mirror of
https://github.com/NixOS/nixpkgs.git
synced 2026-11-06 21:00:34 +00:00
e0a0d6c13b
Diff: https://github.com/bxlab/bx-python/compare/v0.14.0...v0.16.0 Changelog: https://github.com/bxlab/bx-python/releases/tag/v0.16.0
89 lines
1.9 KiB
Nix
89 lines
1.9 KiB
Nix
{
|
||
lib,
|
||
fetchFromGitHub,
|
||
buildPythonPackage,
|
||
python,
|
||
|
||
# build-system
|
||
cython,
|
||
numpy,
|
||
setuptools,
|
||
|
||
# buildInputs
|
||
zlib,
|
||
|
||
# dependencies
|
||
pyparsing,
|
||
|
||
# tests
|
||
pytestCheckHook,
|
||
python-lzo,
|
||
}:
|
||
|
||
buildPythonPackage (finalAttrs: {
|
||
pname = "bx-python";
|
||
version = "0.16.0";
|
||
pyproject = true;
|
||
|
||
src = fetchFromGitHub {
|
||
owner = "bxlab";
|
||
repo = "bx-python";
|
||
tag = "v${finalAttrs.version}";
|
||
hash = "sha256-jSS5amnDy25oz9rKW5KFEqROYCdF0P30vtokxqwudIY=";
|
||
};
|
||
|
||
# pytest-cython, which provides this option, isn't packaged
|
||
postPatch = ''
|
||
substituteInPlace pytest.ini \
|
||
--replace-fail "--doctest-cython" ""
|
||
'';
|
||
|
||
build-system = [
|
||
cython
|
||
numpy
|
||
setuptools
|
||
];
|
||
|
||
buildInputs = [ zlib ];
|
||
|
||
dependencies = [
|
||
numpy
|
||
pyparsing
|
||
];
|
||
|
||
pythonImportsCheck = [ "bx" ];
|
||
|
||
nativeCheckInputs = [
|
||
pytestCheckHook
|
||
python-lzo
|
||
];
|
||
|
||
# Upstream tests against an editable install: the in-tree `lib/bx` shadows the installed
|
||
# package, so copy the compiled extensions next to their sources.
|
||
# https://github.com/bxlab/bx-python/issues/101
|
||
preCheck = ''
|
||
pushd $out/${python.sitePackages}
|
||
find bx -name "*.so" -exec cp --parents {} $OLDPWD/lib/ \;
|
||
popd
|
||
'';
|
||
|
||
postInstall = ''
|
||
cp -r scripts/* $out/bin
|
||
''
|
||
# This is a small hack; the test suite uses the scripts which need to be patched.
|
||
# Linking the patched scripts in $out back to the working directory allows the tests to run.
|
||
+ ''
|
||
rm -rf scripts
|
||
ln -s $out/bin scripts
|
||
'';
|
||
|
||
meta = {
|
||
description = "Tools for manipulating biological data, particularly multiple sequence alignments";
|
||
homepage = "https://github.com/bxlab/bx-python";
|
||
changelog = "https://github.com/bxlab/bx-python/releases/tag/${finalAttrs.src.tag}";
|
||
license = lib.licenses.mit;
|
||
maintainers = with lib.maintainers; [ jbedo ];
|
||
platforms = [ "x86_64-linux" ];
|
||
};
|
||
})
|