updated clean command to match nifti-mrs 1.4.1 release

CHANGELOG.md

@@ -1,9 +1,10 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
-0.8.12 (WIP)
+0.8.12 (Wednesday 20th May 2026)
 ------------
 - Handle DICOMs missing series and instance numbers (generated through Siemens retrorecon).
 - Special case handling of ViennaCrt sequence for VE DICOM.
+- Bumped dependency to nifti-mrs 1.4.1
 
 0.8.11 (Monday 20th April 2026)
 ----------------------------------

pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
   "scipy>=1.13",
   "brukerapi>=0.1.8,<0.1.9",
   "pandas",
-  "nifti-mrs>=1.3.2",
+  "nifti-mrs>=1.4.1",
   "chardet"
 ]
 

spec2nii/other.py

@@ -107,7 +107,7 @@ def clean_hdr_ext(args):
         nifti_mrs_img = NIFTI_MRS(args.file, validate_on_creation=False)
         print("'intent_name' is valid.")
     except NotNIFTI_MRS as exc:
-        if str(exc) != 'NIFTI-MRS intent code not set.':
+        if 'NIFTI-MRS intent code not valid' not in str(exc):
             raise
         # if failed, read as a regular NIfTI, update intent and re-save
         from fsl.data.image import Image

tests/test_other_func.py

@@ -226,6 +226,8 @@ def test_clean_intent(tmp_path):
     nib.save(img, tmp_path / 'invalid1.nii.gz')
     img.header['intent_name'] = None
     nib.save(img, tmp_path / 'invalid2.nii.gz')
+    img.header['intent_name'] = 'test_v2_1'.encode()
+    nib.save(img, tmp_path / 'invalid3.nii.gz')
 
     # Create reference intent_name
     data_text = files('nifti_mrs.standard').joinpath('definitions.json').read_text(encoding='utf-8')
@@ -235,8 +237,8 @@ def test_clean_intent(tmp_path):
     intent_name = f'mrs_v{v_major}_{v_minor}'.encode()
 
     # Test clean call on this file
-    for file, intent in zip(['valid', 'invalid1', 'invalid2'],
-                            ['mrs_v2_1'.encode(), intent_name, intent_name]):
+    for file, intent in zip(['valid', 'invalid1', 'invalid2', 'invalid3'],
+                            ['mrs_v2_1'.encode(), intent_name, intent_name, intent_name]):
         subprocess.check_call(['spec2nii', 'clean',
                             '-o', tmp_path,
                             '-f', 'cleaned',