1463 Remove log outputs from testing

cpp/memilio/utils/parameter_distributions.h

@@ -20,7 +20,6 @@
 #ifndef PARAMETER_DISTRIBUTIONS_H
 #define PARAMETER_DISTRIBUTIONS_H
 
-#include "memilio/utils/compiler_diagnostics.h"
 #include "memilio/utils/logging.h"
 #include "memilio/utils/visitor.h"
 #include "memilio/utils/random_number_generator.h"
@@ -275,11 +274,6 @@ class ParameterDistributionNormal : public VisitableParameterDistribution<Parame
         return m_standard_dev;
     }
 
-    void log_stddev_changes(bool log_stddev_change)
-    {
-        m_log_stddev_change = log_stddev_change;
-    }
-
     void set_lower_bound(ScalarType lower_bound)
     {
         m_lower_bound = lower_bound;
@@ -338,7 +332,7 @@ class ParameterDistributionNormal : public VisitableParameterDistribution<Parame
 
         int i            = 0;
         int retries      = 10;
-        ScalarType rnumb = m_distribution.get_distribution_instance()(thread_local_rng(), m_distribution.params);
+        ScalarType rnumb = m_distribution.get_distribution_instance()(rng, m_distribution.params);
         while ((rnumb > m_upper_bound || rnumb < m_lower_bound) && i < retries) {
             rnumb = m_distribution.get_distribution_instance()(rng, m_distribution.params);
             i++;
@@ -430,7 +424,6 @@ class ParameterDistributionNormal : public VisitableParameterDistribution<Parame
     ScalarType m_lower_bound = std::numeric_limits<ScalarType>::min();
     ScalarType m_quantile    = 2.5758; // default is 0.995 quartile
     NormalDistribution<ScalarType>::ParamType m_distribution;
-    bool m_log_stddev_change = true;
 };
 
 template <class IOObj>

cpp/tests/random_number_test.h

@@ -59,9 +59,9 @@ class RandomNumberTest : public ::testing::Test
 protected:
     void SetUp() override
     {
-        log_rng_seeds(m_rng, mio::LogLevel::warn);
+        m_rng.set_counter(mio::Counter<uint64_t>{0});
     }
 
 private:
-    mio::RandomNumberGenerator m_rng{}; ///< Seeded rng used by this test fixture.
+    static inline mio::RandomNumberGenerator m_rng = mio::thread_local_rng(); ///< Seeded rng used by this test fixture.
 };

cpp/tests/test_abstract_parameter_dist.cpp

@@ -23,13 +23,10 @@
 #include "memilio/utils/random_number_generator.h"
 #include "models/abm/personal_rng.h"
 #include <gtest/gtest.h>
-#include <stdio.h>
 #include <vector>
 
 TEST(AbstractParameterDist, test_abstract_normal_distribution)
 {
-    mio::log_thread_local_rng_seeds(mio::LogLevel::warn);
-
     mio::AbstractParameterDistribution p1(mio::ParameterDistributionNormal(10., 0.5));
     mio::AbstractParameterDistribution p2(mio::ParameterDistributionNormal(20., 0.3));
     auto params1 = std::vector<double>{10., 0.5};
@@ -52,8 +49,6 @@ TEST(AbstractParameterDist, test_abstract_normal_distribution)
 
 TEST(AbstractParameterDist, test_abstract_uniform_distribution)
 {
-    mio::log_thread_local_rng_seeds(mio::LogLevel::warn);
-
     mio::AbstractParameterDistribution p1(mio::ParameterDistributionUniform(0., 1.));
     mio::AbstractParameterDistribution p2(mio::ParameterDistributionUniform(2., 3.));
     auto params1 = std::vector<double>{0., 1.};
@@ -78,8 +73,6 @@ TEST(AbstractParameterDist, test_abstract_uniform_distribution)
 
 TEST(AbstractParameterDist, test_abstract_lognormal_distribution)
 {
-    mio::log_thread_local_rng_seeds(mio::LogLevel::warn);
-
     mio::AbstractParameterDistribution p1(mio::ParameterDistributionLogNormal(1., 0.25));
     mio::AbstractParameterDistribution p2(mio::ParameterDistributionLogNormal(2., 0.1));
     auto params1 = std::vector<double>{1., 0.25};
@@ -102,8 +95,6 @@ TEST(AbstractParameterDist, test_abstract_lognormal_distribution)
 
 TEST(AbstractParameterDist, test_abstract_exponential_distribution)
 {
-    mio::log_thread_local_rng_seeds(mio::LogLevel::warn);
-
     mio::AbstractParameterDistribution p1(mio::ParameterDistributionExponential(1.));
     mio::AbstractParameterDistribution p2(mio::ParameterDistributionExponential(2.));
     auto params1 = std::vector<double>{1.};
@@ -126,8 +117,6 @@ TEST(AbstractParameterDist, test_abstract_exponential_distribution)
 
 TEST(AbstractParameterDist, test_abstract_constant_distribution)
 {
-    mio::log_thread_local_rng_seeds(mio::LogLevel::warn);
-
     mio::AbstractParameterDistribution p1(mio::ParameterDistributionConstant(1.));
     mio::AbstractParameterDistribution p2(mio::ParameterDistributionConstant(2.));
     auto params1 = std::vector<double>{1.};

cpp/tests/test_analyze_result.cpp

@@ -26,6 +26,7 @@
 #include "memilio/utils/time_series.h"
 #include "ode_secir/analyze_result.h"
 #include "ode_secir/model.h"
+#include "utils.h"
 
 #include "gtest/gtest.h"
 #include "gmock/gmock.h"
@@ -679,15 +680,19 @@ TEST(TestMergeTimeSeries, joint_tp_add)
 
 TEST(TestMergeTimeSeries, joint_tp)
 {
+    mio::RedirectLogger logger;
+    logger.capture();
+
     mio::TimeSeries<double> ts1(2);
     mio::TimeSeries<double> ts2(2);
     ts1.add_time_point(0., mio::TimeSeries<double>::Vector::Constant(2, 1.));
     ts2.add_time_point(0., mio::TimeSeries<double>::Vector::Constant(2, 2.));
 
     //Check for both TimeSeries having only one time point
     auto merged_ts_status = mio::merge_time_series(ts1, ts2, false);
-    auto merged_ts        = merged_ts_status.value();
+    EXPECT_THAT(logger.read(), testing::HasSubstr("Both TimeSeries have values for t=0"));
     ASSERT_TRUE(merged_ts_status);
+    auto merged_ts = merged_ts_status.value();
     ASSERT_EQ(merged_ts.get_num_time_points(), 1);
     EXPECT_NEAR(merged_ts.get_time(0), 0., 1e-12);
     EXPECT_NEAR(merged_ts.get_value(0)[0], 1., 1e-12);
@@ -698,13 +703,16 @@ TEST(TestMergeTimeSeries, joint_tp)
     ts2.add_time_point(1., mio::TimeSeries<double>::Vector::Constant(2, 3.));
 
     merged_ts_status = mio::merge_time_series(ts1, ts2, false);
-    merged_ts        = merged_ts_status.value();
+    EXPECT_THAT(logger.read(), testing::AllOf(testing::HasSubstr("Both TimeSeries have values for t=0"),
+                                              testing::HasSubstr("Both TimeSeries have values for t=1")));
     ASSERT_TRUE(merged_ts_status);
+    merged_ts = merged_ts_status.value();
     ASSERT_EQ(merged_ts.get_num_time_points(), 2);
     EXPECT_NEAR(merged_ts.get_time(0), 0., 1e-12);
     EXPECT_NEAR(merged_ts.get_value(0)[0], 1., 1e-12);
     EXPECT_NEAR(merged_ts.get_value(0)[1], 1., 1e-12);
     EXPECT_NEAR(merged_ts.get_time(1), 1., 1e-12);
     EXPECT_NEAR(merged_ts.get_value(1)[0], 2., 1e-12);
     EXPECT_NEAR(merged_ts.get_value(1)[1], 2., 1e-12);
+    logger.release();
 }

cpp/tests/test_binary_serializer.cpp

@@ -17,22 +17,17 @@
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
-#include "boost/none.hpp"
-#include "boost/none_t.hpp"
 #include "matchers.h"
-#include "memilio/epidemiology/damping.h"
-#include "memilio/epidemiology/damping_sampling.h"
 #include "memilio/io/binary_serializer.h"
 #include "memilio/io/io.h"
 #include "memilio/utils/logging.h"
-#include "memilio/utils/parameter_distributions.h"
 #include "memilio/utils/time_series.h"
-#include "memilio/utils/uncertain_value.h"
 #include "ode_secir/model.h"
 #include "ode_secir/parameter_space.h"
-#include "ode_secir/parameters.h"
+#include "utils.h"
+
+#include "boost/none.hpp"
 #include "gtest/gtest.h"
-#include <memory>
 
 namespace
 {
@@ -180,10 +175,9 @@ TEST(BinarySerializer, model)
     //this test is only to make sure the correct number of bytes are serialized/deserialized
     //in a very complex object. correct serializing of single values is tested by other tests.
     mio::osecir::Model<double> model{5};
-    mio::set_log_level(mio::LogLevel::err);
     mio::osecir::set_params_distributions_normal<double>(model, 0, 10, 0.01);
-    mio::set_log_level(mio::LogLevel::warn);
     auto stream = mio::serialize_binary(model);
+    mio::LogLevelOverride llo(mio::LogLevel::off); // suppress warnings from model constructor
     auto result = mio::deserialize_binary(stream, mio::Tag<mio::osecir::Model<double>>{});
     EXPECT_THAT(result, IsSuccess());
 }
@@ -233,4 +227,4 @@ TEST(ByteStream, reset)
     auto p = (unsigned char*)&i;
     EXPECT_TRUE(stream.read(p, sizeof(i)));
     EXPECT_EQ(i, 0);
-}
+}

cpp/tests/test_epi_data_io.cpp

@@ -17,21 +17,19 @@
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
-
-#include "abm/infection_state.h"
 #include "memilio/epidemiology/age_group.h"
 #include "memilio/geography/regions.h"
 #include "memilio/io/epi_data.h"
 #include "matchers.h"
 #include "memilio/io/io.h"
-#include "memilio/io/mobility_io.h"
 #include "test_data_dir.h"
 #include "gtest/gtest.h"
 #include "json/value.h"
 #include "ode_secirts/model.h"
 #include "ode_secirts/parameters_io.h"
 #include "memilio/utils/stl_util.h"
 #include "boost/optional/optional_io.hpp"
+#include "utils.h"
 #include <gmock/gmock-matchers.h>
 
 TEST(TestEpiDataIo, read_rki)
@@ -423,9 +421,12 @@ TEST(TestEpiData, set_vaccination_data)
     model.parameters.set<mio::osecirts::DaysUntilEffectiveBoosterImmunity<double>>(1);
     std::vector<mio::osecirts::Model<double>> model_vector{model};
 
-    auto f = mio::osecirts::details::set_vaccination_data(model_vector,
-                                                          mio::path_join(TEST_DATA_DIR, "vaccination_test.json"),
-                                                          mio::Date(2022, 4, 15), county_ids, num_days);
+    {
+        mio::LogLevelOverride llo(mio::LogLevel::off); // suppress "Vaccination data only available from [...]"
+        mio::unused(mio::osecirts::details::set_vaccination_data(model_vector,
+                                                                 mio::path_join(TEST_DATA_DIR, "vaccination_test.json"),
+                                                                 mio::Date(2022, 4, 15), county_ids, num_days));
+    }
 
     auto expected_values_PI =
         (Eigen::ArrayXd(num_age_groups * (num_days + 1)) << 7, 10, 20, 15, 10, 5, 2, 15, 8, 0).finished();

cpp/tests/test_graph.cpp

@@ -35,10 +35,13 @@
 #include "matchers.h"
 #include "temp_file_register.h"
 #include "memilio/utils/stl_util.h"
+#include "utils.h"
 #include "gmock/gmock-matchers.h"
+#include "gmock/gmock.h"
 #include <cstddef>
 #include <gtest/gtest.h>
 #include <gmock/gmock.h>
+#include <sys/types.h>
 #include <type_traits>
 #include <string>
 
@@ -148,7 +151,7 @@ TEST(TestGraph, graph_without_edges)
     std::vector<int> ids          = {1, 2};
 
     mio::Graph<MockModel, MockMobility> g(ids, models);
-    
+
     EXPECT_EQ(g.edges().size(), 0);
     EXPECT_EQ(g.nodes().size(), 2);
     EXPECT_EQ(g.nodes()[0].id, 1);
@@ -373,7 +376,11 @@ TEST(TestGraphBuilder, Build_unique)
     builder.add_edge(1, 2, 200);
     builder.add_edge(2, 1, 300);
 
+    mio::RedirectLogger logger;
+    logger.capture();
     auto g = std::move(builder).build(true);
+    EXPECT_THAT(logger.read(), testing::HasSubstr("[warning] Removed duplicate edge(s)"));
+    logger.release();
 
     EXPECT_EQ(g.nodes().size(), 3);
     EXPECT_EQ(g.edges().size(), 3);

cpp/tests/test_graph_abm.cpp

@@ -29,13 +29,10 @@
 #include "graph_abm/graph_abm_mobility.h"
 #include "memilio/epidemiology/age_group.h"
 #include "memilio/utils/logging.h"
-#include "memilio/utils/miompi.h"
 #include "memilio/mobility/graph.h"
-#include "abm_helpers.h"
-#include <algorithm>
-#include <cstddef>
+#include "utils.h"
+
 #include <gtest/gtest.h>
-#include <iostream>
 
 struct MockHistory {
 
@@ -253,10 +250,15 @@ TEST(TestGraphABM, test_get_person)
     auto& p1 = model.get_person(pid1);
     EXPECT_EQ(p1.get_location(), home);
     EXPECT_EQ(p1.get_age(), mio::AgeGroup(0));
-    model.remove_person(model.get_person_index(pid1));
-    EXPECT_EQ(model.get_person_index(pid1), std::numeric_limits<uint32_t>::max());
 
-    auto& p2 = model.get_person(pid2);
-    EXPECT_EQ(p2.get_location(), work);
-    EXPECT_EQ(p2.get_age(), mio::AgeGroup(1));
+    {
+        model.remove_person(model.get_person_index(pid1));
+
+        mio::LogLevelOverride llo(mio::LogLevel::off);
+        EXPECT_EQ(model.get_person_index(pid1), std::numeric_limits<uint32_t>::max());
+
+        auto& p2 = model.get_person(pid2);
+        EXPECT_EQ(p2.get_location(), work);
+        EXPECT_EQ(p2.get_age(), mio::AgeGroup(1));
+    }
 }

cpp/tests/test_odemseirs4.cpp

@@ -23,6 +23,7 @@
 #include "ode_mseirs4/model.h"
 #include "ode_mseirs4/infection_state.h"
 #include "ode_mseirs4/parameters.h"
+#include "utils.h"
 
 #include <gtest/gtest.h>
 
@@ -113,6 +114,7 @@ TEST_F(ModelTestOdeMseirs4, checkPopulationConservation)
 
 TEST(TestOdeMseirs4, apply_constraints_parameters)
 {
+    mio::LogLevelOverride llo(mio::LogLevel::off); // hide contstraint warnings/errors
     mio::omseirs4::Model<double> model;
 
     auto& params = model.parameters;
@@ -148,6 +150,7 @@ TEST(TestOdeMseirs4, apply_constraints_parameters)
 
 TEST(TestOdeMseirs4, check_constraints_parameters)
 {
+    mio::LogLevelOverride llo(mio::LogLevel::off); // hide contstraint warnings/errors
     mio::omseirs4::Model<double> model;
     auto& params = model.parameters;