Description updated, membership made optional

Makefile

@@ -11,38 +11,38 @@ AR = ar
 LD = g++
 WINDRES = windres
 
-INC = -Iinclude -Iautogen
+INC = -Iautogen -Iinclude
 CFLAGS = -Wnon-virtual-dtor -Winit-self -Wcast-align -Wundef -Wfloat-equal -Wunreachable-code -Wmissing-include-dirs -Weffc++ -Wzero-as-null-pointer-constant -std=c++14 -fexceptions
 RESINC = 
 LIBDIR = 
-LIB = 
+LIB = -lstdc++fs
 LDFLAGS = 
 
 INC_DEBUG = $(INC)
-CFLAGS_DEBUG = $(CFLAGS) -Wredundant-decls -Winline -Wswitch-default -Wmain -Wall -g -DDEBUG
+CFLAGS_DEBUG = $(CFLAGS) -Wredundant-decls -Winline -Wswitch-default -Wmain -Wall -g -DDEBUG -DHEAVY_VALIDATION=2 -DTRACE=2
 RESINC_DEBUG = $(RESINC)
 RCFLAGS_DEBUG = $(RCFLAGS)
 LIBDIR_DEBUG = $(LIBDIR)
 LIB_DEBUG = $(LIB)
 LDFLAGS_DEBUG = $(LDFLAGS)
 OBJDIR_DEBUG = obj/Debug
 DEP_DEBUG = 
-OUT_DEBUG = bin/Debug/onmi
+OUT_DEBUG = bin/Debug/resmerge
 
 INC_RELEASE = $(INC)
-CFLAGS_RELEASE = $(CFLAGS) -march=core2 -fomit-frame-pointer -O3
+CFLAGS_RELEASE = $(CFLAGS) -march=core2 -fomit-frame-pointer -O3 -DHEAVY_VALIDATION=1 -DTRACE=1
 RESINC_RELEASE = $(RESINC)
 RCFLAGS_RELEASE = $(RCFLAGS)
 LIBDIR_RELEASE = $(LIBDIR)
 LIB_RELEASE = $(LIB)
 LDFLAGS_RELEASE = $(LDFLAGS) -s
 OBJDIR_RELEASE = obj/Release
 DEP_RELEASE = 
-OUT_RELEASE = bin/Release/onmi
+OUT_RELEASE = bin/Release/resmerge
 
-OBJ_DEBUG = $(OBJDIR_DEBUG)/autogen/cmdline.o $(OBJDIR_DEBUG)/onmi.o
+OBJ_DEBUG = $(OBJDIR_DEBUG)/autogen/cmdline.o $(OBJDIR_DEBUG)/src/fileio.o $(OBJDIR_DEBUG)/src/main.o
 
-OBJ_RELEASE = $(OBJDIR_RELEASE)/autogen/cmdline.o $(OBJDIR_RELEASE)/onmi.o
+OBJ_RELEASE = $(OBJDIR_RELEASE)/autogen/cmdline.o $(OBJDIR_RELEASE)/src/fileio.o $(OBJDIR_RELEASE)/src/main.o
 
 all: debug release
 
@@ -51,7 +51,7 @@ clean: clean_debug clean_release
 before_debug: 
 	test -d bin/Debug || mkdir -p bin/Debug
 	test -d $(OBJDIR_DEBUG)/autogen || mkdir -p $(OBJDIR_DEBUG)/autogen
-	test -d $(OBJDIR_DEBUG) || mkdir -p $(OBJDIR_DEBUG)
+	test -d $(OBJDIR_DEBUG)/src || mkdir -p $(OBJDIR_DEBUG)/src
 
 after_debug: 
 
@@ -63,19 +63,22 @@ out_debug: before_debug $(OBJ_DEBUG) $(DEP_DEBUG)
 $(OBJDIR_DEBUG)/autogen/cmdline.o: autogen/cmdline.c
 	$(CC) $(CFLAGS_DEBUG) $(INC_DEBUG) -c autogen/cmdline.c -o $(OBJDIR_DEBUG)/autogen/cmdline.o
 
-$(OBJDIR_DEBUG)/onmi.o: onmi.cpp
-	$(CXX) $(CFLAGS_DEBUG) $(INC_DEBUG) -c onmi.cpp -o $(OBJDIR_DEBUG)/onmi.o
+$(OBJDIR_DEBUG)/src/fileio.o: src/fileio.cpp
+	$(CXX) $(CFLAGS_DEBUG) $(INC_DEBUG) -c src/fileio.cpp -o $(OBJDIR_DEBUG)/src/fileio.o
+
+$(OBJDIR_DEBUG)/src/main.o: src/main.cpp
+	$(CXX) $(CFLAGS_DEBUG) $(INC_DEBUG) -c src/main.cpp -o $(OBJDIR_DEBUG)/src/main.o
 
 clean_debug: 
 	rm -f $(OBJ_DEBUG) $(OUT_DEBUG)
 	rm -rf bin/Debug
 	rm -rf $(OBJDIR_DEBUG)/autogen
-	rm -rf $(OBJDIR_DEBUG)
+	rm -rf $(OBJDIR_DEBUG)/src
 
 before_release: 
 	test -d bin/Release || mkdir -p bin/Release
 	test -d $(OBJDIR_RELEASE)/autogen || mkdir -p $(OBJDIR_RELEASE)/autogen
-	test -d $(OBJDIR_RELEASE) || mkdir -p $(OBJDIR_RELEASE)
+	test -d $(OBJDIR_RELEASE)/src || mkdir -p $(OBJDIR_RELEASE)/src
 
 after_release: 
 
@@ -87,14 +90,17 @@ out_release: before_release $(OBJ_RELEASE) $(DEP_RELEASE)
 $(OBJDIR_RELEASE)/autogen/cmdline.o: autogen/cmdline.c
 	$(CC) $(CFLAGS_RELEASE) $(INC_RELEASE) -c autogen/cmdline.c -o $(OBJDIR_RELEASE)/autogen/cmdline.o
 
-$(OBJDIR_RELEASE)/onmi.o: onmi.cpp
-	$(CXX) $(CFLAGS_RELEASE) $(INC_RELEASE) -c onmi.cpp -o $(OBJDIR_RELEASE)/onmi.o
+$(OBJDIR_RELEASE)/src/fileio.o: src/fileio.cpp
+	$(CXX) $(CFLAGS_RELEASE) $(INC_RELEASE) -c src/fileio.cpp -o $(OBJDIR_RELEASE)/src/fileio.o
+
+$(OBJDIR_RELEASE)/src/main.o: src/main.cpp
+	$(CXX) $(CFLAGS_RELEASE) $(INC_RELEASE) -c src/main.cpp -o $(OBJDIR_RELEASE)/src/main.o
 
 clean_release: 
 	rm -f $(OBJ_RELEASE) $(OUT_RELEASE)
 	rm -rf bin/Release
 	rm -rf $(OBJDIR_RELEASE)/autogen
-	rm -rf $(OBJDIR_RELEASE)
+	rm -rf $(OBJDIR_RELEASE)/src
 
 .PHONY: before_debug after_debug clean_debug before_release after_release clean_release
 

README.md

@@ -42,23 +42,26 @@ _Applicability Note:_ OvpNMI is extremely fast, but does not suitable to evaluat
 Execution Options:
 ```
 $ ./onmi -h
-onmi 0.2
+onmi 0.3
 
 Compare sets of clusters by their members (nodes) using various measures (NMI,
 Omega) and considering overlaps
 
 Usage: onmi [OPTIONS] clsfile1 clsfile2
 
--h, --help     Print help and exit
--V, --version  Print version and exit
--s, --sync     synchronize the node base, for example to fairly evaluate
-                 against top K selected clusters that are subset of the
-                 original nodes  (default=off)
--a, --allnmis  output all NMIs (sum-denominator and LFK besides the
-                 max-denominator one)  (default=off)
--o, --omega    print the Omega measure (can be slow)  (default=off)
--t, --textid   use text ids of nodes instead of .cnl format  (default=off)
--v, --verbose  detailed debugging  (default=off)
+  -h, --help              Print help and exit
+  -V, --version           Print version and exit
+  -s, --sync              synchronize the node base, for example to fairly
+                            evaluate against the top K selected clusters that
+                            are subset of the original nodes  (default=off)
+  -a, --allnmis           output all NMIs (sum-denominator and LFK besides the
+                            max-denominator one)  (default=off)
+  -m, --membership=FLOAT  average expected membership of nodes in the clusters,
+                            > 0, typically >= 1  (default=`1')
+  -o, --omega             print the Omega measure (can be slow)  (default=off)
+  -t, --textid            use text ids of nodes instead of .cnl format
+                            (default=off)
+  -v, --verbose           detailed debugging  (default=off)
 ```
 The input files contain list of clusters (communities, modules). A typical use case is to have
 the "true" communities in one file and and those found by your algorithm in the other file.

args.ggo

@@ -1,7 +1,7 @@
 # Configuration file for the automatic generation of the ONMI input options parsing
 
 package "onmi"
-version "0.2"
+version "0.3"
 
 purpose "Compare sets of clusters by their members (nodes) using various measures (NMI, Omega) and considering overlaps"
 
@@ -13,7 +13,7 @@ option  "omega" o  "print the Omega measure (can be slow)"  flag off
 option  "textid" t  "use text ids of nodes instead of .cnl format"  flag off
 option  "verbose" v  "detailed debugging"  flag off
 
-args "--unamed-opts=clusterings"   # Allow input files to be unnamed parameters
+args "--default-optional --unamed-opts=clusterings"   # Set opional opions, allow input files to be unnamed parameters
 
 # Basic structure, see https://www.gnu.org/software/gengetopt/gengetopt.html#Basic-Usage
 #     package "<packname>"

autogen/cmdline.c

@@ -1,7 +1,7 @@
 /*
   File autogenerated by gengetopt version 2.22.6
   generated with the following command:
-  gengetopt --output-dir autogen -i args.ggo --unamed-opts=clusterings
+  gengetopt --output-dir autogen -i args.ggo --default-optional --unamed-opts=clusterings
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
@@ -59,8 +59,6 @@ static int
 cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
                         struct cmdline_parser_params *params, const char *additional_error);
 
-static int
-cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
 
 static char *
 gengetopt_strdup (const char *s);
@@ -338,37 +336,9 @@ cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, i
 int
 cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
 {
-  int result = EXIT_SUCCESS;
-
-  if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
-    result = EXIT_FAILURE;
-
-  if (result == EXIT_FAILURE)
-    {
-      cmdline_parser_free (args_info);
-      exit (EXIT_FAILURE);
-    }
-
-  return result;
-}
-
-int
-cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
-{
-  int error_occurred = 0;
-  FIX_UNUSED (additional_error);
-
-  /* checks for required options */
-  if (! args_info->membership_given)
-    {
-      fprintf (stderr, "%s: '--membership' ('-m') option required%s\n", prog_name, (additional_error ? additional_error : ""));
-      error_occurred = 1;
-    }
-
-
-  /* checks for dependences among options */
-
-  return error_occurred;
+  FIX_UNUSED (args_info);
+  FIX_UNUSED (prog_name);
+  return EXIT_SUCCESS;
 }
 
 
@@ -619,10 +589,6 @@ cmdline_parser_internal (
 
 
 
-  if (check_required)
-    {
-      error_occurred += cmdline_parser_required2 (args_info, argv[0], additional_error);
-    }
 
   cmdline_parser_release (&local_args_info);
 

autogen/cmdline.h

@@ -31,7 +31,7 @@ extern "C" {
 
 #ifndef CMDLINE_PARSER_VERSION
 /** @brief the program version */
-#define CMDLINE_PARSER_VERSION "0.2"
+#define CMDLINE_PARSER_VERSION "0.3"
 #endif
 
 /** @brief Where the command line options are stored */