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{ lib
, buildPythonPackage
, fetchPypi
, click
, dataclasses
, jsonschema
, matplotlib
, numpy
, pandas
, regional
, semantic-version
, scikitimage
, scikitlearn
, scipy
, showit
, slicedimage
, sympy
, tqdm
, trackpy
, validators
, xarray
, ipywidgets
, pytest
, pythonOlder
}:
buildPythonPackage rec {
pname = "starfish";
version = "0.1.10";
src = fetchPypi {
inherit pname version;
sha256 = "0340e37b732e184081b150f21bbbd4eed3643ab49f74633b9c4d827bda663235";
};
propagatedBuildInputs = [
click
jsonschema
matplotlib
numpy
pandas
regional
semantic-version
scikitimage
scikitlearn
scipy
showit
slicedimage
sympy
tqdm
trackpy
validators
xarray
ipywidgets
] ++ lib.optionals (pythonOlder "3.7") [ dataclasses ];
checkInputs = [
pytest
];
postConfigure = ''
substituteInPlace REQUIREMENTS.txt \
--replace "slicedimage==3.1.1" "slicedimage"
'';
checkPhase = ''
# a few tests < 5% require
rm -rf starfish/test/full_pipelines/*
pytest starfish \
--ignore starfish/core/config/test/test_config.py \
--ignore starfish/core/experiment/builder/test/test_build.py \
--ignore starfish/core/experiment/test/test_experiment.py \
--ignore starfish/core/image/_filter/test/test_reduce.py \
--ignore starfish/core/image/_registration/_apply_transform/test/test_warp.py \
--ignore starfish/core/image/_registration/_learn_transform/test/test_translation.py \
--ignore starfish/core/image/_registration/test/test_transforms_list.py \
--ignore starfish/core/imagestack/test/test_max_proj.py \
--ignore starfish/core/recipe/test/test_recipe.py \
--ignore starfish/core/recipe/test/test_runnable.py \
--ignore starfish/core/test/test_profiler.py
'';
meta = with lib; {
description = "Pipelines and pipeline components for the analysis of image-based transcriptomics data";
homepage = https://spacetx-starfish.readthedocs.io/en/latest/;
license = licenses.mit;
maintainers = [ maintainers.costrouc ];
broken = true; # incompatible with latest python-dateutil, scikit-image
};
}
|