Merge branch 'develop' of github.com:stan-dev/stan into release/v2.16.0

make/os_win

@@ -5,7 +5,7 @@
 #   - CFLAGS_GTEST
 #   - OPT
 #   - EXE
-# 
+#
 # Additionally, set the following variables to build
 # demo/lang using the Microsoft Visual Studio compiler.
 #   - CC_STANC
@@ -20,9 +20,9 @@ PATH_SEPARATOR = '\'
 ## Detecting Process Bitness:
 ## http://blogs.msdn.com/b/david.wang/archive/2006/03/26/howto-detect-process-bitness.aspx
 ifeq ($(PROCESSOR_ARCHITECTURE)$(PROCESSOR_ARCHITEW6432),x86)
-  BIT=32
+  BIT?=32
 else
-  BIT=64
+  BIT?=64
 endif
 ifeq (g++,$(CC_TYPE))
   CFLAGS += -m$(BIT)
@@ -40,4 +40,3 @@ ifeq (mingw32-g++,$(CC_TYPE))
 endif
 ifeq (clang++,$(CC_TYPE))
 endif
-

make/tests

@@ -128,6 +128,23 @@ test/dummy.cpp:
 .PHONY: test-headers
 test-headers: $(HEADER_TESTS)
 
+##
+# Adding a test for multiple translation units. If this fails,
+# a new function is probably missing an inline
+##
+
+test/unit/multiple_translation_units%.o : src/test/unit/multiple_translation_units%.cpp
+	@mkdir -p $(dir $@)
+	$(COMPILE.c) -O$O $< $(OUTPUT_OPTION)
+
+test/unit/libmultiple.so : test/unit/multiple_translation_units1.o test/unit/multiple_translation_units2.o
+	@mkdir -p $(dir $@)
+	$(CC) $(CFLAGS) -shared $(OUTPUT_OPTION) $^
+
+src/test/unit/multiple_translation_units_test.cpp : test/unit/libmultiple.so
+
+
+
 ############################################################
 ##
 # Use the stanc compiler to generate C++ from Stan programs

src/docs/stan-reference/acknowledgements.tex

@@ -15,7 +15,7 @@ \section*{Grants and Corporate Support}
 \subsection*{Current Grants}
 
 \begin{itemize}
-\item 
+\item
  U.~S.\ Department of Education Institute of Education Sciences
 \begin{itemize}\small
 \item Statistical and Research Methodology: Solving
@@ -39,13 +39,13 @@ \subsection*{Previous Grants}
 %
 \begin{itemize}
 \item
-U.~S.\ Department of Energy 
+U.~S.\ Department of Energy
 \begin{itemize}\small
 \item DE-SC0002099: Petascale Computing
 \end{itemize}
 %
 \item
-U.~S.\ National Science Foundation 
+U.~S.\ National Science Foundation
 \begin{itemize}\small
 \item
 ATM-0934516: Reconstructing Climate from Tree Ring Data
@@ -54,7 +54,7 @@ \subsection*{Previous Grants}
 \end{itemize}
 %
 \item
-U.~S.\ Department of Education Institute of Education Sciences 
+U.~S.\ Department of Education Institute of Education Sciences
 \begin{itemize}\small
 \item ED-GRANTS-032309-005:
 Practical Tools for Multilevel Hierarchical Modeling in Education
@@ -92,12 +92,12 @@ \subsection*{Code  and Doc Patches}
 to:
 Ethan Adams,
 Avraham Adler,
-Jarret Barber, 
+Jarret Barber,
 David R.~Blair,
-Miguel de Val-Borro, 
-Ross Boylan, 
-Eric N.~Brown, 
-Devin Caughey, 
+Miguel de Val-Borro,
+Ross Boylan,
+Eric N.~Brown,
+Devin Caughey,
 Emmanuel Charpentier,
 Daniel Chen,
 Jacob Egner,
@@ -116,6 +116,7 @@ \subsection*{Code  and Doc Patches}
 Dan Lakeland,
 Devin Leopold,
 Nathanael I.~Lichti,
+Jussi M\"a\"att\"a,
 Titus van der Malsburg,
 P.~D.~Metcalfe,
 Kyle Meyer,
@@ -155,8 +156,9 @@ \subsection*{Code  and Doc Patches}
 Alex Chase,
 Daniel Chen,
 Roman Cheplyaka,
-Andy Choi, 
+Andy Choi,
 David Chudzicki,
+Michael Clerx,
 Andria Dawson,
 daydreamt (GitHub handle),
 Conner DiPaolo,
@@ -190,15 +192,18 @@ \subsection*{Code  and Doc Patches}
 Tobias Madsen,
 Stefano Mangiola,
 David Manheim,
+Stephen Martin,
 Sean Matthews,
 David Mawdsley,
 Dieter Menne,
 Evelyn Mitchell,
+Javier Moreno,
 Robert Myles,xs
 Sunil Nandihalli,
 Eric Novik,
 Julia Palacios,
-Tamas Papp, 
+Tamas Papp,
+Anders Gorm Pedersen,
 Tomi Peltola,
 Andre Pfeuffer,
 Sergio Polini,
@@ -224,6 +229,7 @@ \subsection*{Code  and Doc Patches}
 Dougal Sutherland,
 John Sutton,
 Maciej Swat,
+J.~Takoua,
 Andrew J.~Tanentzap,
 Shravan Vashisth,
 Aki Vehtari,
@@ -234,8 +240,9 @@ \subsection*{Code  and Doc Patches}
 Sam Weiss,
 Luke Wiklendt,
 wrobell (GitHub handle),
-Howard Zail, and
-Jon Zelner.
+Howard Zail,
+Jon Zelner, and
+Xiubo Zhang
 
 Thanks to Kevin van Horn for install instructions for Cygwin and to
 Kyle Foreman for instructions on using the MKL compiler.

src/docs/stan-reference/algorithms.tex

@@ -169,11 +169,11 @@ \subsection{Leapfrog Integrator}
 repetitions of the above three steps) will be denoted
 $(\rho^{*},\theta^{*})$.
 
-The leapgrog integrator's error is on the order of $\epsilon^3$ per
+The leapfrog integrator's error is on the order of $\epsilon^3$ per
 step and $\epsilon^2$ globally, where $\epsilon$ is the time interval
 (also known as the step size);  \cite{LeimkuhlerReich:2004} provide a
 detailed analysis of numerical integration for Hamiltonian systems,
-including a derivation of the error bound for the leapforg
+including a derivation of the error bound for the leapfrog
 integrator.
 
 

src/docs/stan-reference/appendices.tex

@@ -52,7 +52,7 @@ \section{Boost License}
 \end{quote}
 %
 The copyright for each Boost package is held by its developers or their
-assginees.
+assignees.
 
 
 \section{Eigen License}
@@ -70,7 +70,7 @@ \section{Eigen License}
 \section{SUNDIALS License}
 
 Stan uses the SUNDIALS package for solving stiff differential
-equations.  SUNDIALS is distrubted under the new BSD (3-clause) license.
+equations.  SUNDIALS is distributed under the new BSD (3-clause) license.
 %
 \begin{quote}
 \url{https://opensource.org/licenses/BSD-3-Clause}
@@ -583,7 +583,7 @@ \subsection{Syntactic Conventions}
 of \code{A}.  The notation \code{A \% B}, following the Boost Spirit
 parser library's notation, is shorthand for \code{?(A (B A)*)}, i.e.,
 any number of \code{A} (including zero), separated by \code{B}.  A
-postfixed, curly-braced number indicates a fixed number of repetions;
+postfixed, curly-braced number indicates a fixed number of repetitions;
 e.g., \code{A\{6\}} is equivalent to a sequence of six copies of \code{A}.
 
 \subsection{Programs}
@@ -862,7 +862,7 @@ \section{Warnings vs.\ Errors}
 errors.  Error messages arise when a fatal problem occurs under the
 hood from which there is no way to recover.  Warning messages arise
 in circumstances from which the underlying program can continue to
-operaate.
+operate.
 
 An example warning message is an informational message about
 ill-formed input to an underlying function, which results in a
@@ -893,7 +893,7 @@ \section{Parsing and Compilation}
 \section{Initialization}
 
 \begin{itemize}
-\item {\it vanishing density.} This message arrises when there is a
+\item {\it vanishing density.} This message arises when there is a
   problem with initialization not providing a finite log probability.
 %
 \end{itemize}
@@ -964,7 +964,7 @@ \section{\code{increment\_log\_prob} Statement}
 \section{\code{lp\_\_} Variable}
 
 \begin{description}
-\item[Depcreated]
+\item[Deprecated]
 The variable \code{lp\_\_} is available wherever log density increment
 statements are allowed (\code{target~+=} and \Verb|~| shorthand
 statements).
@@ -1113,7 +1113,7 @@ \section{\code{if\_else} Function}
   otherwise.
 %
 \item[Replacement] Use the conditional operator which allows more
-  flexiblity in the types of \code{b} and \code{c} and is much more
+  flexibility in the types of \code{b} and \code{c} and is much more
   efficient in that it only evaluates whichever of \code{b} or
   \code{c} is returned.  See \refsection{conditional-operator} for
   full details of the conditional operator.  Replace
@@ -1126,7 +1126,7 @@ \section{\code{if\_else} Function}
 \end{stancode}
 \end{description}
 
-\section{\code{\#} Commens}
+\section{\code{\#} Comments}
 
 \begin{description}
 \item[Deprecated] The use of \code{\#} for line-based comments is