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{
lib,
buildPythonPackage,
fetchFromGitHub,
pythonOlder,
pytestCheckHook,
lxml,
matplotlib,
networkx,
pandas,
requests,
setuptools,
}:
buildPythonPackage rec {
pname = "pyxnat";
version = "1.6.2";
pyproject = true;
disabled = pythonOlder "3.8";
# PyPI dist missing test configuration files:
src = fetchFromGitHub {
owner = "pyxnat";
repo = "pyxnat";
rev = "refs/tags/${version}";
hash = "sha256-21nTIYbIYlFWNJTxqsuijamqRunpdc7/VBawvrWadWI=";
};
build-system = [ setuptools ];
propagatedBuildInputs = [
lxml
requests
];
# pathlib is installed part of python38+ w/o an external package
prePatch = ''
substituteInPlace setup.py --replace-fail "pathlib>=1.0" ""
sed -i '/--cov/d' setup.cfg
'';
nativeCheckInputs = [
pytestCheckHook
matplotlib
networkx
pandas
];
preCheck = ''
export PYXNAT_SKIP_NETWORK_TESTS=1
'';
pytestFlagsArray = [ "pyxnat" ];
disabledTestPaths = [
# require a running local XNAT instance e.g. in a docker container:
"pyxnat/tests/attributes_test.py"
"pyxnat/tests/custom_variables_test.py"
"pyxnat/tests/interfaces_test.py"
"pyxnat/tests/pipelines_test.py"
"pyxnat/tests/provenance_test.py"
"pyxnat/tests/prearchive_test.py"
"pyxnat/tests/repr_test.py"
"pyxnat/tests/resources_test.py"
"pyxnat/tests/search_test.py"
"pyxnat/tests/sessionmirror_test.py"
"pyxnat/tests/test_resource_functions.py"
"pyxnat/tests/user_and_project_management_test.py"
];
disabledTests = [
# try to access network even though PYXNAT_SKIP_NETWORK_TESTS is set:
"test_inspector_structure"
"test_project_manager"
];
pythonImportsCheck = [ "pyxnat" ];
meta = with lib; {
homepage = "https://pyxnat.github.io/pyxnat";
description = "Python API to XNAT";
mainProgram = "sessionmirror.py";
changelog = "https://github.com/pyxnat/pyxnat/releases/tag/${version}";
license = licenses.bsd3;
maintainers = with maintainers; [ bcdarwin ];
};
}
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