guix_mirror_bot pushed a commit to branch master
in repository guix.
commit df8015fd265f08873814ddf6545b65575b7ae045
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 58fefa5820..a56f61fc21 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
@@ -6867,16 +6867,16 @@ 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.
@@ -6884,74 +6884,104 @@ 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")
@@ -10719,7 +10749,7 @@ 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
@@ -10746,7 +10776,7 @@ 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
