Added pytest skip for Hyperspy MRC errors

usnistgov · Mar 14, 2024 · 30ef226 · 30ef226
1 parent a3f370f
commit 30ef226
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Showing 2 changed files with 20 additions and 2 deletions.
diff --git a/tomotools/tests/test_io.py b/tomotools/tests/test_io.py
@@ -201,7 +201,7 @@ def test_load_dm_series(self):
         assert stack.axes_manager[2].units == signal.axes_manager[2].units
 
 
-# @pytest.mark.skipif(hspy_mrc_broken is True, reason="Hyperspy MRC reader broken")
+@pytest.mark.skipif(hspy_mrc_broken is True, reason="Hyperspy MRC reader broken")
 class TestSerialEM:
     def test_load_serialem_series(self):
         dirname = os.path.join(tomotools_path, "tests",

diff --git a/tomotools/tests/test_utils.py b/tomotools/tests/test_utils.py
@@ -4,13 +4,31 @@
 import pytest
 import numpy
 from tomotools.base import TomoStack
-# import hyperspy.api as hs
+import hyperspy.api as hs
 import os
 import glob
 
 tomotools_path = os.path.dirname(tomotools.__file__)
 
 
+def hspy_mrc_reader_check():
+    dirname = os.path.join(tomotools_path, "tests",
+                           "test_data", "SerialEM_Multiframe_Test")
+    files = glob.glob(dirname + "/*.mrc")
+    file = files[0]
+    s = hs.load(file)
+    return s
+
+
+try:
+    hspy_mrc_reader_check()
+except TypeError:
+    hspy_mrc_broken = True
+else:
+    hspy_mrc_broken = False
+
+
+@pytest.mark.skipif(hspy_mrc_broken is True, reason="Hyperspy MRC reader broken")
 class TestMultiframeAverage:
     def test_register_serialem_stack(self):
         dirname = os.path.join(tomotools_path, "tests",