Merge branch 'contribution_guide' into 'master'

Contribution guide

See merge request !3

CONTRIBUTING.md

+# Topic-based branch development
+A topic branch is a short-lived branch that you create for a single focus of work.
+Generally, short-lived is less than 6 months. The work can be bug fixes, feature development or design testing.
+It is good practice to always use a branch when introducing changes.
+This allows the master to remain passing and all subsequent branches to start clean.
+
+## In pratice
+### Getting started
+After you have cloned the project
+```
+git clone git@code.ornl.gov:jap/radix radix
+Cloning into 'radix'...
+remote: Counting objects: 893, done.
+remote: Compressing objects: 100% (384/384), done.
+remote: Total 893 (delta 523), reused 852 (delta 484)
+Receiving objects: 100% (893/893), 247.71 KiB | 95.00 KiB/s, done.
+Resolving deltas: 100% (523/523), done.
+Checking connectivity... done.
+```
+Checkout and create a local branch
+```
+git checkout -b featurex
+Switched to a new branch 'contribution_guide'
+```
+You now have a local branch `contribution_guide`
+```
+git branch -l
+* contribution_guide
+  master
+```
+This branch is not in the originating repository.
+```
+git branch -r
+  origin/HEAD -> origin/master
+  origin/master
+```
+### Making the first push
+When you are ready to push your changes, you will get a fatal error about `no upstream branch`.
+```
+git push
+fatal: The current branch contribution_guide has no upstream branch.
+To push the current branch and set the remote as upstream, use
+
+    git push --set-upstream origin contribution_guide
+```
+Follow the suggested command
+```
+git push --set-upstream origin contribution_guide
+Counting objects: 6, done.
+Delta compression using up to 8 threads.
+Compressing objects: 100% (6/6), done.
+Writing objects: 100% (6/6), 1.25 KiB | 0 bytes/s, done.
+Total 6 (delta 3), reused 0 (delta 0)
+remote:
+remote: Create merge request for contribution_guide:
+remote:   https://code.ornl.gov/jap/radix/merge_requests/new?merge_request%5Bsource_branch%5D=contribution_guide
+remote:
+To git@code.ornl.gov:jap/radix
+ * [new branch]      contribution_guide -> contribution_guide
+Branch contribution_guide set up to track remote branch contribution_guide from origin.
+```
+The remote server will return a quick link for creating a merge request if one hasn't already been created for this branch.
+
+
+# Formatting
+The use of the utility [astyle](http://astyle.sourceforge.net/) makes for a quick processing of the desired format.
+From the root directory running the following command will load default options for style formatting.
+```
+astyle --options=options.astyle *.cc *.hh
+```
+# Naming convention
+## File naming
+C++ files should end in `.cc` and header files in `.hh`.
+Template implementations should end in `.i.hh`.
+**File names should be all lowercase with no underscores.**
+
+## Class naming
+Classes should be **CamelCase**.
+```
+class CommandLine
+{
+};
+```
+Class members should be prefixed with **m** and be **lazyCamelCase**.
+```
+class CommandLine
+{
+private:
+  int mArgc;
+  char ** mArgv;
+};
+```
+Class methods should be **lazyCamelCase**.
+Class member getter methods should be the members name **lazyCamelCase**  `int argc() const`.
+```
+class Commandline
+{
+private:
+  int mArgc;
+public:
+  int argc() const;
+  int myMethod() const;
+};
+```

options.astyle

+--suffix=none
+--lineend=linux
+--indent=spaces=4
+--convert-tabs
+--style=bsd
+--recursive
+--exclude=testframework
+--exclude=googletest
+--exclude=TriBITS

radixams/main.cc

@@ -50,10 +50,10 @@ int main(int argc, char **argv)
     if(std::fabs(z) > 1e-16)
     {
         sigma = 1.911515e-16 * (z * z * z * z)
-              - 9.857582e-13 * (z * z * z)
-              + 5.3399174e-9 * (z * z)
-              - 1.180686e-4  * z
-              + 1.22507;
+                - 9.857582e-13 * (z * z * z)
+                + 5.3399174e-9 * (z * z)
+                - 1.180686e-4  * z
+                + 1.22507;
     }
 
     // absorption/attenuation of gamma ray as it passes through air

radixbug/tests/tstBug.cc

@@ -10,7 +10,8 @@ TEST(radixbug, Timer)
     radix_timer_2(timer2);
     radix_timer_3(timer3);
     double value = 0;
-    auto func = [](double value)->double{
+    auto func = [](double value)->double
+    {
         return value * value;
     };
     //
@@ -29,17 +30,17 @@ TEST(radixbug, Timer)
     }
     radix_timer_stop(timer1);
     radix_timer_block(std::cout << "First Timer duration: " << timer1.duration()
-              << " nanoseconds with "
-              << timer1.intervals()
-              << " invervals" << std::endl);
+                      << " nanoseconds with "
+                      << timer1.intervals()
+                      << " invervals" << std::endl);
     radix_timer_block_2(std::cout << "Second Timer duration: " << timer2.duration()
-              << " nanoseconds with "
-              << timer2.intervals()
-              << " invervals" << std::endl);
+                        << " nanoseconds with "
+                        << timer2.intervals()
+                        << " invervals" << std::endl);
     radix_timer_block_3(std::cout << "Third Timer duration: " << timer3.duration()
-              << " nanoseconds with "
-              << timer3.intervals()
-              << " invervals" << std::endl);
+                        << " nanoseconds with "
+                        << timer3.intervals()
+                        << " invervals" << std::endl);
 
     EXPECT_EQ(timer1.intervals(), 1);
     EXPECT_EQ(timer2.intervals(), 100);

radixcommand/commandline.cc

@@ -11,10 +11,11 @@ CommandLine::CommandLine(int argc, char ** argv)
 {
     if(argc < 1) return;
     mExecutable = argv[0];
-    for (int i = 1; i < argc; i++) {
+    for (int i = 1; i < argc; i++)
+    {
         std::string temp = std::string(argv[i]);
         std::tuple<std::string, std::string, bool> data
-                = std::make_tuple("", "", false);
+            = std::make_tuple("", "", false);
         //
         // Check for '-' as first character
         //
@@ -27,13 +28,15 @@ CommandLine::CommandLine(int argc, char ** argv)
                 //
                 size_t index = temp.find('=');
                 if (index == std::string::npos)
-                {//we didn't find equal sign
+                {
+                    //we didn't find equal sign
                     //
                     // This is just a flag with empty value
                     //
                     std::get<0>(data) = std::string("");
                     mData.insert(std::make_pair(temp.substr(1), data));
-                } else
+                }
+                else
                 {
                     //
                     // We found equal sign, so we must divide into flag and value
@@ -70,10 +73,12 @@ void CommandLine::addOption(const std::string &name
         // create a new tuple with no value
         mData.insert(std::make_pair(name,
                                     std::make_tuple(std::string("")
-                                                    , description
-                                                    , required)));
-    } else
-    { // update existing entry
+                                            , description
+                                            , required)));
+    }
+    else
+    {
+        // update existing entry
         std::get<1>(it->second) = description;
         std::get<2>(it->second) = required;
     }
@@ -104,12 +109,14 @@ void CommandLine::printParsedLine(std::ostream &out) const
             if(required)
             {
                 out << "[" << it.first << "] " << value;
-            } else
+            }
+            else
             {
                 out << "<" << it.first << "> " << value;
             }
             out << " -- " << std::get<1>(it.second) << std::endl;
-        } else
+        }
+        else
         {
             out << "*" << it.first << " " << value << std::endl;
         }
@@ -121,7 +128,8 @@ void CommandLine::printParsedLine(std::ostream &out) const
         {
             out << "\t" << mArgs[i] << std::endl;
         }
-    } else
+    }
+    else
     {
         out << "No arguments." << std::endl;
     }
@@ -147,7 +155,8 @@ void CommandLine::help(std::ostream &out) const
             if(required)
             {
                 out << " [-" << it.first << "=var]";
-            } else
+            }
+            else
             {
                 out << " <-" << it.first << "<=var>>";
             }
@@ -171,7 +180,8 @@ void CommandLine::help(std::ostream &out) const
             if(required)
             {
                 out << "[" << it.first << "] ";
-            } else
+            }
+            else
             {
                 out << "<" << it.first << "> ";
             }
@@ -183,9 +193,10 @@ void CommandLine::help(std::ostream &out) const
         out << "\t" << mDeclArgs[i].first;
         if(!mDeclArgs[i].second.empty())
         {
-           out << " -- "
-              << mDeclArgs[i].second << std::endl;
-        } else
+            out << " -- "
+                << mDeclArgs[i].second << std::endl;
+        }
+        else
         {
             out << std::endl;
         }
@@ -254,16 +265,19 @@ bool CommandLine::validate(std::vector<std::string> &errors) const
         if((mDeclArgs.size() - mArgs.size())==1)
         {
             ss << " '" << mDeclArgs[mArgs.size()].first << "'";
-        } else {
+        }
+        else
+        {
             ss << "s:" << std::endl;
             for(size_t i = mArgs.size(); i < mDeclArgs.size(); ++i)
             {
                 ss << "\t'" << mDeclArgs[i].first;
                 if(!mDeclArgs[i].second.empty())
                 {
-                   ss << "' -- "
-                      << mDeclArgs[i].second << std::endl;
-                } else
+                    ss << "' -- "
+                       << mDeclArgs[i].second << std::endl;
+                }
+                else
                 {
                     ss << "'" << std::endl;
                 }
@@ -296,7 +310,8 @@ std::string CommandLine::get(const std::string& name) const
         std::stringstream ss;
         ss << "No such option: " << name;
         throw std::logic_error(ss.str());
-    } else
+    }
+    else
     {
         std::string value = std::get<0>(it->second);
         if(value.empty())

radixcommand/commandline.i.hh

@@ -17,7 +17,8 @@ return_type CommandLine::get(const std::string& name) const
         std::stringstream ss;
         ss << "No such option: " << name;
         throw std::logic_error(ss.str());
-    } else
+    }
+    else
     {
         std::string value = std::get<0>(it->second);
         if(value.empty())

radixcommand/tests/tstCommandLine.cc

@@ -22,7 +22,8 @@ TEST(radixcommand, mixed)
                           (char*)"-M=machine.txt",
                           (char*)"-load=3.4",
                           (char*)"-flag",
-                          (char*)"inputB"};
+                          (char*)"inputB"
+                         };
     CommandLine line(fake_argc, fake_argv);
     line.addOption("o"
                    , "Output filepath, whitespace must be escaped."
@@ -50,7 +51,8 @@ TEST(radixcommand, declared)
 {
     int fake_argc = 2;
     char * fake_argv[] = {(char*)("/Users/jap/build/release/dummy"),
-                          (char*)"-o=path/to a/file"};
+                          (char*)"-o=path/to a/file"
+                         };
     CommandLine line(fake_argc, fake_argv);
     line.declareArgument("input", "Path to input file.");
     line.addOption("o"
@@ -84,7 +86,8 @@ TEST(radixcommand, args)
                           (char*)"inputA",
                           (char*)"machine.txt",
                           (char*)"3.4",
-                          (char*)"input 6"};
+                          (char*)"input 6"
+                         };
 
     CommandLine line(fake_argc, fake_argv);
     std::string a0 = line.arg<std::string>(0);

radixgeometry/aabb.cc

@@ -14,24 +14,29 @@
 namespace radix
 {
 AABB::AABB(void)
-    : x0(-1), x1(1), y0(-1), y1(1), z0(-1), z1(1) {
+    : x0(-1), x1(1), y0(-1), y1(1), z0(-1), z1(1)
+{
 }
 
 AABB::AABB(const Real _x0, const Real _x1,
            const Real _y0, const Real _y1,
            const Real _z0, const Real _z1)
-    : x0(_x0), x1(_x1), y0(_y0), y1(_y1), z0(_z0), z1(_z1) {
+    : x0(_x0), x1(_x1), y0(_y0), y1(_y1), z0(_z0), z1(_z1)
+{
 }
 
 AABB::AABB(const Point3D p0, const Point3D p1)
-    : x0(p0.x), x1(p1.x), y0(p0.y), y1(p1.y), z0(p0.z), z1(p1.z) {
+    : x0(p0.x), x1(p1.x), y0(p0.y), y1(p1.y), z0(p0.z), z1(p1.z)
+{
 }
 
 AABB::AABB(const AABB& aabb)
-    : x0(aabb.x0), x1(aabb.x1), y0(aabb.y0), y1(aabb.y1), z0(aabb.z0), z1(aabb.z1) {
+    : x0(aabb.x0), x1(aabb.x1), y0(aabb.y0), y1(aabb.y1), z0(aabb.z0), z1(aabb.z1)
+{
 }
 
-AABB& AABB::operator=(const AABB& rhs) {
+AABB& AABB::operator=(const AABB& rhs)
+{
     if (this == &rhs)
         return (*this);
 
@@ -45,76 +50,102 @@ AABB& AABB::operator=(const AABB& rhs) {
     return (*this);
 }//operation=
 
-AABB::~AABB(void) {
+AABB::~AABB(void)
+{
 }
 
-bool AABB::hit(const Ray& ray, Real& t) const {
+bool AABB::hit(const Ray& ray, Real& t) const
+{
 
     Real tx_min, ty_min, tz_min;
     Real tx_max, ty_max, tz_max;
     Real t_near, t_far;
-    if( ray.d.x == 1 || ray.d.x == -1){
+    if( ray.d.x == 1 || ray.d.x == -1)
+    {
         if( ray.o.y < y0 || ray.o.y > y1 ) return false;
         if( ray.o.z < z0 || ray.o.z > z1 ) return false;
-        if( ray.d.x > 0 ){
+        if( ray.d.x > 0 )
+        {
             tx_min = (x0-ray.o.x) * ray.d.x;
             tx_max = (x1-ray.o.x) * ray.d.x;
-        }else{
+        }
+        else
+        {
             tx_min = (x1-ray.o.x) * ray.d.x;
             tx_max = (x0-ray.o.x) * ray.d.x;
         }
         if( tx_max < kEpsilon ) return false;
-        if( tx_min <= kEpsilon ){
+        if( tx_min <= kEpsilon )
+        {
             t = tx_max;
-        }else{
+        }
+        else
+        {
             t = tx_min;
         }
         return true;
     }
-    if(  ray.d.y == 1 || ray.d.y == -1){
+    if(  ray.d.y == 1 || ray.d.y == -1)
+    {
         if( ray.o.x < x0 || ray.o.x > x1 ) return false;
         if( ray.o.z < z0 || ray.o.z > z1 ) return false;
-        if( ray.d.y > 0 ){
+        if( ray.d.y > 0 )
+        {
             ty_min = (y0-ray.o.y) * ray.d.y;
             ty_max = (y1-ray.o.y) * ray.d.y;
-        }else{
+        }
+        else
+        {
             ty_min = (y1-ray.o.y) * ray.d.y;
             ty_max = (y0-ray.o.y) * ray.d.y;
         }
         if( ty_max < kEpsilon ) return false;
-        if( ty_min <= kEpsilon ){
+        if( ty_min <= kEpsilon )
+        {
             t = ty_max;
-        }else{
+        }
+        else
+        {
             t = ty_min;
         }
         return true;
     }
-    if(  ray.d.z == 1 || ray.d.z == -1 ){
+    if(  ray.d.z == 1 || ray.d.z == -1 )
+    {
         if( ray.o.y < y0 || ray.o.y > y1 ) return false;
         if( ray.o.x < x0 || ray.o.x > x1 ) return false;
-        if( ray.d.z > 0 ){
+        if( ray.d.z > 0 )
+        {
             tz_min = (z0-ray.o.z) * ray.d.z;
             tz_max = (z1-ray.o.z) * ray.d.z;
-        }else{
+        }
+        else
+        {
             tz_min = (z1-ray.o.z) * ray.d.z;
             tz_max = (z0-ray.o.z) * ray.d.z;
         }
         if( tz_max < kEpsilon ) return false;
-        if( tz_min <= kEpsilon ){
+        if( tz_min <= kEpsilon )
+        {
             t = tz_max;
-        }else{
+        }
+        else
+        {
             t = tz_min;
         }
 
         return true;
     }
     Real a = 1.0 / ray.d.x;
-    if (a >= 0) {
+    if (a >= 0)
+    {
         Real a1 = x0 - ray.o.x;
         Real a2 = x1 - ray.o.x;
         tx_min = (a1) * a;
         tx_max = (a2) * a;
-    } else {
+    }
+    else
+    {
         Real a1 = x0 - ray.o.x;
         Real a2 = x1 - ray.o.x;
         tx_min = (a2) * a;
@@ -122,12 +153,15 @@ bool AABB::hit(const Ray& ray, Real& t) const {
     }
 
     Real b = 1.0 / ray.d.y;
-    if (b >= 0) {
+    if (b >= 0)
+    {
         Real b1 = y0 - ray.o.y;
         Real b2 = y1 - ray.o.y;
         ty_min = (b1) * b;
         ty_max = (b2) * b;
-    } else {
+    }
+    else
+    {
         Real b1 = y0 - ray.o.y;
         Real b2 = y1 - ray.o.y;
         ty_min = (b2) * b;
@@ -135,12 +169,15 @@ bool AABB::hit(const Ray& ray, Real& t) const {
     }
 
     Real c = 1.0 / ray.d.z;
-    if (c >= 0) {
+    if (c >= 0)
+    {
         Real c1 = z0 - ray.o.z;
         Real c2 = z1 - ray.o.z;
         tz_min = (c1) * c;
         tz_max = (c2) * c;
-    } else {
+    }
+    else
+    {
         Real c1 = z0 - ray.o.z;
         Real c2 = z1 - ray.o.z;
         tz_min = (c2) * c;
@@ -150,35 +187,47 @@ bool AABB::hit(const Ray& ray, Real& t) const {
 
     //int face_in, face_out;
     // find the largest entering t value
-    if (tx_min > ty_min) {
+    if (tx_min > ty_min)
+    {
         t_near = tx_min;
         //face_in = (a >= 0.0) ? 0 : 3;
-    } else {
+    }
+    else
+    {
         t_near = ty_min;
         //face_in = (b >= 0.0) ? 1 : 4;
     }
 
-    if (tz_min > t_near) {
+    if (tz_min > t_near)
+    {
         t_near = tz_min;
         //face_in = (c >= 0.0) ? 2 : 5;
     }
 
     //find smallest exiting t value
-    if (tx_max < ty_max) {
+    if (tx_max < ty_max)
+    {
         t_far = tx_max;
         //face_out = (a >= 0.0) ? 3 : 0;
-    } else {
+    }
+    else
+    {
         t_far = ty_max;
         //face_out = (b >= 0.0) ? 4 : 1;
     }
-    if (tz_max < t_far) {
+    if (tz_max < t_far)
+    {
         t_far = tz_max;
         //face_out = (c >= 0.0) ? 5 : 2;
     }
-    if (t_near < t_far && t_far > kEpsilon) {
-        if (t_near > kEpsilon) {
+    if (t_near < t_far && t_far > kEpsilon)
+    {
+        if (t_near > kEpsilon)
+        {
             t = t_near;
-        }else{
+        }
+        else
+        {
             t = t_far;
         }
         return true;
@@ -186,12 +235,14 @@ bool AABB::hit(const Ray& ray, Real& t) const {
     return false;
 }//hit
 
-bool AABB::inside(const Point3D& p) const {
+bool AABB::inside(const Point3D& p) const
+{
     return ((p.x > x0 && p.x < x1)
             && (p.y > y0 && p.y < y1)
             && (p.z > z0 && p.z < z1));
 }//inside
-bool AABB::on(const Point3D& p) const {
+bool AABB::on(const Point3D& p) const
+{
     return ( ((p.x == x0 || p.x == x1)
               && (p.y >= y0 && p.y <= y1)
               && (p.z >= z0 && p.z <= z1))
@@ -202,7 +253,8 @@ bool AABB::on(const Point3D& p) const {
                  && (p.x >= x0 && p.x <= x1)
                  && (p.y >= y0 && p.y <= y1)));