Merge pull request #38584 from peterfpeterson/38332_nexus_sorted_incl…

…udes Remove clang-format suppressions
mantidproject · Jan 10, 2025 · a411fec · a411fec
2 parents f579a71 + 9c6d1b1
commit a411fec
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Showing 43 changed files with 116 additions and 255 deletions.
diff --git a/Framework/API/src/FileBackedExperimentInfo.cpp b/Framework/API/src/FileBackedExperimentInfo.cpp
@@ -6,15 +6,12 @@
 // SPDX - License - Identifier: GPL - 3.0 +
 #include "MantidAPI/FileBackedExperimentInfo.h"
 #include "MantidKernel/Logger.h"
+#include "MantidNexusCpp/NeXusException.hpp"
+#include "MantidNexusCpp/NeXusFile.hpp"
 
 #include <sstream>
 #include <utility>
 
-// clang-format off
-#include "MantidNexusCpp/NeXusFile.hpp"
-#include "MantidNexusCpp/NeXusException.hpp"
-// clang-format on
-
 namespace Mantid::API {
 
 namespace {

diff --git a/Framework/API/test/WorkspaceHistoryIOTest.h b/Framework/API/test/WorkspaceHistoryIOTest.h
@@ -203,15 +203,11 @@ class WorkspaceHistoryIOTest : public CxxTest::TestSuite {
       testHistory.addHistory(std::make_shared<AlgorithmHistory>(algHist));
     }
 
-    // clang-format off
-    auto savehandle = std::make_shared< ::NeXus::File >("WorkspaceHistoryTest_test_SaveNexus.nxs",NXACC_CREATE5);
-    // clang-format on
+    auto savehandle = std::make_shared<::NeXus::File>("WorkspaceHistoryTest_test_SaveNexus.nxs", NXACC_CREATE5);
     TS_ASSERT_THROWS_NOTHING(testHistory.saveNexus(savehandle.get()));
     savehandle->close();
 
-    // clang-format off
-    auto loadhandle = std::make_shared< ::NeXus::File >("WorkspaceHistoryTest_test_SaveNexus.nxs");
-    // clang-format on
+    auto loadhandle = std::make_shared<::NeXus::File>("WorkspaceHistoryTest_test_SaveNexus.nxs");
     std::string rootstring = "/process/";
     for (int i = 1; i < 5; i++) {
       TS_ASSERT_THROWS_NOTHING(
@@ -237,15 +233,11 @@ class WorkspaceHistoryIOTest : public CxxTest::TestSuite {
     algHist.addChildHistory(std::make_shared<AlgorithmHistory>(childHist));
     testHistory.addHistory(std::make_shared<AlgorithmHistory>(algHist));
 
-    // clang-format off
-    auto savehandle = std::make_shared< ::NeXus::File >("WorkspaceHistoryTest_test_SaveNexus.nxs",NXACC_CREATE5);
-    // clang-format on
+    auto savehandle = std::make_shared<::NeXus::File>("WorkspaceHistoryTest_test_SaveNexus.nxs", NXACC_CREATE5);
     TS_ASSERT_THROWS_NOTHING(testHistory.saveNexus(savehandle.get()));
     savehandle->close();
 
-    // clang-format off
-    auto loadhandle = std::make_shared< ::NeXus::File >("WorkspaceHistoryTest_test_SaveNexus.nxs");
-    // clang-format on
+    auto loadhandle = std::make_shared<::NeXus::File>("WorkspaceHistoryTest_test_SaveNexus.nxs");
     std::string rootstring = "/process/";
     TS_ASSERT_THROWS_NOTHING(loadhandle->openPath(rootstring + "MantidAlgorithm_1/"));
     TS_ASSERT_THROWS_NOTHING(loadhandle->openPath(rootstring + "MantidAlgorithm_1/author"));
@@ -264,15 +256,11 @@ class WorkspaceHistoryIOTest : public CxxTest::TestSuite {
   void test_SaveNexus_Empty() {
     WorkspaceHistory testHistory;
 
-    // clang-format off
-    auto savehandle = std::make_shared< ::NeXus::File >("WorkspaceHistoryTest_test_SaveNexus.nxs",NXACC_CREATE5);
-    // clang-format on
+    auto savehandle = std::make_shared<::NeXus::File>("WorkspaceHistoryTest_test_SaveNexus.nxs", NXACC_CREATE5);
     TS_ASSERT_THROWS_NOTHING(testHistory.saveNexus(savehandle.get()));
     savehandle->close();
 
-    // clang-format off
-    auto loadhandle = std::make_shared< ::NeXus::File >("WorkspaceHistoryTest_test_SaveNexus.nxs");
-    // clang-format on
+    auto loadhandle = std::make_shared<::NeXus::File>("WorkspaceHistoryTest_test_SaveNexus.nxs");
     std::string rootstring = "/process/";
     TS_ASSERT_THROWS_NOTHING(loadhandle->openPath(rootstring));
     TS_ASSERT_THROWS_NOTHING(loadhandle->openPath(rootstring + "MantidEnvironment"));
@@ -284,9 +272,7 @@ class WorkspaceHistoryIOTest : public CxxTest::TestSuite {
 
   void test_LoadNexus() {
     std::string filename = FileFinder::Instance().getFullPath("GEM38370_Focussed_Legacy.nxs");
-    // clang-format off
-    auto loadhandle = std::make_shared< ::NeXus::File >(filename);
-    // clang-format on
+    auto loadhandle = std::make_shared<::NeXus::File>(filename);
     loadhandle->openPath("/mantid_workspace_1");
 
     WorkspaceHistory emptyHistory;
@@ -306,9 +292,7 @@ class WorkspaceHistoryIOTest : public CxxTest::TestSuite {
 
   void test_LoadNexus_NestedHistory() {
     std::string filename = FileFinder::Instance().getFullPath("HistoryTest_CreateTransmissionAuto.nxs");
-    // clang-format off
-    auto loadhandle = std::make_shared< ::NeXus::File >(filename);
-    // clang-format on
+    auto loadhandle = std::make_shared<::NeXus::File>(filename);
     loadhandle->openPath("/mantid_workspace_1");
 
     WorkspaceHistory wsHistory;

diff --git a/Framework/Algorithms/test/RebinByPulseTimesTest.h b/Framework/Algorithms/test/RebinByPulseTimesTest.h
@@ -125,10 +125,8 @@ class RebinByPulseTimesTest : public CxxTest::TestSuite, public Super {
 //=====================================================================================
 // Performance Tests
 //=====================================================================================
-// clang-format off
-class RebinByPulseTimesTestPerformance : public CxxTest::TestSuite, public RebinByTimeBaseTestPerformance<RebinByPulseTimes>
-// clang-format on
-{
+class RebinByPulseTimesTestPerformance : public CxxTest::TestSuite,
+                                         public RebinByTimeBaseTestPerformance<RebinByPulseTimes> {
 
 public:
   static RebinByPulseTimesTestPerformance *createSuite() { return new RebinByPulseTimesTestPerformance(); }

diff --git a/Framework/Algorithms/test/RebinByTimeAtSampleTest.h b/Framework/Algorithms/test/RebinByTimeAtSampleTest.h
@@ -245,11 +245,8 @@ class RebinByTimeAtSampleTest : public CxxTest::TestSuite, public Super {
 //=====================================================================================
 // Performance Tests
 //=====================================================================================
-// clang-format off
-class RebinByTimeAtSampleTestPerformance: public CxxTest::TestSuite,
-    public RebinByTimeBaseTestPerformance<RebinByTimeAtSample>
-// clang-format on
-{
+class RebinByTimeAtSampleTestPerformance : public CxxTest::TestSuite,
+                                           public RebinByTimeBaseTestPerformance<RebinByTimeAtSample> {
 
 public:
   static RebinByTimeAtSampleTestPerformance *createSuite() { return new RebinByTimeAtSampleTestPerformance(); }

diff --git a/Framework/Crystal/src/AddPeakHKL.cpp b/Framework/Crystal/src/AddPeakHKL.cpp
@@ -40,9 +40,8 @@ const std::string AddPeakHKL::summary() const { return "Add a peak in the hkl fr
 void AddPeakHKL::init() {
   declareProperty(std::make_unique<WorkspaceProperty<Mantid::API::IPeaksWorkspace>>("Workspace", "", Direction::InOut),
                   "An input workspace.");
-  // clang-format off
-    declareProperty(std::make_unique<ArrayProperty<double>>("HKL", std::make_shared<ArrayLengthValidator<double> > (3)), "HKL point to add");
-  // clang-format on
+  declareProperty(std::make_unique<ArrayProperty<double>>("HKL", std::make_shared<ArrayLengthValidator<double>>(3)),
+                  "HKL point to add");
 }
 
 //----------------------------------------------------------------------------------------------

diff --git a/Framework/Crystal/src/SetUB.cpp b/Framework/Crystal/src/SetUB.cpp
@@ -38,10 +38,8 @@ void SetUB::init() {
   auto reasonableAngle = std::make_shared<BoundedValidator<double>>();
   reasonableAngle->setLower(5.0);
   reasonableAngle->setUpper(175.0);
-  // clang-format off
-  auto mustBe3D = std::make_shared<ArrayLengthValidator<double> >(3);
-  auto threeVthree = std::make_shared<ArrayLengthValidator<double> >(9);
-  // clang-format on
+  auto mustBe3D = std::make_shared<ArrayLengthValidator<double>>(3);
+  auto threeVthree = std::make_shared<ArrayLengthValidator<double>>(9);
   std::vector<double> zeroes(9, 0.), u0(3, 0), v0(3, 0);
   u0[0] = 1.;
   v0[1] = 1.;

diff --git a/Framework/Crystal/src/TransformHKL.cpp b/Framework/Crystal/src/TransformHKL.cpp
@@ -48,9 +48,7 @@ void TransformHKL::init() {
   identity_matrix[0] = 1;
   identity_matrix[4] = 1;
   identity_matrix[8] = 1;
-  // clang-format off
-  auto threeBythree = std::make_shared<ArrayLengthValidator<double> >(9);
-  // clang-format on
+  auto threeBythree = std::make_shared<ArrayLengthValidator<double>>(9);
   this->declareProperty(
       std::make_unique<ArrayProperty<double>>("HKLTransform", std::move(identity_matrix), std::move(threeBythree)),
       "Specify 3x3 HKL transform matrix as a comma separated list of 9 "

diff --git a/Framework/Crystal/test/IndexPeaksTest.h b/Framework/Crystal/test/IndexPeaksTest.h
@@ -73,16 +73,12 @@ PeaksWorkspace_sptr createTestPeaksWorkspaceMainReflOnly() {
                                   0.0045884,  0.0273738,  -0.08973560, 0.0252595};
   // peaks from TOPAZ_3007.peaks: 0, 1, 2, 10, 42 with sign for Q swapped
   // as we don't use the crystallographic convention
-  // clang-format off
-  GNU_DIAG_OFF("missing-braces")
-  // clang-format on
+  GNU_DIAG_OFF("missing-braces");
   constexpr std::array<MinimalPeak, npeaks> testPeaksInfo = {
       MinimalPeak{3008, V3D(-3.52961, 3.13589, 1.0899)}, MinimalPeak{3007, V3D(-2.42456, 2.29581, 1.71147)},
       MinimalPeak{3007, V3D(-3.04393, 3.05739, 2.03727)}, MinimalPeak{3007, V3D(-4.02271, 2.4073, 1.62228)},
       MinimalPeak{3008, V3D(-4.04552, 1.59916, 3.71776)}};
-  // clang-format off
-  GNU_DIAG_ON("missing-braces")
-  // clang-format on
+  GNU_DIAG_ON("missing-braces");
   return createPeaksWorkspace<npeaks>(testPeaksInfo, ub);
 }
 
@@ -91,19 +87,15 @@ PeaksWorkspace_sptr createTestPeaksWorkspaceWithSatellites(const int maxOrder =
                                                            const bool crossTerms = false) {
   constexpr int npeaks{5};
   const std::vector<double> ub = {0.269, -0.01, 0.033, 0.081, -0.191, -0.039, 0.279, 0.347, -0.02};
-  // clang-format off
-  GNU_DIAG_OFF("missing-braces")
-  // clang-format on
+  GNU_DIAG_OFF("missing-braces");
   constexpr std::array<MinimalPeak, npeaks> testPeaksInfo = {
       MinimalPeak{1, V3D(-3.691, -0.694, 3.762)},     // main
       MinimalPeak{2, V3D(-1.234, -0.225, 1.25212)},   // satellite
       MinimalPeak{1, V3D(-3.824, 0.728, 1.711)},      // main
       MinimalPeak{1, V3D(0.872, -0.1998, 2.7476)},    // satellite
       MinimalPeak{2, V3D(-1.54093, 0.129343, 1.445)}, // satellite
   };
-  // clang-format off
-  GNU_DIAG_ON("missing-braces")
-  // clang-format on
+  GNU_DIAG_ON("missing-braces");
   return createPeaksWorkspace<npeaks>(testPeaksInfo, ub, maxOrder, modVectors, crossTerms);
 }
 

diff --git a/Framework/Crystal/test/IntegratePeaksUsingClustersTest.h b/Framework/Crystal/test/IntegratePeaksUsingClustersTest.h
@@ -248,10 +248,7 @@ class IntegratePeaksUsingClustersTest : public CxxTest::TestSuite, public Cluste
 //=====================================================================================
 // Performance Tests
 //=====================================================================================
-// clang-format off
-class IntegratePeaksUsingClustersTestPerformance : public CxxTest::TestSuite, public ClusterIntegrationBaseTest
-// clang-format on
-{
+class IntegratePeaksUsingClustersTestPerformance : public CxxTest::TestSuite, public ClusterIntegrationBaseTest {
 
 private:
   // Input data

diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadEventNexus.h b/Framework/DataHandling/inc/MantidDataHandling/LoadEventNexus.h
@@ -23,18 +23,16 @@
 #include "MantidKernel/Exception.h"
 #include "MantidKernel/NexusHDF5Descriptor.h"
 #include "MantidKernel/OptionalBool.h"
-#include "MantidKernel/TimeSeriesProperty.h"
 
-#include <Poco/Path.h>
-#include <boost/lexical_cast.hpp>
-#include <boost/scoped_array.hpp>
+#include "MantidKernel/TimeSeriesProperty.h"
 
-// clang-format off
-#include "MantidNexusCpp/NeXusFile.hpp"
 #include "MantidNexusCpp/NeXusException.hpp"
-// clang-format on
+#include "MantidNexusCpp/NeXusFile.hpp"
 
+#include <Poco/Path.h>
 #include <algorithm>
+#include <boost/lexical_cast.hpp>
+#include <boost/scoped_array.hpp>
 #include <cstdint>
 #include <functional>
 #include <memory>
@@ -389,9 +387,9 @@ void adjustTimeOfFlightISISLegacy(::NeXus::File &file, T localWorkspace, const s
   if (classType == "NXmonitor") {
     std::vector<std::string> bankNames;
     for (string_map_t::const_iterator it = entries.begin(); it != entries.end(); ++it) {
-      std::string entryName(it->first);
-      std::string entry_class(it->second);
+      const std::string entry_class(it->second);
       if (entry_class == classType) {
+        const std::string entryName(it->first);
         bankNames.emplace_back(entryName);
       }
     }
@@ -703,17 +701,15 @@ void LoadEventNexus::loadEntryMetadata(const std::string &nexusfilename, T WS, c
     file.getDataCoerce(duration);
     if (duration.size() == 1) {
       // get the units
-      // clang-format off
-    std::vector< ::NeXus::AttrInfo> infos = file.getAttrInfos();
-    std::string units;
-    for (std::vector< ::NeXus::AttrInfo>::const_iterator it = infos.begin();
-         it != infos.end(); ++it) {
-      if (it->name == "units") {
-        units = file.getStrAttr(*it);
-        break;
+      std::vector<::NeXus::AttrInfo> infos = file.getAttrInfos();
+      std::string units;
+      for (auto it = infos.begin(); it != infos.end(); ++it) {
+        // cppcheck-suppress useStlAlgorithm
+        if (it->name == "units") {
+          units = file.getStrAttr(*it);
+          break;
+        }
       }
-    }
-      // clang-format on
 
       // set the property
       WS->mutableRun().addProperty("duration", duration[0], units, true);

diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadISISNexus2.h b/Framework/DataHandling/inc/MantidDataHandling/LoadISISNexus2.h
@@ -168,9 +168,7 @@ class MANTID_DATAHANDLING_DLL LoadISISNexus2 : public API::IFileLoader<Kernel::N
   /// Personal wrapper for sqrt to allow msvs to compile
   static double dblSqrt(double in);
   // Handle to the NeXus file
-  // clang-format off
-  boost::scoped_ptr< ::NeXus::File> m_nexusFile;
-  // clang-format on
+  boost::scoped_ptr<::NeXus::File> m_nexusFile;
 
   bool findSpectraDetRangeInFile(const NeXus::NXEntry &entry, std::vector<specnum_t> &spectrum_index, int64_t ndets,
                                  int64_t n_vms_compat_spectra, const std::map<specnum_t, std::string> &monitors,

diff --git a/Framework/DataHandling/inc/MantidDataHandling/PrecompiledHeader.h b/Framework/DataHandling/inc/MantidDataHandling/PrecompiledHeader.h
@@ -14,10 +14,8 @@
 // STL
 
 // NeXus
-// clang-format off
 #include "MantidNexusCpp/NeXusException.hpp"
 #include "MantidNexusCpp/NeXusFile.hpp"
-// clang-format on
 
 // Poco
 #include <Poco/DOM/DOMParser.h>

diff --git a/Framework/DataHandling/inc/MantidDataHandling/SaveToSNSHistogramNexus.h b/Framework/DataHandling/inc/MantidDataHandling/SaveToSNSHistogramNexus.h
@@ -14,11 +14,10 @@
 #include "MantidDataObjects/EventWorkspace.h"
 #include "MantidDataObjects/Workspace2D_fwd.h"
 #include "MantidGeometry/Instrument/RectangularDetector.h"
-#include <climits>
-// clang-format off
-#include "MantidNexusCpp/NeXusFile.hpp"
 #include "MantidNexusCpp/NeXusException.hpp"
-// clang-format on
+#include "MantidNexusCpp/NeXusFile.hpp"
+
+#include <climits>
 
 namespace Mantid {
 namespace DataHandling {

diff --git a/Framework/DataHandling/src/CreateChunkingFromInstrument.cpp b/Framework/DataHandling/src/CreateChunkingFromInstrument.cpp
@@ -15,11 +15,11 @@
 #include "MantidGeometry/IDetector.h"
 #include "MantidKernel/ListValidator.h"
 #include "MantidKernel/OptionalBool.h"
+
 #include "MantidKernel/StringTokenizer.h"
-// clang-format off
-#include "MantidNexusCpp/NeXusFile.hpp"
+
 #include "MantidNexusCpp/NeXusException.hpp"
-// clang-format on
+#include "MantidNexusCpp/NeXusFile.hpp"
 
 #include <algorithm>
 

diff --git a/Framework/DataHandling/src/CreateSimulationWorkspace.cpp b/Framework/DataHandling/src/CreateSimulationWorkspace.cpp
@@ -5,29 +5,23 @@
 //   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
 // SPDX - License - Identifier: GPL - 3.0 +
 #include "MantidDataHandling/CreateSimulationWorkspace.h"
+#include "LoadRaw/isisraw2.h"
 #include "MantidAPI/Axis.h"
 #include "MantidAPI/FileProperty.h"
 #include "MantidAPI/MatrixWorkspace.h"
 #include "MantidAPI/Run.h"
 #include "MantidAPI/WorkspaceFactory.h"
-#include "MantidDataHandling/StartAndEndTimeFromNexusFileExtractor.h"
-
 #include "MantidDataHandling/LoadRawHelper.h"
+#include "MantidDataHandling/StartAndEndTimeFromNexusFileExtractor.h"
 #include "MantidKernel/ArrayProperty.h"
 #include "MantidKernel/ListValidator.h"
 #include "MantidKernel/MandatoryValidator.h"
 #include "MantidKernel/OptionalBool.h"
 #include "MantidKernel/RebinParamsValidator.h"
 #include "MantidKernel/UnitFactory.h"
 #include "MantidKernel/VectorHelper.h"
-
-#include "LoadRaw/isisraw2.h"
-// clang-format off
-#include "MantidNexusCpp/NeXusFile.hpp"
 #include "MantidNexusCpp/NeXusException.hpp"
-// clang-format on
-
-#include <Poco/File.h>
+#include "MantidNexusCpp/NeXusFile.hpp"
 
 namespace {
 

diff --git a/Framework/DataHandling/src/DetermineChunking.cpp b/Framework/DataHandling/src/DetermineChunking.cpp
@@ -15,11 +15,8 @@
 #include "MantidDataHandling/LoadTOFRawNexus.h"
 #include "MantidKernel/BinaryFile.h"
 #include "MantidKernel/BoundedValidator.h"
-
-// clang-format off
-#include "MantidNexusCpp/NeXusFile.hpp"
 #include "MantidNexusCpp/NeXusException.hpp"
-// clang-format on
+#include "MantidNexusCpp/NeXusFile.hpp"
 
 #include <Poco/File.h>
 #include <exception>

diff --git a/Framework/DataHandling/src/LoadBankFromDiskTask.cpp b/Framework/DataHandling/src/LoadBankFromDiskTask.cpp
@@ -14,11 +14,8 @@
 #include "MantidKernel/Unit.h"
 #include "MantidKernel/VectorHelper.h"
 #include "MantidNexus/NexusIOHelper.h"
-
-// clang-format off
-#include "MantidNexusCpp/NeXusFile.hpp"
 #include "MantidNexusCpp/NeXusException.hpp"
-// clang-format on
+#include "MantidNexusCpp/NeXusFile.hpp"
 
 #include <algorithm>
 #include <utility>

diff --git a/Framework/DataHandling/src/LoadMcStasNexus.cpp b/Framework/DataHandling/src/LoadMcStasNexus.cpp
@@ -12,10 +12,8 @@
 #include "MantidAPI/WorkspaceFactory.h"
 #include "MantidAPI/WorkspaceGroup.h"
 #include "MantidKernel/Unit.h"
-// clang-format off
-#include "MantidNexusCpp/NeXusFile.hpp"
 #include "MantidNexusCpp/NeXusException.hpp"
-// clang-format on
+#include "MantidNexusCpp/NeXusFile.hpp"
 
 namespace Mantid::DataHandling {
 using namespace Kernel;