From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
To: 55104@debbugs.gnu.org
Cc: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Subject: [bug#55104] [PATCH 075/232] gnu: python-scipy: Update to 1.8.0 and enable parallel build.
Date: Sun, 24 Apr 2022 23:56:41 -0400 [thread overview]
Message-ID: <20220425035918.25683-75-maxim.cournoyer@gmail.com> (raw)
In-Reply-To: <20220425035918.25683-1-maxim.cournoyer@gmail.com>
* gnu/packages/python-science.scm (python-scipy): Update to 1.8.0.
[modules]: New argument.
[phases]{disable-broken-tests}: Delete phase.
{configure-openblas}: Streamline configuration template.
{parallelize-build}: New phase.
{install-doc}: Move before 'check phase. Remove now extraneous
'add-installed-pythonpath' call. Remove the SPHINXBUILD and PYVER Make
variables, as well as conf.py patching. Provide SPHINXOPTS to build doc in
parallel. Simply recursively copy the 'html' output directory to install the
doc.
{check}: Remove extraneous INPUTS and OUTPUTS arguments. Start tests with the
'runtests.py' launcher, which accepts a '-j' argument to run the tests in
parallel.
[native-inputs]: Sort inputs. Add python-pytest-xdist and
python-threadpoolctl.
[home-page]: Update.
---
gnu/packages/python-science.scm | 91 +++++++++++++--------------------
1 file changed, 36 insertions(+), 55 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index dfe6a66e61..1852a16047 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -72,17 +72,20 @@ (define-module (gnu packages python-science)
(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
@@ -92,81 +95,59 @@ (define-public python-scipy
(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
--
2.34.0
next prev parent reply other threads:[~2022-04-25 4:21 UTC|newest]
Thread overview: 111+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-04-25 3:57 [bug#55104] [PATCH 000/232] Update IPython to latest, fix texlive-polyglossia, add more Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 001/232] gnu: python-ipython: Re-order fields Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 002/232] gnu: python-astroid: Propagate python-typing-extensions Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 003/232] gnu: Add python-pure-eval Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 004/232] gnu: Add python-asttokens Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 005/232] gnu: Add python-littleutils Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 006/232] gnu: Add python-stack-data Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 007/232] gnu: python-traitlets: Update to 5.1.1 Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 008/232] gnu: python-jinja2: Update to 3.1.1 Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 009/232] gnu: python-prompt-toolkit: Update to 3.0.29 Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 010/232] gnu: python-ipython: Update to 8.2.0 [fixes CVE-2022-21699] Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 011/232] gnu: python-nbformat: Update to 5.3.0 Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 012/232] gnu: Add texlive-paralist Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 013/232] gnu: Add texlive-stix2-otf Maxim Cournoyer
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2022-04-25 3:55 ` [bug#55104] [PATCH 015/232] gnu: Add texlive-makecmds Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 016/232] gnu: Add texlive-csplain Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 017/232] gnu: Add texlive-cs Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 018/232] gnu: Add texlive-zref Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 019/232] gnu: Add python-pcpp Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 020/232] gnu: Add opentype-sanitizer Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 021/232] gnu: Add python-opentype-sanitizer Maxim Cournoyer
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2022-04-25 3:55 ` [bug#55104] [PATCH 024/232] gnu: Add python-unicodedata2 Maxim Cournoyer
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2022-04-25 3:55 ` [bug#55104] [PATCH 027/232] gnu: Add python-fontpens-bootstrap Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 028/232] gnu: Add python-booleanoperations Maxim Cournoyer
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2022-04-25 3:55 ` [bug#55104] [PATCH 030/232] gnu: Add python-fontpens Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 031/232] gnu: Add python-defcon Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 032/232] gnu: Add python-fontparts Maxim Cournoyer
2022-04-25 3:55 ` [bug#55104] [PATCH 033/232] gnu: Add python-cu2qu Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 034/232] gnu: Add python-ufoprocessor Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 035/232] gnu: Add python-ufonormalizer Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 036/232] gnu: Add python-types-toml Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 037/232] gnu: Add python-pytest-mypy Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 038/232] gnu: Add python-jaraco-context-bootstrap Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 039/232] gnu: Add python-jaraco-functools-bootstrap Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 040/232] gnu: Add python-autocommand Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 041/232] gnu: Add python-types-freezegun Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 042/232] gnu: Add python-types-pytz Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 043/232] gnu: Add python-pytest-freezegun Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 044/232] gnu: Add python-pytest-enabler-bootstrap Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 045/232] gnu: Add python-path-bootstrap Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 046/232] gnu: Add python-pip-run-bootstrap Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 047/232] gnu: python-importlib-metadata: Update to 4.11.3 Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 048/232] gnu: python-pytest-black: Update to 0.3.12 Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 049/232] gnu: python-mypy: Update to 0.942 and fix search path Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 050/232] gnu: Add python-types-docutils Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 051/232] gnu: python-pytest-checkdocs: Update to 2.7.1 Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 052/232] gnu: Add python-jaraco-classes Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 053/232] gnu: Add python-jaraco-context Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 054/232] gnu: Add python-jaraco-functools Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 055/232] gnu: Add python-pytest-enabler Maxim Cournoyer
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2022-04-25 3:56 ` [bug#55104] [PATCH 057/232] gnu: Add python-pip-run Maxim Cournoyer
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2022-04-25 3:56 ` [bug#55104] [PATCH 059/232] gnu: Add python-pytest-perf Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 060/232] gnu: python-factory-boy: Update to 3.2.1 Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 061/232] gnu: python-faker: Update to 13.3.4 and honor TESTS? Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 062/232] gnu: Add python-pytest-randomly Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 063/232] gnu: Add psautohint-font-data Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 064/232] gnu: Add psautohint Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 065/232] gnu: Add python-ordered-set Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 066/232] gnu: Add python-xdoctest Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 067/232] gnu: Add python-ubelt Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 068/232] gnu: python-setuptools: Update to 62.0.0 Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 069/232] gnu: python-pathpy: Deprecate by python-path Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 070/232] gnu: python-pytest-shutil: Adjust to use python-path Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 071/232] gnu: python-pytest-cov: Update to 3.0.0 Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 072/232] gnu: Add python-scikit-build Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 073/232] gnu: python-jupyter-packaging: Update to 0.12.0, run test suite Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 074/232] gnu: python-scipy: Move input fields below arguments field Maxim Cournoyer
2022-04-25 3:56 ` Maxim Cournoyer [this message]
2022-04-25 3:56 ` [bug#55104] [PATCH 076/232] gnu: Add java-antlr4-runtime-cpp Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 077/232] gnu: Add python-fonttools-next Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 078/232] gnu: Add python-afdko Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 079/232] gnu: Add python-cffsubr Maxim Cournoyer
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2022-04-25 3:56 ` [bug#55104] [PATCH 081/232] gnu: Add python-skia-pathops Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 082/232] gnu: Add python-ufolib2 Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 083/232] gnu: Add python-compreffor Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 084/232] gnu: Add python-ufo2ft Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 085/232] gnu: Add python-sfdlib Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 086/232] gnu: Add font-amiri Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 087/232] gnu: Add font-sil-ezra Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 088/232] gnu: Add texlive-bidi Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 089/232] gnu: Add font-gfs-ambrosia Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 090/232] gnu: python-click: Update to 8.1.2 and honor TESTS? Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 091/232] gnu: python-flask: Update to 2.1.1 Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 092/232] gnu: Add python-untangle Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 093/232] gnu: python-black: Update to 22.3.0 Maxim Cournoyer
2022-04-25 3:57 ` [bug#55104] [PATCH 094/232] gnu: pylint: Run tests in parallel Maxim Cournoyer
2022-04-25 3:57 ` [bug#55104] [PATCH 095/232] gnu: python-trio: Update to 0.20.0 Maxim Cournoyer
2022-04-25 3:57 ` [bug#55104] [PATCH 096/232] gnu: Add python-pydevd Maxim Cournoyer
2022-04-25 3:57 ` [bug#55104] [PATCH 097/232] gnu: Add python-debugpy Maxim Cournoyer
2022-04-25 3:57 ` [bug#55104] [PATCH 098/232] gnu: python-greenlet: Update to 1.1.2 Maxim Cournoyer
2022-04-25 3:57 ` [bug#55104] [PATCH 099/232] gnu: Add python-pytest-forked-next Maxim Cournoyer
2022-04-25 3:57 ` [bug#55104] [PATCH 100/232] gnu: python-pytest-xdist-next: Update to 2.5.0 Maxim Cournoyer
2022-04-25 3:57 ` [bug#55104] [PATCH 101/232] gnu: Add python-ipyparallel-bootstrap Maxim Cournoyer
2022-04-25 9:53 ` [bug#55104] [PATCH 000/232] Update IPython to latest, fix texlive-polyglossia, add more Lars-Dominik Braun
2022-04-25 13:15 ` Maxim Cournoyer
2022-04-26 7:36 ` Lars-Dominik Braun
2022-04-27 3:09 ` Maxim Cournoyer
2022-04-27 11:50 ` Lars-Dominik Braun
2022-05-12 1:31 ` Maxim Cournoyer
2022-04-26 11:21 ` zimoun
2022-04-25 11:36 ` Julien Lepiller
2022-04-25 13:23 ` Maxim Cournoyer
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