From dd24b5cd68e9621edd3dc27254a2d8a346d4c957 Mon Sep 17 00:00:00 2001 From: Mitzi Morris Date: Wed, 2 Oct 2024 12:36:47 -0400 Subject: [PATCH 1/4] tests and data files for warmup draws bug --- src/test/unit/io/stan_csv_reader_test.cpp | 43 +- .../unit/io/test_csv_files/bernoulli_thin.csv | 1057 +++++++++ .../io/test_csv_files/bernoulli_warmup.csv | 2057 +++++++++++++++++ .../io/test_csv_files/fixed_param_output.csv | 55 + 4 files changed, 3208 insertions(+), 4 deletions(-) create mode 100644 src/test/unit/io/test_csv_files/bernoulli_thin.csv create mode 100644 src/test/unit/io/test_csv_files/bernoulli_warmup.csv create mode 100644 src/test/unit/io/test_csv_files/fixed_param_output.csv diff --git a/src/test/unit/io/stan_csv_reader_test.cpp b/src/test/unit/io/stan_csv_reader_test.cpp index 8ee33547d2..6de6a9d99d 100644 --- a/src/test/unit/io/stan_csv_reader_test.cpp +++ b/src/test/unit/io/stan_csv_reader_test.cpp @@ -1,5 +1,6 @@ #include #include +#include #include #include #include @@ -15,13 +16,17 @@ class StanIoStanCsvReader : public testing::Test { header3_stream.open("src/test/unit/io/test_csv_files/header3.csv"); adaptation1_stream.open("src/test/unit/io/test_csv_files/adaptation1.csv"); samples1_stream.open("src/test/unit/io/test_csv_files/samples1.csv"); - epil0_stream.open("src/test/unit/io/test_csv_files/epil.0.csv"); - blocker_nondiag0_stream.open( "src/test/unit/io/test_csv_files/blocker_nondiag.0.csv"); eight_schools_stream.open( "src/test/unit/io/test_csv_files/eight_schools.csv"); + bernoulli_thin_stream.open( + "src/test/unit/io/test_csv_files/bernoulli_thin.csv"); + bernoulli_warmup_stream.open( + "src/test/unit/io/test_csv_files/bernoulli_warmup.csv"); + fixed_param_stream.open( + "src/test/unit/io/test_csv_files/fixed_param_output.csv"); } void TearDown() { @@ -33,10 +38,11 @@ class StanIoStanCsvReader : public testing::Test { header3_stream.close(); adaptation1_stream.close(); samples1_stream.close(); - epil0_stream.close(); - blocker_nondiag0_stream.close(); + bernoulli_thin_stream.close(); + bernoulli_warmup_stream.close(); + fixed_param_stream.close(); } std::ifstream blocker0_stream, epil0_stream; @@ -46,6 +52,9 @@ class StanIoStanCsvReader : public testing::Test { std::ifstream metadata3_stream, header2_stream; std::ifstream eight_schools_stream; std::ifstream header3_stream; + std::ifstream bernoulli_thin_stream; + std::ifstream bernoulli_warmup_stream; + std::ifstream fixed_param_stream; }; TEST_F(StanIoStanCsvReader, read_metadata1) { @@ -537,3 +546,29 @@ TEST_F(StanIoStanCsvReader, ParseEightSchools) { EXPECT_EQ("", out.str()); } + +TEST_F(StanIoStanCsvReader, skip_warmup) { + stan::io::stan_csv bernoulli_warmup; + std::stringstream out; + bernoulli_warmup + = stan::io::stan_csv_reader::parse(bernoulli_warmup_stream, &out); + ASSERT_EQ(1000, bernoulli_warmup.samples.rows()); + ASSERT_EQ(1000, bernoulli_warmup.metadata.num_warmup); + ASSERT_EQ(1000, bernoulli_warmup.metadata.num_samples); + ASSERT_NE(0, bernoulli_warmup.adaptation.step_size); +} + +TEST_F(StanIoStanCsvReader, thinned_data) { + stan::io::stan_csv bernoulli_thin; + std::stringstream out; + bernoulli_thin + = stan::io::stan_csv_reader::parse(bernoulli_thin_stream, &out); + ASSERT_EQ(1000, bernoulli_thin.samples.rows()); +} + +TEST_F(StanIoStanCsvReader, fixed_param) { + stan::io::stan_csv fixed_param; + std::stringstream out; + fixed_param = stan::io::stan_csv_reader::parse(fixed_param_stream, &out); + ASSERT_EQ(10, fixed_param.samples.rows()); +} diff --git a/src/test/unit/io/test_csv_files/bernoulli_thin.csv b/src/test/unit/io/test_csv_files/bernoulli_thin.csv new file mode 100644 index 0000000000..b0874d8ead --- /dev/null +++ b/src/test/unit/io/test_csv_files/bernoulli_thin.csv @@ -0,0 +1,1057 @@ +# stan_version_major = 2 +# stan_version_minor = 35 +# stan_version_patch = 0 +# model = bernoulli_model +# start_datetime = 2024-07-23 15:13:19 UTC +# method = sample (Default) +# sample +# num_samples = 2000 +# num_warmup = 1000 (Default) +# save_warmup = false (Default) +# thin = 2 +# adapt +# engaged = true (Default) +# gamma = 0.05 (Default) +# delta = 0.8 (Default) +# kappa = 0.75 (Default) +# t0 = 10 (Default) +# init_buffer = 75 (Default) +# term_buffer = 50 (Default) +# window = 25 (Default) +# save_metric = false (Default) +# algorithm = hmc (Default) +# hmc +# engine = nuts (Default) +# nuts +# max_depth = 10 (Default) +# metric = diag_e (Default) +# metric_file = (Default) +# stepsize = 1 (Default) +# stepsize_jitter = 0 (Default) +# num_chains = 1 (Default) +# id = 1 (Default) +# data +# file = examples/bernoulli/bernoulli.data.json +# init = 2 (Default) +# random +# seed = 3880845880 (Default) +# output +# file = bernoulli_thin.csv +# diagnostic_file = (Default) +# refresh = 100 (Default) +# sig_figs = -1 (Default) +# profile_file = profile.csv (Default) +# save_cmdstan_config = false (Default) +# num_threads = 1 (Default) +# stanc_version = stanc3 v2.35.0 +# stancflags = +lp__,accept_stat__,stepsize__,treedepth__,n_leapfrog__,divergent__,energy__,theta +# Adaptation terminated +# Step size = 0.893542 +# Diagonal elements of inverse mass matrix: +# 0.483503 +-8.91945,1,0.893542,1,1,0,9.73374,0.0619604 +-8.90814,1,0.893542,1,1,0,9.95846,0.545008 +-7.21915,1,0.893542,1,1,0,7.56642,0.382112 +-6.99262,0.974315,0.893542,1,1,0,6.99262,0.170032 +-7.177,0.949564,0.893542,2,7,0,7.19028,0.147604 +-7.02071,0.934256,0.893542,2,3,0,7.30094,0.348894 +-6.75447,0.998729,0.893542,2,3,0,6.76944,0.264366 +-6.99389,0.954672,0.893542,1,3,0,7.04803,0.169846 +-8.10147,0.867196,0.893542,1,3,0,8.27154,0.0887819 +-7.83949,1,0.893542,1,1,0,8.36851,0.100831 +-7.20348,0.899977,0.893542,1,3,0,7.65125,0.379758 +-7.12214,0.820496,0.893542,1,3,0,8.08646,0.153481 +-6.75619,1,0.893542,2,3,0,7.17582,0.266194 +-6.80721,0.968917,0.893542,1,3,0,7.36674,0.294557 +-7.03198,1,0.893542,1,1,0,7.76254,0.351031 +-6.85284,0.960446,0.893542,1,3,0,7.15062,0.195876 +-6.77208,0.987924,0.893542,1,3,0,7.03182,0.278062 +-6.91359,1,0.893542,2,3,0,8.13328,0.18305 +-6.81561,0.956574,0.893542,2,7,0,7.45532,0.297719 +-6.76032,1,0.893542,2,7,0,6.80503,0.230743 +-6.76597,0.998846,0.893542,1,1,0,6.76725,0.22683 +-6.7594,0.993657,0.893542,1,3,0,6.82523,0.231466 +-7.25866,0.839089,0.893542,2,3,0,8.4433,0.139735 +-7.1134,0.971276,0.893542,1,1,0,7.1556,0.365446 +-7.52094,0.727841,0.893542,1,3,0,8.73414,0.11935 +-7.67112,0.993503,0.893542,1,1,0,7.78017,0.109972 +-6.75103,0.998383,0.893542,2,3,0,6.83417,0.259776 +-8.62702,0.934538,0.893542,2,3,0,9.21545,0.0701174 +-6.85649,0.909432,0.893542,1,3,0,8.95293,0.310994 +-6.87955,0.968041,0.893542,1,3,0,6.94534,0.317443 +-6.84001,0.965601,0.893542,1,3,0,7.07766,0.199102 +-7.88997,1,0.893542,2,3,0,8.09487,0.0983237 +-7.06055,0.900192,0.893542,1,3,0,8.68948,0.356282 +-6.74805,0.996745,0.893542,1,3,0,6.97881,0.250856 +-7.19725,1,0.893542,1,1,0,7.28556,0.145563 +-6.78602,0.995476,0.893542,1,1,0,6.78705,0.285469 +-6.79545,0.966991,0.893542,2,7,0,8.83762,0.289747 +-6.85701,0.986415,0.893542,2,3,0,6.9222,0.194874 +-8.13779,0.808085,0.893542,2,7,0,8.15821,0.0872819 +-6.77475,1,0.893542,2,3,0,6.80685,0.221869 +-6.755,1,0.893542,1,1,0,6.76348,0.235428 +-7.72282,0.995936,0.893542,2,3,0,7.81505,0.107027 +-6.85068,0.991723,0.893542,2,7,0,7.67011,0.309272 +-6.78351,0.96595,0.893542,1,3,0,7.29485,0.217724 +-7.01992,0.916257,0.893542,1,3,0,7.27688,0.166148 +-6.75058,0.983401,0.893542,1,3,0,7.38448,0.259018 +-8.06771,0.664252,0.893542,1,3,0,9.09338,0.0902102 +-6.82585,1,0.893542,2,3,0,7.7661,0.202972 +-7.00359,0.957838,0.893542,1,1,0,7.00467,0.345568 +-7.16065,0.965784,0.893542,2,7,0,7.16072,0.373134 +-6.74805,0.99626,0.893542,1,3,0,6.98927,0.24901 +-6.90231,1,0.893542,2,3,0,7.05968,0.185192 +-7.20636,0.93361,0.893542,1,3,0,9.402,0.144665 +-7.84106,1,0.893542,1,1,0,8.44831,0.456603 +-6.75385,0.986687,0.893542,1,3,0,7.15744,0.236668 +-7.73869,0.848859,0.893542,1,1,0,7.76537,0.446112 +-9.04616,0.923365,0.893542,2,3,0,9.28102,0.554505 +-7.16253,1,0.893542,1,1,0,7.26087,0.149103 +-6.75061,0.953379,0.893542,2,3,0,7.55278,0.241086 +-6.87201,0.983579,0.893542,2,3,0,6.89287,0.315394 +-8.37334,0.780237,0.893542,2,3,0,8.91045,0.504589 +-7.31022,1,0.893542,1,1,0,8.08813,0.39512 +-7.13369,0.836937,0.893542,1,3,0,7.87458,0.152199 +-7.55607,0.978527,0.893542,1,1,0,7.60506,0.117035 +-6.7799,0.995845,0.893542,2,3,0,6.81306,0.219357 +-6.87584,0.978011,0.893542,1,1,0,6.87584,0.316441 +-6.90665,1,0.893542,2,3,0,7.03415,0.184358 +-8.366,0.954237,0.893542,2,7,0,8.64308,0.503988 +-7.31371,1,0.893542,2,3,0,7.59964,0.395598 +-7.42729,1,0.893542,1,1,0,8.24438,0.410478 +-9.83769,0.367101,0.893542,1,3,0,12.9683,0.0429592 +-11.7092,0.971359,0.893542,1,1,0,11.7472,0.0215426 +-7.94546,0.93523,0.893542,2,7,0,11.9231,0.466816 +-7.74281,0.747755,0.893542,1,3,0,8.44191,0.105922 +-6.84047,0.920699,0.893542,2,3,0,7.68591,0.198981 +-8.60661,0.827904,0.893542,1,1,0,8.82479,0.522995 +-7.29777,1,0.893542,2,3,0,7.39398,0.136273 +-6.97269,1,0.893542,1,1,0,7.22693,0.339296 +-6.86249,1,0.893542,1,1,0,7.01724,0.312728 +-6.97125,0.913468,0.893542,1,3,0,7.58656,0.173264 +-7.8638,0.989915,0.893542,1,1,0,7.9762,0.0996114 +-6.86197,1,0.893542,2,3,0,7.63776,0.193713 +-7.22206,0.850919,0.893542,1,3,0,7.71338,0.143146 +-7.22681,0.99046,0.893542,1,1,0,7.27628,0.142693 +-7.09726,1,0.893542,1,1,0,7.36621,0.156335 +-9.96351,0.978531,0.893542,2,3,0,11.1987,0.0409345 +-7.34497,1,0.893542,2,3,0,10.5413,0.132321 +-6.81305,0.938689,0.893542,2,3,0,7.24819,0.206825 +-6.81323,0.996598,0.893542,1,1,0,6.81843,0.206767 +-6.83142,0.971003,0.893542,1,3,0,6.96602,0.201408 +-6.83125,1,0.893542,1,1,0,6.94813,0.30315 +-6.7882,0.950841,0.893542,2,3,0,7.15238,0.215732 +-9.17868,0.966705,0.893542,1,1,0,9.2473,0.0557102 +-10.1185,0.944434,0.893542,1,1,0,10.1239,0.0385895 +-7.53536,0.731681,0.893542,2,3,0,8.955,0.423587 +-7.17139,0.844452,0.893542,2,3,0,7.87684,0.148181 +-7.10769,0.986547,0.893542,1,1,0,7.17427,0.364485 +-6.94717,0.935748,0.893542,2,3,0,7.17961,0.17714 +-6.84534,0.989334,0.893542,1,1,0,6.84994,0.307647 +-6.8368,0.954327,0.893542,1,3,0,7.1096,0.304961 +-6.74879,0.996744,0.893542,1,3,0,6.85754,0.245111 +-6.99263,0.97013,0.893542,2,3,0,7.04979,0.170031 +-8.34668,1,0.893542,1,1,0,9.31823,0.502398 +-7.78992,0.97634,0.893542,1,1,0,7.8495,0.103392 +-6.96885,0.97489,0.893542,1,3,0,7.75062,0.173638 +-7.13219,0.920703,0.893542,1,3,0,7.2178,0.368554 +-6.74834,0.99754,0.893542,1,3,0,8.20523,0.246878 +-6.82781,0.98513,0.893542,1,3,0,6.83699,0.301999 +-8.51144,0.8241,0.893542,2,3,0,8.59822,0.0737269 +-6.8833,0.990012,0.893542,2,3,0,7.1302,0.189023 +-7.727,0.933842,0.893542,2,7,0,7.72929,0.444881 +-6.92808,1,0.893542,2,3,0,7.01247,0.180418 +-7.46481,0.853946,0.893542,1,3,0,7.74876,0.123222 +-7.52531,0.818528,0.893542,1,1,0,8.12529,0.422404 +-7.53784,1,0.893542,2,7,0,7.5663,0.118227 +-8.66406,0.93062,0.893542,1,1,0,8.66529,0.0690104 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+-10.5954,0.978406,0.893542,1,1,0,10.7078,0.0322776 +-9.03458,1,0.893542,1,1,0,10.0862,0.0590819 +-7.58478,0.886552,0.893542,1,3,0,7.73728,0.115201 +-9.91973,1,0.893542,1,1,0,10.5231,0.0416263 +-7.48944,1,0.893542,2,3,0,9.43402,0.121496 +-7.71315,0.865118,0.893542,2,7,0,7.71389,0.107568 +# +# Elapsed Time: 0.005 seconds (Warm-up) +# 0.015 seconds (Sampling) +# 0.02 seconds (Total) +# diff --git a/src/test/unit/io/test_csv_files/bernoulli_warmup.csv b/src/test/unit/io/test_csv_files/bernoulli_warmup.csv new file mode 100644 index 0000000000..799f5c8260 --- /dev/null +++ b/src/test/unit/io/test_csv_files/bernoulli_warmup.csv @@ -0,0 +1,2057 @@ +# stan_version_major = 2 +# stan_version_minor = 35 +# stan_version_patch = 0 +# model = bernoulli_model +# start_datetime = 2024-07-22 12:26:39 UTC +# method = sample (Default) +# sample +# num_samples = 1000 (Default) +# num_warmup = 1000 (Default) +# save_warmup = true +# thin = 1 (Default) +# adapt +# engaged = true (Default) +# gamma = 0.05 (Default) +# delta = 0.8 (Default) +# kappa = 0.75 (Default) +# t0 = 10 (Default) +# init_buffer = 75 (Default) +# term_buffer = 50 (Default) +# window = 25 (Default) +# save_metric = false (Default) +# algorithm = hmc (Default) +# hmc +# engine = nuts (Default) +# nuts +# max_depth = 10 (Default) +# metric = diag_e (Default) +# metric_file = (Default) +# stepsize = 1 (Default) +# stepsize_jitter = 0 (Default) +# num_chains = 1 (Default) +# id = 1 (Default) +# data +# file = examples/bernoulli/bernoulli.data.json +# init = 2 (Default) +# random +# seed = 3784445287 (Default) +# output +# file = output.csv (Default) +# diagnostic_file = (Default) +# refresh = 100 (Default) +# sig_figs = -1 (Default) +# profile_file = profile.csv (Default) +# save_cmdstan_config = false (Default) +# num_threads = 1 (Default) +# stanc_version = stanc3 v2.35.0-25-gbb9ce42 +# stancflags = +lp__,accept_stat__,stepsize__,treedepth__,n_leapfrog__,divergent__,energy__,theta +-9.8506,1,0.5,1,1,0,11.6894,0.604056 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kappa = 0.75 (Default) +# t0 = 10 (Default) +# init_buffer = 75 (Default) +# term_buffer = 50 (Default) +# window = 25 (Default) +# save_metric = false (Default) +# algorithm = fixed_param +# num_chains = 1 (Default) +# id = 1 (Default) +# data +# file = linear_data.json +# init = 2 (Default) +# random +# seed = 3892335730 (Default) +# output +# file = output.csv (Default) +# diagnostic_file = (Default) +# refresh = 100 (Default) +# sig_figs = -1 (Default) +# profile_file = profile.csv (Default) +# save_cmdstan_config = false (Default) +# num_threads = 1 (Default) +# stanc_version = stanc3 v2.35.0 +# stancflags = --filename-in-msg=linear_model_dgp.stan 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+# +# Elapsed Time: 0 seconds (Warm-up) +# 0.001 seconds (Sampling) +# 0.001 seconds (Total) +# From 7704ba4890bfd6b27554e61ba6952b4257f68537 Mon Sep 17 00:00:00 2001 From: Mitzi Morris Date: Wed, 2 Oct 2024 12:51:38 -0400 Subject: [PATCH 2/4] bugfix in, all unit tests passing --- src/stan/io/stan_csv_reader.hpp | 107 +++++++++++----------- src/test/unit/io/stan_csv_reader_test.cpp | 21 ++--- 2 files changed, 63 insertions(+), 65 deletions(-) diff --git a/src/stan/io/stan_csv_reader.hpp b/src/stan/io/stan_csv_reader.hpp index 5ded3d49c9..6d8fa9490d 100644 --- a/src/stan/io/stan_csv_reader.hpp +++ b/src/stan/io/stan_csv_reader.hpp @@ -29,8 +29,6 @@ inline void prettify_stan_csv_name(std::string& variable) { } } -// FIXME: should consolidate with the options from -// the command line in stan::lang struct stan_csv_metadata { int stan_version_major; int stan_version_minor; @@ -47,6 +45,7 @@ struct stan_csv_metadata { bool save_warmup; size_t thin; bool append_samples; + std::string method; std::string algorithm; std::string engine; int max_depth; @@ -64,8 +63,9 @@ struct stan_csv_metadata { num_samples(0), num_warmup(0), save_warmup(false), - thin(0), + thin(1), append_samples(false), + method(""), algorithm(""), engine(""), max_depth(10) {} @@ -101,13 +101,12 @@ class stan_csv_reader { stan_csv_reader() {} ~stan_csv_reader() {} - static bool read_metadata(std::istream& in, stan_csv_metadata& metadata, - std::ostream* out) { + static void read_metadata(std::istream& in, stan_csv_metadata& metadata) { std::stringstream ss; std::string line; if (in.peek() != '#') - return false; + return; while (in.peek() == '#') { std::getline(in, line); ss << line << '\n'; @@ -161,9 +160,15 @@ class stan_csv_reader { metadata.model = value; } else if (name.compare("num_samples") == 0) { std::stringstream(value) >> metadata.num_samples; + } else if (name.compare("output_samples") == 0) { // ADVI config name + std::stringstream(value) >> metadata.num_samples; } else if (name.compare("num_warmup") == 0) { std::stringstream(value) >> metadata.num_warmup; } else if (name.compare("save_warmup") == 0) { + // cmdstan args can be "true" and "false", was "1", "0" + if (value.compare("true") == 0) { + value = "1"; + } std::stringstream(value) >> metadata.save_warmup; } else if (name.compare("thin") == 0) { std::stringstream(value) >> metadata.thin; @@ -177,6 +182,8 @@ class stan_csv_reader { metadata.random_seed = false; } else if (name.compare("append_samples") == 0) { std::stringstream(value) >> metadata.append_samples; + } else if (name.compare("method") == 0) { + metadata.method = value; } else if (name.compare("algorithm") == 0) { metadata.algorithm = value; } else if (name.compare("engine") == 0) { @@ -185,14 +192,10 @@ class stan_csv_reader { std::stringstream(value) >> metadata.max_depth; } } - if (ss.good() == true) - return false; - - return true; } // read_metadata static bool read_header(std::istream& in, std::vector& header, - std::ostream* out, bool prettify_name = true) { + bool prettify_name = true) { std::string line; if (!std::isalpha(in.peek())) @@ -216,62 +219,53 @@ class stan_csv_reader { return true; } - static bool read_adaptation(std::istream& in, stan_csv_adaptation& adaptation, - std::ostream* out) { + static void read_adaptation(std::istream& in, + stan_csv_adaptation& adaptation) { std::stringstream ss; std::string line; int lines = 0; - if (in.peek() != '#' || in.good() == false) - return false; - + return; while (in.peek() == '#') { std::getline(in, line); ss << line << std::endl; lines++; } ss.seekg(std::ios_base::beg); + if (lines < 2) + return; - if (lines < 4) - return false; + std::getline(ss, line); // comment adaptation terminated - char comment; // Buffer for comment indicator, # - - // Skip first two lines - std::getline(ss, line); - - // Stepsize - std::getline(ss, line, '='); + // parse stepsize + std::getline(ss, line, '='); // stepsize boost::trim(line); ss >> adaptation.step_size; + if (lines == 2) // ADVI reports stepsize, no metric + return; - // Metric parameters - std::getline(ss, line); - std::getline(ss, line); - std::getline(ss, line); + std::getline(ss, line); // consume end of stepsize line + std::getline(ss, line); // comment elements of mass matrix + std::getline(ss, line); // diagonal metric or row 1 of dense metric int rows = lines - 3; int cols = std::count(line.begin(), line.end(), ',') + 1; adaptation.metric.resize(rows, cols); + char comment; // Buffer for comment indicator, # + // parse metric, row by row, element by element for (int row = 0; row < rows; row++) { std::stringstream line_ss; line_ss.str(line); line_ss >> comment; - for (int col = 0; col < cols; col++) { std::string token; std::getline(line_ss, token, ','); boost::trim(token); std::stringstream(token) >> adaptation.metric(row, col); } - std::getline(ss, line); // Read in next line + std::getline(ss, line); } - - if (ss.good()) - return false; - else - return true; } static bool read_samples(std::istream& in, Eigen::MatrixXd& samples, @@ -290,7 +284,6 @@ class stan_csv_reader { bool empty_line = (in.peek() == '\n'); std::getline(in, line); - if (empty_line) continue; if (!line.length()) @@ -316,11 +309,10 @@ class stan_csv_reader { if (cols == -1) { cols = current_cols; } else if (cols != current_cols) { - if (out) - *out << "Error: expected " << cols << " columns, but found " - << current_cols << " instead for row " << rows + 1 - << std::endl; - return false; + std::stringstream msg; + msg << "Error: expected " << cols << " columns, but found " + << current_cols << " instead for row " << rows + 1; + throw std::invalid_argument(msg.str()); } rows++; } @@ -348,36 +340,45 @@ class stan_csv_reader { /** * Parses the file. * + * Throws exception if contents can't be parsed into header + data rows. + * + * Emits warning message + * * @param[in] in input stream to parse * @param[out] out output stream to send messages */ static stan_csv parse(std::istream& in, std::ostream* out) { stan_csv data; + std::string line; - if (!read_metadata(in, data.metadata, out)) { - if (out) - *out << "Warning: non-fatal error reading metadata" << std::endl; + read_metadata(in, data.metadata); + if (!read_header(in, data.header)) { + throw std::invalid_argument("Error: no column names found in csv file"); } - if (!read_header(in, data.header, out)) { - if (out) - *out << "Error: error reading header" << std::endl; - throw std::invalid_argument("Error with header of input file in parse"); + // skip warmup draws, if any + if (data.metadata.algorithm != "fixed_param" && data.metadata.num_warmup > 0 + && data.metadata.save_warmup) { + while (in.peek() != '#') { + std::getline(in, line); + } } - if (!read_adaptation(in, data.adaptation, out)) { - if (out) - *out << "Warning: non-fatal error reading adaptation data" << std::endl; + if (data.metadata.algorithm != "fixed_param") { + read_adaptation(in, data.adaptation); } data.timing.warmup = 0; data.timing.sampling = 0; + if (data.metadata.method == "variational") { + std::getline(in, line); // discard variational estimate + } + if (!read_samples(in, data.samples, data.timing, out)) { if (out) *out << "Warning: non-fatal error reading samples" << std::endl; } - return data; } }; diff --git a/src/test/unit/io/stan_csv_reader_test.cpp b/src/test/unit/io/stan_csv_reader_test.cpp index 6de6a9d99d..43b8f68dfa 100644 --- a/src/test/unit/io/stan_csv_reader_test.cpp +++ b/src/test/unit/io/stan_csv_reader_test.cpp @@ -16,11 +16,14 @@ class StanIoStanCsvReader : public testing::Test { header3_stream.open("src/test/unit/io/test_csv_files/header3.csv"); adaptation1_stream.open("src/test/unit/io/test_csv_files/adaptation1.csv"); samples1_stream.open("src/test/unit/io/test_csv_files/samples1.csv"); + epil0_stream.open("src/test/unit/io/test_csv_files/epil.0.csv"); + blocker_nondiag0_stream.open( "src/test/unit/io/test_csv_files/blocker_nondiag.0.csv"); eight_schools_stream.open( "src/test/unit/io/test_csv_files/eight_schools.csv"); + bernoulli_thin_stream.open( "src/test/unit/io/test_csv_files/bernoulli_thin.csv"); bernoulli_warmup_stream.open( @@ -59,8 +62,7 @@ class StanIoStanCsvReader : public testing::Test { TEST_F(StanIoStanCsvReader, read_metadata1) { stan::io::stan_csv_metadata metadata; - EXPECT_TRUE( - stan::io::stan_csv_reader::read_metadata(metadata1_stream, metadata, 0)); + stan::io::stan_csv_reader::read_metadata(metadata1_stream, metadata); EXPECT_EQ(2, metadata.stan_version_major); EXPECT_EQ(9, metadata.stan_version_minor); @@ -86,8 +88,7 @@ TEST_F(StanIoStanCsvReader, read_metadata1) { TEST_F(StanIoStanCsvReader, read_metadata3) { stan::io::stan_csv_metadata metadata; - EXPECT_TRUE( - stan::io::stan_csv_reader::read_metadata(metadata3_stream, metadata, 0)); + stan::io::stan_csv_reader::read_metadata(metadata3_stream, metadata); EXPECT_EQ(2, metadata.stan_version_major); EXPECT_EQ(9, metadata.stan_version_minor); @@ -113,8 +114,7 @@ TEST_F(StanIoStanCsvReader, read_metadata3) { TEST_F(StanIoStanCsvReader, read_header1) { std::vector header; - EXPECT_TRUE( - stan::io::stan_csv_reader::read_header(header1_stream, header, 0)); + EXPECT_TRUE(stan::io::stan_csv_reader::read_header(header1_stream, header)); ASSERT_EQ(55, header.size()); EXPECT_EQ("lp__", header[0]); @@ -141,8 +141,7 @@ TEST_F(StanIoStanCsvReader, read_header1) { TEST_F(StanIoStanCsvReader, read_header2) { std::vector header; - EXPECT_TRUE( - stan::io::stan_csv_reader::read_header(header2_stream, header, 0)); + EXPECT_TRUE(stan::io::stan_csv_reader::read_header(header2_stream, header)); ASSERT_EQ(5, header.size()); EXPECT_EQ("d", header[0]); @@ -156,8 +155,7 @@ TEST_F(StanIoStanCsvReader, read_header2) { TEST_F(StanIoStanCsvReader, read_header_tuples) { std::vector header; - EXPECT_TRUE( - stan::io::stan_csv_reader::read_header(header3_stream, header, 0)); + EXPECT_TRUE(stan::io::stan_csv_reader::read_header(header3_stream, header)); ASSERT_EQ(46, header.size()); @@ -190,8 +188,7 @@ TEST_F(StanIoStanCsvReader, read_header_tuples) { TEST_F(StanIoStanCsvReader, read_adaptation1) { stan::io::stan_csv_adaptation adaptation; - EXPECT_TRUE(stan::io::stan_csv_reader::read_adaptation(adaptation1_stream, - adaptation, 0)); + stan::io::stan_csv_reader::read_adaptation(adaptation1_stream, adaptation); EXPECT_FLOAT_EQ(0.118745, adaptation.step_size); ASSERT_EQ(47, adaptation.metric.size()); From 7f4204285f5605f94342fd4b750be529f128400f Mon Sep 17 00:00:00 2001 From: Mitzi Morris Date: Thu, 3 Oct 2024 13:19:47 -0400 Subject: [PATCH 3/4] more cleanup, unit tests --- src/stan/io/stan_csv_reader.hpp | 8 +- src/test/unit/io/stan_csv_reader_test.cpp | 22 +- .../test_csv_files/bernoulli_no_samples.csv | 57 + .../test_csv_files/bernoulli_variational.csv | 1039 +++++++++++++++++ 4 files changed, 1121 insertions(+), 5 deletions(-) create mode 100644 src/test/unit/io/test_csv_files/bernoulli_no_samples.csv create mode 100644 src/test/unit/io/test_csv_files/bernoulli_variational.csv diff --git a/src/stan/io/stan_csv_reader.hpp b/src/stan/io/stan_csv_reader.hpp index 6d8fa9490d..a5dfc9f0d0 100644 --- a/src/stan/io/stan_csv_reader.hpp +++ b/src/stan/io/stan_csv_reader.hpp @@ -269,7 +269,7 @@ class stan_csv_reader { } static bool read_samples(std::istream& in, Eigen::MatrixXd& samples, - stan_csv_timing& timing, std::ostream* out) { + stan_csv_timing& timing) { std::stringstream ss; std::string line; @@ -277,7 +277,7 @@ class stan_csv_reader { int cols = -1; if (in.peek() == '#' || in.good() == false) - return false; + return false; // need at least one data row while (in.good()) { bool comment_line = (in.peek() == '#'); @@ -375,9 +375,9 @@ class stan_csv_reader { std::getline(in, line); // discard variational estimate } - if (!read_samples(in, data.samples, data.timing, out)) { + if (!read_samples(in, data.samples, data.timing)) { if (out) - *out << "Warning: non-fatal error reading samples" << std::endl; + *out << "Unable to parse sample" << std::endl; } return data; } diff --git a/src/test/unit/io/stan_csv_reader_test.cpp b/src/test/unit/io/stan_csv_reader_test.cpp index 43b8f68dfa..a4df51281b 100644 --- a/src/test/unit/io/stan_csv_reader_test.cpp +++ b/src/test/unit/io/stan_csv_reader_test.cpp @@ -246,7 +246,7 @@ TEST_F(StanIoStanCsvReader, read_samples1) { stan::io::stan_csv_timing timing; EXPECT_TRUE(stan::io::stan_csv_reader::read_samples(samples1_stream, samples, - timing, 0)); + timing)); ASSERT_EQ(5, samples.rows()); ASSERT_EQ(55, samples.cols()); @@ -569,3 +569,23 @@ TEST_F(StanIoStanCsvReader, fixed_param) { fixed_param = stan::io::stan_csv_reader::parse(fixed_param_stream, &out); ASSERT_EQ(10, fixed_param.samples.rows()); } + + +TEST_F(StanIoStanCsvReader, no_samples) { + std::ifstream no_samples_stream; + no_samples_stream.open("src/test/unit/io/test_csv_files/bernoulli_no_samples.csv"); + std::stringstream out; + stan::io::stan_csv no_samples = stan::io::stan_csv_reader::parse(no_samples_stream, &out); + no_samples_stream.close(); + ASSERT_EQ(out.str(), "Unable to parse sample\n"); +} + + +TEST_F(StanIoStanCsvReader, variational) { + std::ifstream variational_stream; + variational_stream.open("src/test/unit/io/test_csv_files/bernoulli_variational.csv"); + std::stringstream out; + stan::io::stan_csv variational = stan::io::stan_csv_reader::parse(variational_stream, &out); + variational_stream.close(); + ASSERT_EQ(1000, variational.metadata.num_samples); +} diff --git a/src/test/unit/io/test_csv_files/bernoulli_no_samples.csv b/src/test/unit/io/test_csv_files/bernoulli_no_samples.csv new file mode 100644 index 0000000000..3244c03f7c --- /dev/null +++ b/src/test/unit/io/test_csv_files/bernoulli_no_samples.csv @@ -0,0 +1,57 @@ +# stan_version_major = 2 +# stan_version_minor = 35 +# stan_version_patch = 0 +# model = bernoulli_model +# start_datetime = 2024-10-03 16:54:16 UTC +# method = sample (Default) +# sample +# num_samples = 0 +# num_warmup = 1000 (Default) +# save_warmup = false (Default) +# thin = 1 (Default) +# adapt +# engaged = true (Default) +# gamma = 0.05 (Default) +# delta = 0.8 (Default) +# kappa = 0.75 (Default) +# t0 = 10 (Default) +# init_buffer = 75 (Default) +# term_buffer = 50 (Default) +# window = 25 (Default) +# save_metric = false (Default) +# algorithm = hmc (Default) +# hmc +# engine = nuts (Default) +# nuts +# max_depth = 10 (Default) +# metric = diag_e (Default) +# metric_file = (Default) +# stepsize = 1 (Default) +# stepsize_jitter = 0 (Default) +# num_chains = 1 (Default) +# id = 1 (Default) +# data +# file = examples/bernoulli/bernoulli.data.json +# init = 2 (Default) +# random +# seed = 1517767693 (Default) +# output +# file = output.csv (Default) +# diagnostic_file = (Default) +# refresh = 100 (Default) +# sig_figs = -1 (Default) +# profile_file = profile.csv (Default) +# save_cmdstan_config = false (Default) +# num_threads = 1 (Default) +# stanc_version = stanc3 v2.35.0 +# stancflags = +lp__,accept_stat__,stepsize__,treedepth__,n_leapfrog__,divergent__,energy__,theta +# Adaptation terminated +# Step size = 1.22726 +# Diagonal elements of inverse mass matrix: +# 0.489285 +# +# Elapsed Time: 0.005 seconds (Warm-up) +# 0 seconds (Sampling) +# 0.005 seconds (Total) +# diff --git a/src/test/unit/io/test_csv_files/bernoulli_variational.csv b/src/test/unit/io/test_csv_files/bernoulli_variational.csv new file mode 100644 index 0000000000..613de2e786 --- /dev/null +++ b/src/test/unit/io/test_csv_files/bernoulli_variational.csv @@ -0,0 +1,1039 @@ +# stan_version_major = 2 +# stan_version_minor = 35 +# stan_version_patch = 0 +# model = bernoulli_model +# start_datetime = 2024-10-03 17:01:50 UTC +# method = variational +# variational +# algorithm = meanfield (Default) +# meanfield +# iter = 10000 (Default) +# grad_samples = 1 (Default) +# elbo_samples = 100 (Default) +# eta = 1 (Default) +# adapt +# engaged = true (Default) +# iter = 50 (Default) +# tol_rel_obj = 0.01 (Default) +# eval_elbo = 100 (Default) +# output_samples = 1000 (Default) +# id = 1 (Default) +# data +# file = examples/bernoulli/bernoulli.data.json +# init = 2 (Default) +# random +# seed = 1518221616 (Default) +# output +# file = output.csv (Default) +# diagnostic_file = (Default) +# refresh = 100 (Default) +# sig_figs = -1 (Default) +# profile_file = profile.csv (Default) +# save_cmdstan_config = false (Default) +# num_threads = 1 (Default) +# stanc_version = stanc3 v2.35.0 +# stancflags = +lp__,log_p__,log_g__,theta +# Stepsize adaptation complete. +# eta = 1 +0,0,0,0.227641 +0,-7.53537,-0.958087,0.423587 +0,-6.78149,-0.0986588,0.283229 +0,-7.35647,-0.775269,0.401351 +0,-6.93635,-0.104432,0.178975 +0,-7.15947,-0.307329,0.149425 +0,-7.2294,-0.641377,0.38363 +0,-7.46285,-0.627355,0.123362 +0,-6.75207,-0.00452421,0.238868 +0,-7.20934,-0.357072,0.144374 +0,-6.81247,-0.0169092,0.207009 +0,-6.75251,-0.00407478,0.238286 +0,-6.82033,-0.0212899,0.204587 +0,-7.60607,-1.02891,0.431705 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Mon Sep 17 00:00:00 2001 From: Stan Jenkins Date: Thu, 3 Oct 2024 13:20:19 -0400 Subject: [PATCH 4/4] [Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1 --- src/test/unit/io/stan_csv_reader_test.cpp | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/test/unit/io/stan_csv_reader_test.cpp b/src/test/unit/io/stan_csv_reader_test.cpp index a4df51281b..ec91cf8684 100644 --- a/src/test/unit/io/stan_csv_reader_test.cpp +++ b/src/test/unit/io/stan_csv_reader_test.cpp @@ -570,22 +570,24 @@ TEST_F(StanIoStanCsvReader, fixed_param) { ASSERT_EQ(10, fixed_param.samples.rows()); } - TEST_F(StanIoStanCsvReader, no_samples) { std::ifstream no_samples_stream; - no_samples_stream.open("src/test/unit/io/test_csv_files/bernoulli_no_samples.csv"); + no_samples_stream.open( + "src/test/unit/io/test_csv_files/bernoulli_no_samples.csv"); std::stringstream out; - stan::io::stan_csv no_samples = stan::io::stan_csv_reader::parse(no_samples_stream, &out); + stan::io::stan_csv no_samples + = stan::io::stan_csv_reader::parse(no_samples_stream, &out); no_samples_stream.close(); ASSERT_EQ(out.str(), "Unable to parse sample\n"); } - TEST_F(StanIoStanCsvReader, variational) { std::ifstream variational_stream; - variational_stream.open("src/test/unit/io/test_csv_files/bernoulli_variational.csv"); + variational_stream.open( + "src/test/unit/io/test_csv_files/bernoulli_variational.csv"); std::stringstream out; - stan::io::stan_csv variational = stan::io::stan_csv_reader::parse(variational_stream, &out); + stan::io::stan_csv variational + = stan::io::stan_csv_reader::parse(variational_stream, &out); variational_stream.close(); ASSERT_EQ(1000, variational.metadata.num_samples); }