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authorMarius Bakke <marius@gnu.org>2022-09-14 23:42:10 +0200
committerGuix Patches Tester <>2022-09-14 22:44:35 +0100
commit4c409e0e13666986018091e52f60cb0dadb6cad9 (patch)
tree0d32b6fefbb5aca54bce73cecbdedcf9d78164f3
parent17baad745133b6db4ff68cec67d2d91ed79f59e8 (diff)
downloadguix-patches-4c409e0e13666986018091e52f60cb0dadb6cad9.tar
guix-patches-4c409e0e13666986018091e52f60cb0dadb6cad9.tar.gz
gnu: python-scipy: Update to 1.9.1.
* gnu/packages/python-science.scm (python-scipy): Update to 1.9.1. [source]: Switch to GIT-FETCH. [outputs]: Remove. [arguments]: Don't disable Pythran. Don't configure OpenBLAS which is now discovered by pkg-config. Do a "manual" PEP 517 style build. Make install-doc phase conditional on the presence of Sphinx. Simplify tests. [propagated-inputs]: Add PYTHON-PYTHRAN. [native-inputs]: Remove PERL, WHICH, PYTHON-NUMPYDOC, PYTHON-PYDATA-SPHINX-THEME, PYTHON-SPHINX, and PYTHON-SPHINX-PANELS. Add GCC, PKG-CONFIG, PYTHON-PYPA-BUILD and PYTHON-MESON.
-rw-r--r--gnu/packages/python-science.scm112
1 files changed, 59 insertions, 53 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index e2a0fb3a95..0d97a9de4b 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