Clang tidy

.clang-format

@@ -2,7 +2,7 @@ Language:        Cpp
 BasedOnStyle:  LLVM
 # AccessModifierOffset: -2
 # AlignAfterOpenBracket: Align
-# AlignConsecutiveAssignments: false
+AlignConsecutiveAssignments: true
 # AlignConsecutiveDeclarations: false
 # AlignEscapedNewlinesLeft: false
 # AlignOperands:   true
@@ -16,7 +16,7 @@ BasedOnStyle:  LLVM
 # AlwaysBreakAfterDefinitionReturnType: None
 # AlwaysBreakAfterReturnType: None
 # AlwaysBreakBeforeMultilineStrings: false
-# AlwaysBreakTemplateDeclarations: false
+AlwaysBreakTemplateDeclarations: true
 BinPackArguments: false
 BinPackParameters: false
 # BraceWrapping:   
@@ -31,10 +31,10 @@ BinPackParameters: false
 #   BeforeCatch:     false
 #   BeforeElse:      false
 #   IndentBraces:    false
-# BreakBeforeBinaryOperators: None
+BreakBeforeBinaryOperators: All
 # BreakBeforeBraces: Attach
 # BreakBeforeTernaryOperators: true
-# BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializersBeforeComma: true
 # BreakAfterJavaFieldAnnotations: false
 # BreakStringLiterals: true
 ColumnLimit:     120
@@ -53,7 +53,7 @@ IndentWidth:     4
 # IndentWrappedFunctionNames: false
 # JavaScriptQuotes: Leave
 # JavaScriptWrapImports: true
-# KeepEmptyLinesAtTheStartOfBlocks: true
+KeepEmptyLinesAtTheStartOfBlocks: false
 # MacroBlockBegin: ''
 # MacroBlockEnd:   ''
 # MaxEmptyLinesToKeep: 1
@@ -71,7 +71,7 @@ IndentWidth:     4
 # ReflowComments:  true
 SortIncludes:    false
 # SpaceAfterCStyleCast: false
-# SpaceAfterTemplateKeyword: true
+SpaceAfterTemplateKeyword: false
 # SpaceBeforeAssignmentOperators: true
 SpaceBeforeParens: Never
 # SpaceInEmptyParentheses: false

CMakeLists.txt

@@ -64,7 +64,7 @@ endif()
 
 if(CMAKE_VERSION VERSION_GREATER 3.6)
 # Add clang-tidy if available
-option(GOOFIT_TIDY_FIX "Perform fixes for Clang-Tidy (resets to OFF)" OFF)
+option(GOOFIT_TIDY_FIX "Perform fixes for Clang-Tidy - changes source inplace" OFF)
     find_program(
         CLANG_TIDY_EXE
         NAMES "clang-tidy"
@@ -305,10 +305,15 @@ endif()
 
 # Adding simple libraries
 add_subdirectory("extern/CLI11")
+mark_as_advanced(CLI_EXAMPLES CLI_SINGLE_FILE CLI_SINGLE_FILE_TESTS CLI_TESTING)
 add_subdirectory("extern/FeatureDetector")
 set_target_properties(FeatureDetector PROPERTIES FOLDER extern)
+
+## Format
 add_subdirectory("extern/fmt")
 set_target_properties(fmt PROPERTIES FOLDER extern)
+mark_as_advanced(FMT_CPPFORMAT FMT_DOC FMT_INSTALL FMT_PEDANTIC FMT_TEST FMT_USE_CPP11)
+
 
 add_library(rang INTERFACE)
 target_include_directories(rang INTERFACE "${PROJECT_SOURCE_DIR}/extern/rang/include")
@@ -486,4 +491,3 @@ if(GOOFIT_TESTS)
     add_subdirectory(tests)
 endif()
 
-set(GOOFIT_TIDY_FIX OFF CACHE BOOL "Perform fixes for Clang-Tidy (resets to OFF)" FORCE)

CONTRIBUTING.md

@@ -4,6 +4,27 @@
 
 See [adding a package](doc/ADDING_EXTERN.md).
 
+## C++
+
+You should verify that the LLVM 4.0 based requirements pass. To fix the clang-tidy requirements:
+
+```bash
+cmake -DGOOFIT_TIDY_FIX=ON ..
+make -j1
+```
+
+To run `clang-format` to correct source code spacing:
+
+```bash
+git ls-files -- '*.cu' '*.cc' '*.h' '*.cpp' | xargs clang-format -i -style=file
+```
+
+The modernize script should also not make any changes:
+
+```bash
+git ls-files -- '*.cu' '*.cc' '*.h' '*.cpp' | xargs ModernizeGoofit.py
+```
+
 ## Git
 
 GooFit is hosted as a [git](http://git-scm.com) repository on [GitHub](https://github.com).
@@ -27,6 +48,7 @@ There's no point in repeating all that info specifically for GooFit here, we do
 If you don't have time to learn about git and pull requests, we still do want your contribution to GooFit. In that case please make an issue on GitHub and link to your updated files or patches e.g. in [gists](https://gist.github.com).
 Note that this way you won't get credit for you contribution though in the commit history, so we prefer you make a GitHub pull request or ask for help in a GitHub issue on where you got stuck (fork -> clone -> branch -> edit -> commit -> push -> pull request) with making the pull request.
 
+
 ## Contact
 
 Please use [Issues](https://github.com/GooFit/GooFit/issues) for suggestions,

README.md

@@ -87,7 +87,7 @@ Advanced Options:
 * `-DGOOFIT_PYTHON=OFF`: Preliminary python bindings using [PyBind11].
 * `-DGOOFIT_MAXPAR=1800`: The maximum number of parameters to allow. May cause memory issues if too large.
 * You can enable sanitizers on non-CUDA builds with `-DSANITIZE_ADDRESS=ON`, `-DSANITIZE_MEMORY=ON`, `-DSANITIZE_THREAD=ON` or `-DSANITIZE_UNDEFINED=ON`.
-* If `clang-tidy` is available, it will automatically be used to check the source. If you set `-DGOOFIT_TIDY_FIX=ON`, fixes will be applied to the GooFit source (This must be passed on command line, will not be cached).
+* If `clang-tidy` is available, it will automatically be used to check the source. If you set `-DGOOFIT_TIDY_FIX=ON`, fixes will be applied to the GooFit source.
 
 Note for targeting Tesla P100 or any `arch=6.0` device:
 * Please use `-DGOOFIT_SEPARATE_COMP=ON` flags to compile.

docs/SYSTEM_INSTALL.md

@@ -34,7 +34,7 @@ source root-6/bin/thisroot.sh
 A truly minimal system, Alpine gives you a working Docker system under 3 MB.
 
 ```bash
-docker run -it alpine sh
+docker run -it alpine
 apk add --no-cache make cmake g++ git libexecinfo-dev
 git clone --recursive https://github.com/GooFit/GooFit.git
 cd GooFit
@@ -48,7 +48,7 @@ ctest
 In the spirit of minimality, this is less instructive and contains more magic, but also would also work:
 
 ```bash
-docker run -it alpine sh
+docker run -it alpine
 apk add --no-cache make cmake g++ git
 git clone https://github.com/GooFit/GooFit.git
 cd GooFit

examples/2d_plot/2d_plot.cu

@@ -18,16 +18,15 @@
 using namespace std;
 using namespace GooFit;
 
-int main(int argc, char** argv) {
-
+int main(int argc, char **argv) {
     GooFit::Application app("2D plot example", argc, argv);
 
     try {
         app.run();
-    } catch (const GooFit::ParseError &e) {
+    } catch(const GooFit::ParseError &e) {
         return app.exit(e);
     }
-    
+
     // In real code, use a random device here
     std::mt19937 gen(137);
     std::normal_distribution<> dx(0.2, 1.1);
@@ -50,13 +49,16 @@ int main(int argc, char** argv) {
     Variable yvar{"yvar", -5, 5};
     UnbinnedDataSet data({&xvar, &yvar});
 
-    TH2F dataHist("dataHist", "",
-                  xvar.getNumBins(), xvar.getLowerLimit(), xvar.getUpperLimit(),
-                  yvar.getNumBins(), yvar.getLowerLimit(), yvar.getUpperLimit());
-    TH1F xvarHist("xvarHist", "",
-                  xvar.getNumBins(), xvar.getLowerLimit(), xvar.getUpperLimit());
-    TH1F yvarHist("yvarHist", "",
-                  yvar.getNumBins(), yvar.getLowerLimit(), yvar.getUpperLimit());
+    TH2F dataHist("dataHist",
+                  "",
+                  xvar.getNumBins(),
+                  xvar.getLowerLimit(),
+                  xvar.getUpperLimit(),
+                  yvar.getNumBins(),
+                  yvar.getLowerLimit(),
+                  yvar.getUpperLimit());
+    TH1F xvarHist("xvarHist", "", xvar.getNumBins(), xvar.getLowerLimit(), xvar.getUpperLimit());
+    TH1F yvarHist("yvarHist", "", yvar.getNumBins(), yvar.getLowerLimit(), yvar.getUpperLimit());
 
     dataHist.SetStats(false);
     xvarHist.SetStats(false);
@@ -77,33 +79,36 @@ int main(int argc, char** argv) {
         }
     }
 
-    Variable xmean {"xmean", 0, 1, -10, 10};
-    Variable xsigm {"xsigm", 1, 0.5, 1.5};
+    Variable xmean{"xmean", 0, 1, -10, 10};
+    Variable xsigm{"xsigm", 1, 0.5, 1.5};
     GaussianPdf xgauss("xgauss", &xvar, &xmean, &xsigm);
 
     Variable ymean{"ymean", 0, 1, -10, 10};
-    Variable ysigm {"ysigm", 0.4, 0.1, 0.6};
+    Variable ysigm{"ysigm", 0.4, 0.1, 0.6};
     GaussianPdf ygauss{"ygauss", &yvar, &ymean, &ysigm};
 
     ProdPdf total("total", {&xgauss, &ygauss});
     total.setData(&data);
-    
+
     FitManager fitter(&total);
     fitter.fit();
 
-    TH2F pdfHist("pdfHist", "",
-                 xvar.getNumBins(), xvar.getLowerLimit(), xvar.getUpperLimit(),
-                 yvar.getNumBins(), yvar.getLowerLimit(), yvar.getUpperLimit());
-    TH1F xpdfHist("xpdfHist", "",
-                  xvar.getNumBins(), xvar.getLowerLimit(), xvar.getUpperLimit());
-    TH1F ypdfHist("ypdfHist", "",
-                  yvar.getNumBins(), yvar.getLowerLimit(), yvar.getUpperLimit());
+    TH2F pdfHist("pdfHist",
+                 "",
+                 xvar.getNumBins(),
+                 xvar.getLowerLimit(),
+                 xvar.getUpperLimit(),
+                 yvar.getNumBins(),
+                 yvar.getLowerLimit(),
+                 yvar.getUpperLimit());
+    TH1F xpdfHist("xpdfHist", "", xvar.getNumBins(), xvar.getLowerLimit(), xvar.getUpperLimit());
+    TH1F ypdfHist("ypdfHist", "", yvar.getNumBins(), yvar.getLowerLimit(), yvar.getUpperLimit());
 
     pdfHist.SetStats(false);
     xpdfHist.SetStats(false);
     ypdfHist.SetStats(false);
 
-    UnbinnedDataSet grid = total.makeGrid();
+    UnbinnedDataSet grid                     = total.makeGrid();
     std::vector<std::vector<double>> pdfVals = total.getCompProbsAtDataPoints();
 
     TCanvas foo;
@@ -121,23 +126,23 @@ int main(int argc, char** argv) {
     }
 
     for(int i = 0; i < xvar.getNumBins(); ++i) {
-        double val = xpdfHist.GetBinContent(i+1);
+        double val = xpdfHist.GetBinContent(i + 1);
         val /= totalPdf;
         val *= totalData;
-        xpdfHist.SetBinContent(i+1, val);
+        xpdfHist.SetBinContent(i + 1, val);
     }
 
     for(int i = 0; i < yvar.getNumBins(); ++i) {
-        double val = ypdfHist.GetBinContent(i+1);
+        double val = ypdfHist.GetBinContent(i + 1);
         val /= totalPdf;
         val *= totalData;
-        ypdfHist.SetBinContent(i+1, val);
+        ypdfHist.SetBinContent(i + 1, val);
 
         for(int j = 0; j < xvar.getNumBins(); ++j) {
-            val = pdfHist.GetBinContent(j+1, i+1);
+            val = pdfHist.GetBinContent(j + 1, i + 1);
             val /= totalPdf;
             val *= totalData;
-            pdfHist.SetBinContent(j+1, i+1, val);
+            pdfHist.SetBinContent(j + 1, i + 1, val);
         }
     }
 
@@ -146,11 +151,11 @@ int main(int argc, char** argv) {
 
     for(int i = 0; i < yvar.getNumBins(); ++i) {
         for(int j = 0; j < xvar.getNumBins(); ++j) {
-            double pval = pdfHist.GetBinContent(j+1, i+1);
-            double dval = dataHist.GetBinContent(j+1, i+1);
+            double pval = pdfHist.GetBinContent(j + 1, i + 1);
+            double dval = dataHist.GetBinContent(j + 1, i + 1);
             pval -= dval;
             pval /= std::max(1.0, sqrt(dval));
-            pdfHist.SetBinContent(j+1, i+1, pval);
+            pdfHist.SetBinContent(j + 1, i + 1, pval);
         }
     }
 
@@ -174,6 +179,5 @@ int main(int argc, char** argv) {
     ypdfHist.Draw("lsame");
     foo.SaveAs("yhist.png");
 
-
     return fitter;
 }