Assimilate PeleLMeX to look more like PeleC (#245)

PeleC build system framework added to PeleLMeX.

.clang-format

@@ -0,0 +1,94 @@
+# -*- mode: yaml -*-
+---
+Language:        Cpp
+AccessModifierOffset: -2
+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: false
+AlignEscapedNewlines: Left
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: TopLevel
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: false
+BraceWrapping:   
+  AfterClass:      true
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   true 
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     true
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 2
+ContinuationIndentWidth: 2
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeCategories: 
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|isl|json)/)'
+    Priority:        3
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '$'
+IndentCaseLabels: false
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes: false
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        2
+UseTab:          Never
+

.clang-tidy

@@ -0,0 +1,73 @@
+---
+Checks: 'bugprone-*,
+         -bugprone-easily-swappable-parameters,
+         -bugprone-implicit-widening-of-multiplication-result,
+         -bugprone-exception-escape,
+         clang-diagnostic-*,
+         clang-analyzer-*,
+         corecppguidelines-*,
+         modernize-*,
+         -modernize-avoid-c-arrays,
+         -modernize-use-trailing-return-type,
+         -modernize-use-nodiscard,
+         -modernize-macro-to-enum,
+         readability-*,
+         -readability-magic-numbers,
+         -readability-identifier-naming,
+         -readability-isolate-declaration,
+         -readability-avoid-const-params-in-decls,
+         -readability-static-accessed-through-instance,
+         -readability-identifier-length,
+         -readability-function-cognitive-complexity,
+         -readability-function-size'
+WarningsAsErrors: ''
+HeaderFilterRegex: '.*'
+AnalyzeTemporaryDtors: false
+FormatStyle:     none
+User:            user
+CheckOptions:
+  - key:             cert-dcl16-c.NewSuffixes
+    value:           'L;LL;LU;LLU'
+  - key:             cert-oop54-cpp.WarnOnlyIfThisHasSuspiciousField
+    value:           '0'
+  - key:             cert-str34-c.DiagnoseSignedUnsignedCharComparisons
+    value:           '0'
+  - key:             cppcoreguidelines-explicit-virtual-functions.IgnoreDestructors
+    value:           '1'
+  - key:             cppcoreguidelines-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic
+    value:           '1'
+  - key:             google-readability-braces-around-statements.ShortStatementLines
+    value:           '1'
+  - key:             google-readability-function-size.StatementThreshold
+    value:           '800'
+  - key:             google-readability-namespace-comments.ShortNamespaceLines
+    value:           '10'
+  - key:             google-readability-namespace-comments.SpacesBeforeComments
+    value:           '2'
+  - key:             llvm-else-after-return.WarnOnConditionVariables
+    value:           '0'
+  - key:             llvm-else-after-return.WarnOnUnfixable
+    value:           '0'
+  - key:             llvm-qualified-auto.AddConstToQualified
+    value:           '0'
+  - key:             modernize-loop-convert.MaxCopySize
+    value:           '16'
+  - key:             modernize-loop-convert.MinConfidence
+    value:           reasonable
+  - key:             modernize-loop-convert.NamingStyle
+    value:           CamelCase
+  - key:             modernize-pass-by-value.IncludeStyle
+    value:           llvm
+  - key:             modernize-replace-auto-ptr.IncludeStyle
+    value:           llvm
+  - key:             modernize-use-nullptr.NullMacros
+    value:           'NULL'
+  - { key: readability-identifier-naming.NamespaceCase,       value: lower_case }
+  - { key: readability-identifier-naming.ClassCase,           value: CamelCase  }
+  - { key: readability-identifier-naming.PrivateMemberPrefix, value: m_         }
+  - { key: readability-identifier-naming.ProtectedMemberPrefix, value: m_         }
+  - { key: readability-identifier-naming.StructCase,          value: CamelCase  }
+  - { key: readability-identifier-naming.FunctionCase,        value: lower_case }
+  - { key: readability-identifier-naming.VariableCase,        value: lower_case }
+  - { key: readability-identifier-naming.GlobalConstantCase,  value: UPPER_CASE }
+...

.github/codeql/codeql-config.yml

@@ -0,0 +1,6 @@
+name: "PeleLMeX CodeQL config"
+
+query-filters:
+  - exclude:
+      id: cpp/poorly-documented-function
+

.github/problem-matchers/cppcheck.json

@@ -0,0 +1,18 @@
+{
+     "__comment": "Modified from vscode-cpptools's Extension/package.json gcc rule",
+     "problemMatcher": [
+         {
+             "owner": "cppcheck-problem-matcher",
+             "pattern": [
+                 {
+                     "regexp": "^(.*):(\\d+):(\\d+):\\s+(?:fatal\\s+)?(error|performance|portability|style|warning):\\s+(.*)$",
+                     "file": 1,
+                     "line": 2,
+                     "column": 3,
+                     "severity": 4,
+                     "message": 5
+                 }
+             ]
+         }
+     ]
+} 

.github/problem-matchers/gcc.json

@@ -0,0 +1,18 @@
+{
+     "__comment": "Taken from vscode-cpptools's Extension/package.json gcc rule",
+     "problemMatcher": [
+         {
+             "owner": "gcc-problem-matcher",
+             "pattern": [
+                 {
+                     "regexp": "^(.*):(\\d+):(\\d+):\\s+(?:fatal\\s+)?(warning|error):\\s+(.*)$",
+                     "file": 1,
+                     "line": 2,
+                     "column": 3,
+                     "severity": 4,
+                     "message": 5
+                 }
+             ]
+         }
+     ]
+} 

.github/problem-matchers/sphinx.json

@@ -37,4 +37,4 @@
              ]           
          }
      ]
-}
+}