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WardBrianWardBrian
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Merge pull request #1298 from stan-dev/update/3301-stan-csv-reader
2 parents b67ab56 + aa6a007 commit 51e7cfd

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3 files changed

+35
-45
lines changed

3 files changed

+35
-45
lines changed

‎src/cmdstan/command_helper.hpp‎

Lines changed: 4 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -284,20 +284,18 @@ void parse_stan_csv(const std::string &fname,
284284
std::stringstream msg;
285285
// parse CSV contents
286286
std::ifstream stream = file::safe_open(fname);
287-
stan::io::stan_csv_reader::read_metadata(stream, fitted_params.metadata,
288-
&msg);
287+
stan::io::stan_csv_reader::read_metadata(stream, fitted_params.metadata);
289288
if (!stan::io::stan_csv_reader::read_header(stream, fitted_params.header,
290-
&msg, false)) {
289+
false)) {
291290
msg << "Error reading fitted param names from sample csv file \"" << fname
292291
<< "\"" << std::endl;
293292
throw std::invalid_argument(msg.str());
294293
}
295-
stan::io::stan_csv_reader::read_adaptation(stream, fitted_params.adaptation,
296-
&msg);
294+
stan::io::stan_csv_reader::read_adaptation(stream, fitted_params.adaptation);
297295
fitted_params.timing.warmup = 0;
298296
fitted_params.timing.sampling = 0;
299297
stan::io::stan_csv_reader::read_samples(stream, fitted_params.samples,
300-
fitted_params.timing, &msg);
298+
fitted_params.timing);
301299
stream.close();
302300
// compute offset, size of parameters block
303301
col_offset = 0;

‎src/test/interface/generated_quantities_test.cpp‎

Lines changed: 28 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -183,23 +183,21 @@ TEST_F(CmdStan, generate_quantities_warmup) {
183183

184184
std::ifstream fp_stream(fp_path.c_str());
185185
stan::io::stan_csv fitted_params;
186-
stan::io::stan_csv_reader::read_metadata(fp_stream, fitted_params.metadata,
187-
&msg);
188-
stan::io::stan_csv_reader::read_header(fp_stream, fitted_params.header, &msg,
186+
stan::io::stan_csv_reader::read_metadata(fp_stream, fitted_params.metadata);
187+
stan::io::stan_csv_reader::read_header(fp_stream, fitted_params.header,
189188
false);
190189
stan::io::stan_csv_reader::read_samples(fp_stream, fitted_params.samples,
191-
fitted_params.timing, &msg);
190+
fitted_params.timing);
192191
fp_stream.close();
193192

194193
std::ifstream gq_stream(gq_output_path.c_str());
195194
stan::io::stan_csv gq_output;
196195
stan::io::stan_csv_reader::read_samples(gq_stream, gq_output.samples,
197-
gq_output.timing, &msg);
198-
stan::io::stan_csv_reader::read_metadata(gq_stream, gq_output.metadata, &msg);
199-
stan::io::stan_csv_reader::read_header(gq_stream, gq_output.header, &msg,
200-
false);
196+
gq_output.timing);
197+
stan::io::stan_csv_reader::read_metadata(gq_stream, gq_output.metadata);
198+
stan::io::stan_csv_reader::read_header(gq_stream, gq_output.header, false);
201199
stan::io::stan_csv_reader::read_samples(gq_stream, gq_output.samples,
202-
gq_output.timing, &msg);
200+
gq_output.timing);
203201
gq_stream.close();
204202

205203
ASSERT_EQ(fitted_params.samples.rows(), gq_output.samples.rows());
@@ -222,23 +220,21 @@ TEST_F(CmdStan, generate_quantities_after_optimization) {
222220

223221
std::ifstream fp_stream(fp_path.c_str());
224222
stan::io::stan_csv fitted_params;
225-
stan::io::stan_csv_reader::read_metadata(fp_stream, fitted_params.metadata,
226-
&msg);
227-
stan::io::stan_csv_reader::read_header(fp_stream, fitted_params.header, &msg,
223+
stan::io::stan_csv_reader::read_metadata(fp_stream, fitted_params.metadata);
224+
stan::io::stan_csv_reader::read_header(fp_stream, fitted_params.header,
228225
false);
229226
stan::io::stan_csv_reader::read_samples(fp_stream, fitted_params.samples,
230-
fitted_params.timing, &msg);
227+
fitted_params.timing);
231228
fp_stream.close();
232229

233230
std::ifstream gq_stream(gq_output_path.c_str());
234231
stan::io::stan_csv gq_output;
235232
stan::io::stan_csv_reader::read_samples(gq_stream, gq_output.samples,
236-
gq_output.timing, &msg);
237-
stan::io::stan_csv_reader::read_metadata(gq_stream, gq_output.metadata, &msg);
238-
stan::io::stan_csv_reader::read_header(gq_stream, gq_output.header, &msg,
239-
false);
233+
gq_output.timing);
234+
stan::io::stan_csv_reader::read_metadata(gq_stream, gq_output.metadata);
235+
stan::io::stan_csv_reader::read_header(gq_stream, gq_output.header, false);
240236
stan::io::stan_csv_reader::read_samples(gq_stream, gq_output.samples,
241-
gq_output.timing, &msg);
237+
gq_output.timing);
242238
gq_stream.close();
243239

244240
ASSERT_EQ(fitted_params.samples.rows(), gq_output.samples.rows());
@@ -261,23 +257,21 @@ TEST_F(CmdStan, generate_quantities_after_vb) {
261257

262258
std::ifstream fp_stream(fp_path.c_str());
263259
stan::io::stan_csv fitted_params;
264-
stan::io::stan_csv_reader::read_metadata(fp_stream, fitted_params.metadata,
265-
&msg);
266-
stan::io::stan_csv_reader::read_header(fp_stream, fitted_params.header, &msg,
260+
stan::io::stan_csv_reader::read_metadata(fp_stream, fitted_params.metadata);
261+
stan::io::stan_csv_reader::read_header(fp_stream, fitted_params.header,
267262
false);
268263
stan::io::stan_csv_reader::read_samples(fp_stream, fitted_params.samples,
269-
fitted_params.timing, &msg);
264+
fitted_params.timing);
270265
fp_stream.close();
271266

272267
std::ifstream gq_stream(gq_output_path.c_str());
273268
stan::io::stan_csv gq_output;
274269
stan::io::stan_csv_reader::read_samples(gq_stream, gq_output.samples,
275-
gq_output.timing, &msg);
276-
stan::io::stan_csv_reader::read_metadata(gq_stream, gq_output.metadata, &msg);
277-
stan::io::stan_csv_reader::read_header(gq_stream, gq_output.header, &msg,
278-
false);
270+
gq_output.timing);
271+
stan::io::stan_csv_reader::read_metadata(gq_stream, gq_output.metadata);
272+
stan::io::stan_csv_reader::read_header(gq_stream, gq_output.header, false);
279273
stan::io::stan_csv_reader::read_samples(gq_stream, gq_output.samples,
280-
gq_output.timing, &msg);
274+
gq_output.timing);
281275
gq_stream.close();
282276

283277
ASSERT_EQ(fitted_params.samples.rows(), gq_output.samples.rows());
@@ -300,23 +294,21 @@ TEST_F(CmdStan, generate_quantities_thin) {
300294

301295
std::ifstream fp_stream(fp_path.c_str());
302296
stan::io::stan_csv fitted_params;
303-
stan::io::stan_csv_reader::read_metadata(fp_stream, fitted_params.metadata,
304-
&msg);
305-
stan::io::stan_csv_reader::read_header(fp_stream, fitted_params.header, &msg,
297+
stan::io::stan_csv_reader::read_metadata(fp_stream, fitted_params.metadata);
298+
stan::io::stan_csv_reader::read_header(fp_stream, fitted_params.header,
306299
false);
307300
stan::io::stan_csv_reader::read_samples(fp_stream, fitted_params.samples,
308-
fitted_params.timing, &msg);
301+
fitted_params.timing);
309302
fp_stream.close();
310303

311304
std::ifstream gq_stream(gq_output_path.c_str());
312305
stan::io::stan_csv gq_output;
313306
stan::io::stan_csv_reader::read_samples(gq_stream, gq_output.samples,
314-
gq_output.timing, &msg);
315-
stan::io::stan_csv_reader::read_metadata(gq_stream, gq_output.metadata, &msg);
316-
stan::io::stan_csv_reader::read_header(gq_stream, gq_output.header, &msg,
317-
false);
307+
gq_output.timing);
308+
stan::io::stan_csv_reader::read_metadata(gq_stream, gq_output.metadata);
309+
stan::io::stan_csv_reader::read_header(gq_stream, gq_output.header, false);
318310
stan::io::stan_csv_reader::read_samples(gq_stream, gq_output.samples,
319-
gq_output.timing, &msg);
311+
gq_output.timing);
320312
gq_stream.close();
321313

322314
ASSERT_EQ(fitted_params.samples.rows(), gq_output.samples.rows());

‎src/test/interface/variational_output_test.cpp‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -50,7 +50,7 @@ TEST_F(CmdStan, variational_default) {
5050

5151
stan::mcmc::chains<> chains = parse_output_file();
5252
ASSERT_EQ(1, chains.num_chains());
53-
ASSERT_EQ(1001, chains.num_samples());
53+
ASSERT_EQ(1000, chains.num_samples());
5454
}
5555

5656
TEST_F(CmdStan, variational_meanfield) {
@@ -61,7 +61,7 @@ TEST_F(CmdStan, variational_meanfield) {
6161

6262
stan::mcmc::chains<> chains = parse_output_file();
6363
ASSERT_EQ(1, chains.num_chains());
64-
ASSERT_EQ(1001, chains.num_samples());
64+
ASSERT_EQ(1000, chains.num_samples());
6565
}
6666

6767
TEST_F(CmdStan, variational_fullrank) {
@@ -72,5 +72,5 @@ TEST_F(CmdStan, variational_fullrank) {
7272

7373
stan::mcmc::chains<> chains = parse_output_file();
7474
ASSERT_EQ(1, chains.num_chains());
75-
ASSERT_EQ(1001, chains.num_samples());
75+
ASSERT_EQ(1000, chains.num_samples());
7676
}

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