Remove some warnings (#1345)

* removed startpoint method from minimize as its depracated and per default in the problem.

* Changed offset to one that should definitely catch the warning and test for warning.

* When loading a problem, we expect a warning.

* Trust-exact cannot handle bounds is an expected warning here.

* If hess is not traced, no need to compute imo

* Revert last changes, instead expect additional warning.

* Better catching of warnings

* Catch warnings?

* Removed startpoint methods from functions, all were uniform.

* added match as parameter to pytest.warns

* Removed warning, is already tested elsewhere.

pypesto/optimize/optimizer.py

@@ -469,7 +469,7 @@ def minimize(
                     "evaluated again. This can lead to increased "
                     "computation times. If possible, separate fun "
                     "and hess.",
-                    stacklevel=1,
+                    stacklevel=2,
                 )
             if objective.grad is True:
 

test/base/test_history.py

@@ -433,8 +433,8 @@ def test_trace_grad(self):
             trace_record_grad=True,
             trace_record_hess=False,
         )
-
-        self.check_history()
+        with pytest.warns(RuntimeWarning, match="cannot handle bounds"):
+            self.check_history()
 
     def test_trace_grad_integrated(self):
         self.obj = rosen_for_sensi(
@@ -447,13 +447,18 @@ def test_trace_grad_integrated(self):
             trace_record_grad=True,
             trace_record_hess=False,
         )
-
-        self.check_history()
+        # Expect RuntimeWarning since we cannot handle bounds and
+        # UserWarning for integrated=True
+        with pytest.warns(Warning) as warninfo:
+            self.check_history()
+        warns = {warn.category for warn in warninfo}
+        expected_warns = {RuntimeWarning, UserWarning}
+        assert warns == expected_warns
 
     def test_trace_all(self):
         self.obj = rosen_for_sensi(
             max_sensi_order=2,
-            integrated=True,
+            integrated=False,
         )["obj"]
 
         self.history_options = HistoryOptions(
@@ -464,10 +469,11 @@ def test_trace_all(self):
             trace_record_sres=True,
         )
         self.fix_pars = False
-        self.check_history()
+        with pytest.warns(RuntimeWarning, match="cannot handle bounds"):
+            self.check_history()
 
     def test_trace_all_aggregated(self):
-        self.obj = rosen_for_sensi(max_sensi_order=2, integrated=True)["obj"]
+        self.obj = rosen_for_sensi(max_sensi_order=2, integrated=False)["obj"]
 
         self.history_options = HistoryOptions(
             trace_record=True,
@@ -478,7 +484,8 @@ def test_trace_all_aggregated(self):
         )
         self.obj = pypesto.objective.AggregatedObjective([self.obj, self.obj])
         self.fix_pars = False
-        self.check_history()
+        with pytest.warns(RuntimeWarning, match="cannot handle bounds"):
+            self.check_history()
 
 
 class CRFunModeHistoryTest(HistoryTest):
@@ -511,7 +518,8 @@ def test_trace_all(self):
         )
 
         self.fix_pars = False
-        self.check_history()
+        with pytest.warns(RuntimeWarning, match="cannot handle bounds"):
+            self.check_history()
 
 
 @pytest.fixture(params=["memory", "csv", "hdf5", ""])

test/base/test_store.py

@@ -4,6 +4,7 @@
 import tempfile
 
 import numpy as np
+import pytest
 import scipy.optimize as so
 
 import pypesto
@@ -94,7 +95,8 @@ def test_storage_problem(hdf5_file):
     problem_writer = ProblemHDF5Writer(hdf5_file)
     problem_writer.write(problem)
     problem_reader = ProblemHDF5Reader(hdf5_file)
-    read_problem = problem_reader.read()
+    with pytest.warns(UserWarning, match="loading a problem"):
+        read_problem = problem_reader.read()
     problem_attrs = [
         value
         for name, value in vars(ProblemHDF5Writer).items()
@@ -369,7 +371,8 @@ def test_storage_all():
     filename = "test_file.hdf5"
     try:
         write_result(result=result, filename=filename)
-        result_read = read_result(filename=filename)
+        with pytest.warns(UserWarning, match="loading a problem"):
+            result_read = read_result(filename=filename)
 
         # test optimize
         for i, opt_res in enumerate(result.optimize_result.list):

test/optimize/test_optimize.py

@@ -219,7 +219,6 @@ def test_unbounded_minimize(optimizer):
                 problem=problem,
                 optimizer=opt,
                 n_starts=1,
-                startpoint_method=pypesto.startpoint.uniform,
                 options=options,
                 progress_bar=False,
             )
@@ -229,7 +228,6 @@ def test_unbounded_minimize(optimizer):
             problem=problem,
             optimizer=opt,
             n_starts=1,
-            startpoint_method=pypesto.startpoint.uniform,
             options=options,
             progress_bar=False,
         )
@@ -295,7 +293,6 @@ def check_minimize(problem, library, solver, allow_failed_starts=False):
         problem=problem,
         optimizer=optimizer,
         n_starts=1,
-        startpoint_method=pypesto.startpoint.uniform,
         options=optimize_options,
         progress_bar=False,
     )
@@ -328,7 +325,6 @@ def test_trim_results(problem):
         problem=prob,
         optimizer=optimizer,
         n_starts=1,
-        startpoint_method=pypesto.startpoint.uniform,
         options=optimize_options,
         progress_bar=False,
     )
@@ -340,7 +336,6 @@ def test_trim_results(problem):
         problem=prob,
         optimizer=optimizer,
         n_starts=1,
-        startpoint_method=pypesto.startpoint.uniform,
         options=optimize_options,
         progress_bar=False,
     )
@@ -369,7 +364,10 @@ def test_mpipoolengine():
         )
 
         # read results
-        result1 = read_result("temp_result.h5", problem=True, optimize=True)
+        with pytest.warns(UserWarning, match="You are loading a problem."):
+            result1 = read_result(
+                "temp_result.h5", problem=True, optimize=True
+            )
         # set optimizer
         optimizer = optimize.FidesOptimizer(verbose=40)
         # initialize problem with x_guesses and objective
@@ -499,7 +497,6 @@ def test_ess(problem, local_optimizer, ess_type, request):
 
     res = ess.minimize(
         problem=problem,
-        startpoint_method=pypesto.startpoint.UniformStartpoints(),
     )
     print("ESS result: ", res.summary())
 
@@ -561,15 +558,15 @@ def test_scipy_integrated_grad():
     optimizer = optimize.ScipyOptimizer(options={"maxiter": 10})
     optimize_options = optimize.OptimizeOptions(allow_failed_starts=False)
     history_options = pypesto.HistoryOptions(trace_record=True)
-    result = optimize.minimize(
-        problem=problem,
-        optimizer=optimizer,
-        n_starts=1,
-        startpoint_method=pypesto.startpoint.uniform,
-        options=optimize_options,
-        history_options=history_options,
-        progress_bar=False,
-    )
+    with pytest.warns(UserWarning, match="fun and hess as one func"):
+        result = optimize.minimize(
+            problem=problem,
+            optimizer=optimizer,
+            n_starts=1,
+            options=optimize_options,
+            history_options=history_options,
+            progress_bar=False,
+        )
     assert (
         len(result.optimize_result.history[0].get_fval_trace())
         == result.optimize_result.history[0].n_fval
@@ -592,7 +589,6 @@ def test_ipopt_approx_grad():
         problem=problem,
         optimizer=optimizer,
         n_starts=1,
-        startpoint_method=pypesto.startpoint.uniform,
         options=optimize_options,
         history_options=history_options,
         progress_bar=False,
@@ -606,7 +602,6 @@ def test_ipopt_approx_grad():
         problem=problem2,
         optimizer=optimizer2,
         n_starts=1,
-        startpoint_method=pypesto.startpoint.uniform,
         options=optimize_options,
         history_options=history_options,
         progress_bar=False,

test/profile/test_profile.py

@@ -113,17 +113,24 @@ def test_engine_profiling(self):
             pypesto.engine.MultiProcessEngine(),
             pypesto.engine.MultiThreadEngine(),
         ]
-        for engine in engines:
+        expected_warns = [
+            pytest.warns(UserWarning, match="fun and hess as one func"),
+            pytest.warns(UserWarning, match="fun and hess as one func"),
+            warnings.catch_warnings(),  # No warnings
+            warnings.catch_warnings(),  # No warnings
+        ]
+        for engine, expected_warn in zip(engines, expected_warns):
             # run profiling, profile results get appended
             # in self.result.profile_result
-            profile.parameter_profile(
-                problem=self.problem,
-                result=self.result,
-                optimizer=self.optimizer,
-                next_guess_method="fixed_step",
-                engine=engine,
-                progress_bar=False,
-            )
+            with expected_warn:
+                profile.parameter_profile(
+                    problem=self.problem,
+                    result=self.result,
+                    optimizer=self.optimizer,
+                    next_guess_method="fixed_step",
+                    engine=engine,
+                    progress_bar=False,
+                )
 
         # check results
         for count, _engine in enumerate(engines[1:]):

test/visualize/test_visualize.py

@@ -172,7 +172,6 @@ def create_optimization_history():
         problem=problem,
         optimizer=optimizer,
         n_starts=5,
-        startpoint_method=pypesto.startpoint.uniform,
         options=optimize_options,
         history_options=history_options,
         progress_bar=False,
@@ -458,7 +457,6 @@ def test_parameters_hist():
         problem=problem,
         optimizer=optimizer,
         n_starts=10,
-        startpoint_method=pypesto.startpoint.uniform,
         progress_bar=False,
     )
 
@@ -772,7 +770,6 @@ def test_optimizer_history_with_options():
         reference=ref3,
         trace_x="time",
         trace_y="gradnorm",
-        offset_y=10.0,
     )
 
 
@@ -814,15 +811,13 @@ def test_optimization_stats():
         problem=problem,
         optimizer=optimizer,
         n_starts=10,
-        startpoint_method=pypesto.startpoint.uniform,
         progress_bar=False,
     )
 
     result_2 = optimize.minimize(
         problem=problem,
         optimizer=optimizer,
         n_starts=10,
-        startpoint_method=pypesto.startpoint.uniform,
         progress_bar=False,
     )