<div dir="ltr">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.<div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Dec 19, 2018 at 1:11 AM <a href="mailto:richard.gildea@diamond.ac.uk">richard.gildea@diamond.ac.uk</a> <<a href="mailto:richard.gildea@diamond.ac.uk">richard.gildea@diamond.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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.<br>
<br>
<br>
iotbx/regression/tst_pdb_as_cif.py<br>
<br>
iotbx/regression/tst_data_manager.py<br>
<br>
<br>
These have been failing since this commit:<br>
<br>
<br>
<a href="https://github.com/cctbx/cctbx_project/commit/2c119fcf012ca4cc60dfce231902c6133b99a228" rel="noreferrer" target="_blank">https://github.com/cctbx/cctbx_project/commit/2c119fcf012ca4cc60dfce231902c6133b99a228</a><br>
<br>
<br>
The tests also fail locally for me (not just on Jenkins).<br>
<br>
Cheers,<br>
<br>
<br>
Richard<br>
<br>
<br>
Traceback (most recent call last):<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 106, in <module><br>
exercise_01()<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 37, in exercise_01<br>
logger=null_out(),<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program<br>
task.run()<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py", line 37, in run<br>
txt = model.model_as_mmcif()<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif<br>
if self.get_restraints_manager() is not None:<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager<br>
self.setup_restraints_manager()<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager<br>
self._process_input_model()<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model<br>
use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__<br>
use_neutron_distances=use_neutron_distances,<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__<br>
use_neutron_distances=use_neutron_distances,<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all<br>
use_neutron_distances=use_neutron_distances,<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom<br>
entry = cif_types.energy_lib_atom(**dict(row))<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__<br>
raise_value_error("Floating-point")<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error<br>
expected_type, looped_id.split(":",1)[0], val))<br>
ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7<br>
<br>
<br>
Traceback (most recent call last):<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 532, in <module><br>
test_model_datatype()<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 233, in test_model_datatype<br>
dm.get_model().model_as_mmcif(), overwrite=True)<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif<br>
if self.get_restraints_manager() is not None:<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager<br>
self.setup_restraints_manager()<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager<br>
self._process_input_model()<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model<br>
use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__<br>
use_neutron_distances=use_neutron_distances,<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__<br>
use_neutron_distances=use_neutron_distances,<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all<br>
use_neutron_distances=use_neutron_distances,<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom<br>
entry = cif_types.energy_lib_atom(**dict(row))<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__<br>
raise_value_error("Floating-point")<br>
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error<br>
expected_type, looped_id.split(":",1)[0], val))<br>
ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7<br>
<br>
<br>
Dr Richard Gildea<br>
Data Analysis Scientist<br>
Tel: +441235 77 8078<br>
<br>
Diamond Light Source Ltd.<br>
Diamond House<br>
Harwell Science & Innovation Campus<br>
Didcot<br>
Oxfordshire<br>
OX11 0DE<br>
<br>
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