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

   1 {
   2   lib,
   3   buildPythonPackage,
   4   fetchFromGitHub,
   5   setuptools,
   6   formulaic,
   7   click,
   8   num2words,
   9   numpy,
  10   scipy,
  11   pandas,
  12   nibabel,
  13   bids-validator,
  14   sqlalchemy,
  15   universal-pathlib,
  16   pytestCheckHook,
  17   versioneer,
  18 }:
  19
  20 buildPythonPackage rec {
  21   pname = "pybids";
  22   version = "0.18.1";
  23   pyproject = true;
  24
  25   src = fetchFromGitHub {
  26     owner = "bids-standard";
  27     repo = "pybids";
  28     rev = version;
  29     hash = "sha256-nSBc4vhkCdRo7CNBwvJreCiwoxJK6ztyI5gvcpzYZ/Y=";
  30   };
  31
  32   postPatch = ''
  33     substituteInPlace pyproject.toml \
  34       --replace-fail 'dynamic = ["version"]' 'version = "${version}"'
  35   '';
  36
  37   pythonRelaxDeps = [
  38     "formulaic"
  39     "sqlalchemy"
  40   ];
  41
  42   build-system = [
  43     setuptools
  44     versioneer
  45   ] ++ versioneer.optional-dependencies.toml;
  46
  47   dependencies = [
  48     bids-validator
  49     click
  50     formulaic
  51     nibabel
  52     num2words
  53     numpy
  54     pandas
  55     scipy
  56     sqlalchemy
  57     universal-pathlib
  58   ];
  59
  60   pythonImportsCheck = [ "bids" ];
  61
  62   nativeCheckInputs = [ pytestCheckHook ];
  63
  64   disabledTestPaths = [
  65     # Could not connect to the endpoint URL
  66     "src/bids/layout/tests/test_remote_bids.py"
  67   ];
  68
  69   disabledTests = [
  70     # Regression associated with formulaic >= 0.6.0
  71     # (see https://github.com/bids-standard/pybids/issues/1000)
  72     "test_split"
  73   ];
  74
  75   meta = {
  76     description = "Python tools for querying and manipulating BIDS datasets";
  77     homepage = "https://github.com/bids-standard/pybids";
  78     changelog = "https://github.com/bids-standard/pybids/blob/${version}/CHANGELOG.rst";
  79     license = lib.licenses.mit;
  80     maintainers = with lib.maintainers; [ wegank ];
  81     mainProgram = "pybids";
  82   };
  83 }