (package (name "calcmysky") - (version "0.3.4") + (version "0.3.5") (source (origin (method git-fetch) @@ -362,7 +364,7 @@ moment, supported SPICE files are: (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0blp1w1bghskfi0ysds51r2a7nvvjc9yqp5nlf8l3gciig97nhdg")))) + (base32 "03h93jxpxfa7gy4z3pvh8xy60z2f5n5id9k2wkzmf81zrvakbvgv")))) (build-system cmake-build-system) (arguments (list #:configure-flags @@ -434,7 +436,6 @@ rendering of the atmosphere model and examine its properties. #:configure-flags #~(list "-DBUILD_PYTHON3=ON" "-DBUILD_PYTHON=OFF" - "-DBUILD_TESTING=TRUE" "-DUSE_HDF5=ON" "-DUSE_OPENMP=OFF" "-DUSE_THREADS=ON" @@ -1359,14 +1360,16 @@ standard astronomy libraries: #:make-flags #~(list (string-append "CC=" #$(cc-for-target)) (string-append "PREFIX=" #$output)) - #:test-target "test" + #:modules '((guix build cmake-build-system) + ((guix build gnu-build-system) #:prefix gnu:) + (guix build utils)) #:phases #~(modify-phases %standard-phases - (add-before 'check 'pre-check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (chdir "../source") - (setenv "CC" #$(cc-for-target)))))))) + (replace 'check + (lambda* (#:rest args) + (with-directory-excursion "../source" + (apply (assoc-ref gnu:%standard-phases 'check) + #:test-target "test" args))))))) (native-inputs (list python-wrapper)) (home-page "https://github.com/kbarbary/sep") @@ -1809,13 +1812,13 @@ Main features: (define-public python-asdf (package (name "python-asdf") - (version "4.2.0") + (version "4.3.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf" version)) (sha256 - (base32 "1xvcli823yqnyylxs817l36w1x9223j1y00f20hfp3g1rl80m86b")))) + (base32 "0z88vzk3z9cdfafv8rbw4l6kz6panxamd21zafs6hj0w3zxpa7cn")))) (build-system pyproject-build-system) (arguments (list @@ -1921,8 +1924,8 @@ Astropy objects.") (define-public python-asdf-compression ;; TODO: No release, change to tag when it's ready. - (let ((commit "68ed09f670a9f1c5f81b3db88ef594e87bdbc9fd") - (revision "2")) + (let ((commit "579c153a453dc0d650f2cca01d2c5dae0dc02051") + (revision "3")) (package (name "python-asdf-compression") (version (git-version "0.0.1" revision commit)) @@ -1934,7 +1937,7 @@ Astropy objects.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0644hn0pris8f872rbb5bklsw2ialryf4sicwshgjs3zcsyxnjf8")))) + (base32 "03cq4x40xy5micipg4qp2j0v1h6hxqrrzpzyjybm6j82zi92c770")))) (build-system pyproject-build-system) (arguments (list @@ -1946,7 +1949,7 @@ Astropy objects.") (native-inputs (list python-numpy python-pytest - python-setuptools + python-setuptools-next python-setuptools-scm python-wheel)) (propagated-inputs @@ -2512,13 +2515,13 @@ astronomy and astrophysics.") (define-public python-astropy-iers-data (package (name "python-astropy-iers-data") - (version "0.2025.6.16.0.38.47") + (version "0.2025.7.21.0.41.39") (source (origin (method url-fetch) (uri (pypi-uri "astropy_iers_data" version)) (sha256 - (base32 "08bifygdnifcmrk3wqn8k0fi31mj8j3zxak9r70sbf06cnbq9jaq")))) + (base32 "14qa0h3jx5iawmb0cpwak1wna0jhjsi18zm4wmdicyb9kly7b0p4")))) (build-system pyproject-build-system) (arguments (list #:tests? #f)) ; no tests @@ -2796,13 +2799,13 @@ Origins Spectrograph}.") (define-public python-camb (package (name "python-camb") - (version "1.6.0") + (version "1.6.2") (source (origin (method url-fetch) (uri (pypi-uri "camb" version)) (sha256 - (base32 "1aqafmc7qf11jwc3y418hsx27m48gd9mb98097kr3db0gylkvxxb")))) + (base32 "1h9zdfsk14vx8hwpsvgs351cid1waggd47hj0yhy69djz935rgq5")))) (build-system pyproject-build-system) (arguments (list @@ -2817,7 +2820,7 @@ Origins Spectrograph}.") (native-inputs (list gfortran python-packaging - python-setuptools + python-setuptools-next python-wheel which)) ; for fortran/Makefile (propagated-inputs @@ -2908,13 +2911,13 @@ astronomy library.") (define-public python-ccdproc (package (name "python-ccdproc") - (version "2.4.3") + (version "2.5.1") (source (origin (method url-fetch) (uri (pypi-uri "ccdproc" version)) (sha256 - (base32 "1crc565n0x1krd59cjm2vnmzyi0p83yc8vpxq6hldj7vdnqgl8yq")))) + (base32 "1ymx9ssapv52m6flfvlhgjnvwmqdgv1qimyjvci8w66k9j4446q5")))) (build-system pyproject-build-system) (native-inputs (list python-hatch-vcs @@ -3103,6 +3106,66 @@ 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-cobaya + (package + (name "python-cobaya") + (version "3.5.7") + (source + (origin + (method git-fetch) ;no tests in pypi release + (uri (git-reference + (url "https://github.com/CobayaSampler/cobaya") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17ccka051lknv05dlr1wfb2ha2qj27av2q2s6ir2vrcgx5c2szfp")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; Test options were taken from GitHub action workflow. + #~(list "--no-flaky-report" + "--numprocesses" (number->string (parallel-job-count)) + "--skip-not-installed" + "-k" "not test_planck_NPIPE_p_CamSpec_camb_install and not test_grid" + "tests") + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + (setenv "HOME" "/tmp") + (setenv "COBAYA_PACKAGES_PATH" "/tmp")))))) + (native-inputs + (list python-flaky + python-pytest + python-pytest-xdist + python-setuptools + python-wheel)) + (propagated-inputs + (list python-dill + python-fuzzywuzzy + python-getdist + python-numpy + python-packaging + python-pandas + python-portalocker + python-py-bobyqa + python-pyyaml + python-scipy + python-tqdm + python-typing-extensions)) + (home-page "https://github.com/CobayaSampler/cobaya") + (synopsis "Code for Bayesian analysis in Cosmology") + (description + "@acronym{Cobaya, COde for BAYesian Analysis}, and Spanish for Guinea +Pig) is a framework for sampling and statistical modelling: it allows you to +explore an arbitrary prior or posterior using a range of Monte Carlo +samplers (including the advanced MCMC sampler from CosmoMC, and the advanced +nested sampler PolyChord). The results of the sampling can be analysed with +GetDist. It supports MPI parallelization (and very soon HPC containerization +with Docker/Shifter and Singularity).") + (license license:lgpl3+))) + (define-public python-colossus ;; There is no source distribution in PyPI and no version tags, use the ;; commit pointing to the version 1.3.8. @@ -3251,13 +3314,13 @@ Spectrograph}.") (define-public python-crds (package (name "python-crds") - (version "12.1.10") + (version "12.1.11") (source (origin (method url-fetch) (uri (pypi-uri "crds" version)) (sha256 - (base32 "07nahxxnw89l8lk8grampdni46a3l52098qdf5vkcfqs1kkq80wz")))) + (base32 "1h4n5wyv23pa1fld2nfqph6app8zxb8zkzv5p1w6dm11n7zbnxih")))) (build-system pyproject-build-system) (arguments (list @@ -3330,7 +3393,7 @@ files and provide related services.") (define-public python-czml3 (package (name "python-czml3") - (version "2.3.4") + (version "2.3.5") (source (origin (method git-fetch) @@ -3341,7 +3404,7 @@ files and provide related services.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1ws26kx975c48s6zzj57fyi1d0aiv0arxcrb4hg7jdvhrcyh3nlk")))) + (base32 "1c2nw1rdllla76z8gkfv2a1dqc302cayhhkqn3xn4b0vgsn1z1k2")))) (build-system pyproject-build-system) (native-inputs (list python-pytest @@ -3365,13 +3428,13 @@ Cesium.") (define-public python-dkist (package (name "python-dkist") - (version "1.13.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (pypi-uri "dkist" version)) (sha256 - (base32 "07mnm9fl6igbhblg4dihg5w187n6ily5aglg40qjxl6yvxr63b2x")))) + (base32 "061hgrg69cpnn2j6gaivjbkxwiz6rpmyf6igxq58h82g4r7yl6ya")))) (build-system pyproject-build-system) (arguments (list @@ -3416,7 +3479,7 @@ Cesium.") python-sunpy python-tqdm)) (home-page "https://github.com/DKISTDC/dkist") - (synopsis "Library for obtaining, processing and interacting with calibrated DKIST data") + (synopsis "Obtaining, processing and interacting with calibrated DKIST data") (description "The @acronym{DKIST, Daniel K. Inouye Solar Telescope} package aims to help you search, obtain and use DKIST data as part of your Python software.") @@ -3425,16 +3488,16 @@ help you search, obtain and use DKIST data as part of your Python software.") (define-public python-drizzle (package (name "python-drizzle") - (version "2.0.1") + (version "2.1.0") (source (origin - (method git-fetch) ;PyPi doesn't have the test data sets + (method git-fetch) ;no test data in PyPI archive (uri (git-reference (url "https://github.com/spacetelescope/drizzle") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "113fqr87glqkvh4szqvbv0b6brr3bwp4d65qy1r1q4b90318p2zf")))) + (base32 "1adp5bhzgrw0csn5wvpij7hzm5wh3zr4nkvpq0a8lb93ifk6k5gh")))) (build-system pyproject-build-system) (arguments (list @@ -3451,7 +3514,7 @@ help you search, obtain and use DKIST data as part of your Python software.") (list python-astropy-minimal python-gwcs python-pytest - python-setuptools + python-setuptools-next python-setuptools-scm python-wheel)) (propagated-inputs @@ -3886,31 +3949,32 @@ pick/FWHM, thumbnails, etc.") (define-public python-glue-astronomy (package (name "python-glue-astronomy") - (version "0.11.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (pypi-uri "glue_astronomy" version)) (sha256 - (base32 "0qaaf3n69ird5b00igkxnwyh80nvwffvfmaz7gbkavxnf6km940p")))) + (base32 "0b65kybnknrnz1nh1kjvsh9k9smia0gyigwn5rc3zrg1qys3wlk4")))) (build-system pyproject-build-system) (arguments (list + ;; 77 passed, 3 deselected #:test-flags #~(list "--pyargs" "glue_astronomy" - ;; XXX: Findout why these tests fail to load: - ;; E ModuleNotFoundError: No module named 'glue.qglue' - ;; E ImportError: cannot import name 'make_2dspec_image' from - ;; 'specreduce.utils.synth_data' - "--ignore=glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py" - "--ignore=glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py" - "--ignore=glue_astronomy/translators/tests/test_trace.py" - "--ignore=glue_astronomy/translators/tests/test_trace.py" - ;; This is a Numpy DeprecationWarning, remove it on next update. - "-k" "not test_spectral_cube_io"))) + "-k" (string-join + ;; Not equal to tolerance rtol=1e-07, atol=0 + (list "not test_from_spectrum1d[wcs3d]" + ;; ValueError: WCS is 1D but flux is + ;; multi-dimensional. Please specify + ;; spectral_axis_index. + "test_spectrum1d_2d_data[2]" + "test_spectrum1d_2d_data[3]") + " and not ")))) (propagated-inputs (list python-astropy python-glue-core + python-glue-qt python-regions python-specreduce python-spectral-cube @@ -4099,13 +4163,13 @@ specifically pulsar timing array signals.") (define-public python-gwcs (package (name "python-gwcs") - (version "0.24.0") + (version "0.25.1") (source (origin (method url-fetch) (uri (pypi-uri "gwcs" version)) (sha256 - (base32 "0q3f2rnl4d1p98kypr1jfkajwih22sbx3smn492yf9dbj92bv1v3")))) + (base32 "0zr2mmad7qk1almw3kc3xqdhfkxbjg7yfc5a9cif4l0m8r11gr0x")))) (build-system pyproject-build-system) (arguments (list @@ -4120,7 +4184,8 @@ specifically pulsar timing array signals.") (list python-pytest python-pytest-astropy python-pyyaml - python-setuptools-scm + python-setuptools-next + python-setuptools-scm-next python-wheel)) (propagated-inputs (list python-asdf @@ -4276,6 +4341,67 @@ is based on the Hierarchical Equal Area isoLatitude Pixelization (HEALPix) scheme and builds with the HEALPix C++ library.") (license license:gpl2+))) +(define-public python-hierarc + (package + (name "python-hierarc") + (version "1.2.0") + (source + (origin + (method git-fetch) ;no tests data in the PyPI archive + (uri (git-reference + (url "https://github.com/sibirrer/hierArc") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "02078a745hrb3m8fj739rwzk4wwxrfk40sr4yvs722aj5xk8j00w")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; Some tests are computation intensive and not thread safe, failing + ;; during parallel invocation: + ;; 109 passed, 32 deselected, 43 warnings in 634.59s + #~(list "--durations" "5" + ;; AttributeError: 'LambdaCDM' object has no attribute '_Ok0'. + "-k" (string-join + (list "not test_cosmo_instance" + "test_kde_likelihood_integration" + "test_log_likelihood" + "test_mcmc_emcee" + "test_sne_likelihood_integration") + " and not ")) + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + ;; RuntimeError: cannot cache function 'rotate': no locator + ;; available for file '<...>/lenstronomy/Util/util.py'. + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (native-inputs + (list python-pytest + python-setuptools + python-wheel)) + (propagated-inputs + (list python-astropy + python-emcee + python-h5py + python-lenstronomy + python-matplotlib + python-mpmath + python-numpy + python-pandas + python-scikit-learn + python-scipy)) + (home-page "https://github.com/sibirrer/hierarc") + (synopsis "Hierarchical analysis of strong lensing systems") + (description + "This package implements a funtionality for hierarchical analysis of +strong lensing systems to infer lens properties and cosmological parameters +simultaneously. It allows to fit lenses with measured time delays, imaging +information, kinematics constraints and standardizable magnifications with +parameters described on the ensemble level.") + (license license:bsd-3))) + (define-public python-holodeck (package (name "python-holodeck") @@ -4378,13 +4504,13 @@ satellite.") (define-public python-jwst (package (name "python-jwst") - (version "1.18.1") + (version "1.19.1") (source (origin (method url-fetch) (uri (pypi-uri "jwst" version)) (sha256 - (base32 "1zhq9816zx0binny80blvwld8zwd52m29b8vspwr2j4nzq1ijyb5")) + (base32 "1bds1a8bgyac19bwr7kf6wcknkmmchji23svhr8mpciga8gm27gv")) (modules '((guix build utils))) (snippet #~(begin @@ -4409,12 +4535,8 @@ satellite.") (add-before 'build 'relax-requirements (lambda _ (substitute* "pyproject.toml" - ;; stcal<1.13.0,>=1.12.0 - ((">=1.12.0,<1.13.0") "") ; main branch points to the latest commit - ;; "stpipe>=0.8.1,<0.9.0", - ((">=0.8.1,<0.9.0") "") - ;; "stdatamodels>=3.0.1,<3.1.0", - ((">=3.0.1,<3.1.0") "") + ;; drizzle>=2.0.1,<2.1.0 + ((">=2.0.1,<2.1.0") ">=2.0.1") ;; scipy>=1.14.1 (("1.14.1") "1.12.0") ;; XXX: Can't detect opencv-python version. The input opencv @@ -4432,7 +4554,7 @@ satellite.") python-pytest-cov python-pytest-doctestplus python-requests-mock - python-setuptools + python-setuptools-next python-setuptools-scm python-wheel)) (propagated-inputs @@ -4540,6 +4662,94 @@ Telescope,JWST} from a set of input dark current files and a set of flat field files.") (license license:bsd-3))) +(define-public python-lenstronomy + (package + (name "python-lenstronomy") + (version "1.13.2") + (source + (origin + (method git-fetch) ;no tests data in the PyPI tarball + (uri (git-reference + (url "https://github.com/lenstronomy/lenstronomy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0j0qc8vw53n9sg5yncilkfd6n5s2jixrm83an0q1gv2m2yk5dsn7")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "--numprocesses" (number->string (parallel-job-count)) + ;; TypeError: SparseSolverBase.__init__() got an + ;; unexpected keyword argument 'num_iter_lens' + "--ignore=test/test_ImSim/test_image_model_pixelbased.py" + "-k" (string-join + ;; AttributeError: 'FlatLambdaCDM' object has no attribute '_Ok0' + (list "not test_angular_diameter_distance" + "test_angular_diameter_distance_array" + "test_angular_diameter_distance_z1z2" + "test_geo_shapiro_delay" + "test_interpol" + "test_set_T_ij_stop" + "test_update_source_redshift" + ;; FileNotFoundError: [Errno 2] No such file or + ;; directory: '/tmp/.../coolest_template.json' + "test_full" + "test_load" + "test_pemd" + "test_pemd_via_epl" + "test_raise" + "test_update" + ;; _flapack.error: (liwork>=max(1,10*n)||liwork==-1) + ;; failed for 10th keyword liwork: dsyevr:liwork=1 + "test_sampler" + ;; TypeError: SLIT_Starlets.function_2d() got an + ;; unexpected keyword argument 'n_pix_x' + "test_pixelbased_modelling" + ;; AssertionError: Arrays are not almost equal to 1 + ;; decimals ACTUAL: 0.8382375738251702 + "test_run_fit") + " and not ")))) + (native-inputs + (list python-colossus + ;; python-nestcheck + ;; python-pymultinest + ;; python-starred-astro + python-coolest + python-pytest + python-pytest-xdist)) + (propagated-inputs + (list python-astropy + python-cobaya + python-configparser + python-corner + python-dynesty + python-emcee + python-h5py + python-matplotlib + python-mpmath + python-multiprocess + python-nautilus-sampler + python-numba + python-numpy + python-pyxdg + python-pyyaml + python-schwimmbad + python-scikit-image + python-scikit-learn + python-scipy + python-slitronomy + python-zeus-mcmc)) + (home-page "https://github.com/lenstronomy/lenstronomy") + (synopsis "Multi-purpose lens modeling software") + (description + "@code{lenstronomy} is a multi-purpose software package to model strong +gravitational lenses. @code{lenstronomy} finds application for time-delay +cosmography and measuring the expansion rate of the Universe, for quantifying +lensing substructure to infer dark matter properties, morphological +quantification of galaxies, quasar-host galaxy decomposition and much more.") + (license license:bsd-3))) + (define-public python-libstempo (package (name "python-libstempo") @@ -4583,6 +4793,40 @@ files.") pulsar timing tool.") (license license:expat))) +(define-public python-linetools + (package + (name "python-linetools") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "linetools" version)) + (sha256 + (base32 "1nljcaz0r60wvsy5dwb040wll2dd764dvib5xzkpc59cbw5lz85h")))) + (build-system pyproject-build-system) + (native-inputs + (list python-pytest + python-pytest-astropy + python-pytest-cov + python-setuptools + python-setuptools-scm + python-wheel)) + (propagated-inputs + (list python-astropy + python-h5py + python-ipython + python-matplotlib + python-numpy + python-pyyaml + python-qtpy + python-scipy)) + (home-page "http://linetools.readthedocs.org/") + (synopsis "Quasar and galaxy spectra 1-D analysis tool") + (description + "This package implements a functionality for analysing absorption and +emission lines in 1-D spectra, especially galaxy and quasar spectra.") + (license license:bsd-3))) + (define-public python-lofar-h5plot (package (name "python-lofar-h5plot") @@ -4724,13 +4968,13 @@ on: (define-public python-mpl-animators (package (name "python-mpl-animators") - (version "1.2.3") + (version "1.2.4") (source (origin (method url-fetch) (uri (pypi-uri "mpl_animators" version)) (sha256 - (base32 "15zsi9apfdj6csr3vpvcw9972xr7036nw6smiwfy0n514l1xh3b1")))) + (base32 "1lwh16f5dilnxjnchw2l2pz7iz3dby7ij6z0l7v3fm6aqhk6fwrg")))) (build-system pyproject-build-system) (arguments (list @@ -4807,6 +5051,7 @@ Carlo.") (build-system pyproject-build-system) (arguments (list + ;; 393 passed, 7 skipped, 31 deselected, 10 xfailed #:test-flags #~(list "--numprocesses" (number->string (parallel-job-count)) "-k" (string-join @@ -4818,7 +5063,10 @@ Carlo.") ;; Introduced with astropy 6.1.3, see ;; <https://github.com/sunpy/ndcube/issues/758>. "test_2d[celestial_2d_ape14_wcs]" - "test_2d[celestial_2d_fitswcs]") + "test_2d[celestial_2d_fitswcs]" + ;; XXX: Not sure why it fails: ValueError: Too many input + ;; arguments - expected 1, got 2. + "test_slice_drop_dimensions") " and not ")) #:phases #~(modify-phases %standard-phases @@ -5025,6 +5273,61 @@ position-frequency slice.") (list python-setuptools python-wheel))))) +(define-public python-pyhalo + (package + (name "python-pyhalo") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pyhalo" version)) + (sha256 + (base32 "06zdcr82fzzn6zkjralmv9qv7qjyjkni1p1rg60bvl8h013v3xp6")))) + (build-system pyproject-build-system) + (arguments + (list + ;; ValueError: The truth value of an array with more than one element is + ;; ambiguous. Use a.any() or a.all() + #:test-flags #~(list "-k" "not test_vmax") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-setupup.py + ;; XXX: ModuleNotFoundError: No module named 'pyHalo.cli'. + (lambda _ + (substitute* "setup.py" + ((".pyHalo=pyHalo.cli:main.*") "")))) + (add-before 'check 'pre-check + (lambda _ + ;; RuntimeError: cannot cache function 'rotate': no locator + ;; available for file '<...>/lenstronomy/Util/util.py'. + (setenv "NUMBA_CACHE_DIR" "/tmp") + ;; PermissionError: [Errno 13] Permission denied: + ;; '/homeless-shelter' + (setenv "HOME" "/tmp")))))) + (native-inputs + (list python-pytest + python-setuptools + python-wheel)) + (propagated-inputs + (list python-astropy + python-click + python-colossus + python-h5py + python-lenstronomy + python-mcfit + python-numpy + python-scipy)) + (home-page "https://github.com/dangilman/pyHalo") + (synopsis "Render populations of dark matter halos") + (description + "pyHalo renders full mass distributions for substructure lensing +simulations with gravitational lensing software package lenstronomy. The main +purpose of the code is to quickly render full populations of dark matter +subhalos and line of sight halos for gravitational lensing simulations. It +also transltes halo properties (mass, concentration, redshift, etc) into +angular units for lensing computations with lenstronomy.") + (license license:expat))) + (define-public python-pyregion (package (name "python-pyregion") @@ -5291,13 +5594,13 @@ solar physics.") (define-public python-regularizepsf (package (name "python-regularizepsf") - (version "1.0.2") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "regularizepsf" version)) (sha256 - (base32 "1ial8i9nshhpn3lsgnjqm94dfrzxwz2qgpd8bjzmml1ls0j7sm9v")))) + (base32 "16kk2rfcs7dkasij225j9z99gwdnxxlamj704d7f3h1lj7yl3vdv")))) (build-system pyproject-build-system) (native-inputs (list python-pytest @@ -5320,6 +5623,104 @@ solar physics.") PSF} describing how the optical system spreads light from sources.") (license license:expat))) +(define-public python-romancal + ;; The compatible version is not released yet, use the latest commit. + (let ((commit "ae864a407fc16001d3a0370779caa381f994f718") + (revision "0")) + (package + (name "python-romancal") + (version (git-version "0.19.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/spacetelescope/romancal") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0dxgwy6qva8ss7xb6hlkck6kysikgmn0byprvj4kx1l82gm1sk0g")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "--color=no" + "--numprocesses" (number->string (min 8 (parallel-job-count))) + ;; XXX: Tests requiring network access or additional setup, + ;; check how to run them locally. + "--ignore=romancal/assign_wcs/tests/test_wcs.py" + "--ignore=romancal/dark_current/tests/test_dark.py" + "--ignore=romancal/dq_init/tests/test_dq_init.py" + "--ignore=romancal/flatfield/tests/test_flatfield.py" + "--ignore=romancal/flux/tests/test_flux_step.py" + "--ignore=romancal/lib/engdb/tests/test_engdb_tools.py" + "--ignore=romancal/linearity/tests/test_linearity.py" + "--ignore=romancal/multiband_catalog/tests/test_multiband_catalog.py" + "--ignore=romancal/orientation/tests/test_set_telescope_pointing.py" + "--ignore=romancal/photom/tests/test_photom.py" + "--ignore=romancal/ramp_fitting/tests/test_ramp_fit_cas22.py" + "--ignore=romancal/ramp_fitting/tests/test_ramp_fit_likelihood.py" + "--ignore=romancal/refpix/tests/test_step.py" + "--ignore=romancal/resample/tests/test_resample.py" + "--ignore=romancal/saturation/tests/test_saturation.py" + "--ignore=romancal/skycell/tests/test_skycell.py" + "--ignore=romancal/skycell/tests/test_skycell_match.py" + "--ignore=romancal/skymatch/tests/test_skymatch.py" + "--ignore=romancal/source_catalog/tests/test_psf.py" + "--ignore=romancal/source_catalog/tests/test_source_catalog.py" + "--ignore=romancal/stpipe/tests/test_core.py" + "--ignore=romancal/tweakreg/tests/test_tweakreg.py") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "pyproject.toml" + ;; XXX: scipy >=1.14.1 + ((" >=1.14.1") "")))) + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" + #$(version-major+minor+point version))))))) + (native-inputs + (list nss-certs-for-test + python-ci-watson + python-deepdiff + ;; python-edp ;not packaged + python-pytest + python-pytest-astropy + python-pytest-xdist + python-setuptools-next + python-setuptools-scm + python-stpreview + python-wheel)) + (propagated-inputs + (list python-asdf + python-asdf-astropy + python-astropy + python-crds + python-drizzle + python-gwcs + python-jsonschema + python-numpy + python-pandas + python-photutils + python-pyarrow + python-pyparsing + python-requests + python-roman-datamodels + python-scipy + python-spherical-geometry + python-stcal + python-stpipe + python-stpsf + python-stsci-imagestats + python-tweakwcs)) + (home-page "https://github.com/spacetelescope/romancal") + (synopsis "Nancy Grace Roman Space Telescope observations processing library") + (description + "This package implements a functionality for calibration of science +observations from the Nancy Grace Roman Space Telescope.") + (license license:bsd-3)))) + (define-public python-sep (package/inherit libsep (name "python-sep") @@ -5677,6 +6078,63 @@ but has evolved to support other missions as well.") ;; known as New or Revised BSD). (license license:bsd-3))) +(define-public python-space-dolphin + (package + (name "python-space-dolphin") + (version "1.1.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "space_dolphin" version)) + (sha256 + (base32 "0qxpb6ss0w4f6mnisri3i3a5g5dfa12a7iimdchzqql7r53x7xiq")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #f ;TODO: Enable when tensorflow is fixed. + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + ;; RuntimeError: cannot cache function 'rotate': no locator + ;; available for file '<...>/lenstronomy/Util/util.py'. + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (native-inputs + (list ;; python-pytest + python-setuptools-next + python-wheel)) + (propagated-inputs + (list python-astropy + python-corner + python-emcee + python-gdown + python-h5py + python-lenstronomy + python-matplotlib + python-numpy + python-pyyaml + python-schwimmbad + python-scipy + python-tqdm + #;tensorflow)) ;XXX: currenlty broken on master, see guix/guix#1436. + (home-page "https://github.com/ajshajib/dolphin") + (synopsis "Automated pipeline for lens modeling based on lenstronomy") + (description + "This package implements a functionality of AI-powered automated pipeline +for lens modeling, with lenstronomy as the modeling engine. + +Features: +@itemize +@item AI-automated forward modeling for large samples of galaxy-scale lenses +@item flexible: supports both fully automated and semi-automated (with user +tweaks) modes +@item multi-band lens modeling made simple +@item supports both galaxy–galaxy and galaxy–quasar systems +@item effortless syncing between local machines and @acronym{High-Performance +Computing Cluster, HPCC} +@end itemize") + (license license:bsd-3))) + (define-public python-specreduce (package (name "python-specreduce") @@ -5690,6 +6148,10 @@ but has evolved to support other missions as well.") (build-system pyproject-build-system) (arguments (list + ;; 21 failed, 55 passed, 24 skipped, 4 errors + ;; + ;; FIXME: More than a half tests are skipped or failed, check why. + #:tests? #f #:test-flags ;; TODO: Try to link some test data availale in ;; specification-specreduce-data package. @@ -6291,13 +6753,13 @@ of axis order, spatial projections, and spectral units that exist in the wild. (define-public python-specutils (package (name "python-specutils") - (version "1.19.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (pypi-uri "specutils" version)) (sha256 - (base32 "1iwkrs436z8xrzwl5rkla8nimyfrx5ydklghm41xgzr27nkvqa12")))) + (base32 "0ngq4r7awkbwdbi7a8isj6iw66xk3s26yjp0c0qvl6wvf9hby59r")))) (build-system pyproject-build-system) (arguments (list @@ -6315,6 +6777,12 @@ of axis order, spatial projections, and spectral units that exist in the wild. " and not ")) #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.cfg" + ;; scipy>=1.14.1; all tests passed, it will remove after + ;; python-team is merged. + ((">=1.14") ">=1.12.0")))) (add-before 'check 'set-home-env (lambda _ ;; Tests require HOME to be set. @@ -6467,13 +6935,13 @@ over many parameters: (define-public python-statmorph (package (name "python-statmorph") - (version "0.6.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (pypi-uri "statmorph" version)) (sha256 - (base32 "0q9h8yqd8w8ckakn3hx7r5mag3vpgaah077rvi3bdmkmix5ky7r9")))) + (base32 "0qrxm0aigsjsqv39vxc85jv1id8b7sry76dx44143ii9hpd9dg4l")))) (build-system pyproject-build-system) (arguments (list @@ -6489,8 +6957,9 @@ over many parameters: (add-after 'unpack 'relax-requirements (lambda _ (substitute* "setup.py" - ;; scikit-image>=0.25.0 - ((">=0.25.0") ">=0.23.2"))))))) + ;; scikit-image>=0.25.0; tests passed, remove when python-team + ;; is merged. + ((">=0.25.2") ">=0.23.2"))))))) (native-inputs (list python-pytest python-setuptools @@ -6512,13 +6981,13 @@ and CAS statistics), as well as fitting 2D Sérsic profiles.") (define-public python-stcal (package (name "python-stcal") - (version "1.13.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (pypi-uri "stcal" version)) (sha256 - (base32 "00xfx7hpcadwf3dm0lddh1raw7qnr5nrg30dclmjcrxhsp27spjg")))) + (base32 "1y3w1nlb4f56f9w7ql1al35mj2xv53cagrnpqknl1kh6r6qg7pqj")))) (build-system pyproject-build-system) (arguments (list @@ -6561,11 +7030,11 @@ and CAS statistics), as well as fitting 2D Sérsic profiles.") python-pytest python-pytest-xdist python-pytest-doctestplus - python-setuptools + python-setuptools-next python-setuptools-scm python-wheel)) (propagated-inputs - (list opencv ;Provides OpenCV-Python + (list opencv ;Provides OpenCV-Python python-asdf python-astropy python-drizzle @@ -6583,16 +7052,17 @@ and CAS statistics), as well as fitting 2D Sérsic profiles.") (define-public python-stdatamodels (package (name "python-stdatamodels") - (version "3.1.0") + (version "4.0.1") (source (origin (method url-fetch) (uri (pypi-uri "stdatamodels" version)) (sha256 - (base32 "03r9nv3d3rjm70ihqg03aj6ydl91527abfmx7nbf6g9598s01fg1")))) + (base32 "1lyxwfq55ngnsjr25bj3v6mjibx17074z28qi3xc9wpib5dn887i")))) (build-system pyproject-build-system) (arguments (list + ;; 1571 passed #:test-flags #~(list "--numprocesses" (number->string (parallel-job-count)) ;; Disable tests requiring access to CRDS servers to download @@ -6631,13 +7101,13 @@ implemented in the @acronym{JWST, James Webb Space Telescope} and (define-public python-stpipe (package (name "python-stpipe") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (pypi-uri "stpipe" version)) (sha256 - (base32 "0am7bb7msa3pa694lsh6q461zybczki806a8llfns0hx721wzipq")) + (base32 "1z5y8sbpkzxccvxwv19as2a8c69f3l01kgmicsk472p91bbm8v31")) (modules '((guix build utils))) (snippet '(begin @@ -6668,6 +7138,36 @@ implementing calibration pipeline software.") ;; LICENSE Association of Universities for Research in Astronomy (AURA) (license license:bsd-3))) +(define-public python-stpreview + (package + (name "python-stpreview") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "stpreview" version)) + (sha256 + (base32 "1z7zpqyg7rl2sf311idzwckdshm86mkbbpknvq90gkxmqdaqas9q")))) + (build-system pyproject-build-system) + (native-inputs + (list python-pytest + python-roman-datamodels + python-setuptools-next + python-setuptools-scm + python-wheel)) + (propagated-inputs + (list python-asdf + python-astropy + python-gwcs + python-matplotlib + python-numpy + python-scikit-image)) + (home-page "https://github.com/spacetelescope/stpreview") + (synopsis "Build downsampled previews of STScI") + (description + "This package provides build downsampled previews of Space Telescope products.") + (license license:bsd-3))) + (define-public python-stpsf (package (name "python-stpsf") @@ -7407,16 +7907,17 @@ and the use of a modern programming language, techniques, and libraries (define-public python-rad (package (name "python-rad") - (version "0.25.0") + (version "0.26.0") (source (origin (method url-fetch) (uri (pypi-uri "rad" version)) (sha256 - (base32 "07pkz0fybhpzrlch5gcw4c90rd2y2mypli23h2lz1pa7q6gyaifd")))) + (base32 "0vxkjsj9bdl84076lbric4jn531jv46i2wwfxak50i5mik8r7zjg")))) (build-system pyproject-build-system) (arguments (list + ;; 1131 passed, 1 skipped #:test-flags ;; Ignore tests requiring python-crds to break cycle: ;; python-rad -> python-roman-datamodels -> python-crds -> python-rad @@ -7428,7 +7929,6 @@ and the use of a modern programming language, techniques, and libraries "--ignore=tests/test_latest.py"))) (native-inputs (list python-pytest - python-pytest python-pytest-doctestplus python-semantic-version python-setuptools-next @@ -7530,13 +8030,13 @@ channels (define-public python-roman-datamodels (package (name "python-roman-datamodels") - (version "0.25.0") + (version "0.26.0") (source (origin (method url-fetch) (uri (pypi-uri "roman_datamodels" version)) (sha256 - (base32 "0sb2zpanklyh5j2rgm27lrscl51fwyny4f6c9gisj373pp7w6h2c")))) + (base32 "0kiv139q6q3pjlalb16nqcyib8hmd9svr4y24s7g0as08x09d7zl")))) (build-system pyproject-build-system) (arguments (list @@ -8266,17 +8766,38 @@ object.") (define-public python-synphot (package (name "python-synphot") - (version "1.5.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (pypi-uri "synphot" version)) (sha256 - (base32 "0xifg0fbh2rj3jn5i504c0qh51dlzgr1l2k962nh38synjhq9csc")))) + (base32 "0vcai5kdfv6286qdyhg58i6f980s028dh5r4fmlhdk872qci574r")))) (build-system pyproject-build-system) (arguments (list - #:test-flags #~(list "--pyargs" "synphot"))) + ;; 394 passed, 29 skipped, 12 deselected, 4 xfailed + #:test-flags + #~(list "--pyargs" "synphot" + ;; Not harmful deprecation warning as synphot is compatible with + ;; specutils now, remove or silent error in the next refresh + ;; cycle. + ;; + ;; See: <https://github.com/spacetelescope/synphot_refactor/issues/411>. + "-k" (string-join + (list "not test_from_spectrum1d_Empirical1D_bandpass" + "test_from_spectrum1d_Empirical1D_bandpass_masked" + "test_from_spectrum1d_Empirical1D_source" + "test_from_spectrum1d_Empirical1D_source_masked" + "test_spectrum1d_source" + "test_to_spectrum1d_Const1D" + "test_to_spectrum1d_ConstFlux1D" + "test_to_spectrum1d_Empirical1D_bandpass" + "test_to_spectrum1d_Empirical1D_source" + "test_to_spectrum1d_GaussianFlux1D" + "test_to_spectrum1d_compound_bandpass" + "test_to_spectrum1d_compound_source") + " and not ")))) (native-inputs (list python-pytest python-pytest-astropy @@ -8288,7 +8809,7 @@ object.") python-dust-extinction python-numpy python-scipy - python-specutils )) + python-specutils)) (home-page "https://github.com/spacetelescope/synphot_refactor") (synopsis "Synthetic photometry using Astropy") (description @@ -8395,13 +8916,13 @@ using (multivariate) polynomials.") (define-public python-yt (package (name "python-yt") - (version "4.4.0") + (version "4.4.1") (source (origin (method url-fetch) (uri (pypi-uri "yt" version)) (sha256 - (base32 "1mf084wp0wrhi17npzbyz42lh3xwlc2hggr8h4pmighsnafdy58f")))) + (base32 "099w4n38c13vk98wsj698wxmskw3pr7zcf56dqiwl8c3nhjn9wrd")))) (build-system pyproject-build-system) (arguments (list @@ -8763,7 +9284,7 @@ It can be used to calculate the trajectory of satellites.") (define-public siril (package (name "siril") - (version "1.3.3") + (version "1.4.0-beta3") (source (origin (method git-fetch) @@ -8771,7 +9292,7 @@ It can be used to calculate the trajectory of satellites.") (url "https://gitlab.com/free-astro/siril") (commit version))) (sha256 - (base32 "1fxjfr9kak9vb899xpgr1vmiv3cc2l4apyp0mn0ghg7mqlyl9qmw")) + (base32 "1frvi6879zh4bzm5smdy0scpjmj5pg2i81wb2wa4ikq1dq227x8k")) (file-name (git-file-name name version)))) (build-system meson-build-system) (arguments @@ -8810,6 +9331,7 @@ It can be used to calculate the trajectory of satellites.") ffms2 fftwf gdk-pixbuf + gtksourceview-4 gsl gtk+ json-glib @@ -8831,7 +9353,8 @@ It can be used to calculate the trajectory of satellites.") lz4 opencv pugixml - wcslib)) + wcslib + yyjson)) (home-page "https://siril.org/") (synopsis "Image processing software for amateur astronomy") (description @@ -8868,11 +9391,14 @@ large number of image formats.") #~(modify-phases %standard-phases (add-after 'unpack 'disable-failing-tests (lambda _ - ;; Two tests fail with SegFAilt: "Cannot allocate GPU memory: - ;; The processing function library was compiled without CUDA - ;; support". (substitute* "tests/CMakeLists.txt" - (("clean") "# clean"))))))) + ;; Two tests fail with SegFAilt: "Cannot allocate GPU memory: + ;; The processing function library was compiled without CUDA + ;; support". + (("clean") "# clean") + ;; test_weighting fails with error: sdp_weighting_uniform: + ;; Expected 'output_weight' not to be read-only. + (("visibility") "# visibility"))))))) (home-page "https://developer.skao.int/projects/ska-sdp-func/en/latest/") (synopsis "SDP Processing Function Library") (description @@ -8945,7 +9471,7 @@ astronomical fields. SkyMaker is part of the (define-public splash (package (name "splash") - (version "3.11.3") + (version "3.11.4") (source (origin (method git-fetch) @@ -8954,7 +9480,7 @@ astronomical fields. SkyMaker is part of the (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0vyshywwbk2746jdhrnn7vn1gj336zzwcifrfyf38byj41691svm")))) + (base32 "13p4hjdpr0yacgh8v3lf5vy1d0hdh5axbwpgi91wafm0xx6zpgkv")))) (build-system gnu-build-system) (arguments ;; FIXME: Tests failed @@ -9077,7 +9603,6 @@ deconvolution). Such post-processing is not performed by Stackistry.") (list ;; FIXME: Tests keep failing on 100% when preparing test-suit for INDI. #:tests? #f - #:test-target "test" #:configure-flags #~(list "-DENABLE_GPS=1" ;; TODO: Enable when all of the dependencies are available for Qt6. @@ -9129,33 +9654,45 @@ objects.") (license license:gpl2+)))) (define-public stuff - (package - (name "stuff") - (version "2.0.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/astromatic/stuff") - ;; XXX: No version tag available in GitHub. - ;; See: https://github.com/astromatic/stuff/issues/6 - (commit "9008dc022ef53331092da248cf0a794abd6783bf"))) - (file-name (git-file-name name version)) - (sha256 - (base32 "004sry5lqqm7s9x4l3agysp3n63y3ga35x1rwwda4m6dc6zvla6b")))) - (build-system gnu-build-system) - (native-inputs - (list autoconf automake libtool pkg-config)) - (home-page "https://www.astromatic.net/software/stuff") - (synopsis "Astronomical catalogue simulation") - (description - "Stuff is a program that simulates \"perfect\" astronomical catalogues. -It generates object lists in ASCII which can read by the SkyMaker program to -produce realistic astronomical fields. Stuff is part of the + ;; XXX: No version tag available in GitHub. + ;; See: https://github.com/astromatic/stuff/issues/6 + (let ((commit "9cf363216a0d5c3d41b3dc759994feee3be0fc4e") + (revision "0")) + (package + (name "stuff") + (version (git-version "2.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/astromatic/stuff") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1n7f2f7llwf1fbliypblia3xyrh69yy1rqbwwhz897qd92fxnl5i")))) + (build-system gnu-build-system) + (native-inputs + (list autoconf automake libtool pkg-config)) + (home-page "https://www.astromatic.net/software/stuff") + (synopsis "Astronomical catalogue simulation") + (description + "Stuff is a program that simulates \"perfect\" astronomical +catalogues. It generates object lists in ASCII which can read by the SkyMaker +program to produce realistic astronomical fields. Stuff is part of the @uref{https://www.astromatic.net/projects/efigi, EFIGI} development project.") - (license license:gpl3+))) + (license license:gpl3+)))) -(define-public sunclock +;; TODO: This is not an original source, and currently fails to build: +;; <https://directory.fsf.org/wiki/Sunclock> +;; -> <https://github.com/mdoege/Sunclock> dead link +;; -> <http://www.arvernes.com/wiki/index.php/Sunclock> dead link +;; <https://github.com/nongiach/Sunclock> is unmaintained. +;; +;; Maybe use Debian's fork instead +;; <https://salsa.debian.org/debian/sunclock>, it would need to apply 12 +;; patches from <debian/patches>? +;; Mark as not public for now. +(define sunclock (let ((commit "f4106eb0a81f7594726d6b2859efd8fc64cc1225") (revision "1")) (package |