I think the best clue was in the origin email you sent me. expected_type, looped_id.split(":",1)[0], val)) ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7 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? 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Dec 19, 2018 at 8:42 AM [email protected] < [email protected]> wrote:

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: [email protected] on behalf of Nigel Moriarty 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.gov

On Wed, Dec 19, 2018 at 1:11 AM [email protected] > 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/2c119fcf012ca4cc60dfce231902c6...

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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_______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

So I suggest you look for "1,7" in the CCP4 monomer library installation... 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Dec 19, 2018 at 9:07 AM [email protected] < [email protected]> wrote:

We have the CCP4 environment loaded (but source before the build/setpath.sh) as it is needed for other dials/xia2 tests.

If I don't load the CCP4 environment then I get a different error:

$ 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 994, in __init__ if(mon_lib_srv is None): self.mon_lib_srv = monomer_library.server.server() File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 399, in __init__ list_cif = mon_lib_list_cif() File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 72, in mon_lib_list_cif strict=strict) File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 65, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON

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: [email protected] on behalf of Nigel Moriarty Sent: 19 December 2018 16:58:09 To: cctbx mailing list Subject: Re: [cctbxbb] Broken iotbx/pdb/cif test

I think the best clue was in the origin email you sent me.

expected_type, looped_id.split(":",1)[0], val)) ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7

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?

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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.gov

On Wed, Dec 19, 2018 at 8:42 AM [email protected] > wrote: 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: [email protected] mailto:[email protected]> on behalf of Nigel Moriarty < [email protected]mailto:[email protected]> 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.gov< http://CCI.LBL.gov>

On Wed, Dec 19, 2018 at 1:11 AM [email protected]> >> 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/2c119fcf012ca4cc60dfce231902c6...

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

-- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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I see from Marcin's email that there is an error in the CCP4 copy of the library. Shouldn't the tests (given that they are in the iotbx module) at least not fail in the absence of a monomer library? E.g. in several other places in iotbx/cctbx modules there is code such as: https://github.com/cctbx/cctbx_project/blob/666f100f60722b554cc7f8e440eb14bf... 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: [email protected] on behalf of Nigel Moriarty Sent: 19 December 2018 17:09:28 To: cctbx mailing list Subject: Re: [cctbxbb] Broken iotbx/pdb/cif test So I suggest you look for "1,7" in the CCP4 monomer library installation... 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.gov On Wed, Dec 19, 2018 at 9:07 AM [email protected]mailto:[email protected] mailto:[email protected]> wrote: We have the CCP4 environment loaded (but source before the build/setpath.sh) as it is needed for other dials/xia2 tests. If I don't load the CCP4 environment then I get a different error: $ 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 994, in __init__ if(mon_lib_srv is None): self.mon_lib_srv = monomer_library.server.server() File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 399, in __init__ list_cif = mon_lib_list_cif() File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 72, in mon_lib_list_cif strict=strict) File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 65, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON 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: [email protected]mailto:[email protected] mailto:[email protected]> on behalf of Nigel Moriarty mailto:[email protected]> Sent: 19 December 2018 16:58:09 To: cctbx mailing list Subject: Re: [cctbxbb] Broken iotbx/pdb/cif test I think the best clue was in the origin email you sent me. expected_type, looped_id.split(":",1)[0], val)) ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7 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? 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.govhttp://CCI.LBL.gov On Wed, Dec 19, 2018 at 8:42 AM [email protected]mailto:[email protected]mailto:[email protected]> mailto:[email protected]mailto:[email protected]>> wrote: 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: [email protected]mailto:[email protected]mailto:[email protected]> mailto:[email protected]mailto:[email protected]>> on behalf of Nigel Moriarty mailto:[email protected]mailto:[email protected]>> 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.govhttp://CCI.LBL.govhttp://CCI.LBL.gov On Wed, Dec 19, 2018 at 1:11 AM [email protected]mailto:[email protected]mailto:[email protected]>mailto:[email protected]mailto:[email protected]>> mailto:[email protected]mailto:[email protected]>mailto:[email protected]mailto:[email protected]>>> 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/2c119fcf012ca4cc60dfce231902c6... 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 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected]mailto:[email protected]>mailto:[email protected]mailto:[email protected]>> http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected]mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb