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
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@ -73,17 +73,20 @@ (define-module (gnu packages python-science)
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(define-public python-scipy
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(package
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(name "python-scipy")
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(version "1.7.3")
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(version "1.8.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scipy" version))
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(sha256
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(base32 "1gxsnw6viz2j3sm8ak2a8l7fcn4b2zm3kzfm8w57xxyyrzx7an5b"))))
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(base32 "1gghkwn93niyasm36333xbqrnn3yiadq9d97wnc9mg14nzbg5m1i"))))
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(outputs '("out" "doc"))
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(build-system python-build-system)
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(arguments
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(list
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#:modules '((guix build utils)
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(guix build python-build-system)
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(ice-9 format))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'disable-pythran
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@ -93,81 +96,59 @@ (define-public python-scipy
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(lambda _
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;; Change from /homeless-shelter to /tmp for write permission.
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(setenv "HOME" "/tmp")))
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(add-after 'unpack 'disable-broken-tests
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(lambda _
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(substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
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(("^( +)def test_threads_parallel\\(self\\):" m indent)
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(string-append indent
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"@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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m)))
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(substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
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(("^def test_parallel_threads\\(\\):" m)
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(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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m)))))
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(add-before 'build 'configure-openblas
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(lambda _
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(call-with-output-file "site.cfg"
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(lambda (port)
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(format port
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"[blas]
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"\
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[blas]
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libraries = openblas
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library_dirs = ~a/lib
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include_dirs = ~a/include
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include_dirs = ~:*~a/include
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# backslash-n to make emacs happy
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\n[atlas]
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library_dirs = ~a/lib
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atlas_libs = openblas
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"
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#$(this-package-input "openblas")
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#$(this-package-input "openblas")
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#$(this-package-input "openblas"))))))
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(add-after 'install 'install-doc
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(lambda* (#:key inputs outputs #:allow-other-keys)
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[atlas]
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library_dirs = ~:*~a/lib
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atlas_libs = openblas~%" #$(this-package-input "openblas"))))))
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(add-before 'build 'parallelize-build
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(lambda _
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(setenv "NPY_NUM_BUILD_JOBS"
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(number->string (parallel-job-count)))))
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(add-before 'check 'install-doc
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
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(doc (string-append data "/doc/" #$name "-" #$version))
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(html (string-append doc "/html"))
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(pyver (string-append "PYVER="
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#$(version-major+minor
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(package-version python))))
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;; By default it tries to run sphinx-build through the Python
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;; interpreter which won't work with our shell wrapper.
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(sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
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;; Make installed package available for building the
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;; documentation
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(add-installed-pythonpath inputs outputs)
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(html (string-append doc "/html")))
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(with-directory-excursion "doc"
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;; Fix generation of images for mathematical expressions.
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(substitute* (find-files "source" "conf\\.py")
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(("pngmath_use_preview = True")
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"pngmath_use_preview = False"))
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;; Build doc.
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(invoke "make" "html"
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;; Building the documentation takes a very long time.
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;; Parallelize it.
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(string-append "SPHINXOPTS=-j"
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(number->string (parallel-job-count))))
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;; Install doc.
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(mkdir-p html)
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(invoke "make" "html" pyver sphinxbuild)
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(with-directory-excursion "build/html"
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(for-each (lambda (file)
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(let* ((dir (dirname file))
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(tgt-dir (string-append html "/" dir)))
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(install-file file html)))
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(find-files ".")))))))
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(copy-recursively "build/html" html)))))
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(replace 'check
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(lambda* (#:key tests? inputs outputs #:allow-other-keys)
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(with-directory-excursion "/tmp"
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(invoke "python" "-c"
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"import scipy; scipy.test(verbose=2)"))))))))
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(invoke "./runtests.py" "-vv" "--no-build" "--mode=fast"
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"-j" (number->string (parallel-job-count)))))))))
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(propagated-inputs (list python-numpy python-matplotlib python-pyparsing))
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(inputs (list openblas pybind11))
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(native-inputs
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(list python-cython
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(list gfortran
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perl
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python-cython
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python-numpydoc
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python-pydata-sphinx-theme
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python-pytest
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python-pytest-xdist
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python-sphinx
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python-sphinx-panels
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python-numpydoc
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gfortran
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perl
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python-threadpoolctl
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which))
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(home-page "https://www.scipy.org/")
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(home-page "https://scipy.org/")
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(synopsis "The Scipy library provides efficient numerical routines")
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(description "The SciPy library is one of the core packages that make up
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the SciPy stack. It provides many user-friendly and efficient numerical
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