Applying clang-format to all packages.

radixalgorithm/ordering.cc

@@ -2,11 +2,9 @@
 
 #include <iostream>
 
-namespace radix
-{
-void super_sad_necessary_hack_for_dll_lib_creation::foo_method()
-{
-    std::cout << "This is a dummy method for compilation symbol" << std::endl;
+namespace radix {
+void super_sad_necessary_hack_for_dll_lib_creation::foo_method() {
+  std::cout << "This is a dummy method for compilation symbol" << std::endl;
 }
 
-} // namespace radix
+}  // namespace radix

radixalgorithm/ordering.hh

-#include <vector>
-#include <numeric>
-#include <utility> // swap
 #include <algorithm>
+#include <numeric>
 #include <radixbug/bug.hh>
+#include <utility>  // swap
+#include <vector>
 #include "radixdl/visibility.hh"
 
-namespace radix
-{
+namespace radix {
 
-struct RADIX_PUBLIC super_sad_necessary_hack_for_dll_lib_creation
-{
-    void foo_method();
+struct RADIX_PUBLIC super_sad_necessary_hack_for_dll_lib_creation {
+  void foo_method();
 };
 
-template<typename list_type
-         , typename compare_type>
-RADIX_PUBLIC std::vector<size_t> sort_permutation(const list_type& data
-                                    , compare_type& comparator)
-{
-    // create list of indices the size of the incoming data
-    std::vector<std::size_t> order(data.size());
-    // initialize list with initial index, starting at zero
-    std::iota(order.begin(), order.end(), 0);
-
-    // order ordering according to comparator
-    std::sort(order.begin(), order.end(),
-              [&](std::size_t data_i, std::size_t data_j)
-              {
-                 radix_line("Comparing [" << data_i
-                            << ", " << data_j << "]");
-                 return comparator(data[data_i], data[data_j]);
-              });
-    return order;
-} // sort_permutation
+template <typename list_type, typename compare_type>
+RADIX_PUBLIC std::vector<size_t> sort_permutation(const list_type &data,
+                                                  compare_type &comparator) {
+  // create list of indices the size of the incoming data
+  std::vector<std::size_t> order(data.size());
+  // initialize list with initial index, starting at zero
+  std::iota(order.begin(), order.end(), 0);
 
+  // order ordering according to comparator
+  std::sort(order.begin(), order.end(),
+            [&](std::size_t data_i, std::size_t data_j) {
+              radix_line("Comparing [" << data_i << ", " << data_j << "]");
+              return comparator(data[data_i], data[data_j]);
+            });
+  return order;
+}  // sort_permutation
 
 template <typename list_type>
-RADIX_PUBLIC void apply_permutation(list_type& data
-                      , const std::vector<size_t>& order)
-{
-    std::vector<bool> done(data.size(), false);
-    for (size_t i = 0; i < data.size(); ++i)
-    {
-        if (done[i]) continue;
-        done[i] = true;
-        // previous ordering is that of the loop, so index i it is
-        size_t prev_j = i;
-        // get the new order lookup
-        size_t j = order[i];
-        //
-        while(i != j)
-        {
-            radix_line( i << ". swapping " << prev_j << " for " << j);
-            std::swap(data[prev_j], data[j]);
-            done[j] = true;
-            prev_j = j;
-            j = order[j];
-        }
+RADIX_PUBLIC void apply_permutation(list_type &data,
+                                    const std::vector<size_t> &order) {
+  std::vector<bool> done(data.size(), false);
+  for (size_t i = 0; i < data.size(); ++i) {
+    if (done[i]) continue;
+    done[i] = true;
+    // previous ordering is that of the loop, so index i it is
+    size_t prev_j = i;
+    // get the new order lookup
+    size_t j = order[i];
+    //
+    while (i != j) {
+      radix_line(i << ". swapping " << prev_j << " for " << j);
+      std::swap(data[prev_j], data[j]);
+      done[j] = true;
+      prev_j  = j;
+      j       = order[j];
     }
-} // apply_permutation
-} // namespace radix
+  }
+}  // apply_permutation
+}  // namespace radix

radixalgorithm/tests/tstOrdering.cc

 #include <iostream>
 #include "gtest/gtest.h"
 
-#include "radixbug/bug.hh"
 #include "radixalgorithm/ordering.hh"
+#include "radixbug/bug.hh"
 
-TEST(radixalgorithm, Ordering)
-{
-
-    std::vector<double> list {2.0, 1.0, 3.0, 4.0, 5.0, 0.0, 10.0};
-    // permutation              5,   1,   0,   2,   3,   4,    6
-    // correct ordering
-    std::vector<int> list2   {  0,   1,   2,   3,   4,   5,    6};
-    auto comparator = [](double a, double b)
-    {
-        radix_line("\t[" << a << "," << b << "]");
-        return a<b;
-    };
-    std::vector<size_t> permutation = radix::sort_permutation(list, comparator);
-    // test edges
-    EXPECT_EQ(permutation[0], 5);
-    EXPECT_EQ(permutation[6], 6);
-    std::cout << "Ordering:" << std::endl;
-    for(size_t i = 0; i < permutation.size(); ++i)
-    {
-        std::cout << "index " << i << ". (" << list[i]
-                     << ") recieves value from "
-                     << permutation[i]
-                     << " (" << list[permutation[i]] << ")"
-                     << std::endl;
-    }
-    //
-    // sort list given the
-    radix::apply_permutation(list, permutation);
-    EXPECT_DOUBLE_EQ(list[0], 0.0);
-    EXPECT_DOUBLE_EQ(list[6], 10.0);
-    radix::apply_permutation(list2, permutation);
-    EXPECT_EQ(list2[0], 5);
-    EXPECT_EQ(list2[6], 6);
-    for(size_t i = 0; i < list.size(); ++i)
-    {
-        std::cout << "[" << list[i] << "," << list2[i] << "]" << std::endl;
-    }
+TEST(radixalgorithm, Ordering) {
+  std::vector<double> list{2.0, 1.0, 3.0, 4.0, 5.0, 0.0, 10.0};
+  // permutation              5,   1,   0,   2,   3,   4,    6
+  // correct ordering
+  std::vector<int> list2{0, 1, 2, 3, 4, 5, 6};
+  auto comparator = [](double a, double b) {
+    radix_line("\t[" << a << "," << b << "]");
+    return a < b;
+  };
+  std::vector<size_t> permutation = radix::sort_permutation(list, comparator);
+  // test edges
+  EXPECT_EQ(permutation[0], 5);
+  EXPECT_EQ(permutation[6], 6);
+  std::cout << "Ordering:" << std::endl;
+  for (size_t i = 0; i < permutation.size(); ++i) {
+    std::cout << "index " << i << ". (" << list[i] << ") recieves value from "
+              << permutation[i] << " (" << list[permutation[i]] << ")"
+              << std::endl;
+  }
+  //
+  // sort list given the
+  radix::apply_permutation(list, permutation);
+  EXPECT_DOUBLE_EQ(list[0], 0.0);
+  EXPECT_DOUBLE_EQ(list[6], 10.0);
+  radix::apply_permutation(list2, permutation);
+  EXPECT_EQ(list2[0], 5);
+  EXPECT_EQ(list2[6], 6);
+  for (size_t i = 0; i < list.size(); ++i) {
+    std::cout << "[" << list[i] << "," << list2[i] << "]" << std::endl;
+  }
 }

radixams/main.cc

@@ -8,87 +8,77 @@
 
 #include <cmath>
 
-
 using namespace radix;
-int main(int argc, char **argv)
-{
-    CommandLine command(argc, argv);
-    command.declareArgument("altitude"
-                            , "Altitude at which to calcuate dose rate (0 for sea level) in m");
-    command.declareArgument("activity"
-                            , "Activity of the area in Ci/m^2");
-    command.declareArgument("energy"
-                            , "Gamma ray energy in MeV");
-
-    // expecting three arguments
-    if(!command.validate(std::cerr))
-    {
-        command.help(std::cerr);
-        return 0;
-    }
-
-    // altitude above sea level - default to 0
-    double z = 0.0;
-    z = command.arg<double>(0);
-
-    // activity in Ci/m^2 of the area of interest - default to 1.767e3
-    double a = 1.767e3;
-    a = command.arg<double>(1);
-
-    // gamma-ray energy in MeV - default to 7e-1
-    double e = 7e-1;
-    e = command.arg<double>(2);
-
-    // radius of area of interest (assumed to be altitude), distance
-//    double r = z;
-//    double s = std::sqrt(z*z + r*r);
-
-    // sigma scalar; constant at sea level
-    double sigma = 1.225;
-
-    // not at sea level, update sigma
-    if(std::fabs(z) > 1e-16)
-    {
-        sigma = 1.911515e-16 * (z * z * z * z)
-                - 9.857582e-13 * (z * z * z)
-                + 5.399174e-9 * (z * z)
-                - 1.180686e-4  * z
-                + 1.22507;
-    }
-
-    // absorption/attenuation of gamma ray as it passes through air
-//    auto mua = radix::gammaRayAbsorptionInAir(e);
-    auto mut = radix::gammaRayAttenuationInAir(e);
-
-    // mu scalars
-    auto mutg = mut * 1.225;
-//    auto muag = -mua * 1.225;
-    auto mutz = mut * sigma;
-//    auto muaz = -mua * sigma;
-
-    // exponential integral values and their ratio
-    auto EIg = 1.0 / radix::exponentialIntegral(mutg);
-    auto EIz = 1.0 / radix::exponentialIntegral(mutz * z);
-    auto EIRatio = EIz / EIg;
-
-    // dose rate at sea level/altitude
-    auto DRg = 9.62 * a;
-    auto DRz = DRg * EIRatio;
-
-    // report dose rate at sea level
-    if(std::fabs(z) < 1e-16)
-    {
-        std::cout << std::scientific << DRg
-                  << " is the Dose Rate at Ground Sea Level in R/hr"
-                  << std::endl;
-    }
-    // report dose rate at altitude above sea level
-    else
-    {
-        std::cout << std::scientific << DRz
-                  << " is the Dose Rate at your Altitude above Ground Sea Level in R/hr"
-                  << std::endl;
-    }
-
+int main(int argc, char **argv) {
+  CommandLine command(argc, argv);
+  command.declareArgument(
+      "altitude",
+      "Altitude at which to calcuate dose rate (0 for sea level) in m");
+  command.declareArgument("activity", "Activity of the area in Ci/m^2");
+  command.declareArgument("energy", "Gamma ray energy in MeV");
+
+  // expecting three arguments
+  if (!command.validate(std::cerr)) {
+    command.help(std::cerr);
     return 0;
+  }
+
+  // altitude above sea level - default to 0
+  double z = 0.0;
+  z        = command.arg<double>(0);
+
+  // activity in Ci/m^2 of the area of interest - default to 1.767e3
+  double a = 1.767e3;
+  a        = command.arg<double>(1);
+
+  // gamma-ray energy in MeV - default to 7e-1
+  double e = 7e-1;
+  e        = command.arg<double>(2);
+
+  // radius of area of interest (assumed to be altitude), distance
+  //    double r = z;
+  //    double s = std::sqrt(z*z + r*r);
+
+  // sigma scalar; constant at sea level
+  double sigma = 1.225;
+
+  // not at sea level, update sigma
+  if (std::fabs(z) > 1e-16) {
+    sigma = 1.911515e-16 * (z * z * z * z) - 9.857582e-13 * (z * z * z) +
+            5.399174e-9 * (z * z) - 1.180686e-4 * z + 1.22507;
+  }
+
+  // absorption/attenuation of gamma ray as it passes through air
+  //    auto mua = radix::gammaRayAbsorptionInAir(e);
+  auto mut = radix::gammaRayAttenuationInAir(e);
+
+  // mu scalars
+  auto mutg = mut * 1.225;
+  //    auto muag = -mua * 1.225;
+  auto mutz = mut * sigma;
+  //    auto muaz = -mua * sigma;
+
+  // exponential integral values and their ratio
+  auto EIg     = 1.0 / radix::exponentialIntegral(mutg);
+  auto EIz     = 1.0 / radix::exponentialIntegral(mutz * z);
+  auto EIRatio = EIz / EIg;
+
+  // dose rate at sea level/altitude
+  auto DRg = 9.62 * a;
+  auto DRz = DRg * EIRatio;
+
+  // report dose rate at sea level
+  if (std::fabs(z) < 1e-16) {
+    std::cout << std::scientific << DRg
+              << " is the Dose Rate at Ground Sea Level in R/hr" << std::endl;
+  }
+  // report dose rate at altitude above sea level
+  else {
+    std::cout
+        << std::scientific << DRz
+        << " is the Dose Rate at your Altitude above Ground Sea Level in R/hr"
+        << std::endl;
+  }
+
+  return 0;
 }

radixbug/bug.hh

@@ -20,32 +20,45 @@
  *
  * Available MACROs:
  * radix(arg) - std::cerr << arg - Pushes content to stderr
- * radix_line(arg) - std::cerr << arg << std::endl - Push newline terminated content to stderr
- * radix(arg) - std::cerr << arg - Pushes content to stderr
- * radix_warning(arg) - std::cerr << arg << std::endl - Push newline terminated content to stderr
- * radix_tagged_line(arg) - Same as radixLine, prefixed with FILE and LINE
- * radix_tagged(arg) - Same as radix, prefixed with FILE and LINE
+ * radix_line(arg) - std::cerr << arg << std::endl - Push newline terminated
+ * content to stderr radix(arg) - std::cerr << arg - Pushes content to stderr
+ * radix_warning(arg) - std::cerr << arg << std::endl - Push newline terminated
+ * content to stderr radix_tagged_line(arg) - Same as radixLine, prefixed with
+ * FILE and LINE radix_tagged(arg) - Same as radix, prefixed with FILE and LINE
  * radix_tagged_warning(arg) - Same as radixWarning, prefixed with FILE and Line
  * radix_block(block) - block - Simply places code block in preprocessor
  */
-#include <iostream>
 #include <cstdio>
+#include <iostream>
 #if DEBUG_OUTPUT & 1
 #ifndef radix_stream
 #define radix_stream std::cerr
 #endif
 #define radix_define_stream
 #define radix_line(arg) radix_stream << arg << std::endl
-#define radix_flush_line(arg) radix_stream << arg << std::endl;fflush(stderr)
+#define radix_flush_line(arg)       \
+  radix_stream << arg << std::endl; \
+  fflush(stderr)
 #define radix(arg) radix_stream << arg
 #define radix_warning(arg) radix_stream << arg << std::endl
-#define radix_tagged_warning(arg) radix_stream << __FILE__ << ":" << __LINE__ << ": " << arg << std::endl
-#define radix_flush_warning(arg) radix_stream << arg << std::endl;fflush(stderr)
-#define radix_tagged_line(arg) radix_stream << __FILE__ << ":" << __LINE__ << ": " << arg << std::endl
-#define radix_flush_tagged_line(arg) radix_stream << __FILE__ << ":" << __LINE__ << ": " << arg << std::endl;fflush(stderr)
-#define radix_tagged(arg) radix_stream << __FILE__ << ":" << __LINE__ << ": "  << arg
-#define radix_flush_tagged_warning(arg) radix_stream << __FILE__ << ":" << __LINE__ << ": " << arg << std::endl;fflush(stderr)
-#define radix_tagged_block(block) radix_stream << __FILE__ << ":" << __LINE__ << ":" << std::endl; block
+#define radix_tagged_warning(arg) \
+  radix_stream << __FILE__ << ":" << __LINE__ << ": " << arg << std::endl
+#define radix_flush_warning(arg)    \
+  radix_stream << arg << std::endl; \
+  fflush(stderr)
+#define radix_tagged_line(arg) \
+  radix_stream << __FILE__ << ":" << __LINE__ << ": " << arg << std::endl
+#define radix_flush_tagged_line(arg)                                       \
+  radix_stream << __FILE__ << ":" << __LINE__ << ": " << arg << std::endl; \
+  fflush(stderr)
+#define radix_tagged(arg) \
+  radix_stream << __FILE__ << ":" << __LINE__ << ": " << arg
+#define radix_flush_tagged_warning(arg)                                    \
+  radix_stream << __FILE__ << ":" << __LINE__ << ": " << arg << std::endl; \
+  fflush(stderr)
+#define radix_tagged_block(block)                                  \
+  radix_stream << __FILE__ << ":" << __LINE__ << ":" << std::endl; \
+  block
 #define radix_block(block) block
 #else
 #define radix(arg)
@@ -62,8 +75,8 @@
 #define radix_block(block)
 #endif /* DEBUG_OUTPUT */
 
-#include <stdexcept>
 #include <sstream>
+#include <stdexcept>
 #ifndef RADIX_DBC
 #define RADIX_DBC 0
 #endif
@@ -76,42 +89,49 @@
 // RADIX_DBC = 7 enables all
 // Insist is always enabled
 #if RADIX_DBC & 1
-#define radix_require(c)  if(!(c)) {\
-    std::ostringstream stream; \
-    stream << __FILE__ << ":" \
-    << __LINE__ << " radix_require("<< #c << ") failed." << std::endl; \
-    throw std::runtime_error(stream.str()); }
+#define radix_require(c)                                             \
+  if (!(c)) {                                                        \
+    std::ostringstream stream;                                       \
+    stream << __FILE__ << ":" << __LINE__ << " radix_require(" << #c \
+           << ") failed." << std::endl;                              \
+    throw std::runtime_error(stream.str());                          \
+  }
 #else
 #define radix_require(c)
 #endif
 #if RADIX_DBC & 2
-#define radix_check(c)  if(!(c)) {\
-    std::ostringstream stream; \
-    stream << __FILE__ << ":" \
-    << __LINE__ << " radix_check("<< #c << ") failed." << std::endl; \
-    throw std::runtime_error(stream.str()); }
+#define radix_check(c)                                             \
+  if (!(c)) {                                                      \
+    std::ostringstream stream;                                     \
+    stream << __FILE__ << ":" << __LINE__ << " radix_check(" << #c \
+           << ") failed." << std::endl;                            \
+    throw std::runtime_error(stream.str());                        \
+  }
 #else
 #define radix_check(c)
 #endif
 #if RADIX_DBC & 4
-#define radix_ensure(c) if(!(c)) {\
-    std::ostringstream stream; \
-    stream << __FILE__ << ":" \
-    << __LINE__ << " radix_ensure("<< #c << ") failed." << std::endl; \
-    throw std::runtime_error(stream.str()); }
+#define radix_ensure(c)                                             \
+  if (!(c)) {                                                       \
+    std::ostringstream stream;                                      \
+    stream << __FILE__ << ":" << __LINE__ << " radix_ensure(" << #c \
+           << ") failed." << std::endl;                             \
+    throw std::runtime_error(stream.str());                         \
+  }
 #define radix_remember(c) c
 #else
 #define radix_ensure(c)
 #define radix_remember(c)
 #endif
 
-#define radix_insist(c, msg) if(!(c)) { \
-    std::ostringstream stream; \
-    stream << __FILE__ << ":" \
-    << __LINE__ << "radix_insist("<< #c \
-    << ") failed with this message:" \
-    << std::endl << msg << std::endl; \
-    throw std::runtime_error(stream.str()); }
+#define radix_insist(c, msg)                                       \
+  if (!(c)) {                                                      \
+    std::ostringstream stream;                                     \
+    stream << __FILE__ << ":" << __LINE__ << "radix_insist(" << #c \
+           << ") failed with this message:" << std::endl           \
+           << msg << std::endl;                                    \
+    throw std::runtime_error(stream.str());                        \
+  }
 
 /// set default timing to off
 #ifndef RADIX_TIMING
@@ -120,48 +140,38 @@
 
 #include <chrono>
 #include <ctime>
-namespace radix
-{
-class Timer
-{
-private:
-    bool mRunning;
-    std::chrono::steady_clock::time_point mStart;
-    std::chrono::steady_clock::time_point mEnd;
-    std::chrono::nanoseconds mDuration;
-    size_t mIntervals;
-public:
-    Timer()
-        : mRunning(false)
-        , mDuration(0)
-        , mIntervals(0)
-    {}
-    void start()
-    {
-        radix_check(!mRunning);
-        mRunning = true;
-        mIntervals++;
-        mStart = std::chrono::steady_clock::now();
-    }
-    void stop()
-    {
-        radix_check(mRunning);
-        mEnd = std::chrono::steady_clock::now();
-        mRunning = false;
-        mDuration += std::chrono::duration_cast<std::chrono::nanoseconds>(mEnd-mStart);
-    }
+namespace radix {
+class Timer {
+ private:
+  bool mRunning;
+  std::chrono::steady_clock::time_point mStart;
+  std::chrono::steady_clock::time_point mEnd;
+  std::chrono::nanoseconds mDuration;
+  size_t mIntervals;
+
+ public:
+  Timer() : mRunning(false), mDuration(0), mIntervals(0) {}
+  void start() {
+    radix_check(!mRunning);
+    mRunning = true;
+    mIntervals++;
+    mStart = std::chrono::steady_clock::now();
+  }
+  void stop() {
+    radix_check(mRunning);
+    mEnd     = std::chrono::steady_clock::now();
+    mRunning = false;
+    mDuration +=
+        std::chrono::duration_cast<std::chrono::nanoseconds>(mEnd - mStart);
+  }
 
-    double duration() const
-    {
-        radix_check(!mRunning);
-        return mDuration.count();
-    }
-    size_t intervals() const
-    {
-        return mIntervals;
-    }
-}; // class Timer
-} // namespace radix
+  double duration() const {
+    radix_check(!mRunning);
+    return mDuration.count();
+  }
+  size_t intervals() const { return mIntervals; }
+};  // class Timer
+}  // namespace radix
 
 #if RADIX_TIMING > 0
 #define radix_timer(name) radix::Timer name
@@ -198,5 +208,4 @@ public:
 #define radix_timer_block_3(content)
 #endif
 
-#endif  /* RADIX_RADIXBUG_BUG_HH_*/
-
+#endif /* RADIX_RADIXBUG_BUG_HH_*/

radixbug/tests/tstBug.cc

@@ -4,49 +4,41 @@
 #define RADIX_TIMING 3
 #include "radixbug/bug.hh"
 
-TEST(radixbug, Timer)
-{
-    radix_timer(timer1);
-    radix_timer_2(timer2);
-    radix_timer_3(timer3);
-    double value = 0;
-    auto func = [](double value)->double
-    {
-        return value * value;
-    };
-    //
-    // demostrate timing metrics
-    radix_timer_start(timer1);
-    for(size_t i = 0; i < 100; ++i)
-    {
-        radix_timer_start_2(timer2);
-        for(size_t j = 0; j < 10000; ++j)
-        {
-            radix_timer_start_3(timer3);
-            value = value + func(value);
-            radix_timer_stop_3(timer3);
-        }
-        radix_timer_stop_2(timer2);
+TEST(radixbug, Timer) {
+  radix_timer(timer1);
+  radix_timer_2(timer2);
+  radix_timer_3(timer3);
+  double value = 0;
+  auto func    = [](double value) -> double { return value * value; };
+  //
+  // demostrate timing metrics
+  radix_timer_start(timer1);