Code Formatting

Adopt clang-format and styler for C++ / R code formatting

- Reformat C++ code using clang-format
- Reformat R code using styler
- Add Travis checks that code is well formatted

  Run clang-format and styler on code and use git to
  check for differences. If any are found, fail the build
- Minor typo corrections

Note that we are not attempting to reformat in the repo: the dev is still required to make sure the code is well formatted before submitting, but this should simplify reviews of future PRs.

.clang-format

@@ -0,0 +1,150 @@
+# Defines the ANGLE style for automatic reformatting.
+# https://code.google.com/p/angleproject/wiki/CodingStandard
+# See Clang docs: http://clang.llvm.org/docs/ClangFormatStyleOptions.html
+Language:        Cpp
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Left
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Inline
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: true
+BinPackParameters: false
+BraceWrapping:   
+  AfterClass:      true
+  AfterControlStatement: true
+  AfterEnum:       true
+  AfterFunction:   true
+  AfterNamespace:  true
+  AfterObjCDeclaration: false
+  AfterStruct:     true
+  AfterUnion:      true
+  AfterExternBlock: false
+  BeforeCatch:     true
+  BeforeElse:      true
+  IndentBraces:    false
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     100
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:   
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Preserve
+IncludeCategories: 
+  - Regex:           '^<ext/.*\.h>'
+    Priority:        2
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentPPDirectives: AfterHash
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Never
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Right
+RawStringFormats: 
+  - Language:        Cpp
+    Delimiters:      
+      - cc
+      - CC
+      - cpp
+      - Cpp
+      - CPP
+      - 'c++'
+      - 'C++'
+    CanonicalDelimiter: ''
+    BasedOnStyle:    google
+  - Language:        TextProto
+    Delimiters:      
+      - pb
+      - PB
+      - proto
+      - PROTO
+    EnclosingFunctions: 
+      - EqualsProto
+      - EquivToProto
+      - PARSE_PARTIAL_TEXT_PROTO
+      - PARSE_TEST_PROTO
+      - PARSE_TEXT_PROTO
+      - ParseTextOrDie
+      - ParseTextProtoOrDie
+    CanonicalDelimiter: ''
+    BasedOnStyle:    google
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+StatementMacros: 
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        8
+UseTab:          Never

.gitignore

@@ -45,3 +45,4 @@ figs/*
 # visualization plots
 tests/testthat/*.pdf
 .vscode/settings.json
+myformat.sh

.travis.yml

@@ -11,6 +11,18 @@ os:
 # Modified from github.com/jeroen/jsonlite
 osx_image: xcode9
 
+addons:
+  apt:
+    sources:
+      # PPA for clang 6.0
+      - llvm-toolchain-trusty-6.0
+      # PPA for clang-format 8
+      - llvm-toolchain-trusty
+      # PPA for a more recen libstdc++
+      - ubuntu-toolchain-r-test
+    packages:
+      - clang-format
+
 r_packages:
   - Rcpp
   - RcppArmadillo
@@ -20,6 +32,7 @@ r_packages:
   - covr
 
 before_install:
+  - bash script/format_check.sh || travis_terminate 1;
   - Rscript -e "source('build_steps.R'); before_install()"
 
 after_success:

R/internals.R

@@ -1,11 +1,11 @@
 #' @importFrom utils packageDescription
-moma_git_hash <- function(){
+moma_git_hash <- function() {
     pd <- packageDescription("moma")
-    gh_file <- system.file("GIT.HASH", package="moma")
+    gh_file <- system.file("GIT.HASH", package = "moma")
 
-    if(!is.null(pd$RemoteSha)){ # devtools install
+    if (!is.null(pd$RemoteSha)) { # devtools install
         return(pd$RemoteSha)
-    } else if(file.exists(gh_file)){
+    } else if (file.exists(gh_file)) {
         return(readLines(gh_file))
     } else {
         NA
@@ -22,18 +22,17 @@ moma_git_hash <- function(){
 #'        only.
 #' @export
 #' @importFrom utils sessionInfo
-moma_session_info <- function(){
-    old_print <- options(max.print=9999)
+moma_session_info <- function() {
+    old_print <- options(max.print = 9999)
     on.exit(options(old_print))
 
     cat("MoMA Git Hash: ", moma_git_hash(), "\n")
 
-    if(requireNamespace("devtools")){
+    if (requireNamespace("devtools")) {
         print(devtools::session_info("moma"))
     } else {
         print(sessionInfo())
     }
 
     invisible(NULL)
 }
-

R/logging.R

@@ -1,11 +1,13 @@
 # Logging infrastructure for MoMA
 
 ## This must be kept consistent with src/moma_logging.h::MoMAoggerLevel
-LEVELS <- c(ERROR    = 40,
-            WARNING  = 30,
-            MESSAGE  = 20,
-            INFO     = 10,
-            DEBUG    = 00)
+LEVELS <- c(
+    ERROR = 40,
+    WARNING = 30,
+    MESSAGE = 20,
+    INFO = 10,
+    DEBUG = 00
+)
 
 
 #' MoMA Package Logging Functionality
@@ -34,67 +36,68 @@ LEVELS <- c(ERROR    = 40,
 #'     \code{moma_logger_level} function can be used to adjust the global
 #'     log level. The \code{INFO} and \code{DEBUG} levels can be quite verbose
 #'     and may significantly slow down the package.
-moma_logger_level <- function(level=c("ERROR",
-                                      "WARNING",
-                                      "MESSAGE",
-                                      "INFO",
-                                      "DEBUG")){
-
+moma_logger_level <- function(level = c(
+                                  "ERROR",
+                                  "WARNING",
+                                  "MESSAGE",
+                                  "INFO",
+                                  "DEBUG"
+                              )) {
     LEVELS_REV <- setNames(names(LEVELS), LEVELS)
 
     old_level <- LEVELS_REV[as.character(moma_get_logger_level_cpp())]
     names(old_level) <- NULL
 
-    if(!missing(level)){
-        level <- match.arg(level);
+    if (!missing(level)) {
+        level <- match.arg(level)
         moma_set_logger_level_cpp(LEVELS[level])
         return(invisible(old_level))
     }
 
     old_level
 }
 
-moma_error <- function(..., call=TRUE){
-    msg <- paste(list(...), collapse="")
+moma_error <- function(..., call = TRUE) {
+    msg <- paste(list(...), collapse = "")
 
     ## Try to add R level calling info
-    if(identical(call, TRUE)){
+    if (identical(call, TRUE)) {
         tryCatch({
             msg <- paste0(msg, " (Called from ", as.character(as.list(sys.call(-1))[[1]]), ")")
-        }, error=function(e){})
-    } else if(is.character(call)){
+        }, error = function(e) {})
+    } else if (is.character(call)) {
         msg <- paste0(msg, " (Called from ", call, ")")
     }
 
     moma_log_cpp(LEVELS["ERROR"], msg)
 }
 
-moma_warning <- function(..., call=TRUE){
-    msg <- paste(list(...), collapse="")
+moma_warning <- function(..., call = TRUE) {
+    msg <- paste(list(...), collapse = "")
 
     ## Try to add R level calling info
-    if(identical(call, TRUE)){
+    if (identical(call, TRUE)) {
         tryCatch({
             msg <- paste0(msg, " (Called from ", as.character(as.list(sys.call(-1))[[1]]), ")")
-        }, error=function(e){})
-    } else if(is.character(call)){
+        }, error = function(e) {})
+    } else if (is.character(call)) {
         msg <- paste0(msg, " (Called from ", call, ")")
     }
 
     moma_log_cpp(LEVELS["WARNING"], msg)
 }
 
-moma_message <- function(...){
-    msg <- paste(list(...), collapse="")
+moma_message <- function(...) {
+    msg <- paste(list(...), collapse = "")
     moma_log_cpp(LEVELS["MESSAGE"], msg)
 }
 
-moma_info <- function(...){
-    msg <- paste(list(...), collapse="")
+moma_info <- function(...) {
+    msg <- paste(list(...), collapse = "")
     moma_log_cpp(LEVELS["INFO"], msg)
 }
 
-moma_debug <- function(...){
-    msg <- paste(list(...), collapse="")
+moma_debug <- function(...) {
+    msg <- paste(list(...), collapse = "")
     moma_log_cpp(LEVELS["DEBUG"], msg)
 }

R/moma_4Dlist_extractor.R

@@ -1,25 +1,27 @@
-get_4Dlist_elem <- function(x, alpha_u_i, lambda_u_i, alpha_v_i, lambda_v_i){
-    if(!inherits(x, "MoMA_4D_list")){
+get_4Dlist_elem <- function(x, alpha_u_i, lambda_u_i, alpha_v_i, lambda_v_i) {
+    if (!inherits(x, "MoMA_4D_list")) {
         moma_error(sQuote("x"), " should be a ", sQuote("MoMA_4D_list"), " object.")
     }
-    n_alpha_u = dim(x)[1]
-    n_lambda_u = dim(x)[2]
-    n_alpha_v = dim(x)[3]
-    n_lambda_v = dim(x)[4]
+    n_alpha_u <- dim(x)[1]
+    n_lambda_u <- dim(x)[2]
+    n_alpha_v <- dim(x)[3]
+    n_lambda_v <- dim(x)[4]
 
     # NOTE: R index starts from 1
-    if(
-        alpha_u_i  <= 0 || alpha_u_i > n_alpha_u ||
-        lambda_u_i <= 0 || lambda_u_i > n_lambda_u ||
-        alpha_v_i  <= 0 || alpha_v_i > n_alpha_v ||
-        lambda_v_i <= 0 || lambda_v_i > n_lambda_v
-    ){
-        moma_error("Invalid index (",alpha_u_i, ",", lambda_u_i, 
-                   ",",alpha_v_i, ",",lambda_v_i,"), dim = ",
-                   dim(x))
+    if (
+        alpha_u_i <= 0 || alpha_u_i > n_alpha_u ||
+            lambda_u_i <= 0 || lambda_u_i > n_lambda_u ||
+            alpha_v_i <= 0 || alpha_v_i > n_alpha_v ||
+            lambda_v_i <= 0 || lambda_v_i > n_lambda_v
+    ) {
+        moma_error(
+            "Invalid index (", alpha_u_i, ",", lambda_u_i,
+            ",", alpha_v_i, ",", lambda_v_i, "), dim = ",
+            dim(x)
+        )
     }
-    return(x[n_lambda_u * n_alpha_v * n_lambda_v * (alpha_u_i-1) + 
-                          n_alpha_v * n_lambda_v * (lambda_u_i-1) + 
-                                      n_lambda_v * (alpha_v_i-1) +
-                                                   lambda_v_i])
+    return(x[n_lambda_u * n_alpha_v * n_lambda_v * (alpha_u_i - 1) +
+        n_alpha_v * n_lambda_v * (lambda_u_i - 1) +
+        n_lambda_v * (alpha_v_i - 1) +
+        lambda_v_i])
 }