pyrox.dev
Merge pull request #119258 from drewrisinger/dr-pr-fix-python-tables
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pkgs/development/python-modules/tables/default.nix
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pkgs/development/python-modules/tables/default.nix
···
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{ lib, fetchPypi, python, buildPythonPackage, isPy38
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, cython, bzip2, lzo, numpy, numexpr, hdf5, six, c-blosc, mock }:
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{ lib
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, fetchPypi
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, fetchurl
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, fetchpatch
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, buildPythonPackage
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, pythonOlder
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, python
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, bzip2
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, c-blosc
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, cython
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, hdf5
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, lzo
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, numpy
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, numexpr
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, setuptools
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# Test inputs
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, pytestCheckHook
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}:
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buildPythonPackage rec {
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version = "3.6.1";
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pname = "tables";
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version = "3.6.1";
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disabled = pythonOlder "3.5";
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src = fetchPypi {
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inherit pname version;
···
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nativeBuildInputs = [ cython ];
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buildInputs = [ hdf5 bzip2 lzo c-blosc ];
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propagatedBuildInputs = [ numpy numexpr six mock ];
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buildInputs = [
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bzip2
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c-blosc
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hdf5
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lzo
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];
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propagatedBuildInputs = [
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numpy
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numexpr
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setuptools # uses pkg_resources at runtime
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];
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patches = [
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(fetchpatch {
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# Needed for numpy >= 1.20.0
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name = "tables-pr-862-use-lowercase-numpy-dtypes.patch";
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url = "https://github.com/PyTables/PyTables/commit/93a3272b8fe754095637628b4d312400e24ae654.patch";
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sha256 = "00czgxnm1dxp9763va9xw1nc7dd7kxh9hjcg9klim52519hkbhi4";
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})
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];
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# When doing `make distclean`, ignore docs
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postPatch = ''
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substituteInPlace Makefile --replace "src doc" "src"
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# Force test suite to error when unittest runner fails
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substituteInPlace tables/tests/test_suite.py \
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--replace "return 0" "assert result.wasSuccessful(); return 0" \
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--replace "return 1" "assert result.wasSuccessful(); return 1"
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'';
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# Regenerate C code with Cython
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make distclean
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'';
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# The setup script complains about missing run-paths, but they are
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# actually set.
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setupPyBuildFlags = [
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"--hdf5=${lib.getDev hdf5}"
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"--lzo=${lib.getDev lzo}"
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"--bzip2=${lib.getDev bzip2}"
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"--blosc=${lib.getDev c-blosc}"
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];
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# Run the test suite.
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# It requires the build path to be in the python search path.
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# These tests take quite some time.
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# If the hdf5 library is built with zlib then there is only one
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# test-failure. That is the same failure as described in the following
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# github issue:
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# https://github.com/PyTables/PyTables/issues/269
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checkPhase = ''
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${python.interpreter} <<EOF
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import sysconfig
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import sys
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import os
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f = "lib.{platform}-{version[0]}.{version[1]}"
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lib = f.format(platform=sysconfig.get_platform(),
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version=sys.version_info)
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build = os.path.join(os.getcwd(), 'build', lib)
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sys.path.insert(0, build)
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import tables
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r = tables.test()
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if not r.wasSuccessful():
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sys.exit(1)
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EOF
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checkInputs = [ pytestCheckHook ];
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preCheck = ''
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cd ..
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'';
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# Runs the test suite as one single test via unittest. The whole "heavy" test suite supposedly takes ~5 hours to run.
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pytestFlagsArray = [
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"--pyargs"
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"tables.tests.test_suite"
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];
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# Disable tests until the failure described above is fixed.
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doCheck = false;
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pythonImportsCheck = [ "tables" ];
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meta = with lib; {
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description = "Hierarchical datasets for Python";
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homepage = "http://www.pytables.org/";
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homepage = "https://www.pytables.org/";
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license = licenses.bsd2;
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maintainers = with maintainers; [ drewrisinger ];
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};
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}
+3
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pkgs/tools/misc/hdf5/1.10.nix
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pkgs/tools/misc/hdf5/1.10.nix
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let inherit (lib) optional optionals; in
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stdenv.mkDerivation rec {
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version = "1.10.7";
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# pinned to 1.10.6 for pythonPackages.tables v3.6.1. tables has test errors for hdf5 > 1.10.6. https://github.com/PyTables/PyTables/issues/845
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version = "1.10.6";
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pname = "hdf5";
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src = fetchurl {
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url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${lib.versions.majorMinor version}/${pname}-${version}/src/${pname}-${version}.tar.bz2";
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sha256 = "0pm5xxry55i0h7wmvc7svzdaa90rnk7h78rrjmnlkz2ygsn8y082";
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sha256 = "1gf38x51128hn00744358w27xgzjk0ff4wra4yxh2lk804ck1mh9";
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};
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outputs = [ "out" "dev" ];