2019-07-13 04:34:46 +01:00
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{ lib
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, buildPythonPackage
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, fetchPypi
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, click
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, dataclasses
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, jsonschema
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, matplotlib
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, numpy
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, pandas
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, regional
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, semantic-version
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, scikitimage
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, scikitlearn
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, scipy
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, showit
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, slicedimage
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, sympy
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, tqdm
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, trackpy
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, validators
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, xarray
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, ipywidgets
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, pytest
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, pythonOlder
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}:
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buildPythonPackage rec {
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pname = "starfish";
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2019-11-19 14:35:39 +00:00
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version = "0.1.9";
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2019-07-13 04:34:46 +01:00
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src = fetchPypi {
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inherit pname version;
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2019-11-19 14:35:39 +00:00
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sha256 = "02002b908572fcd2c7471475936a6c375f143d15df871399ce86ced6d7aef865";
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2019-07-13 04:34:46 +01:00
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};
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propagatedBuildInputs = [
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click
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jsonschema
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matplotlib
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numpy
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pandas
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regional
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semantic-version
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scikitimage
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scikitlearn
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scipy
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showit
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slicedimage
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sympy
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tqdm
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trackpy
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validators
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xarray
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ipywidgets
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] ++ lib.optionals (pythonOlder "3.7") [ dataclasses ];
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checkInputs = [
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pytest
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];
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postConfigure = ''
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substituteInPlace REQUIREMENTS.txt \
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--replace "slicedimage==3.1.1" "slicedimage"
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'';
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checkPhase = ''
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# a few tests < 5% require
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rm -rf starfish/test/full_pipelines/*
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pytest starfish \
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--ignore starfish/core/config/test/test_config.py \
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--ignore starfish/core/experiment/builder/test/test_build.py \
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--ignore starfish/core/experiment/test/test_experiment.py \
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--ignore starfish/core/image/_filter/test/test_reduce.py \
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--ignore starfish/core/image/_registration/_apply_transform/test/test_warp.py \
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--ignore starfish/core/image/_registration/_learn_transform/test/test_translation.py \
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--ignore starfish/core/image/_registration/test/test_transforms_list.py \
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--ignore starfish/core/imagestack/test/test_max_proj.py \
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--ignore starfish/core/recipe/test/test_recipe.py \
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--ignore starfish/core/recipe/test/test_runnable.py \
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--ignore starfish/core/test/test_profiler.py
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'';
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meta = with lib; {
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description = "Pipelines and pipeline components for the analysis of image-based transcriptomics data";
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homepage = https://spacetx-starfish.readthedocs.io/en/latest/;
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license = licenses.mit;
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maintainers = [ maintainers.costrouc ];
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};
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}
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