[cctbxbb] Broken iotbx/pdb/cif test

Wed Dec 19 08:41:48 PST 2018

Hi Nigel,

As I mentioned in my email, this issue also affects my local builds on both mac and linux. I don't think I am doing any thing particularly odd in my local environments, and the fact that Jenkins also thinks the test is broken suggests that the issue is with the test and not my environment. Graeme also confirmed it was failing for him.

Is there anything in the error message that would suggest the underlying issue?

$ libtbx.python $(libtbx.find_in_repositories iotbx/regression/tst_pdb_as_cif.py)

Converting tst_pdb_as_cif_1.pdb to mmCIF format.
Traceback (most recent call last):
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 106, in <module>
    exercise_01()
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 37, in exercise_01
    logger=null_out(),
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program
    task.run()
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py", line 37, in run
    txt = model.model_as_mmcif()
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif
    if self.get_restraints_manager() is not None:
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager
    self.setup_restraints_manager()
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager
    self._process_input_model()
  File "/dls/mx-scratch/rjgildea/software/cctbx/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 "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__
    use_neutron_distances=use_neutron_distances,
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__
    use_neutron_distances=use_neutron_distances,
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all
    use_neutron_distances=use_neutron_distances,
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom
    entry = cif_types.energy_lib_atom(**dict(row))
  File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__
    raise_value_error("Floating-point")
  File "/dls/mx-scratch/rjgildea/software/cctbx/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

Cheers,

Richard

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

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
________________________________
From: cctbxbb-bounces at phenix-online.org <cctbxbb-bounces at phenix-online.org> on behalf of Nigel Moriarty <nwmoriarty at lbl.gov>
Sent: 19 December 2018 16:29:10
To: cctbx mailing list
Subject: Re: [cctbxbb] Broken iotbx/pdb/cif test

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<http://CCI.LBL.gov>

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