--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
+ test.frameName());
for (auto referenceIt = reference.begin(); referenceIt != reference.end(); ++referenceIt)
{
- auto& energyName = referenceIt->first;
+ const auto& energyName = referenceIt->first;
SCOPED_TRACE("Comparing " + energyName + " between frames");
auto testIt = test.find(energyName);
if (testIt != test.end())
{
- auto& energyValueInReference = referenceIt->second;
- auto& energyValueInTest = testIt->second;
+ const auto& energyValueInReference = referenceIt->second;
+ const auto& energyValueInTest = testIt->second;
EXPECT_REAL_EQ_TOL(
energyValueInReference, energyValueInTest, energyTermsToCompare_.at(energyName));
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
std::string requiredEnergiesNotFound =
"Did not find the following required energies in mdrun output:\n";
- for (auto& name : namesOfRequiredEnergyTerms)
+ for (const auto& name : namesOfRequiredEnergyTerms)
{
auto possibleIndex = indicesOfEnergyTerms.find(name);
if (possibleIndex == indicesOfEnergyTerms.end())
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
auto frame = reader.frame();
auto force = frame.f();
int atom = 0;
- for (auto& f : force)
+ for (const auto& f : force)
{
std::string forceName = frame.frameName() + " F[" + toString(atom) + "]";
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
const int nsteps = 1;
const float timestep = 0.001;
- auto integrator = GetParam();
+ const auto* integrator = GetParam();
const std::string integratorName(integrator);
SCOPED_TRACE("Integrating with " + integratorName);
const std::string theMdpFile = formatString(
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#if GMX_OPENMP || defined(DOXYGEN)
//! Number of OpenMP threads for child mdrun call.
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
int g_numOpenMPThreads = 1;
#endif
//! \cond
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
GMX_TEST_OPTIONS(MdrunTestOptions, options)
{
GMX_UNUSED_VALUE(options);
mdpInputContents_ = mdpString;
}
-void SimulationRunner::useStringAsNdxFile(const char* ndxString)
+void SimulationRunner::useStringAsNdxFile(const char* ndxString) const
{
gmx::TextWriter::writeFileFromString(ndxFileName_, ndxString);
}
return callGrompp(CommandLine());
}
-int SimulationRunner::changeTprNsteps(int nsteps)
+int SimulationRunner::changeTprNsteps(int nsteps) const
{
CommandLine caller;
caller.append("convert-tpr");
return gmx::test::CommandLineTestHelper::runModuleFactory(&gmx::ConvertTprInfo::create, &caller);
}
-int SimulationRunner::callNmeig()
+int SimulationRunner::callNmeig() const
{
/* Conforming to style guide by not passing a non-const reference
to this function. Passing a non-const reference might make it
// ====
// static
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
MPI_Comm MdrunTestFixtureBase::communicator_ = MPI_COMM_NULL;
// static
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
std::unique_ptr<gmx_hw_info_t> MdrunTestFixtureBase::hwinfo_;
// static
//! Use a given string as input to grompp
void useStringAsMdpFile(const std::string& mdpString);
//! Use a string as -n input to grompp
- void useStringAsNdxFile(const char* ndxString);
+ void useStringAsNdxFile(const char* ndxString) const;
//! Use a standard .top and .g96 file as input to grompp
void useTopG96AndNdxFromDatabase(const std::string& name);
//! Use a standard .top and .gro file as input to grompp
//! Convenience wrapper for a default call to \c callGromppOnThisRank
int callGromppOnThisRank();
//! Calls nmeig for testing
- int callNmeig();
+ int callNmeig() const;
//! Calls mdrun for testing with a customized command line
int callMdrun(const CommandLine& callerRef);
/*! \brief Convenience wrapper for calling mdrun for testing
* with default command line */
int callMdrun();
//! Calls convert-tpr on this rank to set a new number of steps in the tpr.
- int changeTprNsteps(int nsteps);
+ int changeTprNsteps(int nsteps) const;
//@{
/*! \name Names for frequently used grompp and mdrun output files
~MdrunTestFixtureBase() override;
//! Communicator over which the test fixture works
+ // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static MPI_Comm communicator_;
/*! \brief Hardware information object
*
* Detected within \c communicator_ and available to re-use
* over all tests in the test case of this text fixture. */
+ // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static std::unique_ptr<gmx_hw_info_t> hwinfo_;
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
auto frame = reader.frame();
auto force = frame.f();
int atom = 0;
- for (auto& f : force)
+ for (const auto& f : force)
{
std::string forceName = frame.frameName() + " F[" + toString(atom) + "]";
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff