python312Packages.nilearn: cleanup & fix (#382788)

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

@@ -0,0 +1,45 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  pdm-backend,
+  importlib-resources,
+  pytestCheckHook,
+}:
+
+buildPythonPackage rec {
+  pname = "acres";
+  version = "0.2.0";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "nipreps";
+    repo = "acres";
+    tag = version;
+    hash = "sha256-DSDTOUNInLMR6C1P4NT+121sU+BYBLw67xRCtKobEaM=";
+  };
+
+  build-system = [
+    pdm-backend
+  ];
+
+  dependencies = [
+    importlib-resources
+  ];
+
+  pythonImportsCheck = [
+    "acres"
+  ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  meta = {
+    description = "Data-loading utility for Python";
+    homepage = "https://github.com/nipreps/acres";
+    changelog = "https://github.com/nipreps/acres/blob/${version}/CHANGELOG.md";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+}

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

@@ -2,22 +2,20 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  pythonOlder,
-  pytestCheckHook,
+  setuptools,
   matplotlib,
   pydicom,
   python-dateutil,
-  setuptools,
+  pytestCheckHook,
+  versionCheckHook,
 }:
 
 let
-  deid-data = buildPythonPackage rec {
+  deid-data = buildPythonPackage {
     pname = "deid-data";
     version = "unstable-2022-12-06";
     pyproject = true;
 
-    disabled = pythonOlder "3.7";
-
     build-system = [ setuptools ];
 
     dependencies = [ pydicom ];
@@ -39,18 +37,16 @@ let
 in
 buildPythonPackage rec {
   pname = "deid";
-  version = "0.3.25";
+  version = "0.4.0";
   pyproject = true;
 
-  disabled = pythonOlder "3.7";
-
   # Pypi version has no tests
   src = fetchFromGitHub {
     owner = "pydicom";
-    repo = pname;
+    repo = "deid";
     # the github repo does not contain Pypi version tags:
-    rev = "830966d52846c6b721fabb4cc1c75f39eabd55cc";
-    hash = "sha256-+slwnQSeRHpoCsvZ24Gq7rOBpQL37a6Iqrj4Mqj6PCo=";
+    rev = "14d1e4eb70f2c9fda43fca411794be9d8a5a8516";
+    hash = "sha256-YsLWHIO6whcBQriMYb0tDD9s/RrxlfeKGORF1UCOilI=";
   };
 
   build-system = [ setuptools ];
@@ -64,7 +60,9 @@ buildPythonPackage rec {
   nativeCheckInputs = [
     deid-data
     pytestCheckHook
+    versionCheckHook
   ];
+  versionCheckProgramArg = [ "--version" ];
 
   pythonImportsCheck = [ "deid" ];
 

pkgs/development/python-modules/dicom2nifti/default.nix

@@ -2,16 +2,22 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  pythonOlder,
-  pytestCheckHook,
+
+  # build-system
+  setuptools,
+
+  # dependencies
   gdcm,
   nibabel,
   numpy,
   pydicom,
+  scipy,
+
+  # tests
+  pillow,
   pylibjpeg,
   pylibjpeg-libjpeg,
-  scipy,
-  setuptools,
+  pytestCheckHook,
 }:
 
 buildPythonPackage rec {
@@ -19,8 +25,6 @@ buildPythonPackage rec {
   version = "2.5.1";
   pyproject = true;
 
-  disabled = pythonOlder "3.6";
-
   # no tests in PyPI dist
   src = fetchFromGitHub {
     owner = "icometrix";
@@ -29,9 +33,14 @@ buildPythonPackage rec {
     hash = "sha256-lPaBKqYO8B138fCgeKH6vpwGQhN3JCOnDj5PgaYfRPA=";
   };
 
+  postPatch = ''
+    substituteInPlace tests/test_generic.py --replace-fail "from common" "from dicom2nifti.common"
+    substituteInPlace tests/test_ge.py --replace-fail "import convert_generic" "import dicom2nifti.convert_generic as convert_generic"
+  '';
+
   build-system = [ setuptools ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     gdcm
     nibabel
     numpy
@@ -39,24 +48,37 @@ buildPythonPackage rec {
     scipy
   ];
 
-  postPatch = ''
-    substituteInPlace tests/test_generic.py --replace-fail "from common" "from dicom2nifti.common"
-    substituteInPlace tests/test_ge.py --replace-fail "import convert_generic" "import dicom2nifti.convert_generic as convert_generic"
-  '';
-
-  nativeCheckInputs = [
-    pytestCheckHook
-    pylibjpeg
-    pylibjpeg-libjpeg
-  ];
-
   pythonImportsCheck = [ "dicom2nifti" ];
 
-  meta = with lib; {
+  nativeCheckInputs = [
+    pillow
+    pylibjpeg
+    pylibjpeg-libjpeg
+    pytestCheckHook
+  ];
+
+  disabledTests = [
+    # OverflowError: Python integer -1024 out of bounds for uint16
+    "test_not_a_volume"
+    "test_resampling"
+    "test_validate_orthogonal_disabled"
+
+    # RuntimeError: Unable to decompress 'JPEG 2000 Image Compression (Lossless O...
+    "test_anatomical"
+    "test_compressed_j2k"
+    "test_main_function"
+    "test_rgb"
+
+    # Missing script 'dicom2nifti_scrip'
+    "test_gantry_option"
+    "test_gantry_resampling"
+  ];
+
+  meta = {
     homepage = "https://github.com/icometrix/dicom2nifti";
     description = "Library for converting dicom files to nifti";
     mainProgram = "dicom2nifti";
-    license = licenses.mit;
-    maintainers = with maintainers; [ bcdarwin ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ bcdarwin ];
   };
 }

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

@@ -1,19 +1,24 @@
 {
   lib,
   buildPythonPackage,
-  fetchPypi,
-  pythonOlder,
-  pytestCheckHook,
+  fetchFromGitHub,
+
+  # build-system
   hatch-vcs,
+  hatchling,
+
+  # dependencies
+  joblib,
   lxml,
-  matplotlib,
   nibabel,
   numpy,
   pandas,
+  requests,
   scikit-learn,
   scipy,
-  joblib,
-  requests,
+  packaging,
+
+  pytestCheckHook,
 }:
 
 buildPythonPackage rec {
@@ -21,36 +26,53 @@ buildPythonPackage rec {
   version = "0.11.1";
   pyproject = true;
 
-  disabled = pythonOlder "3.8";
-
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-oB3wj8bI3tPNb7eiEWNGA61Gpt94BQS20FIiwuepcv4=";
+  src = fetchFromGitHub {
+    owner = "nilearn";
+    repo = "nilearn";
+    tag = version;
+    hash = "sha256-ZvodSRJkKwPwpYHOLmxAYIIv7f9AlrjmZS9KLPjz5rM=";
   };
 
-  nativeBuildInputs = [ hatch-vcs ];
+  postPatch = ''
+    substituteInPlace pyproject.toml \
+      --replace-fail " --template=maint_tools/templates/index.html" ""
+  '';
 
-  nativeCheckInputs = [ pytestCheckHook ];
-  disabledTests = [ "test_clean_confounds" ]; # https://github.com/nilearn/nilearn/issues/2608
-  # do subset of tests which don't fetch resources
-  pytestFlagsArray = [ "nilearn/connectome/tests" ];
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     joblib
     lxml
-    matplotlib
     nibabel
     numpy
     pandas
     requests
     scikit-learn
     scipy
+    packaging
   ];
 
-  meta = with lib; {
-    homepage = "https://nilearn.github.io";
+  nativeCheckInputs = [ pytestCheckHook ];
+
+  disabledTests = [
+    # https://github.com/nilearn/nilearn/issues/2608
+    "test_clean_confounds"
+
+    # [XPASS(strict)] invalid checks should fail
+    "test_check_estimator_invalid_group_sparse_covariance"
+  ];
+
+  # do subset of tests which don't fetch resources
+  pytestFlagsArray = [ "nilearn/connectome/tests" ];
+
+  meta = {
     description = "Module for statistical learning on neuroimaging data";
+    homepage = "https://nilearn.github.io";
     changelog = "https://github.com/nilearn/nilearn/releases/tag/${version}";
-    license = licenses.bsd3;
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
   };
 }

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

@@ -2,9 +2,13 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   hatch-vcs,
   hatchling,
-  pytestCheckHook,
+
+  # dependencies
+  acres,
   attrs,
   importlib-resources,
   jinja2,
@@ -26,18 +30,24 @@
   templateflow,
   traits,
   transforms3d,
+
+  # tests
+  pytest-cov-stub,
+  pytest-env,
+  pytestCheckHook,
+  writableTmpDirAsHomeHook,
 }:
 
 buildPythonPackage rec {
   pname = "niworkflows";
-  version = "1.12.0";
+  version = "1.12.2";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "nipreps";
     repo = "niworkflows";
     tag = version;
-    hash = "sha256-OWsfz5YDPy1qPpXomr4YiuCDf40Fy1pW8cNHPjHfqp4=";
+    hash = "sha256-rgnfp12SHlL3LFFMSrHlTd0tWNnA4ekxZ9kKYRvZWlw=";
   };
 
   pythonRelaxDeps = [ "traits" ];
@@ -48,6 +58,7 @@ buildPythonPackage rec {
   ];
 
   dependencies = [
+    acres
     attrs
     importlib-resources
     jinja2
@@ -73,29 +84,38 @@ buildPythonPackage rec {
 
   env.SETUPTOOLS_SCM_PRETEND_VERSION = version;
 
-  nativeCheckInputs = [ pytestCheckHook ];
-  preCheck = ''export HOME=$(mktemp -d)'';
+  nativeCheckInputs = [
+    pytest-cov-stub
+    pytest-env
+    pytestCheckHook
+    writableTmpDirAsHomeHook
+  ];
+
   pytestFlagsArray = [ "niworkflows" ];
-  # try to download data:
+
   disabledTests = [
-    "test_GenerateCifti"
+    # try to download data:
     "ROIsPlot"
     "ROIsPlot2"
+    "niworkflows.interfaces.cifti._prepare_cifti"
+    "niworkflows.utils.misc.get_template_specs"
+    "test_GenerateCifti"
     "test_SimpleShowMaskRPT"
     "test_cifti_surfaces_plot"
-    "niworkflows.utils.misc.get_template_specs"
-    "niworkflows.interfaces.cifti._prepare_cifti"
   ];
-  disabledTestPaths = [ "niworkflows/tests/test_registration.py" ];
+
+  disabledTestPaths = [
+    "niworkflows/tests/test_registration.py"
+  ];
 
   pythonImportsCheck = [ "niworkflows" ];
 
-  meta = with lib; {
+  meta = {
     description = "Common workflows for MRI (anatomical, functional, diffusion, etc.)";
     mainProgram = "niworkflows-boldref";
     homepage = "https://github.com/nipreps/niworkflows";
     changelog = "https://github.com/nipreps/niworkflows/blob/${src.tag}/CHANGES.rst";
-    license = licenses.asl20;
-    maintainers = with maintainers; [ bcdarwin ];
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ bcdarwin ];
   };
 }

pkgs/development/python-modules/pydicom-seg/default.nix

@@ -3,13 +3,18 @@
   buildPythonPackage,
   fetchFromGitHub,
   fetchpatch,
-  pythonOlder,
-  pytest7CheckHook,
+
+  # build-system
   poetry-core,
+
+  # dependencies
   jsonschema,
   numpy,
   pydicom,
   simpleitk,
+
+  # tests
+  pytestCheckHook,
 }:
 
 buildPythonPackage rec {
@@ -17,14 +22,12 @@ buildPythonPackage rec {
   version = "0.4.1";
   pyproject = true;
 
-  disabled = pythonOlder "3.7";
-
   src = fetchFromGitHub {
     owner = "razorx89";
-    repo = pname;
+    repo = "pydicom-seg";
     tag = "v${version}";
-    hash = "sha256-2Y3fZHKfZqdp5EU8HfVsmJ5JFfVGZuAR7+Kj7qaTiPM=";
     fetchSubmodules = true;
+    hash = "sha256-2Y3fZHKfZqdp5EU8HfVsmJ5JFfVGZuAR7+Kj7qaTiPM=";
   };
 
   patches = [
@@ -36,7 +39,10 @@ buildPythonPackage rec {
     })
   ];
 
-  pythonRelaxDeps = [ "jsonschema" ];
+  pythonRelaxDeps = [
+    "jsonschema"
+    "numpy"
+  ];
 
   build-system = [ poetry-core ];
 
@@ -47,15 +53,17 @@ buildPythonPackage rec {
     simpleitk
   ];
 
-  nativeCheckInputs = [ pytest7CheckHook ];
+  nativeCheckInputs = [ pytestCheckHook ];
 
   pythonImportsCheck = [ "pydicom_seg" ];
 
-  meta = with lib; {
+  meta = {
     description = "Medical segmentation file reading and writing";
     homepage = "https://github.com/razorx89/pydicom-seg";
     changelog = "https://github.com/razorx89/pydicom-seg/releases/tag/v${version}";
-    license = licenses.mit;
-    maintainers = with maintainers; [ bcdarwin ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+    # ModuleNotFoundError: No module named 'pydicom._storage_sopclass_uids'
+    broken = true;
   };
 }

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

@@ -3,7 +3,6 @@
   stdenv,
   buildPythonPackage,
   fetchFromGitHub,
-  pythonOlder,
   flit-core,
   numpy,
   pytestCheckHook,
@@ -11,8 +10,8 @@
   # optional/test dependencies
   gdcm,
   pillow,
-  pylibjpeg,
   pylibjpeg-libjpeg,
+  writableTmpDirAsHomeHook,
 }:
 let
   # Pydicom needs pydicom-data to run some tests. If these files aren't downloaded
@@ -29,8 +28,6 @@ buildPythonPackage rec {
   version = "3.0.1";
   pyproject = true;
 
-  disabled = pythonOlder "3.10";
-
   src = fetchFromGitHub {
     owner = "pydicom";
     repo = "pydicom";
@@ -55,13 +52,15 @@ buildPythonPackage rec {
     ];
   };
 
-  nativeCheckInputs = [ pytestCheckHook ] ++ optional-dependencies.pixeldata;
+  nativeCheckInputs = [
+    pytestCheckHook
+    writableTmpDirAsHomeHook
+  ] ++ optional-dependencies.pixeldata;
 
   # Setting $HOME to prevent pytest to try to create a folder inside
   # /homeless-shelter which is read-only.
   # Linking pydicom-data dicom files to $HOME/.pydicom/data
   preCheck = ''
-    export HOME=$TMP/test-home
     mkdir -p $HOME/.pydicom/
     ln -s ${test_data}/data_store/data $HOME/.pydicom/data
   '';
@@ -90,12 +89,20 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "pydicom" ];
 
-  meta = with lib; {
+  meta = {
     description = "Python package for working with DICOM files";
     mainProgram = "pydicom";
     homepage = "https://pydicom.github.io";
     changelog = "https://github.com/pydicom/pydicom/releases/tag/v${version}";
-    license = licenses.mit;
-    maintainers = with maintainers; [ bcdarwin ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+    badPlatforms = [
+      # > 200 tests are failing with errors like:
+      # AttributeError: 'FileDataset' object has no attribute 'BitsStored'
+      # AttributeError: 'FileDataset' object has no attribute 'Rows'
+      # AttributeError: The dataset has no 'Pixel Data', 'Float Pixel Data' or 'Double Float Pixel Data' element, no pixel data to decode
+      # pydicom.errors.InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header.
+      lib.systems.inspect.patterns.isDarwin
+    ];
   };
 }

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

@@ -2,7 +2,6 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  pythonOlder,
   poetry-core,
   httpx,
   pydicom,
@@ -10,20 +9,23 @@
 
 buildPythonPackage rec {
   pname = "pyorthanc";
-  version = "1.19.0";
-  disabled = pythonOlder "3.8";
+  version = "1.19.1";
 
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "gacou54";
-    repo = pname;
+    repo = "pyorthanc";
     tag = "v${version}";
-    hash = "sha256-6//kmkurtaXRGvnYnk/kU2j9F6V1Aui6IEdl+3DHGH0=";
+    hash = "sha256-97i341NXb7QsgN0X808mtz1rSKYSP+SMoGJy43Tkwug=";
   };
 
   build-system = [ poetry-core ];
 
+  pythonRelaxDeps = [
+    "pydicom"
+  ];
+
   dependencies = [
     httpx
     pydicom
@@ -33,11 +35,11 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "pyorthanc" ];
 
-  meta = with lib; {
+  meta = {
     description = "Python library that wraps the Orthanc REST API";
     homepage = "https://github.com/gacou54/pyorthanc";
-    changelog = "https://github.com/gacou54/pyorthanc/releases/tag/${src.tag}";
-    license = licenses.mit;
-    maintainers = with maintainers; [ bcdarwin ];
+    changelog = "https://github.com/gacou54/pyorthanc/releases/tag/v${version}";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ bcdarwin ];
   };
 }

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

@@ -1,42 +1,54 @@
 {
-  stdenv,
   lib,
+  stdenv,
   buildPythonPackage,
   fetchFromGitHub,
-  pytestCheckHook,
-  pythonOlder,
+
+  # build-system
+  hatchling,
+
+  # dependencies
   deprecated,
-  humanize,
   matplotlib,
   nibabel,
   numpy,
-  parameterized,
+  packaging,
+  rich,
   scipy,
   simpleitk,
   torch,
   tqdm,
   typer,
+
+  # tests
+  humanize,
+  parameterized,
+  pytestCheckHook,
 }:
 
 buildPythonPackage rec {
   pname = "torchio";
-  version = "0.20.3";
+  version = "0.20.4";
   pyproject = true;
 
-  disabled = pythonOlder "3.8";
-
   src = fetchFromGitHub {
     owner = "fepegar";
     repo = "torchio";
     tag = "v${version}";
-    hash = "sha256-I91KcrCwHkjY7oh5RFWfV93pRgd4iQVCBVTtd4TqXGo=";
+    hash = "sha256-pcUc0pnpb3qQLMOYU9yh7cljyCQ+Ngf8fJDcrRrK8LQ=";
   };
 
-  propagatedBuildInputs = [
+  build-system = [
+    hatchling
+  ];
+
+  dependencies = [
     deprecated
     humanize
     nibabel
     numpy
+    packaging
+    rich
     scipy
     simpleitk
     torch
@@ -45,10 +57,11 @@ buildPythonPackage rec {
   ];
 
   nativeCheckInputs = [
-    pytestCheckHook
     matplotlib
     parameterized
+    pytestCheckHook
   ];
+
   disabledTests =
     [
       # tries to download models:
@@ -58,15 +71,17 @@ buildPythonPackage rec {
       # RuntimeError: DataLoader worker (pid(s) <...>) exited unexpectedly
       "test_queue_multiprocessing"
     ];
+
   pythonImportsCheck = [
     "torchio"
     "torchio.data"
   ];
 
-  meta = with lib; {
+  meta = {
     description = "Medical imaging toolkit for deep learning";
     homepage = "https://torchio.readthedocs.io";
-    license = licenses.asl20;
-    maintainers = [ maintainers.bcdarwin ];
+    changelog = "https://github.com/TorchIO-project/torchio/blob/v${version}/CHANGELOG.md";
+    license = lib.licenses.asl20;
+    maintainers = [ lib.maintainers.bcdarwin ];
   };
 }

pkgs/top-level/python-packages.nix

@@ -51,6 +51,8 @@ self: super: with self; {
 
   acquire = callPackage ../development/python-modules/acquire { };
 
+  acres = callPackage ../development/python-modules/acres { };
+
   actdiag = callPackage ../development/python-modules/actdiag { };
 
   acunetix = callPackage ../development/python-modules/acunetix { };