From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
To: 55104@debbugs.gnu.org
Cc: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Subject: [bug#55104] [PATCH 074/232] gnu: python-scipy: Move input fields below arguments field.
Date: Sun, 24 Apr 2022 23:56:40 -0400 [thread overview]
Message-ID: <20220425035918.25683-74-maxim.cournoyer@gmail.com> (raw)
In-Reply-To: <20220425035918.25683-1-maxim.cournoyer@gmail.com>
* gnu/packages/python-science.scm (python-scipy): Move inputs fields below the
arguments field.
[phases]: Use gexp.
{configure-openblas}: Use this-package-input.
{check}: Remove extraneous 'add-installed-pythonpath' call.
{install-doc}: Adjust accordingly.
---
gnu/packages/python-science.scm | 155 ++++++++++++++++----------------
1 file changed, 77 insertions(+), 78 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 07d713e013..dfe6a66e61 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -6,7 +6,7 @@
;;; Copyright © 2016, 2022 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net>
@@ -79,49 +79,36 @@ (define-public python-scipy
(uri (pypi-uri "scipy" version))
(sha256
(base32 "1gxsnw6viz2j3sm8ak2a8l7fcn4b2zm3kzfm8w57xxyyrzx7an5b"))))
- (build-system python-build-system)
- (propagated-inputs
- (list python-numpy python-matplotlib python-pyparsing))
- (inputs
- (list openblas pybind11))
- (native-inputs
- (list python-cython
- python-pydata-sphinx-theme
- python-pytest
- python-sphinx
- python-sphinx-panels
- python-numpydoc
- gfortran
- perl
- which))
(outputs '("out" "doc"))
+ (build-system python-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'disable-pythran
- (lambda _
- (setenv "SCIPY_USE_PYTHRAN" "0")))
- (add-before 'build 'change-home-dir
- (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* (#:key inputs #:allow-other-keys)
- (call-with-output-file "site.cfg"
- (lambda (port)
- (format port
- "[blas]
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'disable-pythran
+ (lambda _
+ (setenv "SCIPY_USE_PYTHRAN" "0")))
+ (add-before 'build 'change-home-dir
+ (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]
libraries = openblas
library_dirs = ~a/lib
include_dirs = ~a/include
@@ -131,42 +118,54 @@ (define-public python-scipy
library_dirs = ~a/lib
atlas_libs = openblas
"
- (assoc-ref inputs "openblas")
- (assoc-ref inputs "openblas")
- (assoc-ref inputs "openblas"))))))
- (add-after 'install 'install-doc
- (lambda* (#:key inputs 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)
- (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"))
- (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 ".")))))))
- (replace 'check
- (lambda* (#:key tests? inputs outputs #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (with-directory-excursion "/tmp"
- (invoke "python" "-c"
- "import scipy; scipy.test(verbose=2)"))))))))
+ #$(this-package-input "openblas")
+ #$(this-package-input "openblas")
+ #$(this-package-input "openblas"))))))
+ (add-after 'install 'install-doc
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+ (doc (string-append data "/doc/" #$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)
+ (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"))
+ (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 ".")))))))
+ (replace 'check
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "/tmp"
+ (invoke "python" "-c"
+ "import scipy; scipy.test(verbose=2)"))))))))
+ (propagated-inputs (list python-numpy python-matplotlib python-pyparsing))
+ (inputs (list openblas pybind11))
+ (native-inputs
+ (list python-cython
+ python-pydata-sphinx-theme
+ python-pytest
+ python-sphinx
+ python-sphinx-panels
+ python-numpydoc
+ gfortran
+ perl
+ which))
(home-page "https://www.scipy.org/")
(synopsis "The Scipy library provides efficient numerical routines")
(description "The SciPy library is one of the core packages that make up
--
2.34.0
next prev parent reply other threads:[~2022-04-25 4:23 UTC|newest]
Thread overview: 111+ messages / expand[flat|nested] mbox.gz Atom feed top
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2022-04-25 3:55 ` [bug#55104] [PATCH 009/232] gnu: python-prompt-toolkit: Update to 3.0.29 Maxim Cournoyer
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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 ` Maxim Cournoyer [this message]
2022-04-25 3:56 ` [bug#55104] [PATCH 075/232] gnu: python-scipy: Update to 1.8.0 and enable parallel build Maxim Cournoyer
2022-04-25 3:56 ` [bug#55104] [PATCH 076/232] gnu: Add java-antlr4-runtime-cpp Maxim Cournoyer
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2022-04-25 3:56 ` [bug#55104] [PATCH 083/232] gnu: Add python-compreffor Maxim Cournoyer
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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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