def setup():
global ts1, ts2, sim
testing.init_blank_db_for_testing()
db.config.base = os.path.dirname(os.path.abspath(__file__)) + "/"
session = db.core.get_default_session()
sim = tangos.core.simulation.Simulation("test_stat_files")
session.add(sim)
ts1 = tangos.core.timestep.TimeStep(sim,
"pioneer50h128.1536gst1.bwK1.000832")
ts1.time_gyr = 6 # unimportant
ts1.redshift = 2.323 # matters for AHF filename
ts2 = tangos.core.timestep.TimeStep(
sim, "h242.cosmo50PLK.1536g1bwK1C52.004096")
ts2.time_gyr = 10
ts2.redshift = 0
session.add_all([ts1, ts2])
session.commit()
parallel_tasks.use('null')
def setup():
testing.init_blank_db_for_testing()
creator = tangos.testing.simulation_generator.TestSimulationGenerator()
halo_offset = 0
for ts in range(1, 4):
creator.add_timestep()
creator.add_objects_to_timestep(4)
creator.link_last_halos()
tangos.get_default_session().commit()
tangos.get_item("sim/ts1/halo_1")['test_image'] = np.zeros((500, 500, 3))
for ts in tangos.get_simulation(1).timesteps:
for h in ts.halos:
h['test_value'] = 1.0
tangos.get_default_session().commit()
creator = tangos.testing.simulation_generator.TestSimulationGenerator(
"simname/has/slashes")
creator.add_timestep()
creator.add_objects_to_timestep(1)
creator.add_timestep()
creator.add_objects_to_timestep(1)
creator.link_last_halos()
tangos.get_simulation(2).timesteps[0].halos[0]['test_value'] = 2.0
tangos.get_default_session().commit()
global app
app = TestApp(tangos.web.main({}))
def setup():
testing.init_blank_db_for_testing()
generator = tangos.testing.simulation_generator.TestSimulationGenerator()
generator.add_timestep() # ts1
generator.add_objects_to_timestep(7)
generator.add_timestep() # ts2
generator.add_objects_to_timestep(7)
generator.link_last_halos()
generator.add_timestep() # ts3
generator.add_objects_to_timestep(6)
generator.link_last_halos_using_mapping({1:1, 2:1, 3:2, 4:3, 5:4, 6:5, 7:6}) # ts2->ts3: merger of halos 1 & 2
generator.add_timestep() # ts4
generator.add_objects_to_timestep(6)
generator.link_last_halos()
generator.add_timestep() # ts5
generator.add_objects_to_timestep(5)
generator.link_last_halos_using_mapping({1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 1}) # ts4->ts5: merger of halos 1 & 6
generator.add_timestep() # ts6
generator.add_objects_to_timestep(5)
generator.link_last_halos()
# setup the default options, so that these can change in the config without changing the tests
tree.mergertree_min_fractional_weight = 0.02
tree.mergertree_min_fractional_NDM = 0.0
tree.mergertree_max_nhalos = 30
tree.mergertree_timeout = 15.0
tree.mergertree_max_hops = 500
def setup():
testing.init_blank_db_for_testing()
generator = tangos.testing.simulation_generator.TestSimulationGenerator()
ts1 = generator.add_timestep()
ts1_h1, ts2_h2 = generator.add_objects_to_timestep(2)
ts1_h1['dummy_property_1'] = np.arange(0, 100.0)
angmom = np.empty((100, 3))
angmom[:, :] = np.arange(0, 100.0).reshape((100, 1))
ts1_h1['dummy_property_2'] = angmom
ts1_h1['dummy_property_3'] = -2.5
ts1_h1_bh1 = tangos.core.halo.BH(ts1, 1)
ts1_h1_bh1["BH_mass"] = 1000.0
ts1_h1_bh2 = tangos.core.halo.BH(ts1, 2)
ts1_h1_bh2["BH_mass"] = 900.0
ts1_h1["BH"] = ts1_h1_bh1, ts1_h1_bh2
generator.add_timestep()
generator.add_objects_to_timestep(1)
generator.link_last_halos()
generator.add_timestep() # intentionally empty final timestep
def setup():
testing.init_blank_db_for_testing()
generator = tangos.testing.simulation_generator.TestSimulationGenerator()
generator.add_timestep() # ts1
generator.add_objects_to_timestep(2, NDM=[1000, 600])
generator.add_timestep() # ts2
generator.add_objects_to_timestep(2)
generator.link_last_halos(adjust_masses=True)
generator.add_timestep() # ts3, in which halo 1 and 2 collide
generator.add_objects_to_timestep(2)
generator.link_last_halos_using_mapping(
{
1: 2,
2: 1
}, adjust_masses=True
) # halo 1 becomes 2, 2 becomes 1 due to mass ordering
generator.add_mass_transfer(
1, 1, 0.3, adjust_masses=True
) # halo 1 in previous step loses 30% of its mass to halo 1 in this step... but survives
generator.add_timestep() # ts4
generator.add_objects_to_timestep(2)
generator.link_last_halos(adjust_masses=True)
generator.add_mass_transfer(
2, 1, 0.05, adjust_masses=True) # continued minor stripping of halo 2
generator.add_timestep(
) #ts5, in which halo 1 and 2 finally merge completely
generator.add_objects_to_timestep(1)
generator.link_last_halos_using_mapping({1: 1, 2: 1}, adjust_masses=True)
def test_NDM_cut():
testing.init_blank_db_for_testing()
manager = add_simulation.SimulationAdderUpdater(output_testing.TestInputHandlerReverseHaloNDM("dummy_sim_2"))
manager.min_halo_particles = 2005
manager.scan_simulation_and_add_all_descendants()
ndm, = db.get_timestep("dummy_sim_2/step.1").calculate_all("NDM()")
assert ndm.min()==2005
def setup_module():
testing.init_blank_db_for_testing()
creator = tangos.testing.simulation_generator.SimulationGeneratorForTests()
halo_offset = 0
for ts in range(1,4):
num_halos = 4 if ts<3 else 3
creator.add_timestep()
creator.add_objects_to_timestep(num_halos)
creator.add_properties_to_halos(Mvir=lambda i: i+halo_offset)
creator.add_properties_to_halos(Rvir=lambda i: (i+halo_offset)*0.1)
halo_offset+=num_halos
creator.add_bhs_to_timestep(4)
creator.add_properties_to_bhs(hole_mass = lambda i: float(i*100))
creator.add_properties_to_bhs(hole_spin = lambda i: 1000-float(i)*100)
creator.add_properties_to_bhs(test_array = lambda i: np.array([1.0,2.0,3.0]))
creator.assign_bhs_to_halos({1:1, 2:2, 3:3, 4:3})
if ts>1:
creator.link_last_halos()
creator.link_last_bhs_using_mapping({1:1})
# special timestep 5->6 where there is an exact equal weight link
creator.add_timestep()
creator.add_objects_to_timestep(2, NDM=[5,5])
creator.add_timestep()
creator.add_objects_to_timestep(1, NDM=[10])
creator.link_last_halos_using_mapping({1:1, 2:1})
def setup_module():
testing.init_blank_db_for_testing()
generator = tangos.testing.simulation_generator.SimulationGeneratorForTests(
)
# A second simulation to test linking across
generator_2 = tangos.testing.simulation_generator.SimulationGeneratorForTests(
"sim2")
generator.add_timestep()
generator_2.add_timestep()
generator.add_objects_to_timestep(7)
generator.add_bhs_to_timestep(2)
generator.assign_bhs_to_halos({1: 1, 2: 2})
generator.add_timestep()
generator_2.add_timestep()
generator.add_objects_to_timestep(5)
generator.add_bhs_to_timestep(2)
generator.assign_bhs_to_halos({1: 1, 2: 2})
generator_2.add_objects_to_timestep(2)
generator_2.link_last_halos_across_using_mapping(generator, {1: 2, 2: 1})
# ts1_h1 becomes ts2_h2 but loses 10% of its mass to ts2_h1
# ts1_h2 becomes ts2_h1
# ts1_h3 becomes ts2_h3
# ts1_h4 becomes ts2_h4 but loses 1% of its mass to ts2_h3
# ts1_h6 and ts1_h7 merge into ts2_h5
# ts1_h5 is ORPHANED, i.e has no counterpart in ts2
#
# We do not adjust the masses here because, despite the halos crossing
# over in ordering, the tests were constructed with an earlier version
# of the code which did not ensure this consistency
generator.link_last_halos_using_mapping(
{
1: 2,
2: 1,
3: 3,
4: 4,
6: 5,
7: 5
}, adjust_masses=False)
generator.add_mass_transfer(1, 1, 0.1)
generator.add_mass_transfer(4, 3, 0.01)
generator.add_timestep()
generator.add_objects_to_timestep(5)
generator.add_bhs_to_timestep(2)
generator.assign_bhs_to_halos({1: 1, 2: 2})
# ts2_h1 and ts2_h2 merge to ts3_h1
# ts2_h3 becomes ts3_h2
# ts2_h4 becomes ts3_h3 but loses 5% of its mass to ts3_h2
# ts2_h5 becomes ts3_h4
# ts3_h5 has no counterpart
generator.link_last_halos_using_mapping({1: 1, 2: 1, 3: 2, 4: 3, 5: 4})
generator.add_mass_transfer(4, 2, 0.05)
def test_import():
existing_session = tangos.get_default_session()
testing.init_blank_db_for_testing(testing_db_name='imported_db_test')
new_session = tangos.get_default_session()
manager._db_import_export(new_session, existing_session)
differ = diff.TangosDbDiff(existing_session, new_session)
differ.compare()
assert not differ.failed, "Copied database differs; see log for details"
def setup_func():
parallel_tasks.use('null')
testing.init_blank_db_for_testing()
db.config.base = os.path.join(os.path.dirname(__file__), "test_simulations")
manager = add_simulation.SimulationAdderUpdater(output_testing.TestInputHandler("dummy_sim_1"))
with log.LogCapturer():
manager.scan_simulation_and_add_all_descendants()
def setup_module():
global output_manager
testing.init_blank_db_for_testing()
db.config.base = os.path.join(os.path.dirname(__file__),
"test_simulations")
output_manager = yt_outputs.YtChangaAHFInputHandler("test_tipsy_yt")
add.SimulationAdderUpdater(
output_manager).scan_simulation_and_add_all_descendants()
def init_blank_simulation():
testing.init_blank_db_for_testing(timeout=0.0)
db.config.base = os.path.join(os.path.dirname(__file__),
"test_simulations")
manager = add_simulation.SimulationAdderUpdater(
output_testing.TestInputHandler("dummy_sim_1"))
with log.LogCapturer():
manager.scan_simulation_and_add_all_descendants()
def setup():
pt.use("multiprocessing")
testing.init_blank_db_for_testing(timeout=5.0, verbose=False)
generator = tangos.testing.simulation_generator.TestSimulationGenerator()
generator.add_timestep()
generator.add_objects_to_timestep(9)
tangos.core.get_default_session().commit()
def setup():
testing.init_blank_db_for_testing()
tangos.config.base = os.path.join(os.path.dirname(__file__),
"test_simulations")
manager = tools.add_simulation.SimulationAdderUpdater(
input_handlers.pynbody.ChangaInputHandler("test_ahf_merger_tree"))
with log.LogCapturer():
manager.scan_simulation_and_add_all_descendants()
def test_renumbering():
testing.init_blank_db_for_testing()
manager = add_simulation.SimulationAdderUpdater(output_testing.TestInputHandlerReverseHaloNDM("dummy_sim_2"))
assert not manager.simulation_exists()
with log.LogCapturer():
manager.scan_simulation_and_add_all_descendants()
assert db.get_halo("dummy_sim_2/step.1/halo_2").halo_number==2
assert db.get_halo("dummy_sim_2/step.1/halo_2").finder_id == 7
assert db.get_halo("dummy_sim_2/step.1/halo_2").NDM==2006
def setup():
testing.init_blank_db_for_testing()
generator = tangos.testing.simulation_generator.TestSimulationGenerator()
generator.add_timestep()
ts1_h1, ts1_h2, ts1_h3, ts1_h4, ts1_h5 = generator.add_objects_to_timestep(
5)
ts1_h1['testlink'] = ts1_h2, ts1_h3, ts1_h4, ts1_h5
ts1_h1['testlink_univalued'] = ts1_h2
ts1_h5['nonexistent_link'] = 0 # This is just to generate the results
ts1_h2['testval'] = 1.0
ts1_h2['testvalpartial'] = 1.0
ts1_h3['testval'] = 2.0
ts1_h3['testvalpartial'] = 2.0
ts1_h4['testval'] = 3.0
ts1_h5['testval'] = 0.0
ts1_h2['testval2'] = 10.0
ts1_h3['testval2'] = 20.0
ts1_h4['testval2'] = 30.0
ts1_h5['testval2'] = 40.0
generator.add_timestep()
ts2_h1, ts2_h2 = generator.add_objects_to_timestep(2)
ts2_h1['testval'] = 2.0
ts2_h2['testval'] = 100.0
generator.link_last_halos_using_mapping({2: 1, 3: 2})
generator_sim2 = tangos.testing.simulation_generator.TestSimulationGenerator(
"sim2")
# this is added to offer red herring links that should be ignored
# We add a timestep and links that create an illusory past, but actually it's in another simulation
# so should be ignored. It triggers a problem with the original implementation of find_progenitor.
generator_sim2.add_timestep()
s2_h1, s2_h2 = generator_sim2.add_objects_to_timestep(2)
generator_sim2.link_last_halos_across_using_mapping(
generator, {
1: 1,
2: 2
})
s2_h2['testval'] = 1e6
# end of red herring
generator.add_timestep()
ts3_h1, ts3_h2 = generator.add_objects_to_timestep(2)
generator.link_last_halos()
ts3_h1['testval'] = -1.0
ts3_h2['testval'] = 1000.0
db.core.get_default_session().commit()
def setup():
_ensure_dummy_gadgetsnaps_exist()
testing.init_blank_db_for_testing()
tangos.config.base = os.path.join(os.path.dirname(__file__),
"test_simulations")
manager = tools.add_simulation.SimulationAdderUpdater(
input_handlers.pynbody.GadgetRockstarInputHandler(
"test_gadget_rockstar"))
with log.LogCapturer():
manager.scan_simulation_and_add_all_descendants()
def setup():
testing.init_blank_db_for_testing()
generator = tangos.testing.simulation_generator.TestSimulationGenerator()
ts1 = generator.add_timestep()
generator.add_objects_to_timestep(2)
ts2 = generator.add_timestep()
generator.add_objects_to_timestep(1)
generator.link_last_halos_using_mapping({1:1, 2:1})
_setup_dummy_histogram_data(ts1, ts2)
def setup_func():
parallel_tasks.use('null')
testing.init_blank_db_for_testing()
db.config.base = os.path.join(os.path.dirname(__file__),
"test_simulations")
manager = add_simulation.SimulationAdderUpdater(
output_testing.TestInputHandler("dummy_sim_1"))
manager2 = add_simulation.SimulationAdderUpdater(
output_testing.TestInputHandler("dummy_sim_2"))
with log.LogCapturer():
manager.scan_simulation_and_add_all_descendants()
manager2.scan_simulation_and_add_all_descendants()
writer = property_writer.PropertyWriter()
writer.parse_command_line(['dummy_property'])
writer.run_calculation_loop()
def setup():
pt.use("multiprocessing")
testing.init_blank_db_for_testing(timeout=0.1, verbose=False)
session = db.core.get_default_session()
sim = tangos.core.simulation.Simulation("sim")
session.add(sim)
ts1 = tangos.core.timestep.TimeStep(sim, "ts1")
session.add(ts1)
halo_1 = tangos.core.halo.Halo(ts1, 1, 0, 0, 0, 0)
session.add_all([halo_1])
session.commit()
def setup_module():
testing.init_blank_db_for_testing()
generator = SimulationGeneratorForTests()
generator.add_timestep()
generator.add_objects_to_timestep(10)
generator.add_properties_to_halos(Mvir=lambda i: 1. * i)
halo = tangos.get_halo(1)
session = core.get_default_session()
px = create_property(halo, "Mvir", -1., session)
session.add(px, session)
px = create_property(halo, "Mvir", -2., session)
session.add(px, session)
session.commit()
# Also create links between halos, including duplicates
halo2 = tangos.get_halo(2)
halo3 = tangos.get_halo(3)
halo9 = tangos.get_halo(9)
# two links between halo 1 to halo 2 with the same weight and name (maximal duplicate)
d_test = tangos.core.get_or_create_dictionary_item(session, "test")
l_obj = link.HaloLink(halo, halo2, d_test, 1.0)
session.add(l_obj)
l_obj = link.HaloLink(halo, halo2, d_test, 1.0)
session.add(l_obj)
# and another time but with same weight but different name (not a duplicate)
diff_name = tangos.core.get_or_create_dictionary_item(
session, "other_test")
l_obj = link.HaloLink(halo, halo2, diff_name, 1.0)
session.add(l_obj)
# and another time, with same name but different weight
# (this is a non-maximal duplicate, oldest addition gets deleted and we keep the most recent link)
l_obj = link.HaloLink(halo, halo2, d_test, 0.5)
session.add(l_obj)
# and another time, with same weight and name as previous but linking to a different halo (not a duplicate)
l_obj = link.HaloLink(halo, halo3, d_test, 1.0)
session.add(l_obj)
# and now a completely independent link between halo 2 to halo 9
l_obj = link.HaloLink(halo2, halo9, d_test, 1.0)
session.add(l_obj)
def setup():
testing.init_blank_db_for_testing()
creator = tangos.testing.simulation_generator.TestSimulationGenerator()
halo_offset = 0
for ts in range(1,4):
creator.add_timestep()
creator.add_objects_to_timestep(4)
creator.link_last_halos()
tangos.get_default_session().commit()
tangos.get_item("sim/ts1/halo_1")['test_image'] = np.zeros((500,500,3))
for ts in tangos.get_simulation(1).timesteps:
for h in ts.halos:
h['test_value'] = 1.0
tangos.get_default_session().commit()
creator.add_timestep() # add ts 4
creator.add_objects_to_timestep(3)
tangos.get_default_session().commit()
# now make the object have halo numbers which have a different ordering to the database IDs
tangos.get_item("sim/ts4/1")['test_value'] = 1.0
tangos.get_item("sim/ts4/2")['test_value'] = 2.0
tangos.get_item("sim/ts4/3")['test_value'] = 3.0
tangos.get_item("sim/ts4/1").halo_number = 10
tangos.get_default_session().commit()
creator = tangos.testing.simulation_generator.TestSimulationGenerator("simname/has/slashes")
creator.add_timestep()
creator.add_objects_to_timestep(1)
creator.add_timestep()
creator.add_objects_to_timestep(1)
creator.link_last_halos()
tangos.get_simulation(2).timesteps[0].halos[0]['test_value'] = 2.0
tangos.get_default_session().commit()
global app
app = TestApp(tangos.web.main({}))
def setup_module():
if testing_db_backend != "sqlite":
skip("This test is only relevant for sqlite databases")
pt.use("multiprocessing")
testing.init_blank_db_for_testing(timeout=0.1, verbose=False)
session = db.core.get_default_session()
sim = tangos.core.simulation.Simulation("sim")
session.add(sim)
ts1 = tangos.core.timestep.TimeStep(sim, "ts1")
session.add(ts1)
halo_1 = tangos.core.halo.Halo(ts1, 1, 1, 1, 0, 0, 0, 0)
session.add_all([halo_1])
session.commit()
def setup():
global output_manager, iord_expected_s960, iord_expected_s832
testing.init_blank_db_for_testing()
db.config.base = os.path.join(os.path.dirname(__file__),
"test_simulations")
output_manager = pynbody_outputs.ChangaInputHandler("test_tipsy")
with log.LogCapturer():
add.SimulationAdderUpdater(
output_manager).scan_simulation_and_add_all_descendants()
h1 = db.get_halo("test_tipsy/%640/1").load()
h1_sub = h1[::5]
tracking.new("test_tipsy", h1_sub)
iord_expected_s960 = copy.deepcopy(h1_sub['iord'])
# because the tiny test files are downsampled, only a small number of particles are actually
# in common between the two steps
iord_expected_s832 = np.intersect1d(
iord_expected_s960,
db.get_timestep("test_tipsy/%832").load()['iord'])
def setup():
global sim1, sim2, collection, h1, h2
testing.init_blank_db_for_testing()
session = db.core.get_default_session()
sim1 = tangos.core.simulation.Simulation("sim1")
sim2 = tangos.core.simulation.Simulation("sim2")
ts1 = tangos.core.timestep.TimeStep(sim1, "ts")
h1 = tangos.core.halo.Halo(ts1, 1, 1, 1, 1000, 0, 0, 0)
ts2 = tangos.core.timestep.TimeStep(sim2, "ts")
h2 = tangos.core.halo.Halo(ts2, 1, 1, 1, 1000, 0, 0, 0)
session.add_all([sim1, sim2, ts1, ts2, h1, h2])
sim1['consistent_property'] = 1.0
sim2['consistent_property'] = 1.0
sim1['inconsistent_property'] = 0.5
sim2['inconsistent_property'] = 1.0
collection = cc.ConsistentCollection([sim1, sim2])
def setup():
testing.init_blank_db_for_testing()
creator = tangos.testing.simulation_generator.TestSimulationGenerator()
halo_offset = 0
for ts in range(1, 4):
num_halos = 4 if ts < 3 else 3
creator.add_timestep()
creator.add_objects_to_timestep(num_halos)
creator.add_properties_to_halos(Mvir=lambda i: i + halo_offset)
creator.add_properties_to_halos(Rvir=lambda i: (i + halo_offset) * 0.1)
halo_offset += num_halos
creator.add_bhs_to_timestep(4)
creator.add_properties_to_bhs(hole_mass=lambda i: float(i * 100))
creator.add_properties_to_bhs(
hole_spin=lambda i: 1000 - float(i) * 100)
creator.assign_bhs_to_halos({1: 1, 2: 2, 3: 3, 4: 3})
if ts > 1:
creator.link_last_halos()
creator.link_last_bhs_using_mapping({1: 1})
def setup():
testing.init_blank_db_for_testing()
def setup_module():
testing.init_blank_db_for_testing()
creator = testing.simulation_generator.SimulationGeneratorForTests()
creator.add_timestep()
def setup():
global output_manager
testing.init_blank_db_for_testing()
db.config.base = os.path.join(os.path.dirname(__file__),
"test_simulations")
output_manager = pynbody_outputs.ChangaInputHandler("test_tipsy")
def setup_module():
testing.init_blank_db_for_testing()
