Bad idea to hard-wire package name into lowest level code. Now imagine
we need the same for afit, amber, quantumbio, rosetta, etc.. Are we
going to have a page-long block of "if" statements. Please re-think and
remove. For example, whether you want to shift it or not can be a
parameter that you cast way level up in the context specific code.
Pavel
On 12/20/18 09:53, CCTBX commit wrote:
> Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx
> On branch : master
>
> ------------------------------------------------------------------------
>
>
> commit 1ad3fe05571162839e770c35ed032a7fc38a33b7
> Author: Gydo van Zundert <gydo.vanzundert(a)schrodinger.com>
> Date: Wed Dec 19 14:58:36 2018 -0500
>
> Fix typo geobox
>
>
> ------------------------------------------------------------------------
>
>
> 1ad3fe05571162839e770c35ed032a7fc38a33b7
> mmtbx/refinement/real_space/individual_sites.py | 4 ++--
> 1 file changed, 2 insertions(+), 2 deletions(-)
>
> diff --git a/mmtbx/refinement/real_space/individual_sites.py
> b/mmtbx/refinement/real_space/individual_sites.py
> index c61e88b01..20f38a6b0 100644
> --- a/mmtbx/refinement/real_space/individual_sites.py
> +++ b/mmtbx/refinement/real_space/individual_sites.py
> @@ -350,7 +350,7 @@ class box_refinement_manager(object):
>
> # When using the Schrodinger force field, move the whole
> structure as the
> # selected atoms are environment aware.
> - if geobox.get_source() == 'SCHRODINGER':
> + if geo_box.get_source() == 'SCHRODINGER':
> geo_box.shift_cart(box.shift_cart)
>
> rsr_simple_refiner = simple(
> @@ -377,7 +377,7 @@ class box_refinement_manager(object):
> iselection, sites_cart_refined)
> self.xray_structure.set_sites_cart(sites_cart_moving)
> self.sites_cart = self.xray_structure.sites_cart()
> - if geobox.get_source() == 'SCHRODINGER':
> + if geo_box.get_source() == 'SCHRODINGER':
> geo_box.shift_cart(shift_back)
> else: # NCS constraints are present
> # select on xrs, grm, ncs_groups
>
> ------------------------------------------------------------------------
>
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>
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/2c119fcf012ca4cc60dfce231902c…
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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