Merge pull request #312707 from fabaff/pybids-fix

python312Packages.pybids: disable failing tests

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

@@ -1,27 +1,32 @@
-{ lib
-, buildPythonPackage
-, fetchFromGitHub
-, pythonOlder
-, pytestCheckHook
-, nibabel
-, pydicom
-, pylibjpeg-libjpeg
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  nibabel,
+  pydicom,
+  pylibjpeg-libjpeg,
+  pytestCheckHook,
+  pythonOlder,
+  setuptools,
 }:
 
 buildPythonPackage rec {
   pname = "dcmstack";
   version = "0.9";
-  format = "setuptools";
+  pyproject = true;
+
   disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "moloney";
-    repo = pname;
+    repo = "dcmstack";
     rev = "refs/tags/v${version}";
     hash = "sha256-GVzih9H2m2ZGSuZMRuaDG78b95PI3j0WQw5M3l4KNCs=";
   };
 
-  propagatedBuildInputs = [
+  build-system = [ setuptools ];
+
+  dependencies = [
     nibabel
     pydicom
     pylibjpeg-libjpeg
@@ -29,9 +34,16 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [ pytestCheckHook ];
 
+  pythonImportsCheck = [ "dcmstack" ];
+
+  disabledTestPaths = [
+    # AttributeError: 'TestNitoolCli' object has no attribute 'out_dir'
+    "test/test_cli.py"
+  ];
+
   meta = with lib; {
-    homepage = "https://github.com/moloney/dcmstack";
     description = "DICOM to Nifti conversion preserving metadata";
+    homepage = "https://github.com/moloney/dcmstack";
     license = licenses.mit;
     maintainers = with maintainers; [ bcdarwin ];
   };

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

@@ -1,26 +1,26 @@
-{ lib
-, buildPythonPackage
-, datalad
-, dcm2niix
-, dcmstack
-, etelemetry
-, fetchPypi
-, filelock
-, git
-, nibabel
-, nipype
-, pydicom
-, pytestCheckHook
-, pythonOlder
-, setuptools
-, versioningit
-, wheel
+{
+  lib,
+  buildPythonPackage,
+  datalad,
+  dcm2niix,
+  dcmstack,
+  etelemetry,
+  fetchPypi,
+  filelock,
+  git,
+  nibabel,
+  nipype,
+  pydicom,
+  pytestCheckHook,
+  pythonOlder,
+  setuptools,
+  versioningit,
 }:
 
 buildPythonPackage rec {
   pname = "heudiconv";
   version = "1.1.0";
-  format = "pyproject";
+  pyproject = true;
 
   disabled = pythonOlder "3.8";
 
@@ -31,22 +31,21 @@ buildPythonPackage rec {
 
   postPatch = ''
     substituteInPlace pyproject.toml \
-      --replace "versioningit ~=" "versioningit >="
+      --replace-fail "versioningit ~=" "versioningit >="
   '';
 
-  nativeBuildInputs = [
+  build-system = [
     setuptools
     versioningit
-    wheel
   ];
 
-  propagatedBuildInputs = [
-    nibabel
-    pydicom
-    nipype
+  dependencies = [
     dcmstack
     etelemetry
     filelock
+    nibabel
+    nipype
+    pydicom
   ];
 
   nativeCheckInputs = [
@@ -60,13 +59,16 @@ buildPythonPackage rec {
     export HOME=$(mktemp -d)
   '';
 
-  pythonImportsCheck = [
-    "heudiconv"
+  pythonImportsCheck = [ "heudiconv" ];
+
+  disabledTests = [
+    # No such file or directory
+    "test_bvals_are_zero"
   ];
 
   meta = with lib; {
-    homepage = "https://heudiconv.readthedocs.io";
     description = "Flexible DICOM converter for organizing imaging data";
+    homepage = "https://heudiconv.readthedocs.io";
     changelog = "https://github.com/nipy/heudiconv/releases/tag/v${version}";
     license = licenses.asl20;
     maintainers = with maintainers; [ bcdarwin ];

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

@@ -1,19 +1,20 @@
-{ buildPythonPackage
-, lib
-, fetchPypi
-, setuptools
-, formulaic
-, click
-, num2words
-, numpy
-, scipy
-, pandas
-, nibabel
-, bids-validator
-, sqlalchemy
-, pytestCheckHook
-, versioneer
-, pythonRelaxDepsHook
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  setuptools,
+  formulaic,
+  click,
+  num2words,
+  numpy,
+  scipy,
+  pandas,
+  nibabel,
+  bids-validator,
+  sqlalchemy,
+  pytestCheckHook,
+  versioneer,
+  pythonRelaxDepsHook,
 }:
 
 buildPythonPackage rec {
@@ -49,28 +50,28 @@ buildPythonPackage rec {
     sqlalchemy
   ];
 
-  pythonImportsCheck = [
-    "bids"
-  ];
+  pythonImportsCheck = [ "bids" ];
 
-  nativeCheckInputs = [
-    pytestCheckHook
-  ];
+  nativeCheckInputs = [ pytestCheckHook ];
 
   disabledTests = [
-    # looks for missing data:
+    # Test looks for missing data
     "test_config_filename"
-    # regression associated with formulaic >= 0.6.0
+    # Regression associated with formulaic >= 0.6.0
     # (see https://github.com/bids-standard/pybids/issues/1000)
     "test_split"
+    # AssertionError, TypeError
+    "test_run_variable_collection_bad_length_to_df_all_dense_var"
+    "test_extension_initial_dot"
+    "test_to_df"
   ];
 
   meta = with lib; {
     description = "Python tools for querying and manipulating BIDS datasets";
-    mainProgram = "pybids";
     homepage = "https://github.com/bids-standard/pybids";
     changelog = "https://github.com/bids-standard/pybids/blob/${version}/CHANGELOG.rst";
     license = licenses.mit;
     maintainers = with maintainers; [ jonringer ];
+    mainProgram = "pybids";
   };
 }