python3Packages.multiscale-spatial-image: fix build (#516443)

pkgs/development/python-modules/itkwasm-downsample-emscripten/default.nix

@@ -0,0 +1,42 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  hatch-vcs,
+  hatchling,
+  itkwasm,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "itkwasm-downsample-emscripten";
+  version = "1.8.1";
+  pyproject = true;
+
+  src = fetchPypi {
+    pname = "itkwasm_downsample_emscripten";
+    inherit (finalAttrs) version;
+    hash = "sha256-kF851K6cy1jozPxd5zE8XVnBAHMljmOqtvpmfmQDZy4=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  nativeBuildInputs = [ writableTmpDirAsHomeHook ];
+
+  dependencies = [ itkwasm ];
+
+  pythonImportsCheck = [ "itkwasm_downsample_emscripten" ];
+
+  # No tests available
+  doCheck = false;
+
+  meta = {
+    description = "Pipelines for downsampling images";
+    homepage = "https://pypi.org/project/itkwasm-downsample-emscripten";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ fab ];
+  };
+})

pkgs/development/python-modules/itkwasm-downsample-wasi/default.nix

@@ -0,0 +1,46 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  hatch-vcs,
+  hatchling,
+  importlib-resources,
+  itkwasm,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "itkwasm-downsample-wasi";
+  version = "1.8.1";
+  pyproject = true;
+
+  src = fetchPypi {
+    pname = "itkwasm_downsample_wasi";
+    inherit (finalAttrs) version;
+    hash = "sha256-OykKkZRlRGDw+SsK69z6dqh6LY7eUlyHGdZwmkKsMKQ=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  nativeBuildInputs = [ writableTmpDirAsHomeHook ];
+
+  dependencies = [
+    importlib-resources
+    itkwasm
+  ];
+
+  # No tests available
+  doCheck = false;
+
+  pythonImportsCheck = [ "itkwasm_downsample_wasi" ];
+
+  meta = {
+    description = "Pipelines for downsampling images";
+    homepage = "https://pypi.org/project/itkwasm-downsample-wasi";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ fab ];
+  };
+})

pkgs/development/python-modules/itkwasm-downsample/default.nix

@@ -0,0 +1,48 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  hatch-vcs,
+  hatchling,
+  itkwasm,
+  itkwasm-downsample-emscripten,
+  itkwasm-downsample-wasi,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "itkwasm-downsample";
+  version = "1.8.1";
+  pyproject = true;
+
+  src = fetchPypi {
+    pname = "itkwasm_downsample";
+    inherit (finalAttrs) version;
+    hash = "sha256-tKkct5+39p5jM/vBj3RTSM1YZZoLnajh85Eon4/wavs=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  nativeBuildInputs = [ writableTmpDirAsHomeHook ];
+
+  dependencies = [
+    itkwasm
+    itkwasm-downsample-emscripten
+    itkwasm-downsample-wasi
+  ];
+
+  # No tests available
+  doCheck = false;
+
+  pythonImportsCheck = [ "itkwasm_downsample" ];
+
+  meta = {
+    description = "Pipelines for downsampling images";
+    homepage = "https://pypi.org/project/itkwasm-downsample";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ fab ];
+  };
+})

pkgs/development/python-modules/itkwasm-image-io-emscripten/default.nix

@@ -0,0 +1,39 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  hatch-vcs,
+  hatchling,
+  itkwasm,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "itkwasm-image-io-emscripten";
+  version = "1.6.1";
+  pyproject = true;
+
+  src = fetchPypi {
+    pname = "itkwasm_image_io_emscripten";
+    inherit (finalAttrs) version;
+    hash = "sha256-lFYLpPM4LVSPANpKGg7WSYrrfvpmE2T1w4igidUUL3I=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  nativeBuildInputs = [ writableTmpDirAsHomeHook ];
+
+  dependencies = [ itkwasm ];
+
+  pythonImportsCheck = [ "itkwasm_image_io_emscripten" ];
+
+  meta = {
+    description = "Input and output for scientific and medical image file formats";
+    homepage = "https://pypi.org/project/itkwasm-image-io-emscripten";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ fab ];
+  };
+})

pkgs/development/python-modules/itkwasm-image-io-wasi/default.nix

@@ -0,0 +1,46 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  hatch-vcs,
+  hatchling,
+  importlib-resources,
+  itkwasm,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "itkwasm-image-io-wasi";
+  version = "1.6.1";
+  pyproject = true;
+
+  src = fetchPypi {
+    pname = "itkwasm_image_io_wasi";
+    inherit (finalAttrs) version;
+    hash = "sha256-g3w/OPU9N1GxJkW9kKrOvGtVPRVb6zTy5n2nB5WU7+Q=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  nativeBuildInputs = [ writableTmpDirAsHomeHook ];
+
+  dependencies = [
+    importlib-resources
+    itkwasm
+  ];
+
+  pythonImportsCheck = [ "itkwasm_image_io_wasi" ];
+
+  # No tests available
+  doCheck = false;
+
+  meta = {
+    description = "Input and output for scientific and medical image file formats";
+    homepage = "https://pypi.org/project/itkwasm-image-io-wasi";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ fab ];
+  };
+})

pkgs/development/python-modules/itkwasm-image-io/default.nix

@@ -0,0 +1,48 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  hatch-vcs,
+  hatchling,
+  itkwasm,
+  itkwasm-image-io-emscripten,
+  itkwasm-image-io-wasi,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "itkwasm-image-io";
+  version = "1.6.1";
+  pyproject = true;
+
+  src = fetchPypi {
+    pname = "itkwasm_image_io";
+    inherit (finalAttrs) version;
+    hash = "sha256-Iwb6Xd+N3P+QsWhhu5q1Dx/joUClNgHBaWrgUalx0V4=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  nativeBuildInputs = [ writableTmpDirAsHomeHook ];
+
+  dependencies = [
+    itkwasm
+    itkwasm-image-io-emscripten
+    itkwasm-image-io-wasi
+  ];
+
+  pythonImportsCheck = [ "itkwasm_image_io" ];
+
+  # No tests available
+  doCheck = false;
+
+  meta = {
+    description = "Input and output for scientific and medical image file formats";
+    homepage = "https://pypi.org/project/itkwasm-image-io";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ fab ];
+  };
+})

pkgs/development/python-modules/itkwasm/default.nix

@@ -0,0 +1,47 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  hatchling,
+  importlib-metadata,
+  numpy,
+  platformdirs,
+  typing-extensions,
+  wasmtime,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "itkwasm";
+  version = "1.0b195";
+  pyproject = true;
+
+  src = fetchPypi {
+    inherit (finalAttrs) pname version;
+    hash = "sha256-1OQ0SieMEcrWiIgWT1dQxXdk9lCbWD+1xJ0jfIr0isU=";
+  };
+
+  build-system = [ hatchling ];
+
+  nativeBuildInputs = [ writableTmpDirAsHomeHook ];
+
+  dependencies = [
+    importlib-metadata
+    numpy
+    platformdirs
+    typing-extensions
+    wasmtime
+  ];
+
+  # No test available
+  doCheck = false;
+
+  pythonImportsCheck = [ "itkwasm" ];
+
+  meta = {
+    description = "Python interface to itk-wasm WebAssembly (Wasm) modules";
+    homepage = "https://pypi.org/project/itkwasm";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ fab ];
+  };
+})

pkgs/development/python-modules/multiscale-spatial-image/default.nix

@@ -1,26 +1,23 @@
 {
   lib,
   buildPythonPackage,
-  fetchFromGitHub,
-  hatchling,
+  dask-image,
   dask,
+  fetchFromGitHub,
+  fsspec,
+  hatch-vcs,
+  hatchling,
+  ngff-zarr,
   numpy,
   python-dateutil,
   spatial-image,
-  xarray,
+  writableTmpDirAsHomeHook,
   xarray-dataclass,
+  xarray,
   zarr,
-  dask-image,
-  fsspec,
-  jsonschema,
-  nbmake,
-  pooch,
-  pytestCheckHook,
-  pytest-mypy,
-  urllib3,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "multiscale-spatial-image";
   version = "2.1.0";
   pyproject = true;
@@ -28,14 +25,24 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "spatial-image";
     repo = "multiscale-spatial-image";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-uF9ZccLvP1ref6qn3l6EpedsoK29Q8lAdr68JjsYMis=";
   };
 
-  build-system = [ hatchling ];
+  pythonRelaxDeps = [
+    "dask"
+    "ngff-zarr"
+    "xarray"
+  ];
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
 
   dependencies = [
     dask
+    ngff-zarr
     numpy
     python-dateutil
     spatial-image
@@ -49,20 +56,9 @@ buildPythonPackage rec {
     #itk = [
     #  itk-filtering # not in nixpkgs yet
     #];
-    test = [
-      dask-image
-      fsspec
-      #ipfsspec # not in nixpkgs
-      #itk-filtering # not in nixpkgs
-      jsonschema
-      nbmake
-      pooch
-      pytest-mypy
-      urllib3
-    ];
   };
 
-  nativeCheckInputs = [ pytestCheckHook ] ++ optional-dependencies.test;
+  nativeBuildInputs = [ writableTmpDirAsHomeHook ];
 
   doCheck = false; # all test files try to download data
 
@@ -71,8 +67,8 @@ buildPythonPackage rec {
   meta = {
     description = "Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF";
     homepage = "https://github.com/spatial-image/multiscale-spatial-image";
-    changelog = "https://github.com/spatial-image/multiscale-spatial-image/releases/tag/${src.tag}";
+    changelog = "https://github.com/spatial-image/multiscale-spatial-image/releases/tag/${finalAttrs.src.tag}";
     license = lib.licenses.asl20;
     maintainers = with lib.maintainers; [ bcdarwin ];
   };
-}
+})

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

@@ -0,0 +1,142 @@
+{
+  lib,
+  buildPythonPackage,
+  dask,
+  dask-image,
+  deepdiff,
+  fetchFromGitHub,
+  hatchling,
+  importlib-resources,
+  itk,
+  itkwasm-downsample,
+  itkwasm-image-io,
+  itkwasm,
+  jsonschema,
+  nibabel,
+  imageio,
+  numpy,
+  imagecodecs,
+  platformdirs,
+  pooch,
+  psutil,
+  pytestCheckHook,
+  rich-argparse,
+  rich,
+  tensorstore,
+  tifffile,
+  typing-extensions,
+  writableTmpDirAsHomeHook,
+  zarr,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "ngff-zarr";
+  version = "0.34.0";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "fideus-labs";
+    repo = "ngff-zarr";
+    tag = "py-v${finalAttrs.version}";
+    hash = "sha256-5OiC1NHVEX60oHPwTJ0RN2fQnitwPBMNSfvbMcKAgvc=";
+  };
+
+  sourceRoot = "${finalAttrs.src.name}/py/";
+
+  build-system = [ hatchling ];
+
+  dependencies = [
+    dask
+    importlib-resources
+    itkwasm
+    itkwasm-downsample
+    numpy
+    platformdirs
+    psutil
+    rich
+    rich-argparse
+    typing-extensions
+    zarr
+  ]
+  ++ dask.optional-dependencies.array;
+
+  optional-dependencies = {
+    dask-image = [ dask-image ];
+    # itk = [ itk-filtering ];
+    cli = [
+      # itk-filtering
+      # itk-io
+      # liffile
+      dask
+      dask-image
+      imagecodecs
+      imageio
+      itk
+      itkwasm-image-io
+      nibabel
+      tifffile
+    ]
+    ++ dask.optional-dependencies.distributed;
+    tensorstore = [ tensorstore ];
+    validate = [ jsonschema ];
+  };
+
+  nativeCheckInputs = [
+    deepdiff
+    pooch
+    pytestCheckHook
+    writableTmpDirAsHomeHook
+  ]
+  ++ lib.flatten (builtins.attrValues finalAttrs.passthru.optional-dependencies);
+
+  pythonImportsCheck = [ "ngff_zarr" ];
+
+  disabledTestPaths = [
+    # No CLI tests
+    "test/test_cli_input_to_ngff_image.py"
+    "test/test_cli_output.py"
+    "test/test_cli_relative_paths.py"
+    # Attribute errors
+    "test/test_pyramid_integrity.py"
+    "test/test_multiscales_type.py"
+    "test/test_convert_ome_zarr_version.py"
+    "test/test_itk_image_to_ngff_image.py"
+    # Data missing
+    "test/test_hcs.py"
+    "test/test_hcs_simple.py"
+    "test/test_ngff_validation.py"
+    "test/test_nibabel_image_to_ngff_image.py"
+    # Network access
+    "test/test_from_ngff_zarr_tensorstore.py"
+    "test/test_from_ngff_zarr.py"
+    "test/test_large_serialization.py"
+    "test/test_ngff_image_to_itk_image.py"
+    "test/test_omero.py"
+    "test/test_rfc9_ozx.py"
+    "test/test_to_ngff_zarr_dask_image.py"
+    "test/test_to_ngff_zarr_itk.py"
+    "test/test_to_ngff_zarr_itkwasm.py"
+    "test/test_to_ngff_zarr_rfc2_zarr_v3.py"
+    "test/test_to_ngff_zarr_sharding.py"
+    "test/test_to_ngff_zarr_tensorstore.py"
+    "test/test_to_ngff_zarr_v3_compression.py"
+    # Missing dependencies
+    "test/test_lif_to_ngff_image.py"
+  ];
+
+  disabledTests = [
+    # Assertion errors
+    "test_2d_yx"
+    "test_3d_zyx"
+    "test_smaller_dask_graph"
+    "test_tensorstore_compression"
+  ];
+
+  meta = {
+    description = "Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation";
+    homepage = "https://github.com/fideus-labs/ngff-zarr";
+    changelog = "https://github.com/fideus-labs/ngff-zarr/releases/tag/${finalAttrs.src.tag}";
+    license = lib.licenses.isc;
+    maintainers = with lib.maintainers; [ fab ];
+  };
+})

pkgs/development/python-modules/wasmtime/default.nix

@@ -0,0 +1,83 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  python,
+  pkgs,
+  pycparser,
+  pytest-mypy,
+  pytestCheckHook,
+  setuptools-git-versioning,
+  setuptools,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "wasmtime";
+  version = "44.0.0";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "bytecodealliance";
+    repo = "wasmtime-py";
+    tag = finalAttrs.version;
+    hash = "sha256-7K0j4jMsRB7/wNIj0pXxFTy0y7aN37wgCD1XKM92Ayw=";
+  };
+
+  postPatch = ''
+    substituteInPlace pyproject.toml \
+      --replace-fail "setuptools-git-versioning>=2.0,<3" "setuptools-git-versioning" \
+      --replace-fail 'build-backend = "backend"' 'build-backend = "setuptools.build_meta"'
+
+    substituteInPlace ci/cbindgen.py \
+      --replace-fail "'-D__builtin_va_list=int'," "'-D__builtin_va_list=int', '-Dnullptr_t=void*',"
+
+    sed -i '/^backend-path = \[/,/^\]/d' pyproject.toml
+
+    # Use nixpkgs' wasmtime instead of downloading prebuilt C API artifacts.
+    mkdir -p wasmtime/linux-x86_64 wasmtime/linux-aarch64
+    ln -s ${lib.getLib pkgs.wasmtime}/lib/libwasmtime.so wasmtime/linux-x86_64/_libwasmtime.so
+    ln -s ${lib.getLib pkgs.wasmtime}/lib/libwasmtime.so wasmtime/linux-aarch64/_libwasmtime.so
+  '';
+
+  build-system = [
+    setuptools
+    setuptools-git-versioning
+  ];
+
+  buildInputs = [ pkgs.wasmtime ];
+
+  postInstall = ''
+    # Ensure the installed module can find the shared library at runtime
+    mkdir -p "$out/${python.sitePackages}/wasmtime/linux-x86_64"
+    mkdir -p "$out/${python.sitePackages}/wasmtime/linux-aarch64"
+    ln -sf ${lib.getLib pkgs.wasmtime}/lib/libwasmtime.so "$out/${python.sitePackages}/wasmtime/linux-x86_64/_libwasmtime.so"
+    ln -sf ${lib.getLib pkgs.wasmtime}/lib/libwasmtime.so "$out/${python.sitePackages}/wasmtime/linux-aarch64/_libwasmtime.so"
+  '';
+
+  nativeCheckInputs = [
+    pycparser
+    pytest-mypy
+    pytestCheckHook
+    writableTmpDirAsHomeHook
+  ];
+
+  disabledTestPaths = [
+    "ci/cbindgen.py"
+  ];
+
+  pythonImportsCheck = [ "wasmtime" ];
+
+  preCheck = ''
+    # cbindgen.py checks bindings against C headers during test collection.
+    ln -s ${lib.getDev pkgs.wasmtime}/include wasmtime/include
+  '';
+
+  meta = {
+    description = "Python WebAssembly runtime powered by Wasmtime";
+    homepage = "https://github.com/bytecodealliance/wasmtime-py";
+    changelog = "https://github.com/bytecodealliance/wasmtime-py/releases/tag/{${finalAttrs.src.tag}}";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ fab ];
+  };
+})

pkgs/top-level/python-packages.nix

@@ -7803,6 +7803,24 @@ self: super: with self; {
     }
   );
 
+  itkwasm = callPackage ../development/python-modules/itkwasm { };
+
+  itkwasm-downsample = callPackage ../development/python-modules/itkwasm-downsample { };
+
+  itkwasm-downsample-emscripten =
+    callPackage ../development/python-modules/itkwasm-downsample-emscripten
+      { };
+
+  itkwasm-downsample-wasi = callPackage ../development/python-modules/itkwasm-downsample-wasi { };
+
+  itkwasm-image-io = callPackage ../development/python-modules/itkwasm-image-io { };
+
+  itkwasm-image-io-emscripten =
+    callPackage ../development/python-modules/itkwasm-image-io-emscripten
+      { };
+
+  itkwasm-image-io-wasi = callPackage ../development/python-modules/itkwasm-image-io-wasi { };
+
   itsdangerous = callPackage ../development/python-modules/itsdangerous { };
 
   itunespy = callPackage ../development/python-modules/itunespy { };
@@ -11074,6 +11092,8 @@ self: super: with self; {
 
   nftables = callPackage ../os-specific/linux/nftables/python.nix { inherit (pkgs) nftables; };
 
+  ngff-zarr = callPackage ../development/python-modules/ngff-zarr { };
+
   nglview = callPackage ../development/python-modules/nglview { };
 
   nh3 = callPackage ../development/python-modules/nh3 { };
@@ -21075,6 +21095,8 @@ self: super: with self; {
 
   wasmerPackages = lib.recurseIntoAttrs (callPackage ../development/python-modules/wasmer { });
 
+  wasmtime = callPackage ../development/python-modules/wasmtime { };
+
   wasserstein = callPackage ../development/python-modules/wasserstein { };
 
   wassima = callPackage ../development/python-modules/wassima { };