gnu: python-numpy: Update to 1.21.6 and parallelize build/tests.
* gnu/packages/python-xyz.scm (python-numpy): Update to 1.21.6. Move inputs
and native-inputs fields after arguments. Use gexps.
[modules]: New argument.
[phases]{parallelize-build}: New phase.
{configure-blas}: Format via (ice-9 format).
{fix-executable-paths}: Use search-file-input. Remove obsolete system_info.py
substitution.
{check}: Remove extraneous add-installed-pythonpath and setenv calls. Provide
the '-n' pytest-xdist option.
[native-inputs]: Use python-hypothesis-next.
(python-numpy-next): Inherit from python-numpy.
(python2-numpy): Adjust for gexps.
[phases]{delete-failing-test}: Rename to...
{delete-failing-tests}: ... this.
(python2-numpy-1.8): Likewise, and delete 'delete-failing-tests' phase.
Disable tests.
[native-inputs]: Define as the empty list.
This commit is contained in:
Maxim Cournoyer
parent
bfe7f40650
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411cd4345f
@ -5703,10 +5703,13 @@ writing C extensions for Python as easy as Python itself.")
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"17fqacrpis05w1rpi7d7sbimrk20xf8h6d3vrz5nf6ix3899abil"))))
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(properties '())))
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(define-public python-numpy-next
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;; NOTE: when upgrading numpy please make sure that python-numba,
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;; python-pandas and python-scipy still build, as these three packages are
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;; often used together.
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(define-public python-numpy
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(package
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(name "python-numpy-next")
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(version "1.22.3")
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(name "python-numpy")
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(version "1.21.6")
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(source
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(origin
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(method url-fetch)
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@ -5715,50 +5718,57 @@ writing C extensions for Python as easy as Python itself.")
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version "/numpy-" version ".tar.gz"))
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(sha256
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(base32
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"19dw91pqbqcniw2z57kiyqs1qp56g7kqy1bdyv664g8s62sc01m9"))))
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"0b0c5y35rd3mvwfk5is1d5ppfw9nl4d2rgx9xkwh1p0w394wdvyl"))))
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(build-system python-build-system)
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(inputs
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(list openblas))
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(native-inputs
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(list python-cython python-hypothesis-6.23 python-pytest
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python-pytest-xdist gfortran))
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-before 'build 'configure-blas
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(lambda* (#:key inputs #:allow-other-keys)
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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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(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-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 'build 'configure-blas
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(lambda* (#:key inputs #:allow-other-keys)
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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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[openblas]
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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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"
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(assoc-ref inputs "openblas")
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(assoc-ref inputs "openblas"))))))
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(add-before 'build 'fix-executable-paths
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(lambda* (#:key inputs #:allow-other-keys)
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;; Make /gnu/store/...-bash-.../bin/sh the default shell,
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;; instead of /bin/sh.
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(substitute* "numpy/distutils/exec_command.py"
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(("(os.environ.get\\('SHELL', ')(/bin/sh'\\))" match match-start match-end)
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(string-append match-start (assoc-ref inputs "bash") match-end)))
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;; Use "gcc" executable, not "cc".
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(substitute* "numpy/distutils/system_info.py"
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(("c = distutils\\.ccompiler\\.new_compiler\\(\\)")
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"c = distutils.ccompiler.new_compiler(); c.set_executables(compiler='gcc',compiler_so='gcc',linker_exe='gcc',linker_so='gcc -shared')"))))
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(replace 'check
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(lambda* (#:key tests? outputs inputs #:allow-other-keys)
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(when tests?
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;; Make installed package available for running the tests.
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(add-installed-pythonpath inputs outputs)
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;; Make sure "f2py" etc is found.
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(setenv "PATH" (string-append (assoc-ref outputs "out") "/bin"
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":" (getenv "PATH")))
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(invoke "./runtests.py"
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"-j" (number->string (parallel-job-count)))))))))
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include_dirs = ~:*~a/include~%" #$(this-package-input "openblas"))))))
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(add-before 'build 'fix-executable-paths
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(lambda* (#:key inputs #:allow-other-keys)
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;; Make /gnu/store/...-bash-.../bin/sh the default shell,
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;; instead of /bin/sh.
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(substitute* "numpy/distutils/exec_command.py"
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(("'/bin/sh'")
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(format #f "~s" (search-input-file inputs "bin/bash"))))))
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(replace 'check
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(lambda* (#:key tests? outputs inputs #: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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;; Contrary to scipy, the runtests.py script of numpy
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;; does *not* automatically provide -n when -j is used
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;; (see: https://github.com/numpy/numpy/issues/21359).
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"--" "-n" (number->string (parallel-job-count))
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"-k" (string-append
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;; These tests may fail on 32-bit systems (see:
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;; https://github.com/numpy/numpy/issues/18387).
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"not test_float_remainder_overflow "
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"and not test_pareto"))))))))
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(native-inputs
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(list python-cython
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python-hypothesis-next
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python-pytest
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python-pytest-xdist
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gfortran))
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(inputs (list bash openblas))
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(home-page "https://numpy.org")
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(synopsis "Fundamental package for scientific computing with Python")
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(description "NumPy is the fundamental package for scientific computing
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@ -5769,10 +5779,26 @@ capabilities.")
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(properties `((python2-variant . ,(delay python2-numpy))))
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(license license:bsd-3)))
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(define-public python-numpy-next
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(package
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(inherit python-numpy)
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(name "python-numpy-next")
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(version "1.22.3")
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(source
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(origin
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(inherit (package-source python-numpy))
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(method url-fetch)
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(uri (string-append
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"https://github.com/numpy/numpy/releases/download/v"
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version "/numpy-" version ".tar.gz"))
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(sha256
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(base32
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"19dw91pqbqcniw2z57kiyqs1qp56g7kqy1bdyv664g8s62sc01m9"))))))
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;; Numpy 1.16.x are the last versions that support Python 2.
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(define-public python2-numpy
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(let ((numpy (package-with-python2
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(strip-python2-variant python-numpy-next))))
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(strip-python2-variant python-numpy))))
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(package
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(inherit numpy)
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(name "python2-numpy")
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@ -5788,80 +5814,46 @@ capabilities.")
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(arguments
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(substitute-keyword-arguments (package-arguments numpy)
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((#:phases phases)
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`(modify-phases ,phases
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(add-after 'unpack 'delete-failing-test
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(lambda _
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;; There's just one failing test here.
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(delete-file "numpy/linalg/tests/test_linalg.py")
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;; ...and this one depends on the previous one.
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(delete-file "numpy/matrixlib/tests/test_matrix_linalg.py")))))))
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#~(modify-phases #$phases
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(add-after 'unpack 'delete-failing-tests
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(lambda _
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;; There's just one failing test here.
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(delete-file "numpy/linalg/tests/test_linalg.py")
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;; ...and this one depends on the previous one.
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(delete-file "numpy/matrixlib/tests/test_matrix_linalg.py")))
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(replace 'check
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;; Older versions don't cope well with the extra Pytest
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;; options, so remove them.
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(lambda* (#:key tests? outputs inputs #: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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(native-inputs
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(list python2-cython python2-pytest gfortran)))))
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;; Needed by python-numba, see https://github.com/numba/numba/issues/7176
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(define-public python-numpy-1.20
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(package
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(inherit python-numpy-next)
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(name "python-numpy")
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(version "1.20.3")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/numpy/numpy/releases/download/v"
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version "/numpy-" version ".tar.gz"))
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(sha256
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(base32
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"140zq9snx0di4id4g97vaw9zz8x2rfla5lp3a70j666f5030yd5p"))))
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;; python-numpy-next replaced python-hypothesis with
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;; python-hypothesis-6.23. We switch it back here, to prevent
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;; python-numpy-1.20 and its numerous dependents from being rebuilt.
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(native-inputs
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(list python-cython python-hypothesis python-pytest
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python-pytest-xdist gfortran))
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;; 92 tests fail, many of them because parts of the temp file name
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;; accidentally ends up in a comparison.
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(arguments
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(substitute-keyword-arguments (package-arguments python-numpy-next)
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((#:tests? _ #t) #f)))))
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;; NOTE: when upgrading numpy please make sure that python-pandas and
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;; python-scipy still build, as these three packages are often used together.
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(define-public python-numpy python-numpy-1.20)
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;; NOTE: NumPy 1.8 is packaged only for Python 2 because it is of
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;; interest only for legacy code going back to NumPy's predecessor
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;; Numeric.
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(define-public python2-numpy-1.8
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(package (inherit python2-numpy)
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(package
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(inherit python2-numpy)
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(version "1.8.2")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/numpy/numpy")
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(commit (string-append "v" version))))
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(url "https://github.com/numpy/numpy")
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(commit (string-append "v" version))))
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(file-name (git-file-name "numpy" version))
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(sha256
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(base32
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"0ikgi15rsqwbkfsjjxrwh40lqyal2wvyp3923y6w6ch3dcr82sfk"))))
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(arguments
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(substitute-keyword-arguments (package-arguments python2-numpy)
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((#:phases phases)
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`(modify-phases ,phases
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(replace 'configure-blas
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(lambda* (#:key inputs #:allow-other-keys)
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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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"[openblas]
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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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"
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(assoc-ref inputs "openblas")
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(assoc-ref inputs "openblas"))))))))))
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(native-inputs
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(list python2-nose))
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(arguments (substitute-keyword-arguments (package-arguments python2-numpy)
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((#:tests? _ #f) #f) ;disable tests
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((#:phases phases)
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#~(modify-phases #$phases
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(delete 'delete-failing-tests)))))
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(native-inputs '())
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(description "NumPy is the fundamental package for scientific computing
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with Python. It contains among other things: a powerful N-dimensional array
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object, sophisticated (broadcasting) functions, tools for integrating C/C++
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