Merge branch 'develop' into bugfix/issue-530-no-model-parameters: mov…

…ing test to CmdStan branch bugfix/issue-530-no-model-parameters

Conflicts:
	src/test/CmdStan/fixed_param_sampler_test.cpp

.gitignore

@@ -5,9 +5,6 @@
 /*.dSYM
 /bin
 
-# precompiled model header
-/src/stan/model/model_header.hpp.*ch
-
 # other binary
 *.o
 *.exe
@@ -32,23 +29,18 @@ stan.kdev4
 .Rapp.history
 
 # models:
-src/models/**/*
-!src/models/**/*.stan
-!src/models/**/*.R
-!src/models/**/makefile
+/src/models/**
+!/src/models/**.stan
+!/src/models/**.R
+!/src/models/**/makefile
 
 # tests: compiled models
-src/test/test-models/**/*
-!src/test/test-models/**/*.stan
-!src/test/test-models/**/.gitignore
+/src/test/test-models/**
+!/src/test/test-models/**.stan
+!/src/test/test-models/**/.gitignore
 
 # tests: generated agrad tests
-src/test/unit-distribution/**/**/**/*_generated_test.cpp
+/src/test/unit-distribution/*/*/*/*_generated_test.cpp
 
 # For the Mac
 *.DS_Store
-
-#auto generated by RStan make
-rstan/rstan/R/git_head.R
-rstan/rstan/inst/include/stanlib
-rstan/rstan/inst/include/stansrc

make/os_linux

@@ -24,6 +24,10 @@ ifeq (mingw32-g++,$(CC_TYPE))
 endif
 ifeq (clang++,$(CC_TYPE))
 #  CFLAGS += -stdlib=libc++
+  ifeq (true,$(C++11))
+    CFLAGS += -stdlib=libc++ -std=c++11
+    LDFLAGS += -lc++
+  endif
   CFLAGS_GTEST += -DGTEST_HAS_PTHREAD=0
   CFLAGS_GTEST += -Wno-c++11-long-long
   CFLAGS += -Wno-unused-function

make/os_mac

@@ -12,12 +12,17 @@ ifeq (g++,$(CC_TYPE))
     CFLAGS += -ftemplate-depth-$(TEMPLATE_DEPTH)
   endif
 endif
+
 ifeq (clang++,$(CC_TYPE))
   CFLAGS_GTEST += -Wc++11-extensions
   CFLAGS_GTEST += -Wno-c++11-long-long
   CFLAGS += -Wno-unused-function
   CFLAGS += -Wno-tautological-compare
   CFLAGS += -Wno-c++11-long-long
+  ifeq (true,$(C++11))
+    CFLAGS += -stdlib=libc++ -std=c++11
+  endif
+  #PCH = .pch
   ifeq (4.2,$(CC_MAJOR).$(CC_MINOR))
     TEMPLATE_DEPTH ?= 256
     CFLAGS += -ftemplate-depth=$(TEMPLATE_DEPTH)

make/tests

@@ -172,16 +172,10 @@ endif
 
 ##
 # TEST_MODELS is the set of all the test models.
-# Those in the 'compiled' subdirectory are supposed to be compiled.
 # Those in the 'no_main' subdirectory are supposed to be compiled without a main function.
 ##
 TEST_MODELS := $(shell find src/test/test-models -type f -name '*.stan')
 
-##
-# Compile these with a main.
-## 
-$(patsubst %.stan,%.cpp,$(filter src/test/test-models/compiled/%,$(TEST_MODELS))) : %.cpp : %.stan bin/stanc$(EXE)
-	bin$(PATH_SEPARATOR)stanc$(EXE) --o=$@ $<
 ##
 # Compile these with no main.
 ##
@@ -193,8 +187,6 @@ $(patsubst %.stan,%.cpp,$(filter src/test/test-models/no-main/%,$(TEST_MODELS)))
 # Tests that also depend on generated models.
 ##
 test/unit/io/mcmc_writer.o: src/test/test-models/no-main/io_example.cpp
-test/unit/gm/command_init.o: src/test/test-models/no-main/gm/test_lp.cpp
-test/unit/gm/command_write_iteration.o: src/test/test-models/no-main/gm/test_lp.cpp
 test/unit/gm/generator.o: src/test/test-models/no-main/gm/test_lp.cpp
 
 test/unit/model/util.o: src/test/test-models/no-main/model/valid.cpp src/test/test-models/no-main/model/domain_fail.cpp
@@ -203,21 +195,13 @@ test/unit/mcmc/hmc/hamiltonians/base_hamiltonian.o: src/test/test-models/no-main
 test/unit/mcmc/hmc/hamiltonians/unit_e_metric.o: src/test/test-models/no-main/mcmc/hmc/hamiltonians/funnel.cpp
 test/unit/mcmc/hmc/hamiltonians/diag_e_metric.o: src/test/test-models/no-main/mcmc/hmc/hamiltonians/funnel.cpp
 test/unit/mcmc/hmc/hamiltonians/dense_e_metric.o: src/test/test-models/no-main/mcmc/hmc/hamiltonians/funnel.cpp
-test/unit/mcmc/hmc/integrators/expl_leapfrog.o: src/test/test-models/no-main/mcmc/hmc/integrators/command.cpp src/test/test-models/no-main/mcmc/hmc/integrators/gauss.cpp
-
-##
-# all files that should be compiled as tests
-##
-FILES := $(shell find src/test/test-models/compiled -type f -name '*.stan')
+test/unit/mcmc/hmc/integrators/expl_leapfrog.o: src/test/test-models/no-main/mcmc/hmc/integrators/command.cpp 
+test/unit/mcmc/hmc/integrators/expl_leapfrog2.o: src/test/test-models/no-main/mcmc/hmc/integrators/gauss.cpp
 
-test/integration/compile_models.o : $(patsubst %.stan,%$(EXE),$(FILES)) $(patsubst %.stan,%.cpp-test,$(wildcard src/test/test-models/syntax-only/*stan))
+test/unit/common/command_init.o: src/test/test-models/no-main/common/test_lp.cpp
+test/unit/common/write_iteration.o: src/test/test-models/no-main/common/test_lp.cpp
 
-test/CmdStan/command.o: \
-   $(addprefix src/test/test-models/compiled/CmdStan/,\
-               $(addsuffix $(EXE), printer domain_fail value_fail proper))
-test/CmdStan/gm/argument_configuration.o: src/test/test-models/compiled/CmdStan/test_model$(EXE)
-test/CmdStan/fixed_param_sampler.o: src/test/test-models/compiled/CmdStan/empty$(EXE) src/test/test-models/compiled/CmdStan/proper$(EXE)
-test/CmdStan/optimization_output.o: src/test/test-models/compiled/CmdStan/optimization_output$(EXE)
+test/integration/compile_models.o : $(patsubst %.stan,%.cpp-test,$(wildcard src/test/test-models/syntax-only/*stan))
 
 ##
 # CmdStan specific targets. Should be removed in the future.
@@ -226,12 +210,6 @@ $(patsubst src/%_test.cpp,%.o,$(filter src/test/CmdStan/%,$(ALL_TESTS))): test/%
 	@mkdir -p $(dir $@)
 	$(COMPILE.c) -O$O $(CFLAGS_GTEST) $< $(OUTPUT_OPTION)
 
-##
-# CmdStan model tests. Adding built model as a dependency.
-##
-$(patsubst src/%_test.cpp,%.o,$(filter src/test/CmdStan/models/%,$(ALL_TESTS))): test/CmdStan/%.o : %$(EXE)
-
-
 ##
 # Agrad distributions test generator
 ##
@@ -289,7 +267,7 @@ test-headers: $(HEADER_TESTS)
 # Deprecated test targets
 ##
 .PHONY: test-unit test-distributions test-models test-bugs
-test-unit test-distributions test-models test-bugs test-all:
+test-unit test-distributions test-all:
 	@echo ''
 	@echo ''
 	@echo '  The '$@' target is deprecated. Please use these make targets instead:'
@@ -299,9 +277,23 @@ test-unit: src/test/unit src/test/unit-agrad-rev src/test/unit-agrad-fwd
 
 test-distributions: src/test/unit-distribution
 
-test-models: src/test/CmdStan/models
+test-models:
+	@echo ''
+	@echo 'These tests are now in the CmdStan repository. Run this from'
+	@echo 'the CmdStan directory:'
+	@echo ''
+	@echo '  "> make src/test/models"'
+	@echo ''
+	$(error Tests have moved to the CmdStan repository. Run "> make src/test/models")
 
-test-bugs: src/test/CmdStan/models/bugs_examples
+test-bugs:
+	@echo ''
+	@echo 'These tests are now in the CmdStan repository. Run this from'
+	@echo 'the CmdStan directory:'
+	@echo ''
+	@echo '  "> make src/test/models/bugs_examples"'
+	@echo ''
+	$(error Tests have moved to the CmdStan repository. Run "> make src/test/models/bugs_examples")
 
 
 .PHONY: test-all

makefile

@@ -15,12 +15,14 @@ SUFIXES:
 # - CC: The compiler to use. Expecting g++ or clang++.
 # - O: Optimization level. Valid values are {0, 1, 2, 3}.
 # - AR: archiver (must specify for cross-compiling)
-# - OS: {mac, win, linux}. 
+# - OS: {mac, win, linux}
+# - C++11: Compile with C++11 extensions, Valid values: {true, false}. 
 ##
 CC = g++
 O = 3
 O_STANC = 0
 AR = ar
+C++11 = false
 
 ##
 # Library locations

src/docs/stan-reference/appendices.tex

@@ -1,4 +1,3 @@
-
 \part*{Appendices}
 \addcontentsline{toc}{part}{Appendices}
 
@@ -333,10 +332,11 @@ \subsection{Rtools C++ Development Environment}
    Authoring}, click \code{Next},
 \item \emph{Select Additional Tasks}: check \code{Edit Path} and \code{Save
  Version in Registry}, click \code{Next},
-\item \emph{System Path Report}: click \code{Next},
+\item \emph{System Path Report}: ensure that that the paths to \code{c:\textbackslash{}Rtools\textbackslash{}bin} and \code{c:\textbackslash{}Rtools\textbackslash{}gcc-4.6.3\textbackslash{}bin} are listed at the beginning of the path and click \code{Next},
 \item \emph{Ready to Install}: click \code{Next}, wait for the
   install to complete, then
 \item \emph{Finish}: click \code{Finish}.
+\item \emph{Confirm Path}: After the install has completed, open a command prompt and type \code{PATH} to ensure that the new path is activated and the Rtools folders are in the system path.
 \end{itemize}
 
 \subsection{Downloading and Unpacking Stan}

src/docs/stan-reference/functions.tex

@@ -1243,7 +1243,25 @@ \section{Array Broadcasting}\label{array-broadcasting.section}
 \code{k} in \code{1:4}, \code{m} in \code{1:5}, and \code{n} in
 \code{1:6}.
 
-\section{Other functions}
+\section{Sorting functions}\label{sorting-functions.section}
+
+Sorting can be used to sort values or the indices of those values in
+either ascending or descending order.  For example, if \code{v} is
+declared as a real array of size 3, with values
+\[
+\mbox{\code{v}} = (1, -10.3, 20.987),
+\]
+then the various sort routines produce
+%
+\begin{eqnarray*}
+\mbox{\code{sort\_asc(v)}} & = &  (-10.3,1,20.987)
+\\[4pt]
+\mbox{\code{sort\_desc(v)}} & = &  (20.987,1,-10.3)
+\\[4pt]
+\mbox{\code{sort\_indices\_asc(v)}} & = &  (2,1,3)
+\\[4pt]
+\mbox{\code{sort\_indices\_desc(v)}} & = &  (3,1,2)
+\end{eqnarray*}
 
 \begin{description}
 %
@@ -1259,6 +1277,22 @@ \section{Other functions}
 \fitem{int[]}{sort\_desc}{int[] \farg{v}}{
 Sort the elements of \farg{v} in descending order}
 %
+\fitem{int[]}{sort\_indices\_asc}{real[] \farg{v}}{
+Return an array of indices between 1 and the size of \farg{v},
+sorted to index \farg{v} in ascending order.}
+%
+\fitem{int[]}{sort\_indices\_asc}{int[] \farg{v}}{
+Return an array of indices between 1 and the size of \farg{v},
+sorted to index \farg{v} in ascending order.}
+%
+\fitem{int[]}{sort\_indices\_desc}{real[] \farg{v}}{
+Return an array of indices between 1 and the size of \farg{v},
+sorted to index \farg{v} in descending order.}
+%
+\fitem{int[]}{sort\_indices\_desc}{int[] \farg{v}}{
+Return an array of indices between 1 and the size of \farg{v},
+sorted to index \farg{v} in descending order.}
+%
 \fitem{int}{rank}{real[] \farg{v}, int \farg{s}}{
 Number of components of \farg{v} less than \farg{v[s]}}
 %
@@ -1267,6 +1301,7 @@ \section{Other functions}
 %
 \end{description}
 
+
 \chapter{Matrix Operations}\label{matrix-operations.chapter}
 \noindent
 
@@ -2185,7 +2220,11 @@ \subsubsection{Singular Value Decomposition}
 \end{description}
 
 
-\section{Other functions}
+\section{Sort Functions}
+
+See \refsection{sorting-functions} for examples of how the functions
+work. 
+
 \begin{description}
 %
 \fitem{vector}{sort\_asc}{vector \farg{v}}{
@@ -2200,6 +2239,22 @@ \section{Other functions}
 \fitem{row\_vector}{sort\_desc}{row\_vector \farg{v}}{
 Sort the elements of \farg{v} in descending order}
 %
+\fitem{int[]}{sort\_indices\_asc}{vector \farg{v}}{
+Return an array of indices between 1 and the size of \farg{v},
+sorted to index \farg{v} in ascending order.}
+%
+\fitem{int[]}{sort\_indices\_asc}{row\_vector \farg{v}}{
+Return an array of indices between 1 and the size of \farg{v},
+sorted to index \farg{v} in ascending order.}
+%
+\fitem{int[]}{sort\_indices\_desc}{vector \farg{v}}{
+Return an array of indices between 1 and the size of \farg{v},
+sorted to index \farg{v} in descending order.}
+%
+\fitem{int[]}{sort\_indices\_desc}{row\_vector \farg{v}}{
+Return an array of indices between 1 and the size of \farg{v},
+sorted to index \farg{v} in descending order.}
+%
 \fitem{int}{rank}{vector \farg{v}, int \farg{s}}{
 Number of components of \farg{v} less than \farg{v[s]}}
 %

src/docs/stan-reference/introduction.tex

@@ -898,8 +898,8 @@ \subsubsection{Jacobian Required Warning}
 how to calculate the required Jacobian adjustment and apply it in a model.
 
 In linear transforms or matrix/array slicing, spurious warnings
-arise.  Ane example is the following model, which involves extraction
-of a rwo from a matrix for vectorized sampling.
+arise.  An example is the following model, which involves extraction
+of a row from a matrix for vectorized sampling.
 %
 \begin{quote}
 \begin{Verbatim}

src/stan/common.hpp

@@ -0,0 +1,20 @@
+#ifndef __STAN__COMMON_HPP___
+#define __STAN__COMMON_HPP___
+
+#include <stan/common/command.hpp>
+#include <stan/common/do_print.hpp>
+#include <stan/common/init_adapt.hpp>
+#include <stan/common/init_nuts.hpp>
+#include <stan/common/init_static_hmc.hpp>
+#include <stan/common/init_windowed_adapt.hpp>
+#include <stan/common/print_progress.hpp>
+#include <stan/common/run_markov_chain.hpp>
+#include <stan/common/sample.hpp>
+#include <stan/common/warmup.hpp>
+#include <stan/common/write_error_msg.hpp>
+#include <stan/common/write_iteration.hpp>
+#include <stan/common/write_iteration_csv.hpp>
+#include <stan/common/write_model.hpp>
+#include <stan/common/write_stan.hpp>
+
+#endif