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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
This commit is contained in:
Sharlatan Hellseher
@@ -1037,7 +1037,7 @@ document}.")
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git-minimal/pinned
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highfive
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pkg-config
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python-pynbody
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python-pynbody-1
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python-wrapper))
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(inputs
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(list fftw
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@@ -6867,16 +6867,16 @@ and Sensitivities.")
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(define-public python-pynbody
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(package
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(name "python-pynbody")
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(version "1.6.0.post0")
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(version "2.3.3")
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(source
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(origin
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(method git-fetch) ;PyPi doesn't have not prebuit version.
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pynbody/pynbody")
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(commit (string-append "v" version))))
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(url "https://github.com/pynbody/pynbody")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "0rl9ais4yc6kdijq1il4vi3mplp7z6bcih4x55axhan5n3n7riwi"))
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(base32 "004aq98f65qk7wy0nvm0a71mgvlcn06r6khiblpi2j249zvicqgf"))
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(modules '((guix build utils)))
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(snippet
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;; Symlink goes to not existing directory.
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@@ -6884,74 +6884,104 @@ and Sensitivities.")
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"docs/tutorials/example_code/testdata")))))
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(build-system pyproject-build-system)
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(arguments
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(list #:test-flags #~(list
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;; Disable tests which need to download additional
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;; 1.0GiB+ of test data archive from
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;; http://star.ucl.ac.uk/~app/testdata.tar.gz
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;; https://github.com/pynbody/pynbody/blob/ \
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;; f4bd482dc47532831b3ec115c7cb07149d61bfc5/ \
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;; .github/workflows/build-test.yaml#L41
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;; See <https://github.com/pynbody/pynbody/issues/778>
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"--ignore=tests/copy_on_access_test.py"
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"--ignore=tests/gravity_test.py"
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"--ignore=tests/adaptahop_test.py"
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"--ignore=tests/ahf_halos_test.py"
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"--ignore=tests/array_test.py"
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"--ignore=tests/bridge_test.py"
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"--ignore=tests/family_test.py"
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"--ignore=tests/partial_tipsy_test.py"
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"--ignore=tests/snapshot_test.py"
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"--ignore=tests/test_profile.py"
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"--ignore=tests/gadget_test.py"
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"--ignore=tests/gadgethdf_test.py"
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"--ignore=tests/grafic_test.py"
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"--ignore=tests/halotools_test.py"
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"--ignore=tests/nchilada_test.py"
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"--ignore=tests/ramses_new_ptcl_format_test.py"
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"--ignore=tests/ramses_test.py"
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"--ignore=tests/rockstar_test.py"
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"--ignore=tests/sph_image_test.py"
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"--ignore=tests/sph_smooth_test.py"
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"--ignore=tests/subfind_test.py"
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"--ignore=tests/subfindhdf_gadget4_test.py"
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"--ignore=tests/tipsy_test.py"
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"-k"
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(string-append
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"not test_div_curl_smoothing"
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" and not test_float_kd"
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" and not test_kd_delete"
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" and not test_kd_issue_88"
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" and not test_kdtree_from_existing_kdtree"
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" and not test_kdtree_shared_mem"
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" and not test_neighbour_list"
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" and not test_particles_in_sphere"
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" and not test_periodic_smoothing"
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" and not test_smooth"
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" and not test_smooth_WendlandC2"))
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#:phases
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#~(modify-phases %standard-phases
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(add-before 'build 'set-compiler
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(lambda _
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(setenv "CC" #$(cc-for-target)))))))
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(list
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;; tests: 91 passed, 6 skipped, 12 deselected
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#:test-flags
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;; XXX: testdata is distributed via Zenodo
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;; <https://zenodo.org/records/17084976> with total size more than 2GiB,
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;; refer to the helper script obtaining it
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;; <pynbody/test_utils/__init__.py>.
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#~(list #$@(map (lambda (file) (string-append "--ignore=tests/" file))
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(list "adaptahop_test.py"
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"ahf_halos_test.py"
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"array_test.py"
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"bridge_test.py"
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"copy_on_access_test.py"
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"family_test.py"
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"gadget_test.py"
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"gadgethdf_test.py"
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"gizmo_test.py"
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"grafic_test.py"
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"gravity_test.py"
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"halos_test.py"
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"halotools_test.py"
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"hbtplus_test.py"
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"hmf_test.py"
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"hop_test.py"
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"ionfrac_test.py"
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"kdtree_test.py"
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"luminosity_test.py"
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"morphology_test.py"
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"nchilada_test.py"
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"partial_tipsy_test.py"
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"pkdgravhdf_test.py"
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"plot_stars_test.py"
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"profile_test.py"
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"ramses_new_ptcl_format_test.py"
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"ramses_test.py"
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"rockstar_test.py"
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"snapshot_test.py"
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"sph_image_test.py"
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"subfind_test.py"
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"subfindhdf_gadget4_test.py"
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"subfindhdf_test.py"
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"swift_test.py"
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"tipsy_test.py"
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"velociraptor_test.py"))
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"--deselect=tests/shape_test.py::test_2D_shape"
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"--deselect=tests/shape_test.py::test_3D_shape"
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"--deselect=tests/shape_test.py::test_halo_shape_wrapper"
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"--deselect=tests/test_profile.py::test_unique_hash_generation"
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"--deselect=tests/test_profile.py::test_write_profile"
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;; DeprecationWarning: backend2gui is deprecated since IPython
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;; 8.24, backends are managed in matplotlib and can be
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;; externally registered.
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"--deselect=tests/plot_hist2d_test.py::test_hist2d"
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"--deselect=tests/plot_hist2d_test.py::test_hist2d_massweight"
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"--deselect=tests/schmidtlaw_test.py::test_full_disc"
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"--deselect=tests/schmidtlaw_test.py::test_truncated_disc")
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#:phases
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#~(modify-phases %standard-phases
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(add-before 'check 'pre-check
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(lambda _
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(mkdir-p "testdata/empty_folder_0001")
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(setenv "HOME" "/tmp"))))))
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(native-inputs
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(list python-cython
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python-ipython
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python-pandas
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python-pytest
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python-setuptools
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python-wheel))
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python-setuptools))
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(propagated-inputs
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(list python-h5py
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(list python-certifi
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python-h5py
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python-matplotlib
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python-numpy
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python-posix-ipc
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python-scipy))
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(home-page "https://pynbody.github.io/pynbody/index.html")
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(synopsis "Light-weight astronomical N-body/SPH analysis for python")
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(description "@code{Pynbody} is an analysis framework for N-body and hydrodynamic
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(description
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"@code{Pynbody} is an analysis framework for N-body and hydrodynamic
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astrophysical simulations supporting PKDGRAV/Gasoline, Gadget, Gadget4/Arepo,
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N-Chilada and RAMSES AMR outputs.")
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(license license:gpl3+)))
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(define-public python-pynbody-1
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(package
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(inherit python-pynbody)
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(name "python-pynbody")
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(version "1.6.0.post0")
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(source
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(origin
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(inherit (package-source python-pynbody))
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pynbody/pynbody")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "0rl9ais4yc6kdijq1il4vi3mplp7z6bcih4x55axhan5n3n7riwi"))))))
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(define-public python-pyregion
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(package
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(name "python-pyregion")
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@@ -10719,7 +10749,7 @@ any arbitrary astrometric projection defined in the WCS standard.")
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(arguments
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(list
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;; XXX: Full integration tests require running database, see projects
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;; CI, unit tests are quite compute instance.
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;; CI, unit tests are quite compute-intensive.
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;;
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;; tests: 279 passed, 1 deselected, 105 warnings
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#:test-flags
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@@ -10746,7 +10776,7 @@ any arbitrary astrometric projection defined in the WCS standard.")
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((".*tangos_preprocess_bh =.*") "")))))))
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(native-inputs
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(list python-pymysql
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python-pynbody
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python-pynbody-1
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python-pyquery
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python-pytest
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python-setuptools
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