Merge branch 'release/0.4.0'

Makefile

@@ -6,8 +6,6 @@ READLINE_VERSION = 6.3
 TERMCAP_VERSION = 1.3.1
 GSL_VERSION = 2.0
 
-
-
 ifeq ($(OS),Windows_NT)
     CCFLAGS += -D WIN32
     ifeq ($(PROCESSOR_ARCHITECTURE),AMD64)
@@ -36,17 +34,15 @@ else
     endif
 endif
 
-
 all: cli r_package
 
-cli: libnet readline
+cli: pgmlab readline
 	make -C cli 
 
+r_package: pgmlab
+	make -C R/pgmlabR
 
-r_package: libnet
-	make -C r_package/libnetR
-
-libnet: sha gsl
+pgmlab: sha gsl
 	make -C net
 
 sha: 
@@ -70,8 +66,16 @@ termcap:
 	make; \
 	make install;
 
+make install:
+	make -C net install; \
+	make -C cli install
+
+make uninstall:
+	make -C net uninstall; \
+	make -C cli uninstall
+
 clean:
 	make -C net clean; \
 	make -C cli clean; \
-	make -C r_package/libnetR clean; \
+	make -C R/pgmlabR clean; \
 	rm bin/*

r_package/libnetR/DESCRIPTION → R/pgmlabR/DESCRIPTION

@@ -1,4 +1,4 @@
-Package: libnetR
+Package: pgmlabR
 Type: Package
 Version: 1.0
 Date: 2015-05-01
@@ -10,8 +10,8 @@ Authors@R: c(person("Adam", "Wright", role = c("aut", "cre"),
 Author: Adam Wright [aut, cre], Hossein Radfar [aut]
 Maintainer: Adam Wright <[email protected]>
 Depends: R (>= 3.0.2)
-Description: This is the R interface to LibNet. LibNet Consists of a c library that can be used for learning and inference on binary baysean probabilistic networks. 
+Description: This is the R interface to PGMLAB. PGMLAB Consists of a c library that can be used for learning and inference on binary baysean probabilistic networks. 
 License: GPL (>= 2)
 LazyLoad: yes
-URL: http://www.r-project.org, http://github.com/a8wright/libnet
+URL: http://www.r-project.org, http://github.com/a8wright/PGMLAB
 NeedsCompilation: yes

r_package/libnetR/Makefile → R/pgmlabR/Makefile

@@ -3,8 +3,8 @@ CC = gcc
 
 R_VERSION = 3.2.2_1
 
-TARGET = libnetR
-LIBNET_LIB = ../../net/lib
+TARGET = pgmlabR
+PGMLAB_LIB = ../../net/lib
 
 
 ifeq ($(OS),Windows_NT)
@@ -24,7 +24,7 @@ else
         R_LIB = -L/usr/lib/R/lib -lR
 	INCLUDE_R = -I/usr/share/R/include
         R_FLAGS = -Wl,Bsymbolic-functions -Wl,-z,relro -std=gnu99
-        SOFLAGS +=  -Wl,-rpath=$(LIBNET_LIB),-rpath=../external_lib/gsl/lib -fPIC
+        SOFLAGS +=  -Wl,-rpath=$(PGMLAB_LIB),-rpath=../external_lib/gsl/lib -fPIC
         OFLAGS =  -std=gnu99 -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g 
     endif
     ifeq ($(UNAME_S),Darwin)
@@ -36,7 +36,7 @@ else
         R_FLAGS = -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
         SOFLAGS +=  -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
         OFLAGS = -Wall -mtune=core2 -g -O2 -w 
-        XLINKER = -Xlinker $(LIBNET_LIB)
+        XLINKER = -Xlinker $(PGMLAB_LIB)
     endif
     UNAME_P := $(shell uname -p)
     ifeq ($(UNAME_P),x86_64)
@@ -51,15 +51,15 @@ else
 endif
 
 INCLUDE_GSL = -L../../external_lib/gsl/lib -I../../external_lib/gsl/include -lgsl -lgslcblas
-INCLUDE_LIBNET = -L../../net/lib -lnet -I../../net/include -I../../resources/make_hash_table/include
+INCLUDE_PGMLAB = -L../../net/lib -lpgmlab -I../../net/include -I../../resources/make_hash_table/include
 
 all: object 
 	mkdir -p lib; \
-	$(CC) $(LDFLAGS) $(SOFLAGS) $(R_LIB) -o lib/$(TARGET).$(SHARED_OBJECT_EXTENSION) obj/$(TARGET).o $(INCLUDE_LIBNET) $(RFLAGS)
+	$(CC) $(LDFLAGS) $(SOFLAGS) $(R_LIB) -o lib/$(TARGET).$(SHARED_OBJECT_EXTENSION) obj/$(TARGET).o $(INCLUDE_PGMLAB) $(RFLAGS)
 
 object:
 	mkdir -p obj; \
-	$(CC) -DNDEBUG $(INCLUDE_R) $(OFLAGS) -c src/$(TARGET).c -o obj/$(TARGET).o $(INCLUDE_LIBNET) $(INCLUDE_GSL)  $(XLINKER)
+	$(CC) -DNDEBUG $(INCLUDE_R) $(OFLAGS) -c src/$(TARGET).c -o obj/$(TARGET).o $(INCLUDE_PGMLAB) $(INCLUDE_GSL)  $(XLINKER)
 
 clean:
 	rm lib/* obj/*

r_package/libnetR/src/libnetR.c → R/pgmlabR/src/pgmlabR.c

@@ -12,7 +12,7 @@ SEXP r_reaction_logic_to_factorgraph(SEXP reaction_logic_pathway_filepath_, SEXP
 
     int exit_code = reaction_logic_to_factorgraph(reaction_logic_pathway_filepath, pathway_filepath, number_of_states);
     if (exit_code != 0) {
-        char * strerr = strerror_libnet(exit_code);
+        char * strerr = strerror_pgmlab(exit_code);
         Rprintf("ERROR: %s\n", strerr);
     }
 
@@ -37,7 +37,7 @@ SEXP r_learning_discrete_BayNet(SEXP reaction_logic_pathway_filepath_, SEXP path
     int exit_code = learning_discrete_BayNet(reaction_logic_pathway_filepath, pathway_filepath, observed_data_filepath, estimated_parameters_filepath, 
                              number_of_states, em_max_iterations, em_log_likelihood_change_limit, em_parameters_change_limit, map_flag, logging);
     if (exit_code != 0) {
-        char * strerr = strerror_libnet(exit_code);
+        char * strerr = strerror_pgmlab(exit_code);
         Rprintf("ERROR: %s\n", strerr);
     }
 
@@ -55,7 +55,7 @@ SEXP r_doLBPinference(SEXP reaction_logic_pathway_filepath_, SEXP pathway_filepa
 
     int exit_code = doLBPinference(reaction_logic_pathway_filepath, pathway_filepath, observed_data_filepath, posterior_probabilities_filepath, number_of_states);
     if (exit_code != 0) {
-        char * strerr = strerror_libnet(exit_code);
+        char * strerr = strerror_pgmlab(exit_code);
         Rprintf("ERROR: %s\n", strerr);
     }
 

README.md

@@ -1,8 +1,8 @@
-#LibNet
+#PGMLAB (Probablistic Graphical Model Laboratory)
 
-Libnet performs learning and inference in large discrete baysian networks. Libnet is a standalone C library, which has command line and R interfaces. 
+PGMLAB performs learning and inference in large discrete baysian networks. PGMLAB is a standalone C library, which has command line and R interfaces. 
 
-LibNet developed to fulfill three goals: 
+PGMLAB developed to fulfill three goals: 
 
    - To perform learning and inference in extremely large graphs. 
    - To be used by both expert and non expert in the field of machine learning
@@ -12,19 +12,21 @@ LibNet developed to fulfill three goals:
 
    - Hossein Radfar 
    - Adam Wright 
+##Web Site
+   - Visit the PGMLAB website [here](http://oicr.github.io/PGMLAB)
 
 ##Wiki
-   - Please visit the LibNet wiki [here](https://github.com/OICR/LibNet/wiki) for details and theory. 
-   - Make sure to follow the input file formats specifications [here](https://github.com/OICR/LibNet/wiki/File-Formats).  
+   - Please visit the PGMLAB wiki [here](https://github.com/OICR/PGMLAB/wiki) for details and theory. 
+   - Make sure to follow the input file formats specifications [here](https://github.com/OICR/PGMLAB/wiki/File-Formats).  
 
 ##System requirements
 
-LibNet has been tested on OS X and Ubuntu 14.04.
+PGMLAB has been tested on OS X and Ubuntu 14.04.
 
-###How to download, install and Run LibNet
+###How to download, install and Run PGMLAB
 ####1. Download
 
-   - Download the latest version of LibNet from [here](https://github.com/OICR/LibNet/zipball/master) 
+   - Download the latest version of PGMLAB from [here](https://github.com/OICR/PGMLAB/zipball/master) 
 
 ####2. Installation
 
@@ -33,42 +35,33 @@ LibNet has been tested on OS X and Ubuntu 14.04.
 	Linux: sudo apt-get install texinfo
 	Mac OS X: follow the following instructions http://macappstore.org/texinfo/
 
-#####2.2 Install LibNet Package
+#####2.2 Install PGMLAB Package
 
    - Type the following commands in a terminal:
 
-        cd .../your-download-directory/LibNet  
-	make  
+        cd .../your-download-directory/PGMLAB
+	make 
+        make install (this will link PGMLAB to system paths, making PGMLAB accessible from anywhere on the host) 
 
-####3. Running LibNet
 
-#####3.1 Generate hash for particular network with generateHash
+####3 User Interfaces 
 
-######Library Path
+There are two interaces to the shared object that come with this package: a command line interaface and a C interface. To make either of the interfaces you are required to have already compiled the PGMLAB shared object (3.2).
 
-   - Run the following command if you would like to access this library system wide (not necessary for basic installation) 
+#####3.1Command line interface
 
-	export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<net/lib/libnet.[so|dynlib> 
-
-####4 User Interfaces 
-
-There are two interaces to the shared object that come with this package: a command line interaface and a C interface. To make either of the interfaces you are required to have already compiled the LibNet shared object (3.2).
-
-#####4.1Command line interface
-
-######4.1.2 Interacting with the command line interface
+######3.1.2 Interacting with the command line interface
 
 This command line interface can be used in two distinct ways. The first way is to supply the paths of the files in a config file, in the same way as the example config files in the config folder and flags to customize the parameters to be use and the second way is to input the information through an interactive interface. Further infromation on how to use these interface can be found in the wiki.
 
-   - Run the following commands for a description of the LibNet command line interface. 
+   - Run the following commands for a description of the PGMLAB command line interface. 
 
-	cd bin  
-	./libnet --help  
+	pgmlab --help  
 
    - The following will be outputed from the previous command
 
 ```
-libnet [-gil] [--interactive] [--file-paths=file-paths] [--inference-use-logical-factorgraph] [--number-of-states=<int>] [--em-max-iterations=<int>] [--training-samples=<int>] [--log-likelihood-change-limit=<double>] [--parameters-change-limit=<double>] [--logging-on] [--maximum-a-posteriori-estimation] [--help] [--version] 
+pgmlab [-gil] [--interactive] [--file-paths=file-paths] [--inference-use-logical-factorgraph] [--number-of-states=<int>] [--em-max-iterations=<int>] [--training-samples=<int>] [--log-likelihood-change-limit=<double>] [--parameters-change-limit=<double>] [--logging-on] [--maximum-a-posteriori-estimation] [--help] [--version] 
 
 ###Flag descriptions  
  -g, --generate-factorgraph Generate factor graph from reaction logic
@@ -90,33 +83,30 @@ libnet [-gil] [--interactive] [--file-paths=file-paths] [--inference-use-logical
 
 *If you would like to use the interactive interface select the following flag: "--interactive".
 
-*If you would like to run a new pathway you will need to rerun the generateHash program and then recompile the libnet program.
+#####3.2 R interface
 
+In order to call pgmlab from the R Console you will need to load the PGMLAB R shared object. 
 
-#####4.2 R interface
-
-In order to call libnet from the R Console you will need to load the R LibNet shared object. 
-
-######4.2.1 Running R in order to be able to access the R LibNet shared object
+######3.2.1 Running R in order to be able to access the PGMLAB R shared object
 
    - Run on of the first two commands, depending on your OS, and then run one of the two options in the last line. 
 
-	cd r_package/libnetR/  (for Linux)  
-	cd r_package/ (for OS X)  
+	cd R/pgmlabR/  (for Linux)  
+	cd R/ (for OS X)  
 	type r or rstudio  
-   
+
    - You should now be in a R prompt
 
 *The current working directory needs to be correct to have the shared obejects link to one another correctly
 
-######4.2.2 Loading the LibNet shared ojbect within R or Rstudio
+######3.2.2 Loading the PGMLAB shared ojbect within R or Rstudio
 
    - Run the following command in order to load the shared object 
 
-	dyn.load("<path to repo>/libnet/r_package/libnetR/lib/libnetR.so") (for Linux)
-	dyn.load("libnetR/lib/libnetR.so") (for OS X)
+	dyn.load("<path to repo>/PGMLAB/R/pgmlabR/lib/pgmlabR.so") (for Linux)
+	dyn.load("pgmlabR/lib/pgmlabR.so") (for OS X)
 
-######4.2.3 Description of functions available from the R LibNet library
+######3.2.3 Description of functions available from the PGMLAB R library
 
 	r_reaction_logic_to_factorgraph(SEXP reaction_logic_pathway_filepath_, SEXP pathway_filepath_, SEXP number_of_states_) 
 
@@ -126,7 +116,7 @@ In order to call libnet from the R Console you will need to load the R LibNet sh
 
 *All filepaths can be either full or abolute paths and the rest of the variables should be supplied as integer values. 
 
-######4.2.4 Example R function calls 
+######3.2.4 Example R function calls 
 
 *These relative paths are for linux and should be changed of OS X. In OS X the change should be to remove one of the '../' from the beginning of the each filepath. 
 
@@ -144,16 +134,16 @@ In order to call libnet from the R Console you will need to load the R LibNet sh
 
 *Functions will return 0 upon success and error codes otherwise. 	
 
-####5 Libnet dependencies
+####4 PGMLAB dependencies
 
-All resources are included in the LibNet package. 
+All resources are included in the PGMLAB package. 
 
-#####5.1 Resources
+#####4.1 Resources
 | Name                      |  Description | Link |
 |---------------------------|------------------------|------|
-|  Minimal Perfect Hashing   | Minimal Perfect Hashing wass Created by Bob Jenkins and is used to hashing the names of the nodes. This allows LibNet to very quickely query nodes by their unique hash  |  http://burtleburtle.net/bob/hash/perfect.html    |
+|  Minimal Perfect Hashing   | Minimal Perfect Hashing wass Created by Bob Jenkins and is used to hashing the names of the nodes. This allows PGMLAB to very quickely query nodes by their unique hash  |  http://burtleburtle.net/bob/hash/perfect.html    |
 
-#####5.2 External Libraries
+#####4.2 External Libraries
 | Name                      |  Description | Link |
 |---------------------------|------------------------|------|
 | GNU Scientific Library (GSL) | GSL is a numerical library for C and C++ that provides a wirde range of mathematical routines | http://www.gnu.org/software/gsl/ |

cli/Makefile

@@ -2,7 +2,8 @@
 #
 # other external libraries/tools 
 #
-# 
+#
+CWD = $(shell pwd)
 LIBNET_LIB   = ../net/lib
 SOFLAGS      = 
 ################################
@@ -49,13 +50,13 @@ DEBUGFLAGS   = -O0 -D _DEBUG
 LIBDIRS = -L$(LIBNET_LIB)
 RPATH   = -Wl,-rpath=$(LIBNET_LIB)
 
-TARGET  = libnet
+TARGET  = pgmlab
 TARGET_PATH = ../bin/$(TARGET)
 SOURCES = $(shell echo src/*.c) $(shell echo ../resources/make_hash_table/src/*.c) ../resources/minini/minIni.c
 HEADERS = $(shell echo include/*.h) $(shell echo ../resources/make_hash_table/src/*.h) ../resources/minini/minIni.h ../resources/minini/wxMinIni.h ../resources/minini/minGlue.h
 OBJECTS = $(SOURCES:.c=.o)
 
-INCLUDE_NET = -L../net/lib -I../net/include -lnet
+INCLUDE_NET = -L../net/lib -I../net/include -l$(TARGET)
 INCLUDE_GSL = -L../external_lib/gsl/lib -I../external_lib/gsl/include -lgsl -lgslcblas
 INCLUDE_READLINE = -L../external_lib/readline/lib -I../external_lib/readline/include -lreadline
 INCLUDE_TERMCAP = -L../external_lib/termcap/lib -I../external_lib/termcap/include -ltermcap
@@ -68,12 +69,11 @@ $(TARGET): folders
 folders: 
 	mkdir -p ../bin 
 
-readline:
-	cd ..; \
-	make readline
+make install:
+	ln -s $(CWD)/../bin/$(TARGET) /usr/local/bin/$(TARGET)
+
+make uninstall:
+	rm /usr/local/bin/$(TARGET)
 
 clean:
 	rm -f $(TARGET) $(OBJECTS) 
-
-
-