Fixing failing tests issues

Author: slilonfe5

doc/OnlineDocs/explanation/analysis/parmest/covariance.rst

@@ -106,7 +106,6 @@ the :class:`~pyomo.contrib.parmest.parmest.Estimator.cov_est` function, e.g.,
     >>> import pyomo.contrib.parmest.parmest as parmest
     >>> pest = parmest.Estimator(exp_list, obj_function="SSE")
     >>> obj_val, theta_val = pest.theta_est()
-    WARNING: DEPRECATED: ...
     >>> cov = pest.cov_est()
 
 Optionally, one of the three methods; "reduced_hessian", "finite_difference",
@@ -118,6 +117,5 @@ e.g.,
 
     >>> pest = parmest.Estimator(exp_list, obj_function="SSE")
     >>> obj_val, theta_val = pest.theta_est()
-    WARNING: DEPRECATED: ...
     >>> cov_method = "reduced_hessian"
     >>> cov = pest.cov_est(method=cov_method)

doc/OnlineDocs/explanation/analysis/parmest/datarec.rst

@@ -51,5 +51,4 @@ The following example returns model values from a Pyomo Expression.
 
    >>> pest = parmest.Estimator(exp_list, obj_function=SSE, solver_options=None)
    >>> obj, theta, var_values = pest.theta_est(return_values=['response_function'])
-   WARNING: DEPRECATED: ...
    >>> #print(var_values)

pyomo/contrib/parmest/parmest.py

@@ -985,19 +985,6 @@ def _Q_opt(
         values as well as the objective function value.
 
         """
-        if calc_cov is not NOTSET:
-            deprecation_warning(
-                "theta_est_leaveNout(): `calc_cov` and `cov_n` are deprecated options and "
-                "will be removed in the future. Please use the `cov_est()` function "
-                "for covariance calculation.",
-                version="6.9.4.dev0",
-            )
-        else:
-            calc_cov = False
-
-        if cov_n is NOTSET:
-            cov_n = 0
-
         if solver == "k_aug":
             raise RuntimeError("k_aug no longer supported.")
 
@@ -1093,7 +1080,8 @@ def _Q_opt(
 
                 if not isinstance(cov_n, int):
                     raise TypeError(
-                        f"Expected an integer for the 'cov_n' argument. Got {type(cov_n)}."
+                        f"Expected an integer for the 'cov_n' argument. "
+                        f"Got {type(cov_n)}."
                     )
                 num_unknowns = max(
                     [
@@ -1662,6 +1650,7 @@ def theta_est(
         """
         assert isinstance(solver, str)
         assert isinstance(return_values, list)
+        assert (calc_cov is NOTSET) or isinstance(calc_cov, bool)
 
         if calc_cov is not NOTSET:
             deprecation_warning(
@@ -1673,9 +1662,6 @@ def theta_est(
         else:
             calc_cov = False
 
-        if cov_n is NOTSET:
-            cov_n = 0
-
         # check if we are using deprecated parmest
         if self.pest_deprecated is not None and calc_cov:
             return self.pest_deprecated.theta_est(