guix_mirror_bot pushed a commit to branch astro-updates in repository guix.
commit 6332051b16c4b07afb820bc2f22d434dca2ee6f9 Author: Sharlatan Hellseher <[email protected]> AuthorDate: Thu Nov 13 15:28:03 2025 +0000 gnu: python-pynbody: Update to 2.3.3. * gnu/packages/astronomy.scm (python-pynbody): Update to 2.3.3. [arguments] <test-flags>: Rework ignored test files and deselected tests. <phases>: Remove 'set-compiler; add 'pre-check. [propagated-inputs]: Remove python-posix-ipc; add python-certifi. [native-inputs]: Remove python-wheel; add python-ipython. (python-pynbody-1): New variable. (genetic, tangos)[native-inputs]: Remove python-pynbody; add python-pynbody-1. Change-Id: I0bc626f3111de77169946f13bd415bc67d74597f --- gnu/packages/astronomy.scm | 154 +++++++++++++++++++++++++++------------------ 1 file changed, 92 insertions(+), 62 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 261b210a9e..3c69b1eeef 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1037,7 +1037,7 @@ document}.") git-minimal/pinned highfive pkg-config - python-pynbody + python-pynbody-1 python-wrapper)) (inputs (list fftw @@ -7080,16 +7080,16 @@ and Sensitivities.") (define-public python-pynbody (package (name "python-pynbody") - (version "1.6.0.post0") + (version "2.3.3") (source (origin - (method git-fetch) ;PyPi doesn't have not prebuit version. + (method git-fetch) (uri (git-reference - (url "https://github.com/pynbody/pynbody";) - (commit (string-append "v" version)))) + (url "https://github.com/pynbody/pynbody";) + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0rl9ais4yc6kdijq1il4vi3mplp7z6bcih4x55axhan5n3n7riwi")) + (base32 "004aq98f65qk7wy0nvm0a71mgvlcn06r6khiblpi2j249zvicqgf")) (modules '((guix build utils))) (snippet ;; Symlink goes to not existing directory. @@ -7097,74 +7097,104 @@ and Sensitivities.") "docs/tutorials/example_code/testdata"))))) (build-system pyproject-build-system) (arguments - (list #:test-flags #~(list - ;; Disable tests which need to download additional - ;; 1.0GiB+ of test data archive from - ;; http://star.ucl.ac.uk/~app/testdata.tar.gz - ;; 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" - "--ignore=tests/array_test.py" - "--ignore=tests/bridge_test.py" - "--ignore=tests/family_test.py" - "--ignore=tests/partial_tipsy_test.py" - "--ignore=tests/snapshot_test.py" - "--ignore=tests/test_profile.py" - "--ignore=tests/gadget_test.py" - "--ignore=tests/gadgethdf_test.py" - "--ignore=tests/grafic_test.py" - "--ignore=tests/halotools_test.py" - "--ignore=tests/nchilada_test.py" - "--ignore=tests/ramses_new_ptcl_format_test.py" - "--ignore=tests/ramses_test.py" - "--ignore=tests/rockstar_test.py" - "--ignore=tests/sph_image_test.py" - "--ignore=tests/sph_smooth_test.py" - "--ignore=tests/subfind_test.py" - "--ignore=tests/subfindhdf_gadget4_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 - (lambda _ - (setenv "CC" #$(cc-for-target))))))) + (list + ;; tests: 91 passed, 6 skipped, 12 deselected + #:test-flags + ;; XXX: testdata is distributed via Zenodo + ;; <https://zenodo.org/records/17084976> with total size more than 2GiB, + ;; refer to the helper script obtaining it + ;; <pynbody/test_utils/__init__.py>. + #~(list #$@(map (lambda (file) (string-append "--ignore=tests/" file)) + (list "adaptahop_test.py" + "ahf_halos_test.py" + "array_test.py" + "bridge_test.py" + "copy_on_access_test.py" + "family_test.py" + "gadget_test.py" + "gadgethdf_test.py" + "gizmo_test.py" + "grafic_test.py" + "gravity_test.py" + "halos_test.py" + "halotools_test.py" + "hbtplus_test.py" + "hmf_test.py" + "hop_test.py" + "ionfrac_test.py" + "kdtree_test.py" + "luminosity_test.py" + "morphology_test.py" + "nchilada_test.py" + "partial_tipsy_test.py" + "pkdgravhdf_test.py" + "plot_stars_test.py" + "profile_test.py" + "ramses_new_ptcl_format_test.py" + "ramses_test.py" + "rockstar_test.py" + "snapshot_test.py" + "sph_image_test.py" + "subfind_test.py" + "subfindhdf_gadget4_test.py" + "subfindhdf_test.py" + "swift_test.py" + "tipsy_test.py" + "velociraptor_test.py")) + "--deselect=tests/shape_test.py::test_2D_shape" + "--deselect=tests/shape_test.py::test_3D_shape" + "--deselect=tests/shape_test.py::test_halo_shape_wrapper" + "--deselect=tests/test_profile.py::test_unique_hash_generation" + "--deselect=tests/test_profile.py::test_write_profile" + ;; DeprecationWarning: backend2gui is deprecated since IPython + ;; 8.24, backends are managed in matplotlib and can be + ;; externally registered. + "--deselect=tests/plot_hist2d_test.py::test_hist2d" + "--deselect=tests/plot_hist2d_test.py::test_hist2d_massweight" + "--deselect=tests/schmidtlaw_test.py::test_full_disc" + "--deselect=tests/schmidtlaw_test.py::test_truncated_disc") + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + (mkdir-p "testdata/empty_folder_0001") + (setenv "HOME" "/tmp")))))) (native-inputs (list python-cython + python-ipython python-pandas python-pytest - python-setuptools - python-wheel)) + python-setuptools)) (propagated-inputs - (list python-h5py + (list python-certifi + python-h5py python-matplotlib python-numpy - python-posix-ipc python-scipy)) (home-page "https://pynbody.github.io/pynbody/index.html";) (synopsis "Light-weight astronomical N-body/SPH analysis for python") - (description "@code{Pynbody} is an analysis framework for N-body and hydrodynamic + (description + "@code{Pynbody} is an analysis framework for N-body and hydrodynamic astrophysical simulations supporting PKDGRAV/Gasoline, Gadget, Gadget4/Arepo, N-Chilada and RAMSES AMR outputs.") (license license:gpl3+))) +(define-public python-pynbody-1 + (package + (inherit python-pynbody) + (name "python-pynbody") + (version "1.6.0.post0") + (source + (origin + (inherit (package-source python-pynbody)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/pynbody/pynbody";) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rl9ais4yc6kdijq1il4vi3mplp7z6bcih4x55axhan5n3n7riwi")))))) + (define-public python-pyregion (package (name "python-pyregion") @@ -10991,7 +11021,7 @@ any arbitrary astrometric projection defined in the WCS standard.") (arguments (list ;; XXX: Full integration tests require running database, see projects - ;; CI, unit tests are quite compute instance. + ;; CI, unit tests are quite compute-intensive. ;; ;; tests: 279 passed, 1 deselected, 105 warnings #:test-flags @@ -11018,7 +11048,7 @@ any arbitrary astrometric projection defined in the WCS standard.") ((".*tangos_preprocess_bh =.*") ""))))))) (native-inputs (list python-pymysql - python-pynbody + python-pynbody-1 python-pyquery python-pytest python-setuptools
