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test_fragmenter babel_PC_with_RO_depth fails #3078

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drew-parsons opened this issue Jun 18, 2023 · 1 comment · Fixed by #3093
Closed

test_fragmenter babel_PC_with_RO_depth fails #3078

drew-parsons opened this issue Jun 18, 2023 · 1 comment · Fixed by #3093
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analysis Concerning pymatgen.analysis tests Issues with or changes to the pymatgen test suite

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@drew-parsons
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Description

Testing pymatgen 2023.05.31 on debian unstable, all tests pass except
test_babel_PC_with_RO_depth_0_vs_depth_10 from analysis/tests/test_fragmenter.py

Repro

Steps to reproduce the behavior:

  1. Build from source, including pymatgen test-files
  2. pytest-3 -vv pymatgen/analysis/tests/test_fragmenter.py -k RO_depth
  3. See error

Short error:

_________________________________________________________________________ TestFragmentMolecule.test_babel_PC_with_RO_depth_0_vs_depth_10 __________________________________________________________________________

self = <test_fragmenter.TestFragmentMolecule testMethod=test_babel_PC_with_RO_depth_0_vs_depth_10>

    def test_babel_PC_with_RO_depth_0_vs_depth_10(self):
        pytest.importorskip("openbabel", reason="OpenBabel not installed")
        fragmenter0 = Fragmenter(molecule=self.pc, depth=0, open_rings=True, opt_steps=1000)
>       assert fragmenter0.total_unique_fragments == 509
E       assert 411 == 509
E        +  where 411 = <pymatgen.analysis.fragmenter.Fragmenter object at 0x7f6e6e87bed0>.total_unique_fragments

test_fragmenter.py:118: AssertionError

Long error log:

/projects/pymatgen/pymatgen/analysis/tests$ PMG_TEST_FILES_DIR=/usr/share/doc/pymatgen-test-files/examples/test_files PYTHONPATH=/projects/pymatgen/.pybuild/cpython3_3.11_pymatgen/build/ pytest-3 -vv test_fragmenter.py -k RO_depth 
=============================================================================================== test session starts ===============================================================================================
platform linux -- Python 3.11.4, pytest-7.3.2, pluggy-1.0.0+repack -- /usr/bin/python3
cachedir: .pytest_cache
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/projects/pymatgen/pymatgen/analysis/tests/.hypothesis/examples')
rootdir: /projects/pymatgen
configfile: pyproject.toml
plugins: xvfb-2.0.0, remotedata-0.4.0, asyncio-0.20.3, arraydiff-0.5.0, filter-subpackage-0.1.2, flaky-3.7.0, cov-4.0.0, mpi-0.6, astropy-header-0.2.2, openfiles-0.5.0, hypothesis-6.73.0, mock-3.8.2, doctestplus-0.12.1, astropy-0.10.0
asyncio: mode=Mode.STRICT
collected 11 items / 10 deselected / 1 selected                                                                                                                                                                   

test_fragmenter.py::TestFragmentMolecule::test_babel_PC_with_RO_depth_0_vs_depth_10 FAILED                                                                                                                  [100%]

==================================================================================================== FAILURES =====================================================================================================
_________________________________________________________________________ TestFragmentMolecule.test_babel_PC_with_RO_depth_0_vs_depth_10 __________________________________________________________________________

self = <test_fragmenter.TestFragmentMolecule testMethod=test_babel_PC_with_RO_depth_0_vs_depth_10>

    def test_babel_PC_with_RO_depth_0_vs_depth_10(self):
        pytest.importorskip("openbabel", reason="OpenBabel not installed")
        fragmenter0 = Fragmenter(molecule=self.pc, depth=0, open_rings=True, opt_steps=1000)
>       assert fragmenter0.total_unique_fragments == 509
E       assert 411 == 509
E        +  where 411 = <pymatgen.analysis.fragmenter.Fragmenter object at 0x7f6e6e87bed0>.total_unique_fragments

test_fragmenter.py:118: AssertionError
---------------------------------------------------------------------------------------------- Captured stderr call -----------------------------------------------------------------------------------------------
==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

============================================================================================== slowest 30 durations ===============================================================================================
10.02s call     pymatgen/analysis/tests/test_fragmenter.py::TestFragmentMolecule::test_babel_PC_with_RO_depth_0_vs_depth_10

(2 durations < 0.005s hidden.  Use -vv to show these durations.)
======================================================================================== 1 failed, 10 deselected in 13.08s ========================================================================================

Expected behavior

The test should pass.

Environment

  • OS: Linux (debian unstable)
  • pymatgen 2023.05.31
  • openbabel 3.1.1
@janosh janosh added tests Issues with or changes to the pymatgen test suite analysis Concerning pymatgen.analysis labels Jun 22, 2023
@janosh
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janosh commented Jun 22, 2023

I'm having trouble installing openbabel on Mac so can't run this test myself. Is this value correct?

pymatgen/pymatgen/analysis/tests/test_fragmenter.py

Line 120 in 47af172

assert fragmenter10.total_unique_fragments == 509

I'm concerned these tests are apparently being skipped in CI. I was under the impression openbabel is installed in our Linux CI.

@janosh janosh linked a pull request Jun 22, 2023 that will close this issue
Fix test_babel_pc_with_ro_depth_0_vs_depth_10 #3093
Merged
@janosh janosh mentioned this issue Jun 22, 2023
Merged
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Fix test_babel_pc_with_ro_depth_0_vs_depth_10 materialsproject/pymatgen
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@drew-parsons @janosh