Unverified Commit 3b9c0d92 authored by Mario Rodas's avatar Mario Rodas Committed by GitHub
Browse files

Merge pull request #284103 from bcdarwin/niworkflows 

python311Packages.niworkflows: init at 1.10.0
parents 8c1a6046 7a483d6e

pkgs/development/python-modules/nipreps-versions/default.nix

0 → 100644
+46 −0
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, pythonOlder

, flit-scm

, packaging

, setuptools-scm

, pytestCheckHook

}:



buildPythonPackage rec {

  pname = "nipreps-versions";

  version = "1.0.4";

  pyproject = true;



  disabled = pythonOlder "3.7";



  src = fetchFromGitHub {

    owner = "nipreps";

    repo = "version-schemes";

    rev = "refs/tags/${version}";

    hash = "sha256-B2wtLurzgk59kTooH51a2dewK7aEyA0dAm64Wp+tqhM=";

  };



  env.SETUPTOOLS_SCM_PRETEND_VERSION = version;



  nativeBuildInputs = [

    flit-scm

    setuptools-scm

  ];



  propagatedBuildInputs = [

    packaging

  ];



  nativeCheckInputs = [ pytestCheckHook ];

  pythonImportsCheck = [ "nipreps_versions" ];



  meta = with lib; {

    description = "Setuptools_scm plugin for nipreps version schemes";

    homepage = "https://github.com/nipreps/version-schemes";

    changelog = "https://github.com/nipreps/version-schemes/blob/${src.rev}/CHANGES.md";

    license = licenses.asl20;

    maintainers = with maintainers; [ bcdarwin ];

  };

}

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

0 → 100644
+101 −0
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, hatch-vcs

, hatchling

, pytestCheckHook

, attrs

, importlib-resources

, jinja2

, looseversion

, matplotlib

, nibabel

, nilearn

, nipype

, nitransforms

, numpy

, packaging

, pandas

, pybids

, pyyaml

, scikit-image

, scipy

, seaborn

, svgutils

, templateflow

, traits

, transforms3d

}:



buildPythonPackage rec {

  pname = "niworkflows";

  version = "1.10.0";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "nipreps";

    repo = "niworkflows";

    rev = "refs/tags/${version}";

    hash = "sha256-wQPk9imDvomg+NTWk+VeW1TE2QlvMyi1YYVVaznhktU=";

  };



  postPatch = ''

    substituteInPlace pyproject.toml --replace '"traits < 6.4"' '"traits"'

  '';



  nativeBuildInputs = [

    hatch-vcs

    hatchling

  ];



  propagatedBuildInputs = [

    attrs

    importlib-resources

    jinja2

    looseversion

    matplotlib

    nibabel

    nilearn

    nipype

    nitransforms

    numpy

    packaging

    pandas

    pybids

    pyyaml

    scikit-image

    scipy

    seaborn

    svgutils

    templateflow

    traits

    transforms3d

  ];



  env.SETUPTOOLS_SCM_PRETEND_VERSION = version;



  nativeCheckInputs = [ pytestCheckHook ];

  preCheck = ''export HOME=$(mktemp -d)'';

  pytestFlagsArray = [ "niworkflows" ];

  # try to download data:

  disabledTests = [

    "test_GenerateCifti"

    "ROIsPlot"

    "ROIsPlot2"

    "test_SimpleShowMaskRPT"

    "test_cifti_surfaces_plot"

    "niworkflows.utils.misc.get_template_specs"

    "niworkflows.interfaces.cifti._prepare_cifti"

  ];

  disabledTestPaths = [ "niworkflows/tests/test_registration.py" ];



  pythonImportsCheck = [ "niworkflows" ];



  meta = with lib; {

    description = "Common workflows for MRI (anatomical, functional, diffusion, etc.)";

    homepage = "https://github.com/nipreps/niworkflows";

    changelog = "https://github.com/nipreps/niworkflows/blob/${src.rev}/CHANGES.rst";

    license = licenses.asl20;

    maintainers = with maintainers; [ bcdarwin ];

  };

}

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

0 → 100644
+40 −0
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, setuptools

, lxml

, matplotlib

, pytestCheckHook

, nose

}:



buildPythonPackage rec {

  pname = "svgutils";

  version = "0.3.4";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "btel";

    repo = "svg_utils";

    rev = "refs/tags/v${version}";

    hash = "sha256-ITvZx+3HMbTyaRmCb7tR0LKqCxGjqDdV9/2taziUD0c=";

  };



  nativeBuildInputs = [ setuptools ];



  propagatedBuildInputs = [

    lxml

    matplotlib

  ];



  nativeCheckInputs = [ pytestCheckHook nose ];



  pythonImportsCheck = [ "svgutils" ];



  meta = with lib; {

    description = "Python tools to create and manipulate SVG files";

    homepage = "https://github.com/btel/svg_utils";

    license = licenses.mit;

    maintainers = with maintainers; [ bcdarwin ];

  };

}

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

0 → 100644
+45 −0
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, pythonOlder

, pytestCheckHook

, setuptools-scm

, nipreps-versions

, pybids

, requests

, tqdm

}:



buildPythonPackage rec {

  pname = "templateflow";

  version = "23.1.0";

  pyproject = true;



  disabled = pythonOlder "3.7";



  src = fetchFromGitHub {

    owner = "templateflow";

    repo = "python-client";

    rev = "refs/tags/${version}";

    hash = "sha256-8AdXC1IFGfYZ5cvCAyBz0tD3zia+KBILX0tL9IcO2NA=";

  };



  nativeBuildInputs = [ setuptools-scm ];

  propagatedBuildInputs = [

    nipreps-versions

    pybids

    requests

    tqdm

  ];



  doCheck = false;  # most tests try to download data

  #pythonImportsCheck = [ "templateflow" ];  # touches $HOME/.cache, hence needs https://github.com/NixOS/nixpkgs/pull/120300



  meta = with lib; {

    homepage = "https://templateflow.org/python-client";

    description = "Python API to query TemplateFlow via pyBIDS";

    changelog = "https://github.com/templateflow/python-client/releases/tag/${version}";

    license = licenses.asl20;

    maintainers = with maintainers; [ bcdarwin ];

  };

}

pkgs/top-level/python-packages.nix

+8 −0
Original line number Diff line number Diff line
@@ -8373,6 +8373,8 @@ self: super: with self; { 














  ninja = callPackage ../development/python-modules/ninja { inherit (pkgs) ninja; };



























  nipreps-versions = callPackage ../development/python-modules/nipreps-versions { };



























  nipy = callPackage ../development/python-modules/nipy { };





























  nipype = callPackage ../development/python-modules/nipype {









@@ -8385,6 +8387,8 @@ self: super: with self; {



























  nitransforms = callPackage ../development/python-modules/nitransforms { };



























  niworkflows = callPackage ../development/python-modules/niworkflows { };



























  nix-kernel = callPackage ../development/python-modules/nix-kernel {















    inherit (pkgs) nix;















  };










@@ -14026,6 +14030,8 @@ self: super: with self; {



























  svgelements = callPackage ../development/python-modules/svgelements { };



























  svgutils = callPackage ../development/python-modules/svgutils { };



























  svgwrite = callPackage ../development/python-modules/svgwrite { };





























  sv-ttk = callPackage ../development/python-modules/sv-ttk { };










@@ -14165,6 +14171,8 @@ self: super: with self; {



























  tempita = callPackage ../development/python-modules/tempita { };



























  templateflow = callPackage ../development/python-modules/templateflow { };



























  tempora = callPackage ../development/python-modules/tempora { };





























  tenacity = callPackage ../development/python-modules/tenacity { };