diff options
| -rw-r--r-- | gnu/packages/python-science.scm | 91 |
1 files changed, 36 insertions, 55 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index d192543f5c..2cabdb490c 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -73,17 +73,20 @@ (define-public python-scipy (package (name "python-scipy") - (version "1.7.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (pypi-uri "scipy" version)) (sha256 - (base32 "1gxsnw6viz2j3sm8ak2a8l7fcn4b2zm3kzfm8w57xxyyrzx7an5b")))) + (base32 "1gghkwn93niyasm36333xbqrnn3yiadq9d97wnc9mg14nzbg5m1i")))) (outputs '("out" "doc")) (build-system python-build-system) (arguments (list + #:modules '((guix build utils) + (guix build python-build-system) + (ice-9 format)) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'disable-pythran @@ -93,81 +96,59 @@ (lambda _ ;; Change from /homeless-shelter to /tmp for write permission. (setenv "HOME" "/tmp"))) - (add-after 'unpack 'disable-broken-tests - (lambda _ - (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py" - (("^( +)def test_threads_parallel\\(self\\):" m indent) - (string-append indent - "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - m))) - (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py" - (("^def test_parallel_threads\\(\\):" m) - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - m))))) (add-before 'build 'configure-openblas (lambda _ (call-with-output-file "site.cfg" (lambda (port) (format port - "[blas] + "\ +[blas] libraries = openblas library_dirs = ~a/lib -include_dirs = ~a/include +include_dirs = ~:*~a/include -# backslash-n to make emacs happy -\n[atlas] -library_dirs = ~a/lib -atlas_libs = openblas -" - #$(this-package-input "openblas") - #$(this-package-input "openblas") - #$(this-package-input "openblas")))))) - (add-after 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) +[atlas] +library_dirs = ~:*~a/lib +atlas_libs = openblas~%" #$(this-package-input "openblas")))))) + (add-before 'build 'parallelize-build + (lambda _ + (setenv "NPY_NUM_BUILD_JOBS" + (number->string (parallel-job-count))))) + (add-before 'check 'install-doc + (lambda* (#:key outputs #:allow-other-keys) (let* ((data (string-append (assoc-ref outputs "doc") "/share")) (doc (string-append data "/doc/" #$name "-" #$version)) - (html (string-append doc "/html")) - (pyver (string-append "PYVER=" - #$(version-major+minor - (package-version python)))) - ;; By default it tries to run sphinx-build through the Python - ;; interpreter which won't work with our shell wrapper. - (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build")) - ;; Make installed package available for building the - ;; documentation - (add-installed-pythonpath inputs outputs) + (html (string-append doc "/html"))) (with-directory-excursion "doc" - ;; Fix generation of images for mathematical expressions. - (substitute* (find-files "source" "conf\\.py") - (("pngmath_use_preview = True") - "pngmath_use_preview = False")) + ;; Build doc. + (invoke "make" "html" + ;; Building the documentation takes a very long time. + ;; Parallelize it. + (string-append "SPHINXOPTS=-j" + (number->string (parallel-job-count)))) + ;; Install doc. (mkdir-p html) - (invoke "make" "html" pyver sphinxbuild) - (with-directory-excursion "build/html" - (for-each (lambda (file) - (let* ((dir (dirname file)) - (tgt-dir (string-append html "/" dir))) - (install-file file html))) - (find-files "."))))))) + (copy-recursively "build/html" html))))) (replace 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (lambda* (#:key tests? #:allow-other-keys) (when tests? - (with-directory-excursion "/tmp" - (invoke "python" "-c" - "import scipy; scipy.test(verbose=2)")))))))) + (invoke "./runtests.py" "-vv" "--no-build" "--mode=fast" + "-j" (number->string (parallel-job-count))))))))) (propagated-inputs (list python-numpy python-matplotlib python-pyparsing)) (inputs (list openblas pybind11)) (native-inputs - (list python-cython + (list gfortran + perl + python-cython + python-numpydoc python-pydata-sphinx-theme python-pytest + python-pytest-xdist python-sphinx python-sphinx-panels - python-numpydoc - gfortran - perl + python-threadpoolctl which)) - (home-page "https://www.scipy.org/") + (home-page "https://scipy.org/") (synopsis "The Scipy library provides efficient numerical routines") (description "The SciPy library is one of the core packages that make up the SciPy stack. It provides many user-friendly and efficient numerical |