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python312Packages.bx-python: Drop nose dependency; modernize #330744

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Aug 9, 2024
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python312Packages.bx-python: Drop nose dependency; modernize #330744

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python312Packages.bx-python: Drop nose dependency
pyrox0 Jul 28, 2024
a007b9f
python312Packages.bx-python: Modernize
pyrox0 Jul 28, 2024
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40 changes: 26 additions & 14 deletions pkgs/development/python-modules/bx-python/default.nix
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Original file line number Diff line number Diff line change
Expand Up @@ -2,38 +2,50 @@
lib,
fetchFromGitHub,
buildPythonPackage,
pythonOlder,
numpy,
cython,
zlib,
python-lzo,
nose,
pytestCheckHook,
setuptools,
oldest-supported-numpy,
}:

buildPythonPackage rec {
pname = "bx-python";
version = "0.11.0";
format = "setuptools";

disabled = pythonOlder "3.8";
version = "0.12.0";
pyproject = true;

src = fetchFromGitHub {
owner = "bxlab";
repo = "bx-python";
rev = "refs/tags/v${version}";
hash = "sha256-evhxh/cCZFSK6EgMu7fC9/ZrPd2S1fZz89ItGYrHQck=";
hash = "sha256-ZpZjh7OXdUY7rd692h7VYHzC3qCrDKFme6r+wuG7GP4=";
};

nativeBuildInputs = [ cython ];
postPatch = ''
# pytest-cython, which provides this option, isn't packaged
substituteInPlace pytest.ini \
--replace-fail "--doctest-cython" ""
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'';

build-system = [
setuptools
cython
oldest-supported-numpy
];

buildInputs = [ zlib ];

propagatedBuildInputs = [
numpy
dependencies = [ numpy ];

nativeCheckInputs = [
python-lzo
pytestCheckHook
];

nativeCheckInputs = [ nose ];
# https://github.com/bxlab/bx-python/issues/101
doCheck = false;

postInstall = ''
cp -r scripts/* $out/bin
Expand All @@ -45,12 +57,12 @@ buildPythonPackage rec {
ln -s $out/bin scripts
'';

meta = with lib; {
meta = {
description = "Tools for manipulating biological data, particularly multiple sequence alignments";
homepage = "https://github.com/bxlab/bx-python";
changelog = "https://github.com/bxlab/bx-python/releases/tag/v${version}";
license = licenses.mit;
maintainers = with maintainers; [ jbedo ];
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ jbedo ];
platforms = [ "x86_64-linux" ];
};
}