Codes style cleaning

alea/__init__.py

@@ -1,15 +1,8 @@
-import os
-
-_ROOT = os.path.abspath(os.path.dirname(__file__))
-
 from alea import likelihoods
 
 from alea import plotting
 from alea import simulators
 from alea import template_source
 from alea import toymc_running
 from alea import utils
-
-
-def get_data_path(data_path):
-    return os.path.join(_ROOT, "data", data_path)
+from alea import runner

alea/blueice_extended_model.py

@@ -1,16 +1,17 @@
 from pydoc import locate  # to lookup likelihood class
 from typing import List
 
-from alea.statistical_model import StatisticalModel
-from alea.simulators import BlueiceDataGenerator
-from alea.utils import adapt_likelihood_config_for_blueice
-from alea.parameters import Parameters
 import yaml
 import numpy as np
 import scipy.stats as stats
 from blueice.likelihood import LogAncillaryLikelihood
 from blueice.likelihood import LogLikelihoodSum
 
+from alea.statistical_model import StatisticalModel
+from alea.simulators import BlueiceDataGenerator
+from alea.utils import adapt_likelihood_config_for_blueice
+from alea.parameters import Parameters
+
 
 class BlueiceExtendedModel(StatisticalModel):
     """
@@ -37,7 +38,8 @@ def __init__(self, parameter_definition: dict, likelihood_config: dict):
         self.likelihood_names.append("ancillary_likelihood")
         self.data_generators = self._build_data_generators()
 
-    # TODO analysis_space could be inferred from the data (assert that all sources have the same analysis space)
+    # TODO analysis_space could be inferred from the data
+    # (assert that all sources have the same analysis space)
 
     @classmethod
     def from_config(cls, config_file_path: str) -> "BlueiceExtendedModel":
@@ -62,7 +64,8 @@ def data(self) -> list:
     def data(self, data: list):
         """
         Overrides default setter. Will also set the data of the blueice ll.
-        Data-sets are expected to be in the form of a list of one or more structured arrays-- representing the data-sets of one or more likelihood terms.
+        Data-sets are expected to be in the form of a list of one
+        or more structured arrays-- representing the data-sets of one or more likelihood terms.
         """
         # iterate through all likelihood terms and set the science data in the blueice ll
         # last entry in data are the generate_values
@@ -77,7 +80,8 @@ def get_expectation_values(self, **kwargs) -> dict:
         given a number of named parameters (kwargs)
         """
         ret = dict()
-        for ll in self._likelihood.likelihood_list[:-1]:  # ancillary likelihood does not contribute
+        # ancillary likelihood does not contribute
+        for ll in self._likelihood.likelihood_list[:-1]:
 
             ll_pars = list(ll.rate_parameters.keys()) + list(ll.shape_parameters.keys())
             ll_pars += ["livetime_days"]
@@ -117,8 +121,9 @@ def _build_ll_from_config(self, likelihood_config: dict) -> "LogLikelihoodSum":
 
             # add all parameters to extra_dont_hash for each source unless it is used:
             for i, source in enumerate(config["sources"]):
-                parameters_to_ignore: List[str] = [p.name for p in self.parameters if (p.ptype == "shape")
-                                                   & (p.name not in source["parameters"])]
+                parameters_to_ignore: List[str] = [
+                    p.name for p in self.parameters if (
+                        p.ptype == "shape") & (p.name not in source["parameters"])]
                 # no efficiency affects PDF:
                 parameters_to_ignore += [p.name for p in self.parameters if (p.ptype == "efficiency")]
                 parameters_to_ignore += source.get("extra_dont_hash_settings", [])
@@ -142,7 +147,8 @@ def _build_ll_from_config(self, likelihood_config: dict) -> "LogLikelihoodSum":
                     ll.add_rate_parameter(rate_parameter, log_prior=None)
                 else:
                     raise NotImplementedError(
-                        "Only rate multipliers that end on _rate_multiplier are currently supported.")
+                        "Only rate multipliers that end on _rate_multiplier"
+                        " are currently supported.")
 
                 # Set shape parameters
                 shape_parameters = [
@@ -167,7 +173,8 @@ def _build_ll_from_config(self, likelihood_config: dict) -> "LogLikelihoodSum":
     def _build_data_generators(self) -> list:
         # last one is AncillaryLikelihood
         # IDEA: Also implement data generator for ancillary ll term.
-        return [BlueiceDataGenerator(ll_term) for ll_term in self._likelihood.likelihood_list[:-1]]
+        return [
+            BlueiceDataGenerator(ll_term) for ll_term in self._likelihood.likelihood_list[:-1]]
 
     def _ll(self, **generate_values) -> float:
         return self._likelihood(**generate_values)
@@ -183,8 +190,8 @@ def _generate_data(self, **generate_values) -> list:
         return science_data + [ancillary_measurements] + [generate_values]
 
     def _generate_science_data(self, **generate_values) -> list:
-        science_data = [gen.simulate(**generate_values)
-                        for gen in self.data_generators]
+        science_data = [
+            gen.simulate(**generate_values) for gen in self.data_generators]
         return science_data
 
     def _generate_ancillary_measurements(self, **generate_values) -> dict:
@@ -205,18 +212,28 @@ def _generate_ancillary_measurements(self, **generate_values) -> dict:
         return ancillary_measurements
 
     def _set_efficiency(self, source, ll):
-        assert "efficiency_name" in source, "Unspecified efficiency_name for source {:s}".format(source["name"])
+        if "efficiency_name" not in source:
+            raise ValueError(f"Unspecified efficiency_name for source {source['name']:s}")
         efficiency_name = source["efficiency_name"]
-        assert efficiency_name in source[
-            "parameters"], "The efficiency_name for source {:s} is not in its parameter list".format(source["name"])
+
+        if efficiency_name not in source["parameters"]:
+            raise ValueError(
+                f"The efficiency_name for source {source['name']:s}"
+                " is not in its parameter list")
         efficiency_parameter = self.parameters[efficiency_name]
-        assert efficiency_parameter.ptype == "efficiency", "The parameter {:s} must" \
-            " be an efficiency".format(efficiency_name)
+
+        if efficiency_parameter.ptype != "efficiency":
+            raise ValueError(f"The parameter {efficiency_name:s} must be an efficiency")
         limits = efficiency_parameter.fit_limits
-        assert 0 <= limits[0], 'Efficiency parameters including {:s} must be' \
-                               ' constrained to be nonnegative'.format(efficiency_name)
-        assert np.isfinite(limits[1]), 'Efficiency parameters including {:s} must be' \
-                                       ' constrained to be finite'.format(efficiency_name)
+
+        if limits[0] < 0:
+            raise ValueError(
+                f"Efficiency parameters including {efficiency_name:s}"
+                " must be constrained to be nonnegative")
+        if  ~np.isfinite(limits[1]):
+            raise ValueError(
+                f"Efficiency parameters including {efficiency_name:s}"
+                " must be constrained to be finite")
         ll.add_shape_parameter(efficiency_name, anchors=(limits[0], limits[1]))
 
 
@@ -239,13 +256,16 @@ def __init__(self, parameters: Parameters):
         """
         self.parameters = parameters
         # check that there are no None values in the uncertainties dict
-        assert set(self.parameters.uncertainties.keys()) == set(self.parameters.names)
+        if set(self.parameters.uncertainties.keys()) != set(self.parameters.names):
+            raise ValueError(
+                "The uncertainties dict must contain all parameters as keys.")
         parameter_list = self.parameters.names
 
         self.constraint_functions = self._get_constraint_functions()
-        super().__init__(func=self.ancillary_likelihood_sum,
-                         parameter_list=parameter_list,
-                         config=self.parameters.nominal_values)
+        super().__init__(
+            func=self.ancillary_likelihood_sum,
+            parameter_list=parameter_list,
+            config=self.parameters.nominal_values)
 
     @property
     def constraint_terms(self) -> dict:
@@ -263,7 +283,9 @@ def set_data(self, d: dict):
             d (dict): Data in this case is a dict of ancillary measurements.
         """
         # This results in shifted constraint terms.
-        assert set(d.keys()) == set(self.parameters.names)
+        if set(d.keys()) != set(self.parameters.names):
+            raise ValueError(
+                "The data dict must contain all parameters as keys in CustomAncillaryLikelihood.")
         self.constraint_functions = self._get_constraint_functions(**d)
 
     def ancillary_likelihood_sum(self, evaluate_at: dict) -> float:
@@ -288,8 +310,8 @@ def _get_constraint_functions(self, **generate_values) -> dict:
             if param.relative_uncertainty:
                 uncertainty *= param.nominal_value
             if isinstance(uncertainty, float):
-                func = stats.norm(central_values[name],
-                                  uncertainty)
+                func = stats.norm(
+                    central_values[name], uncertainty)
             else:
                 # TODO: Implement str-type uncertainties
                 NotImplementedError(

alea/examples/gaussian_model.py

@@ -7,8 +7,11 @@
 
 
 class GaussianModel(StatisticalModel):
-    def __init__(self, parameter_definition: Optional[dict or list] = None,
-                 **kwargs):
+    def __init__(
+            self,
+            parameter_definition: Optional[dict or list] = None,
+            **kwargs,
+        ):
         """
         Initialise a model of a gaussian measurement (hatmu),
         where the model has parameters mu and sigma

alea/examples/unbinned_wimp_running.yaml

@@ -7,7 +7,10 @@ computation:
   discovery_power:
     parameters_to_zip: {}
     parameters_to_vary:
-      {poi_expectation: "np.linspace(0, 30, 10)", wimp_mass: [10, 50, 200] }
+      {
+        poi_expectation: "np.linspace(0, 30, 10)",
+        wimp_mass: [10, 50, 200],
+      }
     parameters_in_common:
       {
         hypotheses: ["true", "null", "free"],
@@ -19,7 +22,7 @@ computation:
 
   threshold:
     parameters_to_zip: {}
-    parameters_to_vary: { wimp_mass: [10, 50, 200] }
+    parameters_to_vary: {wimp_mass: [10, 50, 200]}
     parameters_in_common:
       {
         hypotheses: ["true", "null", "free"],
@@ -33,7 +36,7 @@ computation:
 
   sensitivity:
     parameters_to_zip: {}
-    parameters_to_vary: { poi_expectation: [0.], wimp_mass: [10, 50, 200] }
+    parameters_to_vary: {poi_expectation: [0.], wimp_mass: [10, 50, 200]}
     parameters_in_common:
       {
         hypotheses: ["true", "null", "free"],
@@ -51,4 +54,4 @@ OSG_parameters:
   request_memory: "8000Mb"
   singularity_container: null
 
-outputfolder: null
+outputfolder: null

alea/examples/unbinned_wimp_statistical_model.yaml

@@ -120,4 +120,4 @@ likelihood_config:
           - signal_efficiency
         template_filename: wimp50gev_template.h5
         apply_efficiency: True
-        efficiency_name: signal_efficiency
+        efficiency_name: signal_efficiency

alea/statistical_model.py

@@ -1,6 +1,6 @@
 import inspect
 import warnings
-from typing import Tuple, Callable
+from typing import Tuple, Callable, Optional
 
 import numpy as np
 from scipy.stats import chi2
@@ -53,11 +53,11 @@ class StatisticalModel:
     def __init__(
             self,
             data = None,
-            parameter_definition: dict or list = None,
+            parameter_definition: Optional[dict or list] = None,
             confidence_level: float = 0.9,
             confidence_interval_kind: str = "central",  # one of central, upper, lower
             confidence_interval_threshold: Callable[[float], float] = None,
-            **kwargs):
+        ):
         self._data = data
         self._confidence_level = confidence_level
         self._confidence_interval_kind = confidence_interval_kind

setup.cfg

@@ -72,7 +72,9 @@ exclude =
 # WPS519 Found implicit sum() call
 # WPS602 Found using @staticmethod
 # Q000 Remove bad quotes
-ignore = C409, C819, D100, D205, D400, D401, D403, DAR101, DAR201, DAR401, E128, E226, E251, F403, F541, I001, I003, I004, I005, P101, WPS110, WPS111, WPS211, WPS122, WPS210, WPS218, WPS229, WPS231, WPS237, WPS237, WPS300, WPS303, WPS304, WPS305, WPS306, WPS317, WPS318, WPS319, WPS326, WPS331, WPS335, WPS336, WPS420, WPS421, WPS432, WPS433, WPS440, WPS435, WPS437, WPS503, WPS504, WPS519, WPS602, Q000
+# E121 continuation line under-indented for hanging indent
+# E125 continuation line with same indent as next logical line
+ignore = C409, C819, D100, D205, D400, D401, D403, DAR101, DAR201, DAR401, E128, E226, E251, F403, F541, I001, I003, I004, I005, P101, WPS110, WPS111, WPS211, WPS122, WPS210, WPS218, WPS229, WPS231, WPS237, WPS237, WPS300, WPS303, WPS304, WPS305, WPS306, WPS317, WPS318, WPS319, WPS326, WPS331, WPS335, WPS336, WPS420, WPS421, WPS432, WPS433, WPS440, WPS435, WPS437, WPS503, WPS504, WPS519, WPS602, Q000, E121, E125
 
 
 per-file-ignores =