[cctbxbb] Broken iotbx/pdb/cif test

Wed Dec 19 08:29:10 PST 2018

These tests worked when I committed and they work for me now. Also works in
BuildBot. Not sure what is the difference between my normal up-to-date
Phenix environment, BuildBot and Jenkins that is causing the problems for
you.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Wed, Dec 19, 2018 at 1:11 AM richard.gildea at diamond.ac.uk <
richard.gildea at diamond.ac.uk> wrote:

> 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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