Initial commit for the open-source MIT-licensed BCL to be released as…

… a public repository. The commit history leading up to this moment has been preserved in a Meiler Lab copy of the BCL repo.

.clang-format

@@ -0,0 +1,95 @@
+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: false
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: false
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:   
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Allman
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: 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: Right
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: true
+SpacesInSquareBrackets: true
+Standard:        Cpp11
+TabWidth:        2
+UseTab:          Never
+...
+

.clang_complete

@@ -0,0 +1,4 @@
+-std=c++11
+-Wall
+-Wextra
+-Iinclude/

.externalToolBuilders/UpdateCMakeLists.launch

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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ui.externaltools.ProgramBuilderLaunchConfigurationType">
+<booleanAttribute key="org.eclipse.debug.core.capture_output" value="false"/>
+<booleanAttribute key="org.eclipse.debug.ui.ATTR_CONSOLE_OUTPUT_ON" value="false"/>
+<booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="true"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${project_loc}/cmake/scripts/CheckCmakeLists.py"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_RUN_BUILD_KINDS" value="full,incremental,auto,"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_TOOL_ARGUMENTS" value="${project_loc} -o"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_WORKING_DIRECTORY" value="${project_loc}"/>
+</launchConfiguration>

.externalToolBuilders/UpdateForwardHeaders.launch

@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ui.externaltools.ProgramBuilderLaunchConfigurationType">
+<booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${project_loc}/scripts/code/CreateNamespaceForwardHeaders.py"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_RUN_BUILD_KINDS" value="full,incremental,auto,"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_TOOL_ARGUMENTS" value="${project_loc} -o"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="true"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_WORKING_DIRECTORY" value="${project_loc}"/>
+</launchConfiguration>

.gitattributes

@@ -0,0 +1,5 @@
+h.atom_environment_hashmap.four_bonds.txt.gz filter=lfs diff=lfs merge=lfs -text
+fold_templates.input filter=lfs diff=lfs merge=lfs -text
+code_debug.exe filter=lfs diff=lfs merge=lfs -text
+bcl.exe filter=lfs diff=lfs merge=lfs -text
+example_gprof.exe filter=lfs diff=lfs merge=lfs -text

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Please specify steps to reproduce the error, including BCL branch/version, the command-line/script that you ran, and sample input.
+
+**Log file**
+Attach or copy/paste output from the command.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.gitignore

@@ -0,0 +1,3 @@
+**/.DS_Store
+source/bcl_version.cpp
+build/

.project

@@ -0,0 +1,109 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>bcl</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<triggers>auto,full,incremental,</triggers>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+			<triggers>auto,full,incremental,</triggers>
+			<arguments>
+				<dictionary>
+					<key>LaunchConfigHandle</key>
+					<value>&lt;project&gt;/.externalToolBuilders/UpdateCMakeLists.launch</value>
+				</dictionary>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+			<triggers>auto,full,incremental,</triggers>
+			<arguments>
+				<dictionary>
+					<key>LaunchConfigHandle</key>
+					<value>&lt;project&gt;/.externalToolBuilders/UpdateForwardHeaders.launch</value>
+				</dictionary>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
+			<triggers>clean,full,incremental,</triggers>
+			<arguments>
+				<dictionary>
+					<key>?name?</key>
+					<value></value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.append_environment</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
+					<value>all</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildArguments</key>
+					<value>make -k -j120</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildCommand</key>
+					<value>pump</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildLocation</key>
+					<value>${project_loc:/example_release}</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
+					<value>clean</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.contents</key>
+					<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
+					<value>false</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableFullBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.fullBuildTarget</key>
+					<value>all</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.stopOnError</key>
+					<value>false</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
+					<value>false</value>
+				</dictionary>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
+		<nature>org.eclipse.cdt.core.ccnature</nature>
+		<nature>org.eclipse.cdt.core.cnature</nature>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>

.pydevproject

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?><pydev_project>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">python</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.6</pydev_property>
+
+<pydev_pathproperty name="org.python.pydev.PROJECT_EXTERNAL_SOURCE_PATH">
+</pydev_pathproperty>
+</pydev_project>

.settings/CreateMakefilesForAllConfigurations.launch

@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ui.externaltools.ProgramLaunchConfigurationType">
+<stringAttribute key="org.eclipse.debug.core.ATTR_REFRESH_SCOPE" value="${workspace}"/>
+<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+<listEntry value="org.eclipse.ui.externaltools.launchGroup"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${project_loc}/cmake/scripts/create_cmake_lists_arch_if_necessary.csh"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_WORKING_DIRECTORY" value="${project_loc}"/>
+</launchConfiguration>

.settings/FixObviousBclGuidelineViolations.launch

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ui.externaltools.ProgramLaunchConfigurationType">
+<stringAttribute key="org.eclipse.debug.core.ATTR_REFRESH_SCOPE" value="${workspace}"/>
+<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+<listEntry value="org.eclipse.ui.externaltools.launchGroup"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${project_loc}/scripts/code/BclCleaner.sh"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_TOOL_ARGUMENTS" value="./ -o"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_WORKING_DIRECTORY" value="${project_loc}"/>
+</launchConfiguration>

.settings/RemoveCMakeCaches.launch

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ui.externaltools.ProgramLaunchConfigurationType">
+<booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
+<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+<listEntry value="org.eclipse.ui.externaltools.launchGroup"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="/bin/tcsh"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_TOOL_ARGUMENTS" value="-c &quot;/bin/rm -f ./build/*/CMakeCache.txt ./build/*/Makefile &gt;&amp; /dev/null &amp;&amp; /bin/echo 'CMakeCache and makefiles removed' || /bin/echo 'No CMakeCache files to remove'&quot;"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_WORKING_DIRECTORY" value="${project_loc}"/>
+</launchConfiguration>

.settings/RemoveUnnecessaryHeadersFromCpps.launch

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ui.externaltools.ProgramLaunchConfigurationType">
+<stringAttribute key="org.eclipse.debug.core.ATTR_REFRESH_SCOPE" value="${resource}"/>
+<booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
+<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+<listEntry value="org.eclipse.ui.externaltools.launchGroup"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${project_loc}/scripts/deheader/run_deheader"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_TOOL_ARGUMENTS" value="${selected_resource_loc}"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_WORKING_DIRECTORY" value="${project_loc}"/>
+</launchConfiguration>

.settings/ReportObviousBclGuidelineViolations.launch

@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ui.externaltools.ProgramLaunchConfigurationType">
+<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+<listEntry value="org.eclipse.ui.externaltools.launchGroup"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${project_loc}/scripts/code/BclCleaner.sh"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_TOOL_ARGUMENTS" value="./"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_WORKING_DIRECTORY" value="${project_loc}"/>
+</launchConfiguration>