[cctbxbb] Broken iotbx/pdb/cif test

richard.gildea at diamond.ac.uk richard.gildea at diamond.ac.uk
Wed Dec 19 01:10:24 PST 2018


According to Jenkins these two tests have been broken for several days - does anyone know what the issue is and could a fix be applied? Both look like the same error.


iotbx/regression/tst_pdb_as_cif.py

iotbx/regression/tst_data_manager.py


These have been failing since this commit:


https://github.com/cctbx/cctbx_project/commit/2c119fcf012ca4cc60dfce231902c6133b99a228


The tests also fail locally for me (not just on Jenkins).

Cheers,


Richard


Traceback (most recent call last):
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 106, in <module>
    exercise_01()
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 37, in exercise_01
    logger=null_out(),
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program
    task.run()
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py", line 37, in run
    txt = model.model_as_mmcif()
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif
    if self.get_restraints_manager() is not None:
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager
    self.setup_restraints_manager()
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager
    self._process_input_model()
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model
    use_neutron_distances     = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__
    use_neutron_distances=use_neutron_distances,
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__
    use_neutron_distances=use_neutron_distances,
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all
    use_neutron_distances=use_neutron_distances,
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom
    entry = cif_types.energy_lib_atom(**dict(row))
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__
    raise_value_error("Floating-point")
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error
    expected_type, looped_id.split(":",1)[0], val))
ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7


Traceback (most recent call last):
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 532, in <module>
    test_model_datatype()
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 233, in test_model_datatype
    dm.get_model().model_as_mmcif(), overwrite=True)
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif
    if self.get_restraints_manager() is not None:
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager
    self.setup_restraints_manager()
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager
    self._process_input_model()
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model
    use_neutron_distances     = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__
    use_neutron_distances=use_neutron_distances,
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__
    use_neutron_distances=use_neutron_distances,
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all
    use_neutron_distances=use_neutron_distances,
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom
    entry = cif_types.energy_lib_atom(**dict(row))
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__
    raise_value_error("Floating-point")
  File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error
    expected_type, looped_id.split(":",1)[0], val))
ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7


Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

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