<div dir="ltr">I think the best clue was in the origin email you sent me.<div><br></div><div><span style="color:rgb(80,0,80)"> expected_type, looped_id.split(":",1)[0], val))</span><br style="color:rgb(80,0,80)"><span style="color:rgb(80,0,80)">ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7</span></div><div><font color="#500050"><br></font></div><div>It's failing to parse a CIF loop. It can't convert "1,7" to a float. Are you pointing your environment to a different monomer library that Phenix?</div><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 8:42 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">Hi Nigel,<br>
<br>
<br>
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.<br>
<br>
<br>
Is there anything in the error message that would suggest the underlying issue?<br>
<br>
<br>
$ libtbx.python $(libtbx.find_in_repositories iotbx/regression/tst_pdb_as_cif.py)<br>
<br>
Converting tst_pdb_as_cif_1.pdb to mmCIF format.<br>
Traceback (most recent call last):<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 106, in <module><br>
exercise_01()<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 37, in exercise_01<br>
logger=null_out(),<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program<br>
task.run()<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py", line 37, in run<br>
txt = model.model_as_mmcif()<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif<br>
if self.get_restraints_manager() is not None:<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager<br>
self.setup_restraints_manager()<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager<br>
self._process_input_model()<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/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 "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__<br>
use_neutron_distances=use_neutron_distances,<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__<br>
use_neutron_distances=use_neutron_distances,<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all<br>
use_neutron_distances=use_neutron_distances,<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/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 "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__<br>
raise_value_error("Floating-point")<br>
File "/dls/mx-scratch/rjgildea/software/cctbx/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>
Cheers,<br>
<br>
<br>
Richard<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>
From: <a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@phenix-online.org</a> <<a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@phenix-online.org</a>> on behalf of Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>><br>
Sent: 19 December 2018 16:29:10<br>
To: cctbx mailing list<br>
Subject: Re: [cctbxbb] Broken iotbx/pdb/cif test<br>
<br>
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.<br>
<br>
Cheers<br>
<br>
Nigel<br>
<br>
---<br>
Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and Integrated Bioimaging<br>
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" rel="noreferrer" target="_blank">CCI.LBL.gov</a><<a href="http://CCI.LBL.gov" rel="noreferrer" target="_blank">http://CCI.LBL.gov</a>><br>
<br>
<br>
On Wed, Dec 19, 2018 at 1:11 AM <a href="mailto:richard.gildea@diamond.ac.uk" target="_blank">richard.gildea@diamond.ac.uk</a><mailto:<a href="mailto:richard.gildea@diamond.ac.uk" target="_blank">richard.gildea@diamond.ac.uk</a>> <<a href="mailto:richard.gildea@diamond.ac.uk" target="_blank">richard.gildea@diamond.ac.uk</a><mailto:<a href="mailto:richard.gildea@diamond.ac.uk" target="_blank">richard.gildea@diamond.ac.uk</a>>> wrote:<br>
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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