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{
lib,
buildPythonPackage,
stdenv,
fetchFromGitHub,
cmake,
zlib,
pybind11,
pytestCheckHook,
pytest-cov-stub,
pkg-config,
setuptools,
setuptools-scm,
biocutils,
biocframe,
pandas,
scipy,
}:
buildPythonPackage rec {
pname = "rds2py";
version = "0.7.3";
pyproject = true;
src = fetchFromGitHub {
owner = "BiocPy";
repo = "rds2py";
tag = version;
hash = "sha256-GbRpkt+K2HXuAT7KtI4h1SnZ4RtSo5hrea2L92VZj/o=";
};
rds2cpp-src = fetchFromGitHub {
owner = "LTLA";
repo = "rds2cpp";
rev = "v1.1.0";
hash = "sha256-q7C/oORmhgXlqnZnslhyrxBc3RRF2gdgGuQU4TimxtI=";
};
byteme-src = fetchFromGitHub {
owner = "LTLA";
repo = "byteme";
rev = "v1.2.2";
hash = "sha256-rM/pSMGlaMWE69lYORaa8SQYGQyzhdyQnXImmAesxFA=";
};
# Upstream uses CMake's FetchContent to download rds2cpp and byteme into
# build/_deps at configure time. We pre-fetch both repos and copy them
# into build/_deps manually. This way the build tree matches what upstream expects.
prePatch = ''
mkdir -p build/_deps
cp -r ${rds2cpp-src} build/_deps/rds2cpp-src
cp -r ${byteme-src} build/_deps/byteme-src
chmod -R u+w build/_deps
'';
# Patch upstream CMakeLists.txt files to use our vendored sources instead of
# calling FetchContent. We point add_subdirectory() to the copies staged in
# build/_deps above. We also patch rds2cpp's own extern/CMakeLists.txt to
# disable its nested FetchContent call for byteme, since we already provide it.
postPatch = ''
substituteInPlace lib/CMakeLists.txt \
--replace-fail \
"FetchContent_MakeAvailable(byteme)" \
"add_subdirectory(\''${CMAKE_BINARY_DIR}/../_deps/byteme-src \''${CMAKE_CURRENT_BINARY_DIR}/byteme)" \
--replace-fail \
"FetchContent_MakeAvailable(rds2cpp)" \
"add_subdirectory(\''${CMAKE_BINARY_DIR}/../_deps/rds2cpp-src \''${CMAKE_CURRENT_BINARY_DIR}/rds2cpp)"
substituteInPlace build/_deps/rds2cpp-src/extern/CMakeLists.txt \
--replace-fail "FetchContent_MakeAvailable(byteme)" "# FetchContent_MakeAvailable(byteme) -- Patched by Nix"
'';
# We use the MORE_CMAKE_OPTIONS environment variable, which is a hook provided
# by the upstream setup.py, to pass our zlib flags to the CMake configure step.
preConfigure = ''
export MORE_CMAKE_OPTIONS="-DZLIB_INCLUDE_DIR=${lib.getDev zlib}/include -DZLIB_LIBRARY=${lib.getLib zlib}/lib/libz.so"
'';
nativeBuildInputs = [
cmake
pkg-config
pybind11
zlib
];
build-system = [
setuptools
setuptools-scm
];
dependencies = [
biocutils
];
nativeCheckInputs = [
pytest-cov-stub
pytestCheckHook
biocframe
pandas
scipy
];
disabledTestPaths = [
# Requires packages not in Nixpkgs
"tests/test_delayedmatrices.py"
"tests/test_granges.py"
"tests/test_mae.py"
"tests/test_sce.py"
"tests/test_se.py"
];
# setuptools drives the build, so disable cmake configure hook
dontUseCmakeConfigure = true;
pythonImportsCheck = [ "rds2py" ];
meta = {
description = "Read RDS files, in Python";
homepage = "https://github.com/BiocPy/rds2py";
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ b-rodrigues ];
};
}
|
