def test_screen_fake_sims():
from generic import NexusError
from simulation import Simulation
from project_manager import ProjectManager
from test_simulation_module import get_test_workflow, n_test_workflows
sims = []
for n in range(n_test_workflows):
sims.extend(get_test_workflow(n).list())
#end for
pm = ProjectManager()
pm.add_simulations(sims)
pm.screen_fake_sims()
s = sims[len(sims) // 2]
s.fake_sim = True
try:
pm.screen_fake_sims()
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
Simulation.clear_all_sims()
def test_pw2qmcpack_get_result():
from generic import NexusError,obj
sim = get_pw2qmcpack_sim()
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = sim.get_result('orbitals',None)
result_ref = obj(
h5file = './runs/pwscf_output/pwscf.pwscf.h5',
ptcl_xml = './runs/pwscf_output/pwscf.ptcl.xml',
wfs_xml = './runs/pwscf_output/pwscf.wfs.xml',
)
assert(object_eq(result,result_ref))
clear_all_sims()
def test_pyscf_to_afqmc_get_result():
from generic import NexusError,obj
sim = get_pyscf_to_afqmc_sim()
sim.input.output = 'afqmc.h5'
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result_ref = obj(
h5_file = './runs/afqmc.h5',
)
result = sim.get_result('wavefunction',None)
assert(object_eq(result,result_ref))
result = sim.get_result('hamiltonian',None)
assert(object_eq(result,result_ref))
clear_all_sims()
def get_gamess_sim(type='rhf'):
from machines import job
from gamess import Gamess, generate_gamess, GamessInput
from test_gamess_input import get_files
sim = None
Gamess.ericfmt = ''
files = get_files()
if type == 'rhf':
gi_input = GamessInput(files['rhf.inp'])
sim = generate_gamess(
identifier='rhf',
path='rhf',
job=job(machine='ws1', cores=1),
input=gi_input,
)
else:
failed()
#end if
assert (sim is not None)
assert (isinstance(sim, Gamess))
return sim
def test_pw2qmcpack_incorporate_result():
from generic import NexusError,obj
from simulation import Simulation
from test_pwscf_simulation import pseudo_inputs,get_pwscf_sim
tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_check_result',**pseudo_inputs)
other = Simulation()
scf = get_pwscf_sim('scf')
sim = get_pw2qmcpack_sim(path='scf')
try:
sim.incorporate_result('unknown',None,other)
raise TestFailed
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
sim.incorporate_result('orbitals',None,scf)
clear_all_sims()
restore_nexus()
def test_pw2qmcpack_check_sim_status():
import os
from generic import NexusError, obj
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory(
'qmcpack_converter_simulations',
'test_pw2qmcpack_check_sim_status',
divert=True)
nexus_core.runs = ''
sim = get_pw2qmcpack_sim()
assert (sim.locdir.rstrip('/') == tpath.rstrip('/'))
assert (not sim.finished)
assert (not sim.failed)
try:
sim.check_sim_status()
raise FailedTest
except IOError:
None
except Exception as e:
failed(str(e))
#end try
sim.create_directories()
outfile = os.path.join(sim.locdir, sim.outfile)
outfile_text = 'JOB DONE'
out = open(outfile, 'w')
out.write(outfile_text)
out.close()
assert (outfile_text in open(outfile, 'r').read())
prefix = sim.input.inputpp.prefix
outdir = sim.input.inputpp.outdir
outdir_path = os.path.join(tpath, outdir)
if not os.path.exists(outdir_path):
os.makedirs(outdir_path)
#end if
filenames = [
prefix + '.pwscf.h5', prefix + '.ptcl.xml', prefix + '.wfs.xml'
]
for filename in filenames:
filepath = os.path.join(tpath, outdir, filename)
f = open(filepath, 'w')
f.write('')
f.close()
assert (os.path.exists(filepath))
#end for
sim.job.finished = True
sim.check_sim_status()
assert (sim.finished)
assert (not sim.failed)
clear_all_sims()
restore_nexus()
def test_get_result():
from generic import NexusError,obj
sim = get_quantum_package_sim()
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
sim.input.run_control.save_for_qmcpack = True
result = sim.get_result('orbitals',None)
result_ref = obj(
outfile = './runs/qp_savewf.out',
)
assert(object_eq(result,result_ref))
clear_all_sims()
def test_convert4qmc_get_result():
from generic import NexusError,obj
sim = get_convert4qmc_sim()
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = sim.get_result('orbitals',None)
result_ref = obj(
location = './runs/sample.wfj.xml',
)
assert(object_eq(result,result_ref))
result = sim.get_result('particles',None)
result_ref = obj(
location = './runs/sample.structure.xml',
)
assert(object_eq(result,result_ref))
clear_all_sims()
def get_pwscf_sim(type='scf'):
from nexus_base import nexus_core
from machines import job
from pwscf import Pwscf,generate_pwscf
nexus_core.runs = ''
sim = None
if type=='scf':
sim = generate_pwscf(
identifier = 'scf',
path = 'scf',
job = job(machine='ws1',cores=1),
input_type = 'generic',
calculation = 'scf',
input_dft = 'lda',
ecutwfc = 200,
conv_thr = 1e-8,
nosym = True,
wf_collect = True,
system = get_system(),
pseudos = ['C.BFD.upf'],
nogamma = True,
)
else:
failed()
#end if
assert(sim is not None)
assert(isinstance(sim,Pwscf))
return sim
def test_pyscf_to_afqmc_incorporate_result():
import os
from generic import NexusError,obj
from simulation import Simulation
from test_pyscf_simulation import get_pyscf_sim
other = Simulation()
scf = get_pyscf_sim()
sim = get_pyscf_to_afqmc_sim()
try:
sim.incorporate_result('unknown',None,other)
raise TestFailed
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = obj(
chkfile = os.path.join(scf.locdir,'scf.chk'),
)
assert(sim.input.input==None)
sim.incorporate_result('wavefunction',result,scf)
assert(sim.input.input=='scf.chk')
clear_all_sims()
def test_get_result():
import os
from generic import NexusError, obj
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory('gamess_simulation',
'test_get_result',
divert=True)
nexus_core.runs = ''
sim = get_gamess_sim('rhf')
assert (sim.locdir.rstrip('/') == os.path.join(tpath, 'rhf').rstrip('/'))
sim.create_directories()
sim.write_inputs()
if not os.path.exists(sim.imresdir):
os.makedirs(sim.imresdir)
#end if
analyzer = sim.analyzer_type(sim)
analyzer.save(os.path.join(sim.imresdir, sim.analyzer_image))
try:
sim.get_result('unknown', None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = sim.get_result('orbitals', None)
result_ref = obj(
location='rhf/rhf.out',
mos=0,
norbitals=0,
outfile='rhf/rhf.out',
scftyp='rohf',
vec=None,
)
result.location = result.location.replace(tpath, '').lstrip('/')
result.outfile = result.outfile.replace(tpath, '').lstrip('/')
assert (object_eq(result, result_ref))
clear_all_sims()
restore_nexus()
def test_pyscf_to_afqmc_check_sim_status():
import os
from generic import NexusError, obj
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory(
'qmcpack_converter_simulations',
'test_pyscf_to_afqmc_check_sim_status',
divert=True)
nexus_core.runs = ''
sim = get_pyscf_to_afqmc_sim()
assert (sim.locdir.rstrip('/') == tpath.rstrip('/'))
assert (not sim.finished)
assert (not sim.failed)
try:
sim.check_sim_status()
raise FailedTest
except IOError:
None
except Exception as e:
failed(str(e))
#end try
sim.input.output = 'afqmc.h5'
sim.create_directories()
outfile = os.path.join(sim.locdir, sim.outfile)
outfile_text = '# Finished.'
out = open(outfile, 'w')
out.write(outfile_text)
out.close()
assert (outfile_text in open(outfile, 'r').read())
output_file = os.path.join(sim.locdir, sim.input.output)
f = open(output_file, 'w')
f.write('')
f.close()
assert (os.path.exists(output_file))
sim.job.finished = True
sim.check_sim_status()
assert (sim.finished)
assert (not sim.failed)
clear_all_sims()
restore_nexus()
def test_get_result():
from generic import NexusError
tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_get_result',**pseudo_inputs)
sim = get_pwscf_sim('scf')
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = sim.get_result('charge_density',None)
result2 = sim.get_result('restart',None)
assert(object_eq(result,result2))
result_ref = dict(
locdir = 'scf',
outdir = 'scf/pwscf_output',
location = 'scf/pwscf_output/pwscf.save/charge-density.dat',
spin_location = 'scf/pwscf_output/pwscf.save/spin-polarization.dat',
)
assert(set(result.keys())==set(result_ref.keys()))
for k,path in result.items():
path = path.replace(tpath,'').lstrip('/')
assert(path==result_ref[k])
#end for
result = sim.get_result('orbitals',None)
result_ref = dict(
location = 'scf/pwscf_output/pwscf.wfc1',
)
assert(set(result.keys())==set(result_ref.keys()))
for k,path in result.items():
path = path.replace(tpath,'').lstrip('/')
assert(path==result_ref[k])
#end for
clear_all_sims()
restore_nexus()
def test_check_sim_status():
import os
tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_check_sim_status',**pseudo_inputs)
sim = get_pwscf_sim('scf')
assert(sim.locdir.rstrip('/')==os.path.join(tpath,'scf').rstrip('/'))
if not os.path.exists(sim.locdir):
os.makedirs(sim.locdir)
#end if
assert(not sim.finished)
try:
sim.check_sim_status()
except IOError:
None
except Exception as e:
failed(str(e))
#end try
assert(not sim.finished)
out_path = os.path.join(tpath,'scf',sim.outfile)
out_text = ''
outfile = open(out_path,'w')
outfile.write(out_text)
outfile.close()
assert(os.path.exists(out_path))
sim.check_sim_status()
assert(not sim.finished)
out_text = 'JOB DONE'
outfile = open(out_path,'w')
outfile.write(out_text)
outfile.close()
assert(out_text in open(out_path,'r').read())
sim.check_sim_status()
assert(sim.finished)
assert(not sim.failed)
clear_all_sims()
restore_nexus()
def test_get_result():
import os
from generic import NexusError, obj
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory('pyscf_simulation',
'test_get_result',
divert=True)
nexus_core.runs = ''
template_file = 'scf_template.py'
template_text = 'template $chkfile'
template_filepath = os.path.join(tpath, template_file)
f = open(template_filepath, 'w')
f.write(template_text)
f.close()
sim = get_pyscf_sim(
prefix='scf',
checkpoint='scf.chk',
template=template_filepath,
)
try:
sim.get_result('unknown', None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = sim.get_result('orbitals', None)
assert (result.h5_file.replace(tpath, '').lstrip('/') == 'scf.h5')
result = sim.get_result('wavefunction', None)
assert (result.chkfile.replace(tpath, '').lstrip('/') == 'scf.chk')
clear_all_sims()
restore_nexus()
def test_check_sim_status():
import os
from generic import NexusError, obj
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory('gamess_simulation',
'test_check_sim_status',
divert=True)
nexus_core.runs = ''
sim = get_gamess_sim('rhf')
assert (sim.locdir.rstrip('/') == os.path.join(tpath, 'rhf').rstrip('/'))
assert (not sim.finished)
assert (not sim.failed)
try:
sim.check_sim_status()
raise FailedTest
except IOError:
None
except Exception as e:
failed(str(e))
#end try
sim.create_directories()
outfile = os.path.join(sim.locdir, sim.outfile)
outfile_text = 'EXECUTION OF GAMESS TERMINATED NORMALLY'
out = open(outfile, 'w')
out.write(outfile_text)
out.close()
assert (outfile_text in open(outfile, 'r').read())
sim.check_sim_status()
assert (sim.finished)
assert (not sim.failed)
clear_all_sims()
restore_nexus()
def test_incorporate_result():
from generic import NexusError
from machines import job
for cls,gen in get_class_generators():
sim = gen(job=job(machine='ws1',cores=1))
assert(isinstance(sim,cls))
try:
sim.incorporate_result('anything',None,None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
#end for
clear_all_sims()
def test_check_sim_status():
import os
from generic import NexusError,obj
from nexus_base import nexus_core
tpath = testing.setup_unit_test_output_directory('quantum_package_simulation','test_check_sim_status',divert=True)
nexus_core.runs = ''
sim = get_quantum_package_sim()
assert(sim.locdir.rstrip('/')==tpath.rstrip('/'))
assert(not sim.finished)
assert(not sim.failed)
try:
sim.check_sim_status()
raise FailedTest
except IOError:
None
except Exception as e:
failed(str(e))
#end try
sim.create_directories()
outfile = os.path.join(sim.locdir,sim.outfile)
outfile_text = '* SCF energy'
out = open(outfile,'w')
out.write(outfile_text)
out.close()
assert(outfile_text in open(outfile,'r').read())
sim.job.finished = True
sim.check_sim_status()
assert(sim.finished)
assert(not sim.failed)
clear_all_sims()
restore_nexus()
def get_qmcpack_sim(type='rsqmc', **kwargs):
from machines import job
from qmcpack import Qmcpack, generate_qmcpack
if type == 'rsqmc':
tiling = kwargs.pop('tiling', (1, 1, 1))
sim = generate_qmcpack(job=job(machine='ws1', cores=1),
system=get_system(tiling=tiling),
**kwargs)
elif type == 'afqmc':
sim = generate_qmcpack(job=job(machine='ws1', cores=1),
input_type='basic_afqmc',
**kwargs)
else:
failed()
#end if
assert (isinstance(sim, Qmcpack))
return sim
def test_resolve_file_collisions():
from generic import NexusError
from simulation import Simulation
from project_manager import ProjectManager
from test_simulation_module import get_test_workflow, n_test_workflows
divert_nexus_log()
sims = []
for n in range(n_test_workflows):
sims.extend(get_test_workflow(n).list())
#end for
pm = ProjectManager()
pm.add_simulations(sims)
pm.resolve_file_collisions()
s1 = sims[len(sims) // 2]
s2 = sims[len(sims) // 2 + 1]
s2.locdir = s1.locdir
s2.outfile = s1.outfile
try:
pm.resolve_file_collisions()
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
restore_nexus_log()
Simulation.clear_all_sims()
def test_incorporate_result():
import os
from generic import NexusError, obj
tpath = testing.setup_unit_test_output_directory(
'gamess_simulation', 'test_incorporate_result')
sim = get_gamess_sim('rhf')
try:
sim.incorporate_result('unknown', None, None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
result = obj(
vec='vec text',
norbitals=10,
)
input = sim.input
assert ('vec' not in input)
assert ('norb' not in input.guess)
assert ('prtmo' not in input.guess)
sim.incorporate_result('orbitals', result, None)
assert (input.vec.text == 'vec text')
assert (input.guess.guess == 'moread')
assert (input.guess.norb == 10)
assert (input.guess.prtmo == True)
clear_all_sims()
def test_incorporate_result():
from generic import NexusError,obj
from machines import job
from simulation import Simulation
from gamess import generate_gamess,Gamess
Gamess.ericfmt = ''
other = Simulation()
gms = generate_gamess(
job = job(machine='ws1',cores=1),
)
Gamess.ericfmt = None
sim = get_quantum_package_sim()
try:
sim.get_result('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try:
sim.get_result('orbitals',other)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
clear_all_sims()
def test_extensions():
# test obj functions
from generic import obj,NexusError
# make a simple object
o = obj(
a = 1,
b = 'b',
c = (1,1,1),
)
o[3,4,5] = (5,6,7)
# test member values
assert(o.a==1)
assert(o.b=='b')
assert(o.c==(1,1,1))
assert(o[3,4,5]==(5,6,7))
# test member presence and length
assert('a' in o)
assert(2 not in o)
assert(len(o)==4)
# test list interface
vals = [3,'t',6.4,(4,3,2)]
l = list()
lo = obj()
for v in vals:
l.append(v)
lo.append(v)
#end for
assert(len(l)==len(lo))
for i in range(len(l)):
assert(l[i]==lo[i])
#end for
# test representations
# test list representation
l2 = lo.list()
assert(isinstance(l2,list))
assert(l==l2)
l2 = lo.list_optional(1,3)
assert(l2==['t',(4,3,2)])
l2 = o.list_optional('b',(3,4,5))
assert(l2==['b',(5,6,7)])
# test tuple representation
t = lo.tuple()
assert(isinstance(t,tuple))
assert(t==tuple(l))
d = dict(
a = 1,
b = 'b',
c = (1,1,1),
)
d[3,4,5] = (5,6,7)
# test dict representation
do = o.dict()
assert(isinstance(do,dict))
assert(do==d)
d2 = d.copy()
d2['d'] = d
o2 = o.copy()
o2.d = o
d2o = o2.to_dict()
assert(d2o==d2)
# test obj representation
o2 = o.obj()
assert(isinstance(o2,obj))
assert(id(o2)!=id(o))
assert(object_eq(o2,o))
o2 = o.copy().to_obj()
assert(object_eq(o2,o))
# test list extensions
# test first
assert(lo.first()==lo[0])
# test last
assert(lo.last()==lo[3])
# test select_random
v = lo.select_random()
assert(v in lo.list())
# test dict extensions
# test random_key
k = o.random_key()
assert(k in o)
o2 = obj()
assert(o2.random_key() is None)
# test set
o2 = o.copy()
o2.set(
b = 'b2',
d = ('a','b','c'),
)
assert(o2.b=='b2')
assert(o2.d==tuple('abc'))
o1 = obj(a=1,b=2)
o2 = obj(c=3,d=4)
o3 = obj(e=5,f=6)
o4 = obj()
o4.set(o1,o2,o3)
for on in (o1,o2,o3):
for k,v in on.items():
assert(o4[k]==v)
#end for
#end for
# test set optional
o2 = o.copy()
o2.set_optional(
b = 'b2',
d = ('a','b','c'),
)
assert(o2.b=='b')
assert(o2.d==tuple('abc'))
o1 = obj(a=1,b=2)
o2 = obj(c=3,d=4)
o3 = obj(e=5,f=6)
o4 = obj()
o4.set_optional(o1,o2,o3)
for on in (o1,o2,o3):
for k,v in on.items():
assert(o4[k]==v)
#end for
#end for
# test get
assert(o.get('c')==(1,1,1))
assert('d' not in o)
assert(o.get('d') is None)
# test get optional (identical to get)
assert(o.get_optional('c')==(1,1,1))
assert(o.get_optional('d') is None)
# test get required
assert(o.get_required('c')==(1,1,1))
try:
val = o.get_required('d')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test delete
o2 = o.copy()
assert(o2.delete('c')==(1,1,1))
assert('c' not in o2)
keys = 'a','b','c',(3,4,5)
vals = [1,'b',(1,1,1),(5,6,7)]
o2 = o.copy()
assert(o2.delete(*keys)==vals)
assert(len(o2)==0)
for k in keys:
assert(k not in o2)
#end for
o2 = o.copy()
assert(o2.delete(keys)==vals)
assert(len(o2)==0)
for k in keys:
assert(k not in o2)
#end for
o2 = o.copy()
try:
o2.delete('a','d')
raise FailedTest
except KeyError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test delete optional
o2 = o.copy()
o2.delete_optional('c')
assert('c' not in o2)
assert('d' not in o2)
o2.delete_optional('d')
assert('d' not in o2)
# test delete required
o2 = o.copy()
o2.delete_required('c')
assert('c' not in o2)
try:
o2.delete_required('d')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test add
o2 = obj()
o2.add('a',1)
try: # add unhashable type
o2.add([3,4,5],6)
raise FailedTest
except TypeError:
None
#end if
# test add optional
o2 = obj(a=1)
o2.add_optional('a',2)
o2.add_optional('b',3)
assert(o2.a==1)
assert(o2.b==3)
# test transfer/copy/move functions
dref = dict(
a = 1,
b = 'b',
c = (1,1,1),
d = dict(
e = 5.4,
f = [3.3,4.5],
),
)
dref[3,4,5] = (5,6,7)
# test transfer from
o = obj()
o.transfer_from(dref)
assert(o.to_dict()==dref)
assert(id(o.d)==id(dref['d']))
o = obj()
o.transfer_from(dref,copy=True)
assert(o.to_dict()==dref)
assert(id(o.d)!=id(dref['d']))
osmall = obj(b='b',c=(1,1,1))
osmall[3,4,5] = (5,6,7)
o = obj()
oref = obj(dref)
assert(oref.to_dict()==dref)
o.transfer_from(oref,keys=['b','c',(3,4,5)])
assert(object_eq(o,osmall))
o = obj(a=6,b=7)
o.transfer_from(oref,overwrite=False)
assert(object_neq(o,oref))
o.transfer_from(oref,overwrite=True)
assert(object_eq(o,oref))
assert(o.to_dict()==dref)
o = obj()
try:
o.transfer_from(oref,keys=['a','x'])
raise FailedTest
except KeyError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test transfer to
o = obj()
oref.transfer_to(o)
assert(object_eq(o,oref))
assert(id(o.d)==id(oref.d))
o = obj()
oref.transfer_to(o,copy=True)
assert(object_eq(o,oref))
assert(id(o.d)!=id(oref.d))
o = obj()
oref.transfer_to(o,keys=['b','c',(3,4,5)])
assert(object_eq(o,osmall))
o = obj(a=6,b=7)
oref.transfer_to(o,overwrite=False)
assert(object_neq(o,oref))
oref.transfer_to(o,overwrite=True)
assert(object_eq(o,oref))
o = obj()
try:
oref.transfer_to(o,keys=['a','x'])
raise FailedTest
except KeyError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test move from
d2 = dref.copy()
o = obj()
o.move_from(d2)
assert(len(d2)==0)
assert(object_eq(o,oref))
o2 = oref.copy()
o = obj()
o.move_from(o2)
assert(len(o2)==0)
assert(object_eq(o,oref))
osmall2 = oref.copy()
del osmall2.b
del osmall2.c
del osmall2[3,4,5]
o2 = oref.copy()
o = obj()
o.move_from(o2,keys=['b','c',(3,4,5)])
assert(object_eq(o,osmall))
assert(object_eq(o2,osmall2))
o2 = oref.copy()
o = obj()
o.move_from_optional(o2,keys=['b','c',(3,4,5),'alpha','beta'])
assert(object_eq(o,osmall))
assert(object_eq(o2,osmall2))
o2 = oref.copy()
o = obj()
try:
o.move_from(o2,keys=['a','x'])
raise FailedTest
except KeyError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test move to
o2 = oref.copy()
d = dict()
o2.move_to(d)
assert(len(o2)==0)
assert(d==dref)
o2 = oref.copy()
o = obj()
o2.move_to(o)
assert(len(o2)==0)
assert(object_eq(o,oref))
o2 = oref.copy()
o = obj()
o2.move_to(o,keys=['b','c',(3,4,5)])
assert(object_eq(o,osmall))
assert(object_eq(o2,osmall2))
o2 = oref.copy()
o = obj()
o2.move_to_optional(o,keys=['b','c',(3,4,5),'alpha','beta'])
assert(object_eq(o,osmall))
assert(object_eq(o2,osmall2))
o2 = oref.copy()
o = obj()
try:
o2.move_to(o,keys=['a','x'])
raise FailedTest
except KeyError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test copy from
o = obj()
o.copy_from(dref)
assert(o.to_dict()==dref)
assert(id(o.d)!=id(dref['d']))
o = obj()
o.copy_from(dref,deep=False)
assert(o.to_dict()==dref)
assert(id(o.d)==id(dref['d']))
osmall = obj(b='b',c=(1,1,1))
osmall[3,4,5] = (5,6,7)
o = obj()
oref = obj(dref)
assert(oref.to_dict()==dref)
o.copy_from(oref,keys=['b','c',(3,4,5)])
assert(object_eq(o,osmall))
o = obj()
try:
o.copy_from(oref,keys=['a','x'])
raise FailedTest
except KeyError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test copy to
o = obj()
oref.copy_to(o)
assert(object_eq(o,oref))
assert(id(o.d)!=id(oref.d))
o = obj()
oref.copy_to(o,deep=False)
assert(object_eq(o,oref))
assert(id(o.d)==id(oref.d))
o = obj()
oref.copy_to(o,keys=['b','c',(3,4,5)])
assert(object_eq(o,osmall))
o = obj()
try:
oref.copy_to(o,keys=['a','x'])
raise FailedTest
except KeyError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test extract
o = oref.copy()
o2 = o.extract()
assert(len(o)==0)
assert(object_eq(o2,oref))
o = oref.copy()
o2 = o.extract(['b','c',(3,4,5)])
assert(object_eq(o2,osmall))
assert(object_eq(o,osmall2))
o = oref.copy()
o2 = o.extract_optional(['b','c',(3,4,5),'alpha','beta'])
assert(object_eq(o2,osmall))
assert(object_eq(o,osmall2))
# test check_required
oref.check_required(['a','d',(3,4,5)])
try:
oref.check_required(['alpha','beta'])
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test check_types
types = dict(
a = int,
b = str,
c = tuple,
d = dict,
)
types[3,4,5] = tuple
oref.check_types(types)
types['b'] = int
try:
oref.check_types(types)
raise FailedTest
except:
None
#end try
types['b'] = str
types['alpha'] = float
types['beta'] = list
oref.check_types_optional(types)
# test shallow_copy
class DerivedObj(obj):
None
#end class DerivedObj
do = DerivedObj(
a = 1,
b = 'b',
c = (1,1,1),
)
do[3,4,5] = (5,6,7)
do2 = do.shallow_copy()
assert(isinstance(do2,DerivedObj))
assert(object_eq(do2,do))
assert(id(do2.c)==id(do.c))
# test inverse
oi = do.inverse()
assert(set(oi.keys())==set(do.values()))
assert(set(oi.values())==set(do.keys()))
assert(oi[1]=='a')
assert(oi.b=='b')
assert(oi[1,1,1]=='c')
assert(oi[5,6,7]==(3,4,5))
# test path operations
# test path exists
o2 = obj()
o2.this = obj()
o2.this.new = obj()
o2.this.new.variable = 'here'
path1 = ['this','new','variable']
path2 = 'this/new/variable'
assert(o2.path_exists(path1))
assert(o2.path_exists(path2))
# test set path
o3 = obj()
o3.set_path(path1,'here')
assert(o3.path_exists(path1))
assert(o3.path_exists(path2))
assert(object_eq(o2,o3))
o4 = obj()
o4.set_path(path2,'here')
assert(o4.path_exists(path1))
assert(o4.path_exists(path2))
assert(object_eq(o3,o4))
# test get path
assert(o2.get_path(path1)=='here')
assert(o2.get_path(path2)=='here')
# test serial
o = obj(
a = obj(
a0 = 0,
a1 = obj(
a10 = 1,
),
),
b = obj(
b0 = 0,
b1 = obj(
b10 = 1,
),
b2 = obj(
b20 = obj(
b200 = 2,
),
b21 = obj(
b210 = obj(
b2100 = 3,
),
),
),
),
c = obj(
c0 = 0,
c1 = obj(
c10 = 1,
),
c2 = obj(
c20 = obj(
c200 = 2,
),
c21 = obj(
c210 = obj(
c2100 = 3,
),
),
),
c3 = obj(
c30 = obj(
c300 = obj(
c3000 = obj(
c30000 = 4,
),
),
c301 = obj(
c3010 = obj(
c30100 = obj(
c301000 = 5,
),
),
),
),
c31 = obj(
c310 = obj(
c3100 = obj(
c31000 = obj(
c310000 = obj(
c3100000 = 6,
),
),
),
),
c311 = obj(
c3110 = obj(
c31100 = obj(
c311000 = obj(
c3110000 = obj(
c3110000 = 7,
)
),
),
),
),
),
),
),
)
oref = obj({
'a/a0':0,
'a/a1/a10':1,
'b/b0':0,
'b/b1/b10':1,
'b/b2/b20/b200':2,
'b/b2/b21/b210/b2100':3,
'c/c0':0,
'c/c1/c10':1,
'c/c2/c20/c200':2,
'c/c2/c21/c210/c2100':3,
'c/c3/c30/c300/c3000/c30000':4,
'c/c3/c30/c301/c3010/c30100/c301000':5,
'c/c3/c31/c310/c3100/c31000/c310000/c3100000':6,
'c/c3/c31/c311/c3110/c31100/c311000/c3110000/c3110000':7,
})
for k,v in oref.items():
assert(o.get_path(k)==v)
#end for
o2 = o.serial()
assert(object_eq(o2,oref))
def test_intrinsics():
# test object_interface functions
import os
from generic import obj,object_interface
from generic import generic_settings,NexusError
from numpy import array,bool_
tpath = testing.setup_unit_test_output_directory('generic','test_intrinsics')
# test object set/get
# make a simple object
o = obj()
o.a = 1
o.b = 'b'
o['c'] = (1,1,1)
o[3,4,5] = (5,6,7)
# test member values
assert(o.a==1)
assert(o.b=='b')
assert(o.c==(1,1,1))
assert(o[3,4,5]==(5,6,7))
# test member presence and length
assert('a' in o)
assert(2 not in o)
assert(len(o)==4)
del o.a
assert('a' not in o)
assert(len(o)==3)
try:
del o.d
raise FailedTest
except AttributeError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test add/access failures
try: # add unhashable type
o[{1:2,3:4}] = 5
raise FailedTest
except TypeError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try: # access missing member
v = o.d
raise FailedTest
except AttributeError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try: # access missing member
v = o['d']
raise FailedTest
except KeyError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test iterability
# test list-like iterability
l = list()
for v in o:
l.append(v)
#end for
l = set(l)
l2 = {'b', (1, 1, 1), (5, 6, 7)}
assert(l2==l)
# test dict-like iterability
d = dict()
for k,v in o.items():
d[k] = v
#end for
o2 = obj()
o2.__dict__ = d
assert(object_eq(o,o2))
assert(set(o.keys())==set(d.keys()))
assert(set(o.values())==set(d.values()))
assert(set(o.items())==set(d.items()))
# test repr
ro = '''
b str
c tuple
(3, 4, 5) tuple
'''
assert(repr(o)==ro[1:])
o2 = obj(
a = obj(a1=1,a2=2,a3=3),
b = obj(b1='b1',b2='b2'),
c = obj(c1=5,c2=('a',3,4)),
d = array([3,4,5],dtype=int),
)
ro2 = '''
a obj
b obj
c obj
d ndarray
'''
assert(repr(o2)==ro2[1:])
# test str
so = '''
b = b
c = (1, 1, 1)
(3, 4, 5) = (5, 6, 7)
'''
assert(str(o)==so[1:])
so2 = '''
d = [3 4 5]
a
a1 = 1
a2 = 2
a3 = 3
end a
b
b1 = b1
b2 = b2
end b
c
c1 = 5
c2 = ('a', 3, 4)
end c
'''
assert(str(o2)==so2[1:])
o3 = o2
# test tree
# not committed to output, only check execution
assert(isinstance(o2.tree(),str))
assert(isinstance(o2.tree(depth=1),str))
assert(isinstance(o2.tree(types=True),str))
assert(isinstance(o2.tree(all=True),str))
assert(isinstance(o2.tree(nindent=2),str))
# test deepcopy
o2 = o.copy()
assert(id(o)!=id(o2))
assert(object_eq(o,o2))
o2.a=1
assert(object_neq(o,o2))
# test eq
assert(o==o2)
o4 = o3.copy()
v = o3==o4
assert(isinstance(v,bool_))
assert(bool(v))
assert(object_eq(o3,o4))
# test clear
o2.clear()
assert(len(o2)==0)
assert('a' not in o2)
# test save/load
save_file = os.path.join(tpath,'o.p')
o.save(save_file)
o2 = obj()
o2.load(save_file)
assert(object_eq(o,o2))
# test class-level set/get methods
class objint(object_interface):
a = 1
b = 'b'
c = (1,1,1)
#end class objint
# test class_has
assert(objint.class_has('c'))
# test class_get
assert(objint.class_get('c')==(1,1,1))
try:
val = objint.class_get('d')
raise FailedTest
except AttributeError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# test class_keys
ck = objint.class_keys()
for v in 'abc':
assert(v in ck)
#end for
# test class_set_single
objint.class_set_single('d',1.34)
assert(objint.class_has('d'))
# test class_set
objint.class_set(
e = 45,
f = 'a phrase',
g = {4:6,'a':2}
)
for v in 'efg':
assert(objint.class_has(v))
#end for
# test class_set_optional
objint.class_set_optional(h=2)
assert(objint.class_has('h'))
assert(objint.class_get('h')==2)
objint.class_set_optional(a=6)
assert(objint.class_get('a')==1)
# test logging functions
# test open log, write, close log
o = obj()
o.open_log('log.out')
s = 'log output'
o.write(s)
o.close_log()
f = open('log.out','r')
so = f.read()
f.close()
os.remove('log.out')
assert(so==s)
# send messages to object rather than stdout
divert_nexus_log()
logfile = object_interface._logfile
# simple message
class DerivedObj(obj):
None
#end class DerivedObj
o = DerivedObj()
s = 'simple message'
logfile.reset()
o.log(s)
assert(logfile.s==s+'\n')
# list of items
items = ['a','b','c',1,2,3]
logfile.reset()
o.log(*items)
assert(logfile.s=='a b c 1 2 3 \n')
# message with indentation
s = 'a message\nwith indentation'
logfile.reset()
o.log(s,indent=' ')
assert(logfile.s==' a message\n with indentation\n')
logfile.reset()
o.log(s,indent='msg: ')
assert(logfile.s=='msg: a message\nmsg: with indentation\n')
# writing to separate log files
logfile2 = FakeLog()
s1 = 'message to log 1'
s2 = 'message to log 2'
logfile.reset()
logfile2.reset()
o.log(s1)
assert(logfile.s==s1+'\n')
assert(logfile2.s=='')
logfile.reset()
logfile2.reset()
o.log(s2,logfile=logfile2)
assert(logfile.s=='')
assert(logfile2.s==s2+'\n')
# test warn
logfile.reset()
s = 'this is a warning'
o.warn(s)
so = '''
DerivedObj warning:
this is a warning
'''
assert(logfile.s==so)
logfile.reset()
s = 'this is a warning'
o.warn(s,header='Special')
so = '''
Special warning:
this is a warning
'''
assert(logfile.s==so)
# test error
# in testing environment, should raise an error
try:
o.error('testing environment')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# in standard/user environment, should print message
generic_settings.raise_error = False
logfile.reset()
o.error('this is an error',exit=False)
so = '''
DerivedObj error:
this is an error
'''
assert(logfile.s==so)
logfile.reset()
o.error('this is an error',header='User',exit=False)
so = '''
User error:
this is an error
'''
assert(logfile.s==so)
generic_settings.raise_error = True
# in testing environment, should raise an error
try:
o.error('testing environment')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# restore logging function
restore_nexus_log()
def test_get_result():
import os
import shutil
from numpy import array
from generic import obj, NexusError
tpath = testing.setup_unit_test_output_directory('vasp_simulation',
'test_get_result',
**pseudo_inputs)
sim = setup_vasp_sim(tpath, identifier='diamond', files=True)
try:
sim.get_result('unknown', None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
pcfile = os.path.join(tpath, 'diamond_POSCAR')
ccfile = os.path.join(tpath, sim.identifier + '.CONTCAR')
assert (sim.locdir.strip('/') == tpath.strip('/'))
shutil.copy2(pcfile, ccfile)
assert (os.path.exists(ccfile))
result = sim.get_result('structure', None)
result_ref = obj(structure=obj(
axes=array([[3.57, 3.57, 0.], [0., 3.57, 3.57], [3.57, 0., 3.57]],
dtype=float),
background_charge=0,
bconds=array([]),
center=array([3.57, 3.57, 3.57], dtype=float),
dim=3,
elem=array([
'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
'C', 'C', 'C'
],
dtype=object),
folded_structure=None,
frozen=None,
kaxes=array([[0.87999794, 0.87999794, -0.87999794],
[-0.87999794, 0.87999794, 0.87999794],
[0.87999794, -0.87999794, 0.87999794]],
dtype=float),
kpoints=array([], dtype=float),
kweights=array([], dtype=float),
mag=None,
pos=array([[0., 0., 0.], [0.8925, 0.8925, 0.8925], [1.785, 1.785, 0.],
[2.6775, 2.6775, 0.8925], [0., 1.785, 1.785],
[0.8925, 2.6775, 2.6775], [1.785, 3.57, 1.785],
[2.6775, 4.4625, 2.6775], [1.785, 0., 1.785],
[2.6775, 0.8925, 2.6775], [3.57, 1.785, 1.785],
[4.4625, 2.6775, 2.6775], [1.785, 1.785, 3.57],
[2.6775, 2.6775, 4.4625], [3.57, 3.57, 3.57],
[4.4625, 4.4625, 4.4625]],
dtype=float),
scale=1.0,
units='A',
), )
assert (check_object_eq(result, result_ref))
clear_all_sims()
restore_nexus()
def test_unavailable():
from generic import generic_settings, NexusError
from developer import Void
from developer import unavailable, available
gre = generic_settings.raise_error
generic_settings.raise_error = True
try:
import keyword
except:
keyword = unavailable('keyword')
#end try
assert (not isinstance(keyword, Void))
assert (available(keyword))
try:
import an_unavailable_module
except:
an_unavailable_module = unavailable('an_unavailable_module')
#end try
assert (isinstance(an_unavailable_module, Void))
assert (not available(an_unavailable_module))
try:
from an_unavailable_module import a, b, c, d, e, f, g
except:
a, b, c, d, e, f, g = unavailable('an_unavailable_module', 'a', 'b',
'c', 'd', 'e', 'f', 'g')
#end try
void_imports = an_unavailable_module, b, c, d, e, f, g
for v in void_imports:
assert (isinstance(v, Void))
assert (not available(v))
#end for
operations = [
dir,
len,
repr,
str,
complex,
int,
float,
lambda v: v == 0,
lambda v: v != 0,
lambda v: v > 0,
lambda v: v < 0,
lambda v: v >= 0,
lambda v: v <= 0,
lambda v: v(),
lambda v: v.a,
lambda v: v['a'],
lambda v: setattr(v, 'a', 0),
lambda v: getattr(v, 'a'),
lambda v: delattr(v, 'a'),
lambda v: v + 0,
lambda v: v - 0,
lambda v: v * 0,
lambda v: v / 0,
lambda v: v % 0,
lambda v: v & 0,
lambda v: v | 0,
]
for op in operations:
for v in void_imports:
try:
op(v)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
#end for
#end for
generic_settings.raise_error = gre
def test_logging():
from generic import log,message,warn,error
from generic import generic_settings,NexusError
# send messages to object rather than stdout
divert_nexus_log()
logfile = generic_settings.devlog
# test log
# simple message
s = 'simple message'
logfile.reset()
log(s)
assert(logfile.s==s+'\n')
# list of items
items = ['a','b','c',1,2,3]
logfile.reset()
log(*items)
assert(logfile.s=='a b c 1 2 3 \n')
# message with indentation
s = 'a message\nwith indentation'
logfile.reset()
log(s,indent=' ')
assert(logfile.s==' a message\n with indentation\n')
logfile.reset()
log(s,indent='msg: ')
assert(logfile.s=='msg: a message\nmsg: with indentation\n')
# writing to separate log files
logfile2 = FakeLog()
s1 = 'message to log 1'
s2 = 'message to log 2'
logfile.reset()
logfile2.reset()
log(s1)
assert(logfile.s==s1+'\n')
assert(logfile2.s=='')
logfile.reset()
logfile2.reset()
log(s2,logfile=logfile2)
assert(logfile.s=='')
assert(logfile2.s==s2+'\n')
# test warn
logfile.reset()
s = 'this is a warning'
warn(s)
so = '''
warning:
this is a warning
'''
assert(logfile.s==so)
logfile.reset()
s = 'this is a warning'
warn(s,header='Special')
so = '''
Special warning:
this is a warning
'''
assert(logfile.s==so)
# test error
# in testing environment, should raise an error
try:
error('testing environment')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# in standard/user environment, should print message
generic_settings.raise_error = False
logfile.reset()
error('this is an error',header='User',exit=False)
so = '''
User error:
this is an error
'''
assert(logfile.s==so)
generic_settings.raise_error = True
# in testing environment, should raise an error
try:
error('testing environment')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
restore_nexus_log()
def test_convert4qmc_incorporate_result():
from generic import NexusError,obj
from simulation import Simulation
from gamess import Gamess
from pyscf_sim import Pyscf
from quantum_package import QuantumPackage
from test_gamess_simulation import get_gamess_sim
from test_pyscf_simulation import get_pyscf_sim
from test_quantum_package_simulation import get_quantum_package_sim
other = Simulation()
gms = get_gamess_sim('rhf')
Gamess.ericfmt = None
gms_result = obj(
location = './rhf/rhf.out',
mos = 0,
norbitals = 0,
outfile = './rhf/rhf.out',
scftyp = 'rohf',
vec = None,
)
pscf = get_pyscf_sim()
pscf_result = obj(
h5_file = './scf.h5',
)
qp = get_quantum_package_sim()
QuantumPackage.qprc = None
qp_result = obj(
outfile = './qp_savewf.out',
)
sim_start = get_convert4qmc_sim()
sim = sim_start.copy()
try:
sim.incorporate_result('unknown',None,other)
raise TestFailed
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# incorporate orbitals from gamess
sim = sim_start.copy()
assert(sim.input_code is None)
assert(sim.input.gamess_ascii is None)
assert(sim.job.app_command=='convert4qmc')
sim.incorporate_result('orbitals',gms_result,gms)
assert(sim.input_code=='gamess')
assert(sim.input.gamess_ascii=='../rhf/rhf.out')
assert(sim.job.app_command=='convert4qmc -gamessAscii ../rhf/rhf.out')
# incorporate orbitals from pyscf
sim = sim_start.copy()
assert(sim.input_code is None)
assert(sim.input.pyscf is None)
sim.incorporate_result('orbitals',pscf_result,pscf)
assert(sim.input_code=='pyscf')
assert(sim.input.pyscf=='../scf.h5')
# incorporate orbitals from quantum package
sim = sim_start.copy()
assert(sim.input_code is None)
assert(sim.input.qp is None)
sim.incorporate_result('orbitals',qp_result,qp)
assert(sim.input_code=='qp')
assert(sim.input.qp=='../qp_savewf.out')
clear_all_sims()
def test_defined_attribute_base():
from generic import obj,NexusError
from observables import AttributeProperties,DefinedAttributeBase
# empty init
p = AttributeProperties()
o = DefinedAttributeBase()
pref = obj(
assigned = set(),
deepcopy = False,
default = None,
dest = None,
name = None,
no_default = False,
required = False,
type = None,
)
assert(check_object_eq(p,pref))
assert(len(o)==0)
# init
p = AttributeProperties(
default = 2,
dest = 'nest',
deepcopy = True,
)
pref = obj(
assigned = {'dest', 'default', 'deepcopy'},
deepcopy = True,
default = 2,
dest = 'nest',
name = None,
no_default = False,
required = False,
type = None,
)
assert(check_object_eq(p,pref))
# define attributes
class DA(DefinedAttributeBase):
None
#end class DA
da_attributes = obj(
a = obj(
default = 1,
),
b = obj(
default = 2,
type = int,
required = True,
),
c = obj(
dest = 'nest',
type = str,
),
d = obj(
type = dict,
deepcopy = True,
no_default = True,
),
nest = obj(
type = obj,
default = obj,
),
)
DA.define_attributes(**da_attributes)
def get_class_dict(cls):
o = obj()
o.transfer_from(cls.__dict__)
for k in list(o.keys()):
if k.startswith('_'):
del o[k]
#end if
#end for
return o
#end def get_class_dict
o = get_class_dict(DA)
oref = obj(
deepcopy_attributes = {'d'},
required_attributes = {'b'},
sublevel_attributes = {'c'},
toplevel_attributes = {'d', 'a', 'b', 'nest'},
typed_attributes = {'d', 'c', 'b', 'nest'},
attribute_definitions = obj(
a = obj(
assigned = {'default'},
deepcopy = False,
default = 1,
dest = None,
name = 'a',
no_default = False,
required = False,
type = None,
),
b = obj(
assigned = {'required', 'default', 'type'},
deepcopy = False,
default = 2,
dest = None,
name = 'b',
no_default = False,
required = True,
type = int,
),
c = obj(
assigned = {'dest', 'type'},
deepcopy = False,
default = None,
dest = 'nest',
name = 'c',
no_default = False,
required = False,
type = str,
),
d = obj(
assigned = {'deepcopy', 'no_default', 'type'},
deepcopy = True,
default = None,
dest = None,
name = 'd',
no_default = True,
required = False,
type = dict,
),
nest = obj(
assigned = {'default', 'type'},
deepcopy = False,
default = obj,
no_default = False,
dest = None,
name = 'nest',
required = False,
type = obj,
),
),
)
assert(check_object_eq(o,oref))
class DA2(DA):
None
#end class DA2
DA2.define_attributes(
DA,
e = obj(
required = True,
)
)
o = get_class_dict(DA)
assert(check_object_eq(o,oref))
o2 = get_class_dict(DA2)
oref.required_attributes.add('e')
oref.toplevel_attributes.add('e')
oref.attribute_definitions.e = obj(
assigned = {'required'},
deepcopy = False,
default = None,
dest = None,
name = 'e',
no_default = False,
required = True,
type = None,
)
assert(check_object_eq(o2,oref))
# empty init
da = DA()
assert(len(da)==0)
assert(not da.check_attributes())
# set_default_attributes
da.set_default_attributes()
da_ref = obj(
a = 1,
b = 2,
nest = obj(
c = None,
),
)
assert(check_object_eq(da,da_ref))
assert(not da.check_attributes())
# set_attributes/init
da = DA(
a = 2,
b = 3,
c = 'hi',
d = dict(a=2),
)
da_ref = obj(
a = 2,
b = 3,
d = {'a': 2},
nest = obj(
c = 'hi',
),
)
assert(check_object_eq(da,da_ref))
assert(da.check_attributes())
# set_attribute
da = DA()
assert('b' not in da)
da.set_attribute('b',5)
assert('b' in da)
assert(da.b==5)
try:
da.set_attribute('unknown',None)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
da.set_attribute('b',3)
assert(da.b==3)
try:
da.set_attribute('b',3.5)
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# get_attribute
da = DA()
da.set_attribute('b',5)
assert('b' in da)
assert(da.b==5)
assert(da.get_attribute('b')==5)
assert(da.get_attribute('a',None) is None)
assert(da.get_attribute('c',None) is None)
try:
da.get_attribute('unknown')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try:
da.get_attribute('a')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try:
da.get_attribute('c')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# default values
class DA_def(DefinedAttributeBase):
None
#end class DA_def
DA_def.set_unassigned_default(None)
class DA_def2(DA_def):
None
#end class DA_def2
DA_def2.define_attributes(**da_attributes)
assert(not DefinedAttributeBase.class_has('unassigned_default'))
assert(DA_def.class_has('unassigned_default'))
assert(DA_def2.class_has('unassigned_default'))
assert(DA_def.unassigned_default is None)
assert(DA_def2.unassigned_default is None)
da = DA_def2()
assert('a' not in da)
assert('c' not in da)
assert('nest' not in da)
assert(da.get_attribute('a',None) is None)
assert(da.get_attribute('c',None) is None)
try:
da.get_attribute('a')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try:
da.get_attribute('c')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
da.set_default_attributes()
da_ref = obj(
a = 1,
b = 2,
nest = obj(
c = None,
)
)
assert(check_object_eq(da,da_ref))
da.b = None
assert(da.get_attribute('a')==1)
assert(da.get_attribute('b',assigned=False) is None)
assert(da.get_attribute('c',assigned=False) is None)
assert(da.get_attribute('a',2)==1)
assert(da.get_attribute('a',assigned=False)==1)
try:
da.get_attribute('b')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try:
da.get_attribute('c')
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
def test_bundle():
from generic import NexusError
from machines import job, get_machine
from bundle import bundle
from bundle import SimulationBundle
from test_simulation_module import get_test_workflow
# empty init
try:
bundle()
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
# init with wrong types
try:
bundle([1, 2, 3])
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
def get_workflow():
machine = get_machine('theta')
machine.account = 'ABC123'
test_job = job(machine='theta', nodes=1, app_command='test.x')
sims = get_test_workflow(7, job=test_job)
levels = []
levels.append([sims.s0, sims.s1, sims.s2])
levels.append([sims.s3, sims.s5, sims.s7, sims.s10])
levels.append([sims.s4, sims.s6, sims.s8, sims.s11])
levels.append([sims.s9, sims.s12])
return sims, levels
#end def get_workflow
sims, levels = get_workflow()
# attempt to bundle sims that depend on each other
try:
bundle(levels[1] + [sims.s8])
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
try:
bundle(levels[1] + [sims.s9])
raise FailedTest
except NexusError:
None
except FailedTest:
failed()
except Exception as e:
failed(str(e))
#end try
sims, levels = get_workflow()
for n, level in enumerate(levels):
for s in level:
assert (not s.bundled)
assert (s.bundler is None)
assert (not s.skip_submit)
#end for
b = bundle(level, identifier='bundle_' + str(n))
for s in level:
assert (s.bundled)
assert (id(s.bundler) == id(b))
assert (s.skip_submit)
#end for
assert (isinstance(b, SimulationBundle))
assert (isinstance(b.sims, list))
assert (b.system is None)
assert (b.infile is None)
assert (not b.allow_create_directories)
assert (not b.allow_get_dependencies)
assert (not b.allow_write_inputs)
assert (not b.allow_send_files)
assert (not b.allow_submit)
assert (not b.allow_get_output)
assert (not b.allow_analyze)
for sb, s in zip(b.sims, level):
assert (id(sb) == id(s))
#end for
bj = b.job
j = level[0].job
ns = len(level)
assert (bj.nodes == ns * j.nodes)
assert (bj.cores == ns * j.cores)
assert (object_eq(bj.get_time(), j.get_time()))
#end for
testing.clear_all_sims()
