Handle temporary bruker numpy issues.

CHANGELOG.md

@@ -8,6 +8,7 @@ This document contains the Spec2nii release history in reverse chronological ord
 - Modified repository structure. Siemens and Philips files now have dedicated directories.
 - Support Python 3.11
 - Enable automatic Pypi upload and move to pyproject.toml file build.
+- Bruker conversion currently limited to numpy installations <1.20.0. Awaiting brukerapi package update.
 
 0.4.9 (Friday 4th November 2022)
 --------------------------------

spec2nii/spec2nii.py

@@ -33,6 +33,10 @@
 # There are case specific imports below
 
 
+class Spec2niiError(Exception):
+    pass
+
+
 class spec2nii:
     def __init__(self):
         cite_str = "Clarke WT, Bell TK, Emir UE, Mikkelsen M, Oeltzschner G, Shamaei A, Soher BJ, Wilson M. "\
@@ -521,7 +525,16 @@ def raw(self, args):
     # Bruker 2dseq files with FG_COMPLEX
     def bruker(self, args):
         from spec2nii.bruker import read_bruker
-        self.imageOut, self.fileoutNames = read_bruker(args)
+        from warnings import warn
+        from brukerapi.exceptions import MissingProperty
+        warn('Bruker conversion must currently be run with numpy<1.20.0')
+
+        try:
+            self.imageOut, self.fileoutNames = read_bruker(args)
+        except MissingProperty:
+            raise Spec2niiError(
+                'Bruker conversion must currently be run with numpy<1.20.0. '
+                'The underlying brukerapi package requires updating for ongoing compatibility.')
 
     # Varian parser
     def varian(self, args):

tests/test_bruker.py

@@ -9,6 +9,7 @@
 import json
 
 import numpy as np
+import pytest
 
 from .io_for_tests import read_nifti_mrs
 
@@ -17,6 +18,7 @@
 data_path = bruker_path / '20201208_105201_lego_rod_1_3'
 
 
+@pytest.mark.skip(reason="Awaiting fix of brukerapi package")
 def test_fid(tmp_path):
 
     subprocess.check_call(['spec2nii', 'bruker',
@@ -94,6 +96,7 @@ def test_fid(tmp_path):
     assert 'acqp' in hdr_ext
 
 
+@pytest.mark.skip(reason="Awaiting fix of brukerapi package")
 def test_2dseq(tmp_path):
 
     subprocess.check_call(['spec2nii', 'bruker',