From 63262608a702ccbca96980c4058c2d29895658a8 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Sun, 20 Oct 2024 10:14:09 +0200
Subject: [PATCH] Some clang-tidy

---
 .clang-tidy                                              | 1 -
 include/parpeamici/multiConditionDataProvider.h          | 6 +++---
 src/parpeamici/amiciSimulationRunner.cpp                 | 9 +++++++--
 ...erarchicalOptimizationAnalyticalParameterProvider.cpp | 2 +-
 4 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/.clang-tidy b/.clang-tidy
index 3d122ad7e..8895907ae 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -2,7 +2,6 @@
 Checks:          '*,-cppcoreguidelines-pro-type-vararg,-google-readability-braces-around-statements,-google-readability-todo,-llvm-include-order,-fuchsia-default-arguments,-hicpp-vararg,-google-default-arguments'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
-AnalyzeTemporaryDtors: false
 User:            dweindl
 CheckOptions:    
   - key:             google-readability-braces-around-statements.ShortStatementLines
diff --git a/include/parpeamici/multiConditionDataProvider.h b/include/parpeamici/multiConditionDataProvider.h
index a344659d2..60fb1a1d4 100644
--- a/include/parpeamici/multiConditionDataProvider.h
+++ b/include/parpeamici/multiConditionDataProvider.h
@@ -309,14 +309,14 @@ class MultiConditionDataProviderHDF5 : public MultiConditionDataProvider
                                                gsl::span<double> buffer) const;
 
     std::unique_ptr<amici::ExpData> getExperimentalDataForCondition(
-      int conditionIdx) const override;
+      int simulationIdx) const override;
 
     std::vector<std::vector<double>> getAllMeasurements() const override;
     std::vector<std::vector<double>> getAllSigmas() const override;
 
     std::vector<double> getSigmaForSimulationIndex(int simulationIdx) const;
     std::vector<double> getMeasurementForSimulationIndex(
-      int conditionIdx) const;
+      int simulationIdx) const;
 
     /**
      * @brief Writes lower parameter bounds into the provided buffer
@@ -390,7 +390,7 @@ class MultiConditionDataProviderHDF5 : public MultiConditionDataProvider
      * parameters should be taken.
      * @param edata The object to be updated.
      */
-    void updateFixedSimulationParameters(int conditionIdx,
+    void updateFixedSimulationParameters(int simulationIdx,
                                          amici::ExpData& edata) const;
 
 
diff --git a/src/parpeamici/amiciSimulationRunner.cpp b/src/parpeamici/amiciSimulationRunner.cpp
index bc53c864f..0b44347f9 100644
--- a/src/parpeamici/amiciSimulationRunner.cpp
+++ b/src/parpeamici/amiciSimulationRunner.cpp
@@ -7,6 +7,11 @@
 #endif
 
 #include <utility>
+#include <vector>
+#include <string>
+#include <mutex>
+#include <cmath>
+#include <functional>
 
 // #define PARPE_SIMULATION_RUNNER_DEBUG
 
@@ -51,9 +56,9 @@ AmiciSimulationRunner::runDistributedMemory(LoadBalancerMaster* loadBalancer,
 
     // prepare and queue work package
     for (int jobIdx = 0; jobIdx < numJobsTotal; ++jobIdx) {
-        int simulationsLeft =
+        int const simulationsLeft =
           static_cast<int>(condition_indices_.size()) - numConditionsSent;
-        int simulationsCurrentPackage =
+        int const simulationsCurrentPackage =
           std::min(simulationsLeft, maxSimulationsPerPackage);
 
         auto currentConditions = std::vector<int>(
diff --git a/src/parpeamici/hierarchicalOptimizationAnalyticalParameterProvider.cpp b/src/parpeamici/hierarchicalOptimizationAnalyticalParameterProvider.cpp
index 8648c8845..94bfe6a8e 100644
--- a/src/parpeamici/hierarchicalOptimizationAnalyticalParameterProvider.cpp
+++ b/src/parpeamici/hierarchicalOptimizationAnalyticalParameterProvider.cpp
@@ -166,4 +166,4 @@ AnalyticalParameterHdf5Reader::readRawMap(H5::DataSet const& dataset,
     return rawMap;
 }
 
-}
+} // namespace parpe