diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 97 |
1 files changed, 74 insertions, 23 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 108dc8dd2ff..28298c208a1 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -3441,47 +3441,95 @@ cross-validation.") (define-public python-scipy (package (name "python-scipy") - (version "1.12.0") + (version "1.16.3") + ;; TODO: PyPI archive bundles extra in subprojects: + ;; - https://github.com/boostorg/math + ;; - https://github.com/scipy/HiGHS + ;; - https://github.com/scipy/xsf + ;; - qhull (source (origin (method url-fetch) (uri (pypi-uri "scipy" version)) (sha256 - (base32 "18rn15wg3lp58z204fbjjhy0h79c53yg3c4qqs9h3liniamspxab")))) + (base32 "1jxf6mjr3whbh23p8bnlcyiss5rsamq37qgys8xz8qi781cpds01")))) (build-system pyproject-build-system) (arguments (list + ;; tests: 78689 passed, 4982 skipped, 319 xfailed, 19 xpassed, 2660 warnings + #:configure-flags + ''(("setup-args" . #("-Duse-system-libraries=all"))) + #:test-flags + #~(list "--durations=10" + "--numprocesses" (number->string (min 4 (parallel-job-count))) + "--pyargs" "scipy" + "-k" (string-join + ;; Network access is requied. + (list "not test_ascent" + "test_electrocardiogram" + "test_existence_all" + "test_face" + ;; pycparser.ply.yacc.YaccError: Unable to build parser + "test_callbacks" + "test_bad_callbacks" + ;; AssertionError: Items are not equal: ACTUAL: + ;; np.complex128(inf+nanj) DESIRED: (inf+0j) + "test_expm1_complex" + ;; AssertionError: Not equal to tolerance rtol=1e-07, atol=0 + "test_log1p_complex" + ;; AssertionError: Not equal to tolerance rtol=5e-09, atol=0 + "test_nctdtr_accuracy[3.0-5.0--2.0-1.5645373999149622e-09-5e-09]" + ;; Bad results (X out of Y) for the following points + ;; (in output 0): + "test_spherical_in_complex" + "test_spherical_jn_complex" + "test_spherical_kn" + "test_spherical_yn_complex" + ;; Not equal to tolerance rtol=1e-07, atol=0 + "test_negative_real_gh14582[spherical_in-False]" + "test_negative_real_gh14582[spherical_in-True]" + "test_negative_real_gh14582[spherical_jn-False]" + "test_negative_real_gh14582[spherical_jn-True]" + "test_negative_real_gh14582[spherical_yn-False]" + "test_negative_real_gh14582[spherical_yn-True]" + ;; Failed: DID NOT WARN. No warnings of type (<class + ;; 'RuntimeWarning'>,) were emitted. + "test_boost_eval_issue_14606") + " and not ")) #:phases #~(modify-phases %standard-phases - #$@(if (target-x86-32?) - #~((add-after 'unpack 'apply-i686-patch - (lambda _ - (let ((patch-file - #$(local-file - (search-patch "python-scipy-i686.patch")))) - (invoke "patch" "--force" "-p1" "-i" - patch-file))))) - #~()) + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "meson.build" + ;; boost + (("1.88.0") "1.89.0")))) + (add-after 'set-paths 'hide-gfortran + ;; See: <https://issues.guix.gnu.org/73439#45>. + (lambda* (#:key inputs #:allow-other-keys) + (let ((gfortran #$(this-package-native-input "gfortran"))) + (setenv "CPLUS_INCLUDE_PATH" + (string-join + (delete (string-append gfortran "/include/c++") + (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) + ":"))))) (replace 'check - (lambda* (#:key tests? #:allow-other-keys) + (lambda* (#:key test-flags tests? #:allow-other-keys) (when tests? ;; Step out of the source directory to avoid interference. + ;; See: <.github/workflows/linux.yml> for any other posible + ;; tests setup. (with-directory-excursion "/tmp" - (invoke "python" "-c" - (string-append - "import scipy; scipy.test('fast', parallel=" - (number->string (parallel-job-count)) - ", verbose=2)"))))))))) + (setenv "HOME" "/tmp") + (setenv "PYTHONOPTIMIZE" "2") + (apply invoke "pytest" "-vv" test-flags)))))))) (native-inputs (list gfortran - ;; XXX: Adding gfortran shadows GCC headers, causing a compilation - ;; failure. Somehow also providing GCC works around it ... - gcc meson-python pkg-config python-click - python-cython-0 + python-cython python-doit + python-hypothesis python-mpmath python-numpydoc python-pooch @@ -3495,8 +3543,11 @@ cross-validation.") python-threadpoolctl python-typing-extensions)) (inputs - (list openblas - pybind11-2.10)) + (list boost + openblas + pybind11 + qhull + xsimd)) (propagated-inputs (list python-numpy)) (home-page "https://scipy.org/") |