2019-07-13 04:34:46 +01:00
|
|
|
{ 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";
|
2019-10-24 07:47:49 +01:00
|
|
|
version = "0.1.8";
|
2019-07-13 04:34:46 +01:00
|
|
|
|
|
|
|
|
src = fetchPypi {
|
|
|
|
|
inherit pname version;
|
2019-10-24 07:47:49 +01:00
|
|
|
sha256 = "6924404b9ce7c55b427bebc5712656b87d17b5114e9fb610f2821865bd8d70f4";
|
2019-07-13 04:34:46 +01:00
|
|
|
};
|
|
|
|
|
|
|
|
|
|
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 ];
|
|
|
|
|
};
|
|
|
|
|
}
|
