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.
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Marius Bakke
parent
44d73b3370
commit
888dfc8eb6
@ -42,6 +42,7 @@
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#:use-module (gnu packages base)
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#:use-module (gnu packages bioinformatics)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages build-tools)
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#:use-module (gnu packages check)
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#:use-module (gnu packages cpp)
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#:use-module (gnu packages databases)
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@ -75,81 +76,86 @@
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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 "1.8.0")
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(version "1.9.1")
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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 "1gghkwn93niyasm36333xbqrnn3yiadq9d97wnc9mg14nzbg5m1i"))))
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(outputs '("out" "doc"))
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(base32 "1jcb94xal7w7ax80kaivqqics36v8smi4a3xngyxbrh0i538rli6"))))
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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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(add-after 'unpack 'loosen-requirements
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(lambda _
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(setenv "SCIPY_USE_PYTHRAN" "0")))
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(add-before 'build 'change-home-dir
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(substitute* "pyproject.toml"
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(("numpy==") "numpy>=")
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(("meson==") "meson>="))))
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(replace 'build
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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-before 'build 'configure-openblas
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;; ZIP does not support timestamps before 1980.
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(setenv "SOURCE_DATE_EPOCH" "315532800")
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(invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
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(replace 'install
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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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"\
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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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[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 "-" #$version))
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(html (string-append doc "/html")))
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(with-directory-excursion "doc"
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;; Build doc.
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(invoke "make" "html"
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;; Building the documentation takes a very long time.
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;; Parallelize it.
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(string-append "SPHINXOPTS=-j"
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(number->string (parallel-job-count))))
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;; Install doc.
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(mkdir-p html)
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(copy-recursively "build/html" html)))))
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(let ((whl (car (find-files "dist" "\\.whl$"))))
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(invoke "pip" "--no-cache-dir" "--no-input"
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"install" "--no-deps" "--prefix" #$output whl))))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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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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;; Step out of the source directory to avoid interference.
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(with-directory-excursion "/tmp"
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(invoke "python" "-c"
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(string-append
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"import scipy; scipy.test('fast', parallel="
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(number->string (parallel-job-count))
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", verbose=2)"))))))
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(add-after 'check 'install-doc
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(lambda* (#:key outputs #:allow-other-keys)
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;; FIXME: Documentation cannot be built because it requires
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;; a newer version of pydata-sphinx-theme, which currently
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;; cannot build without internet access:
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;; <https://github.com/pydata/pydata-sphinx-theme/issues/628>.
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;; Keep the phase for easy testing.
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(let ((sphinx-build (false-if-exception
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(search-input-file input "bin/sphinx-build"))))
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(if sphinx-build
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(let* ((doc (assoc-ref outputs "doc"))
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(data (string-append doc "/share"))
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(docdir (string-append
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data "/doc/"
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#$(package-name this-package) "-"
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#$(package-version this-package)))
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(html (string-append docdir "/html")))
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(with-directory-excursion "doc"
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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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(copy-recursively "build/html" html)))
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(format #t "sphinx-build not found, skipping~%"))))))))
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(propagated-inputs
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(list python-numpy python-matplotlib python-pyparsing python-pythran))
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(inputs (list openblas pybind11))
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(native-inputs
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(list gfortran
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perl
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;; XXX: Adding gfortran shadows GCC headers, causing a compilation
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;; failure. Somehow also providing GCC works around it ...
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gcc
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meson-python
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pkg-config
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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-pypa-build
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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-threadpoolctl
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which))
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python-threadpoolctl))
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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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