Merge commit '8746c77a383f5c76153c7a181f3616d273acfa2a'

1 files changed, 89 insertions, 0 deletions

diff --git a/nixpkgs/pkgs/development/python-modules/starfish/default.nix b/nixpkgs/pkgs/development/python-modules/starfish/default.nix
new file mode 100644
index 000000000000..d7989d80e8e0
--- /dev/null
+++ b/nixpkgs/pkgs/development/python-modules/starfish/default.nix
@@ -0,0 +1,89 @@
+{ 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 = "0.1.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "19bec2a869affbca0a7e3fc0aee1b9978ff7f0f1a2a8551c2d4ae148a7ddc251";
+  };
+
+  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 ];
+  };
+}