pythonPackages: new functions to build numpy and scipy
This commit is contained in:
Frederik Rietdijk
parent
e5b143a964
commit
63cf61e8d3
@ -1,35 +0,0 @@
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{
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# Python package expression
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python,
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# Name of package (e.g. numpy or scipy)
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pkgName,
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# OpenBLAS math library
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openblas
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}:
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{
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# Re-export openblas here so that it can be sure that the same one will be used
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# in the propagatedBuildInputs.
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inherit openblas;
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# First "install" the package, then import what was installed, and call the
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# .test() function, which will run the test suite.
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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 ${pkgName}; ${pkgName}.test("fast", verbose=10)'
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popd
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runHook postCheck
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'';
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# Creates a site.cfg telling the setup script where to find depended-on
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# math libraries.
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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 = ${openblas}/include
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library_dirs = ${openblas}/lib
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EOF
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'';
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}
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51
pkgs/development/python-modules/numpy.nix
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51
pkgs/development/python-modules/numpy.nix
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@ -0,0 +1,51 @@
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{lib, python, buildPythonPackage, isPyPy, gfortran, nose, blas}:
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args:
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let
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inherit (args) version;
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in buildPythonPackage (args // rec {
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name = "numpy-${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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})
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47
pkgs/development/python-modules/scipy.nix
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47
pkgs/development/python-modules/scipy.nix
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@ -0,0 +1,47 @@
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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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})
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@ -12505,48 +12505,20 @@ in modules // {
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};
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};
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numpy = let
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support = import ../development/python-modules/numpy-scipy-support.nix {
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inherit python;
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openblas = pkgs.openblasCompat;
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pkgName = "numpy";
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};
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in buildPythonPackage ( rec {
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name = "numpy-${version}";
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version = "1.10.4";
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buildNumpyPackage = callPackage ../development/python-modules/numpy.nix {
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gfortran = pkgs.gfortran;
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blas = pkgs.openblasCompat;
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};
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numpy = self.numpy_1_10;
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numpy_1_10 = self.buildNumpyPackage rec {
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version = "1.10.4";
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src = pkgs.fetchurl {
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url = "https://pypi.python.org/packages/source/n/numpy/${name}.tar.gz";
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url = "https://pypi.python.org/packages/source/n/numpy/numpy-${version}.tar.gz";
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sha256 = "7356e98fbcc529e8d540666f5a919912752e569150e9a4f8d869c686f14c720b";
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};
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disabled = isPyPy; # WIP
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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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inherit (support) preBuild checkPhase;
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buildInputs = [ pkgs.gfortran self.nose ];
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propagatedBuildInputs = [ support.openblas ];
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# Disable failing test_f2py test.
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# f2py couldn't be found by test,
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# even though it was used successfully to build numpy
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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_f2py/donttest/' numpy/tests/test_scripts.py
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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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};
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});
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};
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numpydoc = buildPythonPackage rec {
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name = "numpydoc-${version}";
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@ -18488,47 +18460,19 @@ in modules // {
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};
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};
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buildScipyPackage = callPackage ../development/python-modules/scipy.nix {
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gfortran = pkgs.gfortran;
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};
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scipy = let
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support = import ../development/python-modules/numpy-scipy-support.nix {
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inherit python;
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openblas = pkgs.openblasCompat;
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pkgName = "scipy";
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};
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in buildPythonPackage rec {
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name = "scipy-${version}";
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scipy = self.scipy_0_16;
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scipy_0_16 = self.buildScipyPackage rec {
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version = "0.16.1";
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src = pkgs.fetchurl {
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url = "http://pypi.python.org/packages/source/s/scipy/${name}.tar.gz";
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url = "https://pypi.python.org/packages/source/s/scipy/scipy-${version}.tar.gz";
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sha256 = "ecd1efbb1c038accb0516151d1e6679809c6010288765eb5da6051550bf52260";
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};
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buildInputs = [ pkgs.gfortran self.nose ];
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propagatedBuildInputs = [ self.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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# First test: RuntimeWarning: Mean of empty slice.
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# Second: SyntaxError: invalid syntax. Due to wrapper?
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# Third: test checks permissions
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prePatch = ''
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substituteInPlace scipy/stats/tests/test_stats.py --replace "test_chisquare_masked_arrays" "remove_this_one"
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rm scipy/linalg/tests/test_lapack.py
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substituteInPlace scipy/weave/tests/test_catalog.py --replace "test_user" "remove_this_one"
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'';
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inherit (support) preBuild checkPhase;
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patches = [../development/python-modules/scipy-0.16.1-decorator-fix.patch];
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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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};
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numpy = self.numpy_1_10;
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};
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scikitimage = buildPythonPackage rec {
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@ -18563,7 +18507,7 @@ in modules // {
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};
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buildInputs = with self; [ nose pillow pkgs.gfortran pkgs.glibcLocales ];
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propagatedBuildInputs = with self; [ numpy scipy pkgs.openblas ];
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propagatedBuildInputs = with self; [ numpy scipy numpy.blas ];
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LC_ALL="en_US.UTF-8";
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