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