[scipion-users] Xmipp tests

[Lynn R. <lyn...@un...>]

Dear Scipion community,

I'm having some problems with Xmipp. It installed without errors, but it gives a warning that it cannot find the image library. When I run this test:

scipion3 tests pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus

Then it gives me the following error message:

[   FAILED ] TestCtfConsensus.test1

Traceback (most recent call last):
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
    yield
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run
    self._callTestMethod(testMethod)
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
    method()
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", line 186, in test1
    self.checkCTFs(protCTFcons3,
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py", line 71, in checkCTFs
    self.assertAlmostEqual(avgCTF['defocusU'], firstCTF.getDefocusU(), delta=100,
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 966, in assertAlmostEqual
    raise self.failureException(msg)
AssertionError: 24140.0898 != 24025.673242 within 100 delta (114.4165580000008 difference) : DefocusU doesn't match when defocus averaging.

Also, the similar test:

scipion3 tests pwem.tests.workflows.test_workflow_xmipp

Gives the error message:

[   FAILED ] TestXmippWorkflow.testXmippWorkflow

Traceback (most recent call last):
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
    yield
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run
    self._callTestMethod(testMethod)
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
    method()
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp.py", line 198, in testXmippWorkflow
    self.assertAlmostEqual(protExtractCoordsShifts.outputCoordinates.getFirstItem().getPosition(),
  File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py", line 943, in assertAlmostEqual
    diff = abs(first - second)
TypeError: unsupported operand type(s) for -: 'tuple' and 'tuple'



All the other tests (basic and medium) that I ran completed without problems. I'm hoping that you can give me some advice on how to fix these error and get Xmipp running properly.

Kind regards,

Lynn Radamaker