Merge branch 'sb-graph-dev' into sb-graph-tearing

Author: yamilsaer

3rd-party/CMakeLists.txt

@@ -21,3 +21,16 @@ add_custom_target(
 )
 
 add_dependencies(sbgraph 3rd-party-libs)
+
+include(FetchContent)
+
+set(BENCHMARK_ENABLE_GTEST_TESTS OFF CACHE BOOL "" FORCE)
+set(BENCHMARK_ENABLE_TESTING OFF CACHE BOOL "" FORCE)
+set(BENCHMARK_ENABLE_INSTALL OFF CACHE BOOL "" FORCE)
+
+FetchContent_Declare(
+  google_benchmark
+  GIT_REPOSITORY https://github.com/google/benchmark.git
+  GIT_TAG v1.6.1
+)
+FetchContent_MakeAvailable(google_benchmark)

CMakeLists.txt

@@ -81,10 +81,25 @@ install(
   COMPONENT sbgraph
 )
 
+# Documentation
+set(DOC_PATHS "${CMAKE_CURRENT_SOURCE_DIR}")
+string(REPLACE ";" " " DOXYGEN_INPUT_DIR "${DOC_PATHS}")
+
+set(DOXYGEN_OUTPUT_DIR "${CMAKE_CURRENT_SOURCE_DIR}/doc")
+
+set(DOXYGEN_EXCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+
+set(DOXYGEN_MAINPAGE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
+               ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+
 add_custom_target(doc
   COMMAND echo "Generating Project documentation."
+  COMMAND doxygen "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile"
+  #COMMAND ${CMAKE_COMMAND} -E make_directory ${PROJECT_SOURCE_DIR}/doc
+  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+  COMMENT "Generating API documentation with Doxygen"
 )
 
-add_dependencies(doc eval-doc sbg-doc util-doc)
-
 set_target_properties(doc PROPERTIES EXCLUDE_FROM_ALL ON)

sbg/SBG.doxyfile Doxyfile.insbg/SBG.doxyfile renamed to Doxyfile.in

@@ -68,7 +68,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = ../doc/sbg
+OUTPUT_DIRECTORY       = @DOXYGEN_OUTPUT_DIR@
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
 # sub-directories (in 2 levels) under the output directory of each output format
@@ -162,7 +162,7 @@ INLINE_INHERITED_MEMB  = NO
 # shortest path that makes the file name unique will be used
 # The default value is: YES.
 
-FULL_PATH_NAMES        = YES
+FULL_PATH_NAMES        = NO
 
 # The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
 # Stripping is only done if one of the specified strings matches the left-hand
@@ -174,7 +174,7 @@ FULL_PATH_NAMES        = YES
 # will be relative from the directory where doxygen is started.
 # This tag requires that the tag FULL_PATH_NAMES is set to YES.
 
-STRIP_FROM_PATH        =
+STRIP_FROM_PATH        = YES
 
 # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
 # path mentioned in the documentation of a class, which tells the reader which
@@ -933,10 +933,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = sbg \
-                         sbg/util \
-                         sbg/graph_builders \
-                         .
+INPUT                  = @DOXYGEN_INPUT_DIR@
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -976,13 +973,13 @@ INPUT_FILE_ENCODING    =
 # provided as doxygen C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
 # *.f18, *.f, *.for, *.vhd, *.vhdl, *.ucf, *.qsf and *.ice.
 
-FILE_PATTERNS          =
+FILE_PATTERNS          = *.cpp *.hpp *.md
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
 # The default value is: NO.
 
-RECURSIVE              = NO
+RECURSIVE              = YES
 
 # The EXCLUDE tag can be used to specify files and/or directories that should be
 # excluded from the INPUT source files. This way you can easily exclude a
@@ -991,7 +988,13 @@ RECURSIVE              = NO
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                =
+EXCLUDE                = @DOXYGEN_EXCLUDE_DIR@/3rd-party \
+                         @DOXYGEN_EXCLUDE_DIR@/autom4te.cache \
+                         @DOXYGEN_EXCLUDE_DIR@/build \
+                         @DOXYGEN_EXCLUDE_DIR@/deploy \
+                         @DOXYGEN_EXCLUDE_DIR@/install \
+                         @DOXYGEN_EXCLUDE_DIR@/lib \
+                         @DOXYGEN_EXCLUDE_DIR@/obj
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -1007,7 +1010,9 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       = */build/* \
+                         */cmake/* \
+                         */.git/*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -1102,7 +1107,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = @DOXYGEN_MAINPAGE_DIR@/README.md
 
 # The Fortran standard specifies that for fixed formatted Fortran code all
 # characters from position 72 are to be considered as comment. A common
@@ -1137,7 +1142,7 @@ INLINE_SOURCES         = NO
 # Fortran comments will always remain visible.
 # The default value is: YES.
 
-STRIP_CODE_COMMENTS    = YES
+STRIP_CODE_COMMENTS    = NO
 
 # If the REFERENCED_BY_RELATION tag is set to YES then for each documented
 # entity all documented functions referencing it will be listed.

Makefile.in

@@ -37,6 +37,13 @@ bool BFSMatching::ExitCondition::full_match() { return full_match_; }
 
 bool BFSMatching::ExitCondition::found_paths() { return found_paths_; }
 
+bool BFSMatching::ExitCondition::isSatisfied()
+{
+  return full_match_ || !found_paths_;
+}
+
+// Algorithm -------------------------------------------------------------------
+
 BFSMatching::BFSMatching() : M_(SET_FACT.createSet()), dsbg_()
   , direction_(Direction::kForward) {}
 
@@ -157,31 +164,37 @@ BFSMatching::ExitCondition BFSMatching::step(const Set& right_vertices)
   // Calculate exit conditions
   Set matchedU = dsbg_.mapD().image(M_);
   bool full_match = right_vertices.difference(matchedU).isEmpty();
-  bool found_paths = !M_.isEmpty();
+  bool found_paths = !augmenting_edges.isEmpty();
 
   return ExitCondition(full_match, found_paths);
 }
 
-bool BFSMatching::ExitCondition::isSatisfied()
+void BFSMatching::init(const BipartiteSBG& bsbg)
 {
-  return full_match_ || !found_paths_;
-}
+  PWMap map1 = bsbg.map1().compact();
+  PWMap map2 = bsbg.map2().compact();
 
-void BFSMatching::init(const SBG& sbg)
-{
-  dsbg_ = DSBG(sbg.V().compact(), sbg.Vmap().compact(), sbg.map2()
-    , sbg.map1().compact(), sbg.Emap().compact(), sbg.subEmap().compact());
+  Set Y = bsbg.Y();
+  PWMap map1_toY = map1.restrict(map1.preImage(Y));
+  PWMap map2_toY = map2.restrict(map2.preImage(Y));
+  PWMap mapB = map1_toY.concatenation(map2_toY);
 
-  return;
+  Set X = bsbg.X();
+  PWMap map1_toX = map1.restrict(map1.preImage(X));
+  PWMap map2_toX = map2.restrict(map2.preImage(X));
+  PWMap mapD = map1_toX.concatenation(map2_toX);
+
+  dsbg_ = DSBG(bsbg.V().compact(), bsbg.Vmap().compact(), mapB, mapD
+    , bsbg.Emap().compact(), bsbg.subEmap().compact());
 }
 
-MatchData BFSMatching::calculate(const SBG& sbg)
+MatchData BFSMatching::calculate(const BipartiteSBG& bsbg)
 {
-  Util::DEBUG_LOG << "Matching sbg: \n" << sbg << "\n\n";
+  Util::DEBUG_LOG << "Matching bsbg: \n" << bsbg << "\n\n";
 
   auto begin = std::chrono::high_resolution_clock::now();
-  init(sbg);
-  Set right_vertices = dsbg_.mapB().image();
+  init(bsbg);
+  Set right_vertices = bsbg.Y();
 
   ExitCondition exit_cond(false, false);
   do {
@@ -192,7 +205,7 @@ MatchData BFSMatching::calculate(const SBG& sbg)
     end - begin);
   Util::SBG_LOG << "Total matching exec time: " << total.count() << " [μs]\n";
 
-  MatchData result(sbg, M_.compact(), exit_cond.full_match());
+  MatchData result(bsbg, M_.compact(), exit_cond.full_match());
   Util::SBG_LOG << result << "\n\n";
 
   return result;

algorithms/matching/bfs_matching.cpp

@@ -26,6 +26,7 @@
 
 #include "algorithms/matching/bfs_paths.hpp"
 #include "algorithms/matching/matching.hpp"
+#include "sbg/directed_sbg.hpp"
 
 namespace SBG {
 
@@ -50,7 +51,7 @@ class BFSMatching : public MatchStrategy {
   public:
   BFSMatching();
 
-  MatchData calculate(const SBG& sbg) override;
+  MatchData calculate(const BipartiteSBG& bsbg) override;
 
   private:
   /**
@@ -72,9 +73,9 @@ class BFSMatching : public MatchStrategy {
   };
 
   /**
-   * @brief Initializes data members determined by the input SBG.
+   * @brief Initializes data members determined by the input bipartite SBG.
    */
-  void init(const SBG& sbg);
+  void init(const BipartiteSBG& bsbg);
 
   /**
    * @brief Performs an iteration of the algorithm. It looks up alternating
@@ -117,7 +118,7 @@ class BFSMatching : public MatchStrategy {
    */
   Set edgesInPaths(const PWMap& smap, const Set& E) const;
 
-  DSBG dsbg_; ///< Input DSBG
+  DSBG dsbg_; ///< Directed graph according to matching
   Set M_;     ///< Matched edges
   Direction direction_;
 };

algorithms/matching/bfs_matching.hpp

@@ -44,10 +44,10 @@ std::ostream& operator<<(std::ostream& out, const Direction& direction)
   return out;
 }
 
-MatchData::MatchData(SBG sbg, Set M, bool full_match)
-  : sbg_(sbg), M_(M), full_match_(full_match) {}
+MatchData::MatchData(BipartiteSBG bsbg, Set M, bool full_match)
+  : bsbg_(bsbg), M_(M), full_match_(full_match) {}
 
-const SBG& MatchData::sbg() const { return sbg_; }
+const BipartiteSBG& MatchData::bsbg() const { return bsbg_; }
 const Set& MatchData::M() const { return M_; }
 const bool& MatchData::full_match() const { return full_match_; }
 
@@ -74,9 +74,9 @@ MatchStrategy::MatchStrategy() {}
 
 Matching::Matching(MatchStratPtr strat) : strategy_(std::move(strat)) {}
 
-MatchData Matching::calculate(const SBG& sbg)
+MatchData Matching::calculate(const BipartiteSBG& bsbg)
 {
-  return strategy_->calculate(sbg);
+  return strategy_->calculate(bsbg);
 }
 
 } // namespace LIB