diff options
| -rw-r--r-- | gnu/packages/python-science.scm | 112 |
1 files changed, 59 insertions, 53 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 9a75bf3089..d1698e5f67 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -42,6 +42,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) + #:use-module (gnu packages build-tools) #:use-module (gnu packages check) #:use-module (gnu packages cpp) #:use-module (gnu packages databases) @@ -75,81 +76,86 @@ (define-public python-scipy (package (name "python-scipy") - (version "1.8.0") + (version "1.9.1") (source (origin (method url-fetch) (uri (pypi-uri "scipy" version)) (sha256 - (base32 "1gghkwn93niyasm36333xbqrnn3yiadq9d97wnc9mg14nzbg5m1i")))) - (outputs '("out" "doc")) + (base32 "1jcb94xal7w7ax80kaivqqics36v8smi4a3xngyxbrh0i538rli6")))) (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 - (lambda _ - (setenv "SCIPY_USE_PYTHRAN" "0"))) - (add-before 'build 'change-home-dir + (add-after 'unpack 'loosen-requirements (lambda _ - ;; Change from /homeless-shelter to /tmp for write permission. - (setenv "HOME" "/tmp"))) - (add-before 'build 'configure-openblas + (substitute* "pyproject.toml" + (("numpy==") "numpy>=") + (("meson==") "meson>=")))) + (replace 'build (lambda _ - (call-with-output-file "site.cfg" - (lambda (port) - (format port - "\ -[blas] -libraries = openblas -library_dirs = ~a/lib -include_dirs = ~:*~a/include - -[atlas] -library_dirs = ~:*~a/lib -atlas_libs = openblas~%" #$(this-package-input "openblas")))))) - (add-before 'build 'parallelize-build + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'install (lambda _ - (setenv "NPY_NUM_BUILD_JOBS" - (number->string (parallel-job-count))))) - (add-before 'check 'install-doc - (lambda* (#:key outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append data "/doc/" #$name "-" #$version)) - (html (string-append doc "/html"))) - (with-directory-excursion "doc" - ;; Build doc. - (invoke "make" "html" - ;; Building the documentation takes a very long time. - ;; Parallelize it. - (string-append "SPHINXOPTS=-j" - (number->string (parallel-job-count)))) - ;; Install doc. - (mkdir-p html) - (copy-recursively "build/html" html))))) + (let ((whl (car (find-files "dist" "\\.whl$")))) + (invoke "pip" "--no-cache-dir" "--no-input" + "install" "--no-deps" "--prefix" #$output whl)))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? - (invoke "./runtests.py" "-vv" "--no-build" "--mode=fast" - "-j" (number->string (parallel-job-count))))))))) - (propagated-inputs (list python-numpy python-matplotlib python-pyparsing)) + ;; Step out of the source directory to avoid interference. + (with-directory-excursion "/tmp" + (invoke "python" "-c" + (string-append + "import scipy; scipy.test('fast', parallel=" + (number->string (parallel-job-count)) + ", verbose=2)")))))) + (add-after 'check 'install-doc + (lambda* (#:key outputs #:allow-other-keys) + ;; FIXME: Documentation cannot be built because it requires + ;; a newer version of pydata-sphinx-theme, which currently + ;; cannot build without internet access: + ;; <https://github.com/pydata/pydata-sphinx-theme/issues/628>. + ;; Keep the phase for easy testing. + (let ((sphinx-build (false-if-exception + (search-input-file input "bin/sphinx-build")))) + (if sphinx-build + (let* ((doc (assoc-ref outputs "doc")) + (data (string-append doc "/share")) + (docdir (string-append + data "/doc/" + #$(package-name this-package) "-" + #$(package-version this-package))) + (html (string-append docdir "/html"))) + (with-directory-excursion "doc" + ;; 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) + (copy-recursively "build/html" html))) + (format #t "sphinx-build not found, skipping~%")))))))) + (propagated-inputs + (list python-numpy python-matplotlib python-pyparsing python-pythran)) (inputs (list openblas pybind11)) (native-inputs (list gfortran - perl + ;; XXX: Adding gfortran shadows GCC headers, causing a compilation + ;; failure. Somehow also providing GCC works around it ... + gcc + meson-python + pkg-config python-cython - python-numpydoc - python-pydata-sphinx-theme + python-pypa-build python-pytest python-pytest-xdist - python-sphinx - python-sphinx-panels - python-threadpoolctl - which)) + python-threadpoolctl)) (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 |