From c33dc58b14961bd75f0af71e01f3b45a78fb85a7 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@helmholtz-munich.de>
Date: Wed, 13 Dec 2023 10:15:44 +0100
Subject: [PATCH] Cleanup includes

---
 include/parpeamici/hierarchicalOptimization.h          | 2 --
 include/parpeamici/multiConditionProblem.h             | 1 -
 include/parpecommon/hdf5Misc.h                         | 1 -
 include/parpecommon/misc.h                             | 3 ---
 include/parpecommon/model.h                            | 1 -
 include/parpeoptimization/localOptimizationCeres.h     | 1 -
 include/parpeoptimization/localOptimizationIpoptTNLP.h | 2 --
 include/parpeoptimization/multiStartOptimization.h     | 1 -
 src/parpeamici/amiciMisc.cpp                           | 5 ++---
 src/parpecommon/misc.cpp                               | 4 ----
 src/parpeoptimization/localOptimizationIpoptTNLP.cpp   | 4 +---
 src/parpeoptimization/optimizationProblem.cpp          | 2 +-
 12 files changed, 4 insertions(+), 23 deletions(-)

diff --git a/include/parpeamici/hierarchicalOptimization.h b/include/parpeamici/hierarchicalOptimization.h
index c9868cd1b..6620d93a1 100644
--- a/include/parpeamici/hierarchicalOptimization.h
+++ b/include/parpeamici/hierarchicalOptimization.h
@@ -7,9 +7,7 @@
 
 #include <gsl/gsl-lite.hpp>
 
-#include <cmath>
 #include <memory>
-#include <numeric>
 
 
 namespace parpe {
diff --git a/include/parpeamici/multiConditionProblem.h b/include/parpeamici/multiConditionProblem.h
index 101437bf8..7ce634ba4 100644
--- a/include/parpeamici/multiConditionProblem.h
+++ b/include/parpeamici/multiConditionProblem.h
@@ -15,7 +15,6 @@
 #include <gsl/gsl-lite.hpp>
 
 #include <memory>
-#include <cstdlib>
 
 /** @file multiConditionProblem.h
  *  Interfaces between AMICI model and parPE optimization problem */
diff --git a/include/parpecommon/hdf5Misc.h b/include/parpecommon/hdf5Misc.h
index 5247aa9b4..5a5d6fec9 100644
--- a/include/parpecommon/hdf5Misc.h
+++ b/include/parpecommon/hdf5Misc.h
@@ -9,7 +9,6 @@
 #include <exception>
 #include <string>
 #include <mutex>
-#include <cstdarg>
 
 namespace parpe {
 
diff --git a/include/parpecommon/misc.h b/include/parpecommon/misc.h
index c092eccdc..b797c2da4 100644
--- a/include/parpecommon/misc.h
+++ b/include/parpecommon/misc.h
@@ -4,10 +4,7 @@
 #include <parpecommon/parpeConfig.h>
 
 #include <chrono>
-#include <cstdio>
-#include <memory>
 #include <ostream>
-#include <stdlib.h>
 #include <vector>
 
 #include <gsl/gsl-lite.hpp>
diff --git a/include/parpecommon/model.h b/include/parpecommon/model.h
index 121bbbe10..53c9ca98c 100644
--- a/include/parpecommon/model.h
+++ b/include/parpecommon/model.h
@@ -4,7 +4,6 @@
 #include <parpecommon/functions.h>
 
 #include <vector>
-#include <memory>
 
 namespace parpe {
 
diff --git a/include/parpeoptimization/localOptimizationCeres.h b/include/parpeoptimization/localOptimizationCeres.h
index 6a30a0073..2e841dac7 100644
--- a/include/parpeoptimization/localOptimizationCeres.h
+++ b/include/parpeoptimization/localOptimizationCeres.h
@@ -3,7 +3,6 @@
 
 #include <parpeoptimization/optimizer.h>
 
-#include <string>
 
 namespace parpe {
 
diff --git a/include/parpeoptimization/localOptimizationIpoptTNLP.h b/include/parpeoptimization/localOptimizationIpoptTNLP.h
index e0f319b83..3ef15f199 100644
--- a/include/parpeoptimization/localOptimizationIpoptTNLP.h
+++ b/include/parpeoptimization/localOptimizationIpoptTNLP.h
@@ -11,8 +11,6 @@
 #include <IpIpoptApplication.hpp>
 #endif
 
-#include <cmath>
-#include <memory>
 #include <mutex>
 
 #include <parpecommon/misc.h>
diff --git a/include/parpeoptimization/multiStartOptimization.h b/include/parpeoptimization/multiStartOptimization.h
index eba5d81d4..f5c68ef9c 100644
--- a/include/parpeoptimization/multiStartOptimization.h
+++ b/include/parpeoptimization/multiStartOptimization.h
@@ -3,7 +3,6 @@
 
 #include <parpeoptimization/optimizationProblem.h>
 
-#include <vector>
 #include <memory>
 
 namespace parpe {
diff --git a/src/parpeamici/amiciMisc.cpp b/src/parpeamici/amiciMisc.cpp
index 3a0d7929c..0869c2963 100644
--- a/src/parpeamici/amiciMisc.cpp
+++ b/src/parpeamici/amiciMisc.cpp
@@ -5,12 +5,11 @@
 #include <amici/logging.h>
 #include <parpecommon/logging.h>
 
+#include <memory>
+
 namespace parpe {
 
-using amici::ExpData;
-using amici::Model;
 using amici::ReturnData;
-using amici::Solver;
 
 std::unique_ptr<ReturnData> run_amici_simulation(
     amici::Solver &solver,
diff --git a/src/parpecommon/misc.cpp b/src/parpecommon/misc.cpp
index 7d4f9a69d..c09ea370c 100644
--- a/src/parpecommon/misc.cpp
+++ b/src/parpecommon/misc.cpp
@@ -1,13 +1,9 @@
 #include <parpecommon/misc.h>
 #include <parpecommon/logging.h>
 
-#include <cassert>
-#include <cerrno>
 #include <execinfo.h>
 #include <cmath>
-#include <cstdarg>
 #include <cstdio>
-#include <cstring>
 #include <sys/types.h>
 #include <ctime>
 #include <unistd.h>
diff --git a/src/parpeoptimization/localOptimizationIpoptTNLP.cpp b/src/parpeoptimization/localOptimizationIpoptTNLP.cpp
index ba8ea9414..a16d0d836 100644
--- a/src/parpeoptimization/localOptimizationIpoptTNLP.cpp
+++ b/src/parpeoptimization/localOptimizationIpoptTNLP.cpp
@@ -4,8 +4,6 @@
 
 #include <IpDenseVector.hpp>
 #include <IpIpoptData.hpp>
-#include <cassert>
-#include <cstring>
 //#include <IpIpoptCalculatedQuantities.hpp>
 
 namespace parpe {
@@ -202,7 +200,7 @@ LocalOptimizationIpoptTNLP::finalize_solution(
     // obj_value 0.0 along with the respective flag. This does not make too
     // much sense. Set to NAN.
     if(status == INVALID_NUMBER_DETECTED && obj_value == 0.0) {
-        obj_value = NAN;
+        obj_value = std::numeric_limits<double>::quiet_NaN();
     }
 
     reporter.finished(obj_value, gsl::span<double const>(x, n), status);
diff --git a/src/parpeoptimization/optimizationProblem.cpp b/src/parpeoptimization/optimizationProblem.cpp
index d138dcb78..dae0d9e56 100644
--- a/src/parpeoptimization/optimizationProblem.cpp
+++ b/src/parpeoptimization/optimizationProblem.cpp
@@ -404,7 +404,7 @@ void OptimizationReporter::finished(double optimalCost,
         // the optimal parameters from the optimizer. since we don't know them, rather set to nan
         if (logger_)
             logger_->logmessage(loglevel::info, "cachedCost != optimalCost && parameters.empty()");
-        cached_parameters_.assign(cached_parameters_.size(), NAN);
+        cached_parameters_.assign(cached_parameters_.size(), std::numeric_limits<double>::quiet_NaN());
         cached_cost_ = optimalCost;
     } // else: our cached parameters were better. use those