observable

Author: dweindl

petab/v2/core.py

@@ -8,7 +8,6 @@
 import tempfile
 import traceback
 from abc import abstractmethod
-from collections import OrderedDict
 from collections.abc import Sequence
 from enum import Enum
 from itertools import chain
@@ -2280,14 +2279,14 @@ def get_measurements_for_experiment(
         ]
 
     def get_output_parameters(
-        self, observables: bool = True, noise: bool = True
+        self, observable: bool = True, noise: bool = True
     ) -> list[str]:
         """Get output parameters.
 
         Returns IDs of symbols used in observable and noise formulas that are
         not observables and that are not defined in the model.
 
-        :param observables:
+        :param observable:
             Include parameters from observableFormulas
         :param noise:
             Include parameters from noiseFormulas
@@ -2297,7 +2296,7 @@ def get_output_parameters(
         # collect free symbols from observable and noise formulas,
         # skipping observable IDs
         candidates = set()
-        if observables:
+        if observable:
             candidates |= {
                 str_sym
                 for o in self.observables

petab/v2/lint.py

@@ -996,15 +996,15 @@ def append_overrides(overrides):
     for formula_type, placeholder_sources in (
         (
             # Observable formulae
-            {"observables": True, "noise": False},
+            {"observable": True, "noise": False},
             # can only contain observable placeholders
-            {"noise": False, "observables": True},
+            {"noise": False, "observable": True},
         ),
         (
             # Noise formulae
-            {"observables": False, "noise": True},
+            {"observable": False, "noise": True},
             # can contain noise and observable placeholders
-            {"noise": True, "observables": True},
+            {"noise": True, "observable": True},
         ),
     ):
         output_parameters = problem.get_output_parameters(
@@ -1035,15 +1035,15 @@ def append_overrides(overrides):
 
 def get_placeholders(
     problem: Problem,
-    observables: bool = True,
+    observable: bool = True,
     noise: bool = True,
 ) -> list[str]:
     """Get all placeholder parameters from observable table observableFormulas
     and noiseFormulas.
 
     Arguments:
         problem: The PEtab problem
-        observables: Include parameters from observableFormulas
+        observable: Include parameters from observableFormulas
         noise: Include parameters from noiseFormulas
 
     Returns:
@@ -1054,7 +1054,7 @@ def get_placeholders(
     # {observable,noise}Parameters
     placeholders = []
     for o in problem.observables:
-        if observables:
+        if observable:
             placeholders.extend(map(str, o.observable_placeholders))
         if noise:
             placeholders.extend(map(str, o.noise_placeholders))

tests/v2/test_core.py

@@ -804,12 +804,12 @@ def test_get_output_parameters():
     )
     assert (
         petab_problem.get_output_parameters()
-        == petab_problem.get_output_parameters(observables=True, noise=True)
+        == petab_problem.get_output_parameters(observable=True, noise=True)
         == ["p1", "p3", "p4", "p5"]
     )
     assert petab_problem.get_output_parameters(
-        observables=True, noise=False
+        observable=True, noise=False
     ) == ["p1", "p3", "p4"]
     assert petab_problem.get_output_parameters(
-        observables=False, noise=True
+        observable=False, noise=True
     ) == ["p1", "p3", "p5"]