Merge remote-tracking branch 'upstream/develop' into refactor/type_tr…

…aits

.gitignore

@@ -74,3 +74,6 @@ lib/boost_*/stage/
 lib/boost_*/tools/build/*
 !lib/boost_*/tools/build/src*
 lib/boost_*/user-config.jam
+
+# clang-tidy output
+.clang-fixes.log

make/clang-tidy

@@ -0,0 +1,23 @@
+# See full list of checks here
+# https://clang.llvm.org/extra/clang-tidy/checks/list.html
+tidy_base_checks=*perf*,*modernize*,*misc*,*google*,*readability*,*optin*
+modern_excludes=,-modernize-replace-random-shuffle,-modernize-use-override,-modernize-concat-nested-namespaces,-modernize-avoid-c-arrays
+readability_excludes=,-readability-magic-numbers,-readability-convert-member-functions-to-static,-readability-inconsistent-declaration-parameter-name,-readability-function-size,-readability-named-parameter,-readability-container-size-empty,-readability-implicit-bool-conversion,-readability-else-after-return,-readability-container-size-empty
+misc_excludes=,-misc-non-private-member-variables-in-classes,-misc-unused-parameters,-misc-unused-using-decls,-misc-definitions-in-headers,-misc-unconventional-assign-operator
+google_excludes=,-google-runtime-references,-google-global-names-in-headers,-google-build-using-namespace,-google-runtime-int
+things_we_should_look_at=,-google-readability-casting,-google-explicit-constructor,-modernize-use-using,-modernize-pass-by-value,-readability-implicit-bool-conversion,-readability-const-return-type,-readability-avoid-const-params-in-decls,-modernize-return-braced-init-list,-modernize-use-using
+tidy_checks?= $(tidy_base_checks) $(modern_excludes) $(readability_excludes) $(misc_excludes) $(google_excludes) $(things_we_should_look_at)
+files?= *
+folder?= ./test/unit/*
+.PHONY: clang-tidy
+clang-tidy:
+		find $(folder) -path './test/unit/*' -wholename '*$(files).cpp' -type f | xargs -I {} clang-tidy "{}" \
+		 -checks='$(tidy_checks)' -format-style='file' -header-filter='./stan/*' \
+		 -- $(CXXFLAGS) $(LDFLAGS) $(LDLIBS) $(INC_GTEST) $(CXXFLAGS_GTEST) $(CPPFLAGS)
+
+.PHONY: clang-tidy-fix
+clang-tidy-fix:
+		find $(folder) -path './test/unit/*' -wholename '*$(files).cpp' -type f | xargs -I {} clang-tidy "{}" \
+		 -checks='$(tidy_checks)' -format-style='file' -header-filter='./stan/*' \
+		 -fix -export-fixes="./.clang-fixes.log" \
+		 -- $(CXXFLAGS) $(LDFLAGS) $(LDLIBS) $(INC_GTEST) $(CXXFLAGS_GTEST) $(CPPFLAGS)

make/test-math-dependencies

@@ -1,4 +1,4 @@
-## 
+##
 #  Function to search code for warnings.
 #
 #  After all the warnings are found, use

makefile

@@ -19,6 +19,7 @@ include make/dependencies                 # rules for generating dependencies
 include make/libraries
 include make/tests
 include make/cpplint
+include make/clang-tidy
 
 .PHONY: help
 help:
@@ -56,6 +57,22 @@ help:
 	@echo '                    To set the version of python 2, set the PYTHON2 variable:'
 	@echo '                      PYTHON2 = $(PYTHON2)'
 	@echo ''
+	@echo ' Clang Tidy'
+	@echo ' - clang-tidy     : runs the clang-tidy makefile over the test suite.'
+	@echo '                    Options:'
+	@echo '                     files: (Optional) regex for file names to include in the check'
+	@echo '                      Default runs all the tests in unit'
+	@echo '                     tidy_checks: (Optional) A set of checks'
+	@echo '                      Default runs a hand picked selection of tests'
+	@echo ''
+	@echo '     Example: This runs clang-tidy over all the multiply tests in prim'
+	@echo ''
+	@echo '     make clang-tidy files=*prim*multiply*'
+	@echo ''
+	@echo ' - clang-tidy-fix : same as above but runs with the -fix flag.'
+	@echo '                    For automated fixes, outputs a yaml named'
+	@echo '                    .clang-fixes.yml'
+	@echo ''
 	@echo 'Documentation:'
 	@echo '  Doxygen'
 	@echo '  - doxygen       : runs doxygen on source files. requires doxygen.'