merge development into character_history, lots of merge conflicts

.gitignore

@@ -7,6 +7,7 @@
 # Blacklist
 # ----------------------------------------------
 projects/cmake
+src/revlanguage/utils/GitVersion.cpp
 src/revlanguage/constants.h
 src/ui/constants.h
 boost_1_55_0/bootstrap.log
@@ -24,20 +25,20 @@ boost_1_55_0/tools/build/v2/engine/bin.linuxx86_64/bjam
 boost_1_60_0/bootstrap.log
 boost_1_60_0/bin.v2
 boost_1_60_0/stage/lib
+boost_1_60_0/libs/config/checks
 boost_1_60_0/project
 boost_1_60_0/project-config.jam
 boost_1_60_0/tools/build/src/engine/bootstrap
+boost_1_60_0/tools/build/v2/engine/bootstrap
 boost_1_60_0/b2
 boost_1_60_0/bjam
 boost_1_60_0/tools/build/src/engine/bin.macosxx86_64/b2
 boost_1_60_0/tools/build/src/engine/bin.macosxx86_64/bjam
-boost_1_60_0/tools/build/src/engine/bin.linuxx86_64/b2
-boost_1_60_0/tools/build/src/engine/bin.linuxx86_64/bjam
-boost_1_60_0/libs/config/checks/architecture/bin/darwin-4.2.1/debug/64.o
-boost_1_60_0/libs/config/checks/architecture/bin/darwin-4.2.1/debug/x86.o
+boost_1_60_0/tools/build/v2/engine/bin.macosxx86_64/b2
+boost_1_60_0/tools/build/v2/engine/bin.macosxx86_64/bjam
+boost_1_60_0/tools/build/v2/engine/bin.linuxx86_64/b2
+boost_1_60_0/tools/build/v2/engine/bin.linuxx86_64/bjam
 projects/xcode/revbayes.xcodeproj
 .DS_Store
-*.aux
-*.synctex.gz
 .history
 history.txt

.travis.yml

@@ -6,9 +6,14 @@ compiler:
 script:
   - cd projects/cmake
   - ./build.sh
+  - echo "\"Hello World\"" | ./rb
 
 # safelist
 branches:
   only:
   - master
   - development
+
+# notifications
+notifications:
+  slack: revbayes:bQO6VTun0Orhx2NiKktVPDsS

CHANGELOG.md

@@ -0,0 +1,44 @@
+## Change Log
+This file contains a list of notable upgrades and features introduced to each release version of [RevBayes](https://github.com/revbayes/revbayes/releases).
+
+### [1.0.4] - under development
+
+#### Added
+- `CHANGELOG.md` added
+- Support to provide autotuned acceptance rates for `mvScale`, `mvSlide`, and `mvSimplex` moves using the `tuneTarget` argument
+
+#### Changed
+
+#### Fixed
+
+#### Removed
+
+---
+
+## Earlier versions without change log records:
+
+### [1.0.3] - 2016-12-14
+
+### [1.0.2] - 2016-12-06
+
+### [1.0.1] - 2016-07-10
+
+### [1.0.0] - 2016-03-21
+Notes:
+- Official release
+
+### [1.0.0-beta.1] - 2015-12-01
+
+### [1.0.0-beta.0] - 2015-04-01
+Notes:
+- Pre-release
+
+### [0.0.3] - 2015-03-31
+
+### [0.0.2] - 2015-02-23
+Notes:
+- Cesky-Krumlov release
+
+### [0.0.1] - 2014-09-05
+Notes:
+- NesCENT release

GuiExecutable/RevBayesGui.app/Contents/Info.plist

@@ -0,0 +1,123 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>BuildMachineOSBuild</key>
+	<string>15G1004</string>
+	<key>CFBundleDevelopmentRegion</key>
+	<string>en</string>
+	<key>CFBundleDocumentTypes</key>
+	<array>
+		<dict>
+			<key>CFBundleTypeExtensions</key>
+			<array>
+				<string>rvbs</string>
+			</array>
+			<key>CFBundleTypeIconFile</key>
+			<string>blankdocument.icns</string>
+			<key>CFBundleTypeName</key>
+			<string>RevBayes Doc</string>
+			<key>CFBundleTypeRole</key>
+			<string>Editor</string>
+			<key>LSItemContentTypes</key>
+			<array>
+				<string>com.berkeley.file</string>
+			</array>
+			<key>NSDocumentClass</key>
+			<string>AnalysisDocument</string>
+		</dict>
+	</array>
+	<key>CFBundleExecutable</key>
+	<string>RevBayesGui</string>
+	<key>CFBundleHelpBookFolder</key>
+	<string>RevBayesHelp.help</string>
+	<key>CFBundleHelpBookName</key>
+	<string>com.berkeley.revbayes.help</string>
+	<key>CFBundleIconFile</key>
+	<string>aquabayes.icns</string>
+	<key>CFBundleIdentifier</key>
+	<string>com.berkeley.revbayes</string>
+	<key>CFBundleInfoDictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleName</key>
+	<string>RevBayes</string>
+	<key>CFBundlePackageType</key>
+	<string>APPL</string>
+	<key>CFBundleShortVersionString</key>
+	<string>1.0</string>
+	<key>CFBundleSignature</key>
+	<string>????</string>
+	<key>CFBundleSupportedPlatforms</key>
+	<array>
+		<string>MacOSX</string>
+	</array>
+	<key>CFBundleURLTypes</key>
+	<array/>
+	<key>CFBundleVersion</key>
+	<string>1</string>
+	<key>DTCompiler</key>
+	<string>com.apple.compilers.llvm.clang.1_0</string>
+	<key>DTPlatformBuild</key>
+	<string>7D1014</string>
+	<key>DTPlatformVersion</key>
+	<string>GM</string>
+	<key>DTSDKBuild</key>
+	<string>15E60</string>
+	<key>DTSDKName</key>
+	<string>macosx10.11</string>
+	<key>DTXcode</key>
+	<string>0731</string>
+	<key>DTXcodeBuild</key>
+	<string>7D1014</string>
+	<key>LSApplicationCategoryType</key>
+	<string>public.app-category.education</string>
+	<key>LSMinimumSystemVersion</key>
+	<string>10.11</string>
+	<key>NSMainNibFile</key>
+	<string>MainMenu</string>
+	<key>NSPrincipalClass</key>
+	<string>NSApplication</string>
+	<key>NSServices</key>
+	<array/>
+	<key>UTExportedTypeDeclarations</key>
+	<array>
+		<dict>
+			<key>UTTypeConformsTo</key>
+			<array>
+				<string>com.apple.package</string>
+			</array>
+			<key>UTTypeIconFile</key>
+			<string>blankdocument.icns</string>
+			<key>UTTypeIdentifier</key>
+			<string>com.berkeley.file</string>
+			<key>UTTypeTagSpecification</key>
+			<dict>
+				<key>public.filename-extension</key>
+				<array>
+					<string>rvbs</string>
+				</array>
+			</dict>
+		</dict>
+	</array>
+	<key>UTImportedTypeDeclarations</key>
+	<array>
+		<dict>
+			<key>UTTypeConformsTo</key>
+			<array>
+				<string>com.apple.package</string>
+			</array>
+			<key>UTTypeIconFile</key>
+			<string>blankdocument.icns</string>
+			<key>UTTypeIdentifier</key>
+			<string>com.berkeley.file</string>
+			<key>UTTypeTagSpecification</key>
+			<dict>
+				<key>public.filename-extension</key>
+				<array>
+					<string>rvbs</string>
+				</array>
+			</dict>
+		</dict>
+	</array>
+</dict>
+</plist>

GuiExecutable/RevBayesGui.app/Contents/Resources/RevBayesGui-Info.plist

@@ -0,0 +1,103 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>CFBundleDevelopmentRegion</key>
+	<string>en</string>
+	<key>CFBundleDocumentTypes</key>
+	<array>
+		<dict>
+			<key>CFBundleTypeExtensions</key>
+			<array>
+				<string>rvbs</string>
+			</array>
+			<key>CFBundleTypeIconFile</key>
+			<string>blankdocument.icns</string>
+			<key>CFBundleTypeName</key>
+			<string>RevBayes Doc</string>
+			<key>CFBundleTypeRole</key>
+			<string>Editor</string>
+			<key>LSItemContentTypes</key>
+			<array>
+				<string>com.berkeley.file</string>
+			</array>
+			<key>NSDocumentClass</key>
+			<string>AnalysisDocument</string>
+		</dict>
+	</array>
+	<key>CFBundleExecutable</key>
+	<string>${EXECUTABLE_NAME}</string>
+	<key>CFBundleHelpBookFolder</key>
+	<string>RevBayesHelp.help</string>
+	<key>CFBundleHelpBookName</key>
+	<string>RevBayes Help</string>
+	<key>CFBundleIconFile</key>
+	<string>aquabayes.icns</string>
+	<key>CFBundleIdentifier</key>
+	<string>com.berkeley.revbayes</string>
+	<key>CFBundleInfoDictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleName</key>
+	<string>RevBayes</string>
+	<key>CFBundlePackageType</key>
+	<string>APPL</string>
+	<key>CFBundleShortVersionString</key>
+	<string>1.0</string>
+	<key>CFBundleSignature</key>
+	<string>????</string>
+	<key>CFBundleURLTypes</key>
+	<array/>
+	<key>CFBundleVersion</key>
+	<string>1</string>
+	<key>LSApplicationCategoryType</key>
+	<string>public.app-category.education</string>
+	<key>LSMinimumSystemVersion</key>
+	<string>${MACOSX_DEPLOYMENT_TARGET}</string>
+	<key>NSMainNibFile</key>
+	<string>MainMenu</string>
+	<key>NSPrincipalClass</key>
+	<string>NSApplication</string>
+	<key>NSServices</key>
+	<array/>
+	<key>UTExportedTypeDeclarations</key>
+	<array>
+		<dict>
+			<key>UTTypeConformsTo</key>
+			<array>
+				<string>com.apple.package</string>
+			</array>
+			<key>UTTypeIconFile</key>
+			<string>blankdocument.icns</string>
+			<key>UTTypeIdentifier</key>
+			<string>com.berkeley.file</string>
+			<key>UTTypeTagSpecification</key>
+			<dict>
+				<key>public.filename-extension</key>
+				<array>
+					<string>rvbs</string>
+				</array>
+			</dict>
+		</dict>
+	</array>
+	<key>UTImportedTypeDeclarations</key>
+	<array>
+		<dict>
+			<key>UTTypeConformsTo</key>
+			<array>
+				<string>com.apple.package</string>
+			</array>
+			<key>UTTypeIconFile</key>
+			<string>blankdocument.icns</string>
+			<key>UTTypeIdentifier</key>
+			<string>com.berkeley.file</string>
+			<key>UTTypeTagSpecification</key>
+			<dict>
+				<key>public.filename-extension</key>
+				<array>
+					<string>rvbs</string>
+				</array>
+			</dict>
+		</dict>
+	</array>
+</dict>
+</plist>

GuiExecutable/RevBayesGui.app/Contents/Resources/RevBayesHelp.help/Contents/Info.plist

@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>CFBundleDevelopment-Region</key>
+	<string>en_US</string>
+	<key>CFBundleIdentifier</key>
+	<string>com.berkeley.revbayes.help</string>
+	<key>CFBundleInfo-DictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleName</key>
+	<string>RevBayesHelp</string>
+	<key>CFBundlePackageType</key>
+	<string>BNDL</string>
+	<key>CFBundleShortVersion-String</key>
+	<string>1</string>
+	<key>CFBundleSignature</key>
+	<string>hbwr</string>
+	<key>CFBundleVersion</key>
+	<string>1</string>
+	<key>HPDBookAccessPath</key>
+	<string>index.html</string>
+	<key>HPDBookIconPath</key>
+	<string>shrd/bookIcon.png</string>
+	<key>HPDBookKBProduct</key>
+	<string>RevBayesHelp</string>
+	<key>HPDBookTitle</key>
+	<string>RevBayesHelp</string>
+	<key>HPDBookTopic-ListCSSPath</key>
+	<string>sty/topiclist.css</string>
+	<key>HPDBookType</key>
+	<string>3</string>
+</dict>
+</plist>