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Bob Carpenter
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Merge branch 'develop' of https://github.com/stan-dev/cmdstan into develop
2 parents 2d99e9a + 3f23f5f commit dfda127

14 files changed

+422
-202
lines changed

‎make/models

+5-5
Original file line numberDiff line numberDiff line change
@@ -4,15 +4,15 @@
44
MODEL_HEADER := stan/src/stan/model/model_header.hpp
55
CMDSTAN_MAIN := src/cmdstan/main.cpp
66

7-
.PRECIOUS: %.cpp %.o
8-
$(patsubst %.stan,%,$(wildcard $(addsuffix .stan,$(MAKECMDGOALS)))) : %$(EXE) : %.cpp %.stan bin/stanc$(EXE) bin/print$(EXE)
7+
.PRECIOUS: %.hpp %.o
8+
$(patsubst %.stan,%,$(wildcard $(addsuffix .stan,$(MAKECMDGOALS)))) : %$(EXE) : %.hpp %.stan bin/stanc$(EXE) bin/print$(EXE)
99
@echo ''
1010
@echo '--- Linking C++ model ---'
1111
$(LINK.c) -O$O $(OUTPUT_OPTION) $(CMDSTAN_MAIN) -include $< $(LDLIBS)
1212

13-
.PRECIOUS: %.cpp
14-
%.cpp : %.stan $(MODEL_HEADER) bin/stanc$(EXE)
13+
.PRECIOUS: %.hpp
14+
%.hpp : %.stan $(MODEL_HEADER) bin/stanc$(EXE)
1515
@echo ''
1616
@echo '--- Translating Stan model to C++ code ---'
17-
$(WINE) bin$(PATH_SEPARATOR)stanc$(EXE) $< --o=$@ --no_main
17+
$(WINE) bin$(PATH_SEPARATOR)stanc$(EXE) $< --o=$@
1818

‎makefile

+4-5
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@ AR = ar
2626
##
2727
STANAPI_HOME ?= stan/
2828
EIGEN ?= $(STANAPI_HOME)lib/eigen_3.2.2
29-
BOOST ?= $(STANAPI_HOME)lib/boost_1.54.0
29+
BOOST ?= $(STANAPI_HOME)lib/boost_1.55.0
3030
GTEST ?= $(STANAPI_HOME)lib/gtest_1.7.0
3131

3232
##
@@ -69,12 +69,11 @@ PATH_SEPARATOR = /
6969
%.o : %.cpp
7070
$(COMPILE.c) -O$O $(OUTPUT_OPTION) $<
7171

72-
%$(EXE) : %.cpp %.stan
72+
%$(EXE) : %.hpp %.stan
7373
@echo ''
7474
@echo '--- Linking C++ model ---'
7575
$(LINK.c) -O$O $(OUTPUT_OPTION) $(CMDSTAN_MAIN) -include $< $(LDLIBS)
7676

77-
7877
##
7978
# Tell make the default way to compile a .o file.
8079
##
@@ -139,7 +138,7 @@ endif
139138
@echo ''
140139
@echo ' This target will:'
141140
@echo ' 1. Build the Stan compiler: bin/stanc$(EXE).'
142-
@echo ' 2. Use the Stan compiler to generate C++ code, foo/bar.cpp.'
141+
@echo ' 2. Use the Stan compiler to generate C++ code, foo/bar.hpp.'
143142
@echo ' 3. Compile the C++ code using $(CC) to generate foo/bar$(EXE)'
144143
@echo ''
145144
@echo ' Example - Sample from a normal: stan/example-models/basic_distributions/normal.stan'
@@ -192,7 +191,7 @@ build: bin/stanc$(EXE) bin/print$(EXE)
192191

193192
clean: clean-manual
194193
$(RM) -r test
195-
$(RM) $(wildcard $(patsubst %.stan,%.cpp,$(TEST_MODELS)))
194+
$(RM) $(wildcard $(patsubst %.stan,%.hpp,$(TEST_MODELS)))
196195
$(RM) $(wildcard $(patsubst %.stan,%$(EXE),$(TEST_MODELS)))
197196

198197
clean-manual:

‎runCmdStanTests.py

+181
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,181 @@
1+
#!/usr/bin/python
2+
3+
"""
4+
replacement for runtest target in Makefile
5+
arg 1: test dir or test file
6+
"""
7+
8+
import os
9+
import os.path
10+
import platform
11+
import sys
12+
import subprocess
13+
import time
14+
15+
winsfx = ".exe"
16+
testsfx = "_test.cpp"
17+
debug = False
18+
batchSize = 25
19+
20+
def usage():
21+
sys.stdout.write('usage: %s <path/test/dir(/files)>\n' % sys.argv[0])
22+
sys.stdout.write('or\n')
23+
sys.stdout.write(' %s -j<#cores> <path/test/dir(/files)>\n' % sys.argv[0])
24+
sys.exit(0)
25+
26+
def stopErr(msg, returncode):
27+
sys.stderr.write('%s\n' % msg)
28+
sys.stderr.write('exit now (%s)\n' % time.strftime('%x %X %Z'))
29+
sys.exit(returncode)
30+
31+
def isWin():
32+
if (platform.system().lower().startswith("windows")
33+
or os.name.lower().startswith("windows")):
34+
return True
35+
return False
36+
37+
# set up good makefile target name
38+
def mungeName(name):
39+
if (debug):
40+
print("munge input: %s" % name)
41+
if (name.startswith("src")):
42+
name = name.replace("src/","",1)
43+
if (name.endswith(testsfx)):
44+
name = name.replace(testsfx,"_test")
45+
if (isWin()):
46+
name += winsfx
47+
name = name.replace("\\","/")
48+
49+
name = name.replace(" ", "\\ ").replace("(","\\(").replace(")","\\)")
50+
if (debug):
51+
print("munge return: %s" % name)
52+
return name
53+
54+
55+
def doCommand(command):
56+
print("------------------------------------------------------------")
57+
print("%s" % command)
58+
p1 = subprocess.Popen(command,shell=True)
59+
p1.wait()
60+
if (not(p1.returncode == None) and not(p1.returncode == 0)):
61+
stopErr('%s failed' % command, p1.returncode)
62+
63+
def makeTest(name, j):
64+
target = mungeName(name)
65+
if (j == None):
66+
command = 'make %s' % target
67+
else:
68+
command = 'make -j%d %s' % (j,target)
69+
doCommand(command)
70+
71+
def makeBuild(j):
72+
if (j == None):
73+
command = 'make build'
74+
else:
75+
command = 'make -j%d build' % j
76+
doCommand(command)
77+
78+
79+
def makeTestModel(target, j):
80+
if (j == None):
81+
command = 'make %s' % target
82+
else:
83+
command = 'make -j%d %s' % (j,target)
84+
doCommand(command)
85+
86+
87+
def makeTests(dirname, filenames, j):
88+
targets = list()
89+
for name in filenames:
90+
if (not name.endswith(testsfx)):
91+
continue
92+
target = "/".join([dirname,name])
93+
target = mungeName(target)
94+
targets.append(target)
95+
if (len(targets) > 0):
96+
if (debug):
97+
print('# targets: %d' % len(targets))
98+
startIdx = 0
99+
endIdx = batchSize
100+
while (startIdx < len(targets)):
101+
if (j == None):
102+
command = 'make %s' % ' '.join(targets[startIdx:endIdx])
103+
else:
104+
command = 'make -j%d %s' % (j,' '.join(targets[startIdx:endIdx]))
105+
if (debug):
106+
print('start %d, end %d' % (startIdx,endIdx))
107+
print(command)
108+
doCommand(command)
109+
startIdx = endIdx
110+
endIdx = startIdx + batchSize
111+
if (endIdx > len(targets)):
112+
endIdx = len(targets)
113+
114+
115+
def runTest(name):
116+
executable = mungeName(name).replace("/",os.sep)
117+
xml = mungeName(name).replace(winsfx, "")
118+
command = '%s --gtest_output="xml:%s.xml"' % (executable, xml)
119+
doCommand(command)
120+
121+
def main():
122+
if (len(sys.argv) < 2):
123+
usage()
124+
125+
argsIdx = 1
126+
j = None
127+
if (sys.argv[1].startswith("-j")):
128+
argsIdx = 2
129+
if (len(sys.argv) < 3):
130+
usage()
131+
else:
132+
j = sys.argv[1].replace("-j","")
133+
try:
134+
jprime = int(j)
135+
if (jprime < 1 or jprime > 16):
136+
stopErr("bad value for -j flag",-1)
137+
j = jprime
138+
except ValueError:
139+
stopErr("bad value for -j flag",-1)
140+
141+
142+
# pass 0: make build
143+
makeBuild(j)
144+
145+
# pass 1: call make to compile test targets
146+
for i in range(argsIdx,len(sys.argv)):
147+
testname = sys.argv[i]
148+
if (debug):
149+
print("testname: %s" % testname)
150+
if (not(os.path.exists(testname))):
151+
stopErr('%s: no such file or directory' % testname,-1)
152+
if (not(os.path.isdir(testname))):
153+
if (not(testname.endswith(testsfx))):
154+
stopErr('%s: not a testfile' % testname,-1)
155+
if (debug):
156+
print("make single test: %s" % testname)
157+
makeTest(testname,j)
158+
else:
159+
for root, dirs, files in os.walk(testname):
160+
if (debug):
161+
print("make root: %s" % root)
162+
makeTests(root,files,j)
163+
164+
# pass 2: run test targets
165+
for i in range(argsIdx,len(sys.argv)):
166+
testname = sys.argv[i]
167+
if (not(os.path.isdir(testname))):
168+
if (debug):
169+
print("run single test: %s" % testname)
170+
runTest(testname)
171+
else:
172+
for root, dirs, files in os.walk(testname):
173+
for name in files:
174+
if (name.endswith(testsfx)):
175+
if (debug):
176+
print("run dir,test: %s,%s" % (root,name))
177+
runTest(os.sep.join([root,name]))
178+
179+
180+
if __name__ == "__main__":
181+
main()

‎src/docs/cmdstan-guide/stanc.tex

+4-4
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@ \section{The \stanc Compiler}
3939
\begin{quote}
4040
\begin{Verbatim}[fontshape=sl]
4141
> cd <cmdstan-home>
42-
> bin/stanc --name=bernoulli --o=bernoulli.cpp \
42+
> bin/stanc --name=bernoulli --o=bernoulli.hpp \
4343
stan/example-models/basic_estimators/bernoulli.stan
4444
\end{Verbatim}
4545
\end{quote}
@@ -51,7 +51,7 @@ \section{The \stanc Compiler}
5151
\begin{quote}
5252
\begin{Verbatim}[fontshape=sl]
5353
> cd <cmdstan-home>
54-
> bin\stanc.exe --name=bernoulli --o=bernoulli.cpp ^
54+
> bin\stanc.exe --name=bernoulli --o=bernoulli.hpp ^
5555
stan/example-models/basic_estimators/bernoulli.stan
5656
\end{Verbatim}
5757
\end{quote}
@@ -67,7 +67,7 @@ \section{The \stanc Compiler}
6767
any \Cpp reserved keyword.
6868

6969
The \Cpp code implementing the class is written to the file
70-
\code{bernoulli.cpp} in the current directory. The final argument,
70+
\code{bernoulli.hpp} in the current directory. The final argument,
7171
\code{bernoulli.stan}, is the file from which to read the \Stan
7272
program.
7373

@@ -105,7 +105,7 @@ \section{Command-Line Options for {\tt\bfseries stanc}}
105105
\mbox{ } \\
106106
Specify the name of the file into which the generated \Cpp is written.
107107
\\[2pt]
108-
Default: {\tt {\slshape cpp\_file\_name} = {\slshape class\_name}.cpp}
108+
Default: {\tt {\slshape cpp\_file\_name} = {\slshape class\_name}.hpp}
109109
%
110110
\end{description}
111111

‎src/test/interface/command_test.cpp

+6
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,12 @@
66
#include <stdexcept>
77
#include <boost/math/policies/error_handling.hpp>
88

9+
using cmdstan::test::convert_model_path;
10+
using cmdstan::test::count_matches;
11+
using cmdstan::test::multiple_command_separator;
12+
using cmdstan::test::run_command;
13+
using cmdstan::test::run_command_output;
14+
915
TEST(StanUiCommand, countMatches) {
1016
EXPECT_EQ(-1, count_matches("", ""));
1117
EXPECT_EQ(-1, count_matches("", "abc"));

‎src/test/interface/csv_header_consistency_test.cpp

+4
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,10 @@
33
#include <test/utility.hpp>
44
#include <stan/mcmc/chains.hpp>
55

6+
using cmdstan::test::convert_model_path;
7+
using cmdstan::test::run_command;
8+
using cmdstan::test::run_command_output;
9+
610
TEST(gm,csv_header_consistency) {
711
// from stan-dev/stan issue #109
812
std::vector<std::string> model_path;

‎src/test/interface/elapsed_time_test.cpp

+5
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,11 @@
33
#include <fstream>
44
#include <streambuf>
55

6+
using cmdstan::test::count_matches;
7+
using cmdstan::test::get_path_separator;
8+
using cmdstan::test::run_command;
9+
using cmdstan::test::run_command_output;
10+
611
TEST(CommandElapsedTime, PrintToScreen) {
712
std::string path_separator;
813
path_separator.push_back(get_path_separator());

‎src/test/interface/fixed_param_sampler_test.cpp

+3-1
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,12 @@
11
#include <stan/mcmc/chains.hpp>
22
#include <stan/mcmc/fixed_param_sampler.hpp>
33
#include <stan/io/stan_csv_reader.hpp>
4-
54
#include <gtest/gtest.h>
65
#include <test/utility.hpp>
76

7+
using cmdstan::test::convert_model_path;
8+
using cmdstan::test::run_command;
9+
using cmdstan::test::run_command_output;
810

911
void test_constant(const Eigen::VectorXd& samples) {
1012
for (int i = 1; i < samples.size(); i++)

‎src/test/interface/gm/argument_configuration_test.cpp

+5
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,11 @@
1313
#include <vector>
1414
#include <sstream>
1515

16+
using cmdstan::test::convert_model_path;
17+
using cmdstan::test::multiple_command_separator;
18+
using cmdstan::test::run_command;
19+
using cmdstan::test::run_command_output;
20+
1621
void clean_line(std::string& line) {
1722
line.erase(0, 1);
1823
if (line.find("(Default)") != std::string::npos)

‎src/test/interface/optimization_output_test.cpp

+4
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,10 @@
22
#include <test/utility.hpp>
33
#include <stan/mcmc/chains.hpp>
44

5+
using cmdstan::test::convert_model_path;
6+
using cmdstan::test::run_command;
7+
using cmdstan::test::run_command_output;
8+
59
class CmdStan : public testing::Test {
610
public:
711
void SetUp() {

‎src/test/interface/print_test.cpp

+5
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,11 @@
22
#include <gtest/gtest.h>
33
#include <test/utility.hpp>
44

5+
using cmdstan::test::count_matches;
6+
using cmdstan::test::get_path_separator;
7+
using cmdstan::test::run_command;
8+
using cmdstan::test::run_command_output;
9+
510
TEST(CommandPrint, next_index_1d) {
611
std::vector<int> dims(1);
712
std::vector<int> index(1,1);

‎src/test/interface/print_uninitialized_test.cpp

+4
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,10 @@
22
#include <stan/gm/error_codes.hpp>
33
#include <test/utility.hpp>
44

5+
using cmdstan::test::convert_model_path;
6+
using cmdstan::test::run_command;
7+
using cmdstan::test::run_command_output;
8+
59
TEST(gm,print_uninitialized) {
610
// This was stan-dev/stan issue #91
711
std::vector<std::string> model_path;

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