mirror of
https://codeberg.org/guix/guix.git
synced 2025-10-02 02:15:12 +00:00
gnu: python-scipy: Update to 1.8.0 and enable parallel build.
* 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.
This commit is contained in:
Maxim Cournoyer
parent
5a3634f461
commit
cddedb9c5b
1 changed files with 36 additions and 55 deletions
|
|
@ -73,17 +73,20 @@
|
||||||
(define-public python-scipy
|
(define-public python-scipy
|
||||||
(package
|
(package
|
||||||
(name "python-scipy")
|
(name "python-scipy")
|
||||||
(version "1.7.3")
|
(version "1.8.0")
|
||||||
(source
|
(source
|
||||||
(origin
|
(origin
|
||||||
(method url-fetch)
|
(method url-fetch)
|
||||||
(uri (pypi-uri "scipy" version))
|
(uri (pypi-uri "scipy" version))
|
||||||
(sha256
|
(sha256
|
||||||
(base32 "1gxsnw6viz2j3sm8ak2a8l7fcn4b2zm3kzfm8w57xxyyrzx7an5b"))))
|
(base32 "1gghkwn93niyasm36333xbqrnn3yiadq9d97wnc9mg14nzbg5m1i"))))
|
||||||
(outputs '("out" "doc"))
|
(outputs '("out" "doc"))
|
||||||
(build-system python-build-system)
|
(build-system python-build-system)
|
||||||
(arguments
|
(arguments
|
||||||
(list
|
(list
|
||||||
|
#:modules '((guix build utils)
|
||||||
|
(guix build python-build-system)
|
||||||
|
(ice-9 format))
|
||||||
#:phases
|
#:phases
|
||||||
#~(modify-phases %standard-phases
|
#~(modify-phases %standard-phases
|
||||||
(add-after 'unpack 'disable-pythran
|
(add-after 'unpack 'disable-pythran
|
||||||
|
|
@ -93,81 +96,59 @@
|
||||||
(lambda _
|
(lambda _
|
||||||
;; Change from /homeless-shelter to /tmp for write permission.
|
;; Change from /homeless-shelter to /tmp for write permission.
|
||||||
(setenv "HOME" "/tmp")))
|
(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
|
(add-before 'build 'configure-openblas
|
||||||
(lambda _
|
(lambda _
|
||||||
(call-with-output-file "site.cfg"
|
(call-with-output-file "site.cfg"
|
||||||
(lambda (port)
|
(lambda (port)
|
||||||
(format port
|
(format port
|
||||||
"[blas]
|
"\
|
||||||
|
[blas]
|
||||||
libraries = openblas
|
libraries = openblas
|
||||||
library_dirs = ~a/lib
|
library_dirs = ~a/lib
|
||||||
include_dirs = ~a/include
|
include_dirs = ~:*~a/include
|
||||||
|
|
||||||
# backslash-n to make emacs happy
|
[atlas]
|
||||||
\n[atlas]
|
library_dirs = ~:*~a/lib
|
||||||
library_dirs = ~a/lib
|
atlas_libs = openblas~%" #$(this-package-input "openblas"))))))
|
||||||
atlas_libs = openblas
|
(add-before 'build 'parallelize-build
|
||||||
"
|
(lambda _
|
||||||
#$(this-package-input "openblas")
|
(setenv "NPY_NUM_BUILD_JOBS"
|
||||||
#$(this-package-input "openblas")
|
(number->string (parallel-job-count)))))
|
||||||
#$(this-package-input "openblas"))))))
|
(add-before 'check 'install-doc
|
||||||
(add-after 'install 'install-doc
|
(lambda* (#:key outputs #:allow-other-keys)
|
||||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
||||||
(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
|
(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
|
||||||
(doc (string-append data "/doc/" #$name "-" #$version))
|
(doc (string-append data "/doc/" #$name "-" #$version))
|
||||||
(html (string-append doc "/html"))
|
(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"
|
(with-directory-excursion "doc"
|
||||||
;; Fix generation of images for mathematical expressions.
|
;; Build doc.
|
||||||
(substitute* (find-files "source" "conf\\.py")
|
(invoke "make" "html"
|
||||||
(("pngmath_use_preview = True")
|
;; Building the documentation takes a very long time.
|
||||||
"pngmath_use_preview = False"))
|
;; Parallelize it.
|
||||||
|
(string-append "SPHINXOPTS=-j"
|
||||||
|
(number->string (parallel-job-count))))
|
||||||
|
;; Install doc.
|
||||||
(mkdir-p html)
|
(mkdir-p html)
|
||||||
(invoke "make" "html" pyver sphinxbuild)
|
(copy-recursively "build/html" html)))))
|
||||||
(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
|
(replace 'check
|
||||||
(lambda* (#:key tests? inputs outputs #:allow-other-keys)
|
(lambda* (#:key tests? #:allow-other-keys)
|
||||||
(when tests?
|
(when tests?
|
||||||
(with-directory-excursion "/tmp"
|
(invoke "./runtests.py" "-vv" "--no-build" "--mode=fast"
|
||||||
(invoke "python" "-c"
|
"-j" (number->string (parallel-job-count)))))))))
|
||||||
"import scipy; scipy.test(verbose=2)"))))))))
|
|
||||||
(propagated-inputs (list python-numpy python-matplotlib python-pyparsing))
|
(propagated-inputs (list python-numpy python-matplotlib python-pyparsing))
|
||||||
(inputs (list openblas pybind11))
|
(inputs (list openblas pybind11))
|
||||||
(native-inputs
|
(native-inputs
|
||||||
(list python-cython
|
(list gfortran
|
||||||
|
perl
|
||||||
|
python-cython
|
||||||
|
python-numpydoc
|
||||||
python-pydata-sphinx-theme
|
python-pydata-sphinx-theme
|
||||||
python-pytest
|
python-pytest
|
||||||
|
python-pytest-xdist
|
||||||
python-sphinx
|
python-sphinx
|
||||||
python-sphinx-panels
|
python-sphinx-panels
|
||||||
python-numpydoc
|
python-threadpoolctl
|
||||||
gfortran
|
|
||||||
perl
|
|
||||||
which))
|
which))
|
||||||
(home-page "https://www.scipy.org/")
|
(home-page "https://scipy.org/")
|
||||||
(synopsis "The Scipy library provides efficient numerical routines")
|
(synopsis "The Scipy library provides efficient numerical routines")
|
||||||
(description "The SciPy library is one of the core packages that make up
|
(description "The SciPy library is one of the core packages that make up
|
||||||
the SciPy stack. It provides many user-friendly and efficient numerical
|
the SciPy stack. It provides many user-friendly and efficient numerical
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue