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Merge pull request #3056 from aherrmann/pr_tables

Python module tables
This commit is contained in:
Florian Friesdorf 2014-06-23 22:58:04 +02:00
commit ba654b9368
4 changed files with 116 additions and 9 deletions

View file

@ -4,6 +4,6 @@ stdenv.mkDerivation {
name = "szip-2.1";
src = fetchurl {
url = ftp://ftp.hdfgroup.org/lib-external/szip/2.1/src/szip-2.1.tar.gz;
sha256 = "05707lrdhwp8mv0dgzh2b6m2mwamv1z6k29m2v1v7pz0c1w2gb6z";
sha256 = "1vym7r4by02m0yqj10023xyps5b21ryymnxb4nb2gs32arfxj5m8";
};
}
}

View file

@ -0,0 +1,56 @@
{ stdenv, fetchurl, python, buildPythonPackage
, cython, bzip2, lzo, numpy, numexpr, hdf5 }:
buildPythonPackage rec {
version = "3.1.1";
name = "tables-${version}";
src = fetchurl {
url = "mirror://sourceforge/pytables/${name}.tar.gz";
sha256 = "18rdzv9xwiapb5c8y47rk2fi3fdm2dpjf68wfycma67ifrih7f9r";
};
buildInputs = [ hdf5 cython bzip2 lzo ];
propagatedBuildInputs = [ numpy numexpr ];
# The setup script complains about missing run-paths, but they are
# actually set.
setupPyBuildFlags =
[ "--hdf5=${hdf5}"
"--lzo=${lzo}"
"--bzip2=${bzip2}"
];
setupPyInstallFlags = setupPyBuildFlags;
# Run the test suite.
# It requires the build path to be in the python search path.
# These tests take quite some time.
# If the hdf5 library is built with zlib then there is only one
# test-failure. That is the same failure as described in the following
# github issue:
# https://github.com/PyTables/PyTables/issues/269
checkPhase = ''
${python}/bin/${python.executable} <<EOF
import sysconfig
import sys
import os
f = "lib.{platform}-{version[0]}.{version[1]}"
lib = f.format(platform=sysconfig.get_platform(),
version=sys.version_info)
build = os.path.join(os.getcwd(), 'build', lib)
sys.path.insert(0, build)
import tables
r = tables.test()
if not r.wasSuccessful():
sys.exit(1)
EOF
'';
# Disable tests until the failure described above is fixed.
doCheck = false;
meta = {
description = "Hierarchical datasets for Python";
homepage = "http://www.pytables.org/";
};
}

View file

@ -1,14 +1,22 @@
{ stdenv
, fetchurl
, zlib ? null
, szip ? null
}:
stdenv.mkDerivation {
name = "hdf5-1.8.10-patch1";
stdenv.mkDerivation rec {
version = "1.8.13";
name = "hdf5-${version}-patch1";
src = fetchurl {
url = http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.10-patch1.tar.gz;
sha256 = "08ad32fhnci6rdfn6mn3w9v1wcaxdcd326n3ljwkcq4dzhkh28qz";
url = "http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-${version}.tar.gz";
sha256 = "1h9qdl321gzm3ihdhlijbl9sh9qcdrw94j7izg64yfqhxj7b7xl2";
};
buildInputs = [] ;
buildInputs = []
++ stdenv.lib.optional (zlib != null) zlib
++ stdenv.lib.optional (szip != null) szip;
configureFlags = if szip != null then "--with-szlib=${szip}" else "";
patches = [./bin-mv.patch];

View file

@ -146,6 +146,12 @@ rec {
inherit python;
};
tables = import ../development/python-modules/tables {
inherit (pkgs) stdenv fetchurl bzip2 lzo;
inherit python buildPythonPackage cython numpy numexpr;
hdf5 = pkgs.hdf5.override { zlib = pkgs.zlib; };
};
# packages defined here
aafigure = buildPythonPackage rec {
@ -4625,6 +4631,43 @@ rec {
};
};
numexpr = buildPythonPackage rec {
version = "2.4";
name = "numexpr-${version}";
src = fetchgit {
url = https://github.com/pydata/numexpr.git;
rev = "606cc9a110711e947d35ac2770749c00dab184c8";
sha256 = "1gxgkg7ncgjhnifn444iha5nrjhyr8sr6w5yp204186a1ysz858g";
};
propagatedBuildInputs = with pkgs; [ numpy ];
# Run the test suite.
# It requires the build path to be in the python search path.
checkPhase = ''
${python}/bin/${python.executable} <<EOF
import sysconfig
import sys
import os
f = "lib.{platform}-{version[0]}.{version[1]}"
lib = f.format(platform=sysconfig.get_platform(),
version=sys.version_info)
build = os.path.join(os.getcwd(), 'build', lib)
sys.path.insert(0, build)
import numexpr
r = numexpr.test()
if not r.wasSuccessful():
sys.exit(1)
EOF
'';
meta = {
description = "Fast numerical array expression evaluator for NumPy";
homepage = "https://github.com/pydata/numexpr";
};
};
numpy = buildPythonPackage ( rec {
name = "numpy-1.7.1";
@ -4859,11 +4902,11 @@ rec {
});
pandas = buildPythonPackage rec {
name = "pandas-0.12.0";
name = "pandas-0.14.0";
src = fetchurl {
url = "https://pypi.python.org/packages/source/p/pandas/${name}.tar.gz";
sha256 = "0vf865wh1kcq33189ykqgngb25nxhxxch6skfdl3c6w024v4r6xy";
sha256 = "f7997debca756c4dd5ccdf5a010dfe3d1c7dac98ee706b715d994cf7c9d35528";
};
buildInputs = [ nose ];