Merge pull request #214398 from bcdarwin/ome-zarr-py

python310Packages.ome-zarr: init at 0.6.1

pkgs/development/python-modules/ome-zarr/default.nix

@@ -0,0 +1,81 @@
+{ lib
+, buildPythonPackage
+, pythonOlder
+, fetchFromGitHub
+, fetchpatch
+, pytestCheckHook
+, aiohttp
+, dask
+, fsspec
+, numpy
+, requests
+, scikitimage
+, s3fs
+, toolz
+, zarr
+}:
+
+buildPythonPackage rec {
+  pname = "ome-zarr";
+  version = "0.6.1";
+  disabled = pythonOlder "3.6";
+
+  src = fetchFromGitHub {
+    owner = "ome";
+    repo = "ome-zarr-py";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-dpweOuqruh7mAqmSaNbehLCr8OCLe1IZNWV4bpHpTl0=";
+  };
+
+  patches = [
+    # remove after next release:
+    (fetchpatch {
+      name = "fix-writer-bug";
+      url = "https://github.com/ome/ome-zarr-py/commit/c1302e05998dfe2faf94b0f958c92888681f5ffa.patch";
+      hash = "sha256-1WANObABUXkjqeGdnmg0qJ48RcZcuAwgitZyMwiRYUw=";
+    })
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    dask
+    zarr
+    fsspec
+    aiohttp
+    requests
+    s3fs
+    scikitimage
+    toolz
+  ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  disabledTests = [
+    # attempts to access network
+    "test_s3_info"
+  ];
+
+  pythonImportsCheck = [
+    "ome_zarr"
+    "ome_zarr.cli"
+    "ome_zarr.csv"
+    "ome_zarr.data"
+    "ome_zarr.format"
+    "ome_zarr.io"
+    "ome_zarr.reader"
+    "ome_zarr.writer"
+    "ome_zarr.scale"
+    "ome_zarr.utils"
+  ];
+
+  meta = with lib; {
+    description = "Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.";
+    homepage = "https://pypi.org/project/ome-zarr";
+    changelog = "https://github.com/ome/ome-zarr-py/blob/v${version}/CHANGELOG.md";
+    license = licenses.bsd2;
+    maintainers = [ maintainers.bcdarwin ];
+    mainProgram = "ome_zarr";
+  };
+}

pkgs/top-level/all-packages.nix

@@ -10350,6 +10350,8 @@ with pkgs;
 
   ombi = callPackage ../servers/ombi { };
 
+  ome_zarr = with python3Packages; toPythonApplication ome-zarr;
+
   omping = callPackage ../applications/networking/omping { };
 
   onefetch = callPackage ../tools/misc/onefetch {

pkgs/top-level/python-packages.nix

@@ -6595,6 +6595,8 @@ self: super: with self; {
 
   omegaconf = callPackage ../development/python-modules/omegaconf { };
 
+  ome-zarr = callPackage ../development/python-modules/ome-zarr { };
+
   omnikinverter = callPackage ../development/python-modules/omnikinverter { };
 
   omnilogic = callPackage ../development/python-modules/omnilogic { };