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FRidhFRidh
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pythonPackages: new functions to build numpy and scipy
1 parent e5b143a commit 63cf61e

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Lines changed: 117 additions & 110 deletions

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‎pkgs/development/python-modules/numpy-scipy-support.nix‎

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This file was deleted.

‎pkgs/development/python-modules/numpy.nix‎

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{lib, python, buildPythonPackage, isPyPy, gfortran, nose, blas}:
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args:
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let
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inherit (args) version;
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in buildPythonPackage (args // rec {
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name = "numpy-${version}";
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disabled = isPyPy;
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buildInputs = args.buildInputs or [ gfortran nose ];
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propagatedBuildInputs = args.propagatedBuildInputs or [ passthru.blas ];
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preConfigure = ''
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sed -i 's/-faltivec//' numpy/distutils/system_info.py
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'';
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preBuild = ''
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echo "Creating site.cfg file..."
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cat << EOF > site.cfg
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[openblas]
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include_dirs = ${passthru.blas}/include
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library_dirs = ${passthru.blas}/lib
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EOF
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'';
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checkPhase = ''
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runHook preCheck
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pushd dist
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${python.interpreter} -c 'import numpy; numpy.test("fast", verbose=10)'
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popd
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runHook postCheck
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'';
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passthru = {
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blas = blas;
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};
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# The large file support test is disabled because it takes forever
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# and can cause the machine to run out of disk space when run.
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prePatch = ''
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sed -i 's/test_large_file_support/donttest/' numpy/lib/tests/test_format.py
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'';
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meta = {
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description = "Scientific tools for Python";
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homepage = "http://numpy.scipy.org/";
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maintainers = with lib.maintainers; [ fridh ];
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} // (args.meta or {});
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})

‎pkgs/development/python-modules/scipy.nix‎

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{lib, python, buildPythonPackage, isPyPy, gfortran, nose}:
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args:
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let
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inherit (args) version;
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inherit (args) numpy;
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in buildPythonPackage (args // rec {
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name = "scipy-${version}";
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buildInputs = (args.buildInputs or [ gfortran nose ]);
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propagatedBuildInputs = (args.propagatedBuildInputs or [ passthru.blas numpy]);
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preConfigure = ''
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sed -i '0,/from numpy.distutils.core/s//import setuptools;from numpy.distutils.core/' setup.py
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'';
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preBuild = ''
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echo "Creating site.cfg file..."
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cat << EOF > site.cfg
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[openblas]
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include_dirs = ${passthru.blas}/include
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library_dirs = ${passthru.blas}/lib
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EOF
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'';
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checkPhase = ''
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runHook preCheck
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pushd dist
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${python.interpreter} -c 'import scipy; scipy.test("fast", verbose=10)'
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popd
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runHook postCheck
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'';
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passthru = {
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blas = numpy.blas;
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};
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setupPyBuildFlags = [ "--fcompiler='gnu95'" ];
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meta = {
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description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering. ";
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homepage = http://www.scipy.org/;
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maintainers = with lib.maintainers; [ fridh ];
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} // (args.meta or {});
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})

‎pkgs/top-level/python-packages.nix‎

Lines changed: 19 additions & 75 deletions
Original file line numberDiff line numberDiff line change
@@ -12505,48 +12505,20 @@ in modules // {
1250512505
};
1250612506
};
1250712507

12508-
numpy = let
12509-
support = import ../development/python-modules/numpy-scipy-support.nix {
12510-
inherit python;
12511-
openblas = pkgs.openblasCompat;
12512-
pkgName = "numpy";
12513-
};
12514-
in buildPythonPackage ( rec {
12515-
name = "numpy-${version}";
12516-
version = "1.10.4";
12508+
buildNumpyPackage = callPackage ../development/python-modules/numpy.nix {
12509+
gfortran = pkgs.gfortran;
12510+
blas = pkgs.openblasCompat;
12511+
};
12512+
12513+
numpy = self.numpy_1_10;
1251712514

12515+
numpy_1_10 = self.buildNumpyPackage rec {
12516+
version = "1.10.4";
1251812517
src = pkgs.fetchurl {
12519-
url = "https://pypi.python.org/packages/source/n/numpy/${name}.tar.gz";
12518+
url = "https://pypi.python.org/packages/source/n/numpy/numpy-${version}.tar.gz";
1252012519
sha256 = "7356e98fbcc529e8d540666f5a919912752e569150e9a4f8d869c686f14c720b";
1252112520
};
12522-
12523-
disabled = isPyPy; # WIP
12524-
12525-
preConfigure = ''
12526-
sed -i 's/-faltivec//' numpy/distutils/system_info.py
12527-
'';
12528-
12529-
inherit (support) preBuild checkPhase;
12530-
12531-
buildInputs = [ pkgs.gfortran self.nose ];
12532-
propagatedBuildInputs = [ support.openblas ];
12533-
12534-
# Disable failing test_f2py test.
12535-
# f2py couldn't be found by test,
12536-
# even though it was used successfully to build numpy
12537-
12538-
# The large file support test is disabled because it takes forever
12539-
# and can cause the machine to run out of disk space when run.
12540-
prePatch = ''
12541-
sed -i 's/test_f2py/donttest/' numpy/tests/test_scripts.py
12542-
sed -i 's/test_large_file_support/donttest/' numpy/lib/tests/test_format.py
12543-
'';
12544-
12545-
meta = {
12546-
description = "Scientific tools for Python";
12547-
homepage = "http://numpy.scipy.org/";
12548-
};
12549-
});
12521+
};
1255012522

1255112523
numpydoc = buildPythonPackage rec {
1255212524
name = "numpydoc-${version}";
@@ -18488,47 +18460,19 @@ in modules // {
1848818460
};
1848918461
};
1849018462

18463+
buildScipyPackage = callPackage ../development/python-modules/scipy.nix {
18464+
gfortran = pkgs.gfortran;
18465+
};
1849118466

18492-
scipy = let
18493-
support = import ../development/python-modules/numpy-scipy-support.nix {
18494-
inherit python;
18495-
openblas = pkgs.openblasCompat;
18496-
pkgName = "scipy";
18497-
};
18498-
in buildPythonPackage rec {
18499-
name = "scipy-${version}";
18500-
version = "0.16.1";
18467+
scipy = self.scipy_0_16;
1850118468

18469+
scipy_0_16 = self.buildScipyPackage rec {
18470+
version = "0.16.1";
1850218471
src = pkgs.fetchurl {
18503-
url = "http://pypi.python.org/packages/source/s/scipy/${name}.tar.gz";
18472+
url = "https://pypi.python.org/packages/source/s/scipy/scipy-${version}.tar.gz";
1850418473
sha256 = "ecd1efbb1c038accb0516151d1e6679809c6010288765eb5da6051550bf52260";
1850518474
};
18506-
18507-
buildInputs = [ pkgs.gfortran self.nose ];
18508-
propagatedBuildInputs = [ self.numpy ];
18509-
18510-
preConfigure = ''
18511-
sed -i '0,/from numpy.distutils.core/s//import setuptools;from numpy.distutils.core/' setup.py
18512-
'';
18513-
18514-
# First test: RuntimeWarning: Mean of empty slice.
18515-
# Second: SyntaxError: invalid syntax. Due to wrapper?
18516-
# Third: test checks permissions
18517-
prePatch = ''
18518-
substituteInPlace scipy/stats/tests/test_stats.py --replace "test_chisquare_masked_arrays" "remove_this_one"
18519-
rm scipy/linalg/tests/test_lapack.py
18520-
substituteInPlace scipy/weave/tests/test_catalog.py --replace "test_user" "remove_this_one"
18521-
'';
18522-
18523-
inherit (support) preBuild checkPhase;
18524-
18525-
patches = [../development/python-modules/scipy-0.16.1-decorator-fix.patch];
18526-
setupPyBuildFlags = [ "--fcompiler='gnu95'" ];
18527-
18528-
meta = {
18529-
description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering. ";
18530-
homepage = http://www.scipy.org/;
18531-
};
18475+
numpy = self.numpy_1_10;
1853218476
};
1853318477

1853418478
scikitimage = buildPythonPackage rec {
@@ -18563,7 +18507,7 @@ in modules // {
1856318507
};
1856418508

1856518509
buildInputs = with self; [ nose pillow pkgs.gfortran pkgs.glibcLocales ];
18566-
propagatedBuildInputs = with self; [ numpy scipy pkgs.openblas ];
18510+
propagatedBuildInputs = with self; [ numpy scipy numpy.blas ];
1856718511

1856818512
LC_ALL="en_US.UTF-8";
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