def setUp(self):
lp_filedir = os.path.dirname(os.path.realpath(__file__))
with open(lp_filedir + '/tests_launchpad.yaml', 'r') as lp_file:
yaml = YAML()
lp_dict = dict(yaml.load(lp_file))
self.lp = LaunchPad.from_dict(lp_dict)
self.db = self.lp.db
def __init__(self, *args, **kwargs):
super(OptTask, self).__init__(*args, **kwargs)
# Configuration attrs
lp = self.get("launchpad", LaunchPad.auto_load())
if isinstance(lp, LaunchPad):
lp = lp.to_dict()
self.lpad = LaunchPad.from_dict(lp)
self.opt_label = self.get("opt_label", "opt_default")
self.c = getattr(self.lpad.db, self.opt_label)
self.config = self.c.find_one({"doctype": "config"})
if self.config is None:
raise NotConfiguredError("Please use MissionControl().configure to "
"configure the optimization database "
"({} - {}) before running OptTask."
"".format(self.lpad.db, self.opt_label))
self.wf_creator = deserialize(self.config["wf_creator"])
self.x_dims = self.config["dimensions"]
self._xdim_types = self.config["dim_types"]
self.is_discrete_all = self.config["is_discrete_all"]
self.is_discrete_any = self.config["is_discrete_any"]
self.wf_creator_args = self.config["wf_creator_args"] or []
self.wf_creator_kwargs = self.config["wf_creator_kwargs"] or {}
self.predictor = self.config["predictor"]
self.predictor_args = self.config["predictor_args"] or []
self.predictor_kwargs = self.config["predictor_kwargs"] or {}
self.maximize = self.config["maximize"]
self.n_search_pts = self.config["n_search_pts"]
self.n_train_pts = self.config["n_train_pts"]
self.n_bootstraps = self.config["n_bootstraps"]
self.acq = self.config["acq"]
self.space_file = self.config["space_file"]
self.onehot_categorical = self.config["onehot_categorical"]
self.duplicate_check = self.config["duplicate_check"]
self.get_z = self.config["get_z"]
if self.get_z:
self.get_z = deserialize(self.config['get_z'])
else:
self.get_z = lambda *ars, **kws: []
self.get_z_args = self.config["get_z_args"] or []
self.get_z_kwargs = self.config["get_z_kwargs"] or {}
self.z_file = self.config["z_file"]
self.enforce_sequential = self.config["enforce_sequential"]
self.tolerances = self.config["tolerances"]
self.batch_size = self.config["batch_size"]
self.timeout = self.config["timeout"]
# Declared attrs
self.n_objs = None
plist = [RandomForestRegressor, GaussianProcessRegressor,
ExtraTreesRegressor, GradientBoostingRegressor]
self.builtin_predictors = {p.__name__: p for p in plist}
self._n_cats = 0
self._encoding_info = []
# Query formats
self._completed = {'x': {'$exists': 1}, 'y': {'$exists': 1,
'$ne': 'reserved'},
'z': {'$exists': 1}}
self._manager = {'lock': {'$exists': 1}, 'queue': {'$exists': 1}}
def __init__(self,
source,
materials,
wf_function,
material_filter=None,
lpad=None,
**kwargs):
"""
Adds workflows to a launchpad based on material inputs.
This is primarily to be used for derivative property
workflows but could in principles used to generate workflows
for any workflow that can be invoked from structure data
Args:
source (Store): store of properties
materials (Store): Store of materials properties
material_filter (dict): dict filter for getting items to process
e. g. {"elasticity": None}
wf_function (string or method): method to generate a workflow
based on structure in document with missing property
can be a string to be loaded or a custom method.
Note that the builder/runner will not be serializable
with custom methods.
lpad (LaunchPad or dict): fireworks launchpad to use for adding
workflows, can either be None (autoloaded), a LaunchPad
instance, or a dict from which the LaunchPad will be invoked
**kwargs (kwargs): kwargs for builder
"""
self.source = source
self.materials = materials
# Will this be pickled properly for multiprocessing? could just put
# it into the processor if that's the case
if isinstance(wf_function, six.string_types):
self.wf_function = load_class(*wf_function.rsplit('.', 1))
self._wf_function_string = wf_function
elif callable(wf_function):
self.wf_function = wf_function
self._wf_function_string = None
else:
raise ValueError("wf_function must be callable or a string "
"corresponding to a loadable method")
self.material_filter = material_filter
if lpad is None:
self.lpad = LaunchPad.auto_load()
elif isinstance(lpad, dict):
self.lpad = LaunchPad.from_dict(lpad)
else:
self.lpad = lpad
super().__init__(sources=[source, materials], targets=[], **kwargs)
def __init__(self,
pj_store,
lpad,
incremental=True,
query=None,
base_priority=2500,
site_penalty=10,
vote_weight=10,
**kwargs):
"""
Takes a propjockey collection and sets the priority
of a fireworks in a fireworks collection from a LaunchPad
Args:
pj_store (Store): store corresponding to propjockey collection
lpad (LaunchPad): fireworks launchpad
query (dict): query to filter the propjockey store
base_priority (int): base priority to assign to fireworks
site_penalty (int): per-site penalty to priority
vote_weight (int): priority boost per vote
**kwargs (kwargs): kwargs for builder
"""
self.pj_store = pj_store
if isinstance(lpad, dict):
self.lpad = LaunchPad.from_dict(lpad)
else:
self.lpad = lpad
self.fws_store = MongoStore.from_collection(self.lpad.fireworks)
self.fws_store.lu_field = "_pj_lu"
self.incremental = incremental
self.start_date = datetime.utcnow()
self.query = query or {}
self.base_priority = base_priority
self.site_penalty = site_penalty
self.vote_weight = vote_weight
super().__init__(sources=[self.pj_store],
targets=[self.fws_store],
**kwargs)
def test_dict_from_file(self):
lp = LaunchPad.from_file(self.LP_LOC)
lp_dict = lp.to_dict()
new_lp = LaunchPad.from_dict(lp_dict)
self.assertIsInstance(new_lp, LaunchPad)
from fireworks.core.firework import FireTaskBase
from fireworks.scripts.rlaunch_run import launch_multiprocess
from fireworks.utilities.fw_utilities import explicit_serialize
from fw_tutorials.firetask.addition_task import AdditionTask
from rocketsled import OptTask, MissionControl
from rocketsled.utils import ExhaustedSpaceError
__author__ = "Alexander Dunn"
__email__ = "*****@*****.**"
lp_filedir = os.path.dirname(os.path.realpath(__file__))
with open(lp_filedir + '/tests_launchpad.yaml', 'r') as lp_file:
yaml = YAML()
lp_dict = dict(yaml.load(lp_file))
launchpad = LaunchPad.from_dict(lp_dict)
opt_label = "test"
db_info = {"launchpad": launchpad, "opt_label": opt_label}
test_db_name = launchpad.db
common_kwargs = {"predictor": "RandomForestRegressor", "acq": None}
@explicit_serialize
class BasicTestTask(FireTaskBase):
_fw_name = "BasicTestTask"
def run_task(self, fw_spec):
x = fw_spec['_x']
y = np.sum(x[:-1]) # sum all except the final string element
return FWAction(update_spec={'_y': y})
def test_dict_from_file(self):
lp = LaunchPad.from_file(self.LP_LOC)
lp_dict = lp.to_dict()
new_lp = LaunchPad.from_dict(lp_dict)
self.assertIsInstance(new_lp, LaunchPad)
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
Si
2
direct
0.000000 0.000000 0.000000 Si
0.750000 0.500000 0.750000 Si"""
STRUCT = Structure.from_str(POSCAR_STR, fmt='POSCAR')
TEST_DIR = os.path.join(MODULE_DIR, 'tmp_fw_test_dir')
LPAD = LaunchPad.from_dict({
'host': 'localhost',
'logdir': None,
'name': 'prlworkflows_unittest',
'password': None,
'port': 27017,
'ssl_ca_file': None,
'strm_lvl': 'DEBUG',
'user_indices': [],
'username': None,
'wf_user_indices': []
})
# TODO: enable debug mode by having a launchpad that does not reset
# Can this be done by still having other tests pass?
# Should we only run one test?
# Stop on failure?
@pytest.fixture
def lpad():
"""A LaunchPad object for test instances to use. Always gives a clean (reset) LaunchPad. """
LPAD.reset(None, require_password=False, max_reset_wo_password=5)
def __init__(self, *args, **kwargs):
super(OptTask, self).__init__(*args, **kwargs)
# Configuration attrs
lp = self.get("launchpad", LaunchPad.auto_load())
if isinstance(lp, LaunchPad):
lp = lp.to_dict()
self.lpad = LaunchPad.from_dict(lp)
self.opt_label = self.get("opt_label", "opt_default")
self.c = getattr(self.lpad.db, self.opt_label)
self.config = self.c.find_one({"doctype": "config"})
if self.config is None:
raise NotConfiguredError(
"Please use MissionControl().configure to "
"configure the optimization database "
"({} - {}) before running OptTask."
"".format(self.lpad.db, self.opt_label))
self.wf_creator = deserialize(self.config["wf_creator"])
self.x_dims = self.config["dimensions"]
self._xdim_types = self.config["dim_types"]
self.is_discrete_all = self.config["is_discrete_all"]
self.is_discrete_any = self.config["is_discrete_any"]
self.wf_creator_args = self.config["wf_creator_args"] or []
self.wf_creator_kwargs = self.config["wf_creator_kwargs"] or {}
self.predictor = self.config["predictor"]
self.predictor_args = self.config["predictor_args"] or []
self.predictor_kwargs = self.config["predictor_kwargs"] or {}
self.maximize = self.config["maximize"]
self.n_search_pts = self.config["n_search_pts"]
self.n_train_pts = self.config["n_train_pts"]
self.n_bootstraps = self.config["n_bootstraps"]
self.acq = self.config["acq"]
self.space_file = self.config["space_file"]
self.onehot_categorical = self.config["onehot_categorical"]
self.duplicate_check = self.config["duplicate_check"]
self.get_z = self.config["get_z"]
if self.get_z:
self.get_z = deserialize(self.config["get_z"])
else:
self.get_z = lambda *ars, **kws: []
self.get_z_args = self.config["get_z_args"] or []
self.get_z_kwargs = self.config["get_z_kwargs"] or {}
self.z_file = self.config["z_file"]
self.enforce_sequential = self.config["enforce_sequential"]
self.tolerances = self.config["tolerances"]
self.batch_size = self.config["batch_size"]
self.timeout = self.config["timeout"]
# Declared attrs
self.n_objs = None
self.builtin_predictors = {p.__name__: p for p in BUILTIN_PREDICTORS}
self._n_cats = 0
self._encoding_info = []
# Query formats
self._completed = {
"x": {
"$exists": 1
},
"y": {
"$exists": 1,
"$ne": "reserved"
},
"z": {
"$exists": 1
},
}
self._manager = {"lock": {"$exists": 1}, "queue": {"$exists": 1}}
from fireworks.core.firework import FireTaskBase
from fireworks.scripts.rlaunch_run import launch_multiprocess
from fireworks.utilities.fw_utilities import explicit_serialize
from fw_tutorials.firetask.addition_task import AdditionTask
from rocketsled import OptTask, MissionControl
from rocketsled.utils import ExhaustedSpaceError
__author__ = "Alexander Dunn"
__email__ = "*****@*****.**"
lp_filedir = os.path.dirname(os.path.realpath(__file__))
with open(lp_filedir + '/tests_launchpad.yaml', 'r') as lp_file:
yaml = YAML()
lp_dict = dict(yaml.load(lp_file))
launchpad = LaunchPad.from_dict(lp_dict)
opt_label = "test"
db_info = {"launchpad": launchpad, "opt_label": opt_label}
test_db_name = launchpad.db
common_kwargs = {"predictor": "RandomForestRegressor", "acq": None}
@explicit_serialize
class BasicTestTask(FireTaskBase):
_fw_name = "BasicTestTask"
def run_task(self, fw_spec):
x = fw_spec['_x']
y = np.sum(x[:-1]) # sum all except the final string element
return FWAction(update_spec={'_y': y})