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Prepare for quick stanc3 tests.
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‎all.tests

+91
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@@ -0,0 +1,91 @@
1+
stat_comp_benchmarks/benchmarks/arK/arK.stan
2+
stat_comp_benchmarks/benchmarks/arma/arma.stan
3+
stat_comp_benchmarks/benchmarks/eight_schools/eight_schools.stan
4+
stat_comp_benchmarks/benchmarks/garch/garch.stan
5+
stat_comp_benchmarks/benchmarks/gp_pois_regr/gp_pois_regr.stan
6+
stat_comp_benchmarks/benchmarks/gp_regr/gen_gp_data.stan
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stat_comp_benchmarks/benchmarks/gp_regr/gp_regr.stan
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stat_comp_benchmarks/benchmarks/irt_2pl/irt_2pl.stan
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stat_comp_benchmarks/benchmarks/low_dim_corr_gauss/low_dim_corr_gauss.stan
10+
stat_comp_benchmarks/benchmarks/low_dim_gauss_mix/low_dim_gauss_mix.stan
11+
stat_comp_benchmarks/benchmarks/low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan
12+
stat_comp_benchmarks/benchmarks/pkpd/one_comp_mm_elim_abs.stan
13+
stat_comp_benchmarks/benchmarks/pkpd/sim_one_comp_mm_elim_abs.stan
14+
stat_comp_benchmarks/benchmarks/sir/sir.stan
15+
example-models/bugs_examples/vol1/dogs/dogs.stan
16+
example-models/bugs_examples/vol1/epil/epil.stan
17+
example-models/bugs_examples/vol1/inhalers/inhalers.stan
18+
example-models/bugs_examples/vol1/kidney/kidney.stan
19+
example-models/bugs_examples/vol1/litter/litter_old_param.stan
20+
example-models/bugs_examples/vol1/lsat/lsat.stan
21+
example-models/bugs_examples/vol1/oxford/oxford.stan
22+
example-models/bugs_examples/vol1/rats/rats_stanified.stan
23+
example-models/bugs_examples/vol2/birats/birats.stan
24+
example-models/bugs_examples/vol2/cervix/cervix2.stan
25+
example-models/bugs_examples/vol2/jaws/jaws.stan
26+
example-models/bugs_examples/vol2/mvn_orange/mvn_orange.stan
27+
example-models/bugs_examples/vol2/pines/pines-3.stan
28+
example-models/bugs_examples/vol2/pines/pines-4.stan
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example-models/bugs_examples/vol2/pines/pines-independent.stan
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example-models/bugs_examples/vol2/schools/schools-1.stan
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example-models/bugs_examples/vol2/schools/schools-2.stan
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example-models/bugs_examples/vol2/schools/schools-3.stan
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example-models/bugs_examples/vol2/schools/schools-4.stan
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example-models/bugs_examples/vol2/schools/schools.stan
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example-models/bugs_examples/vol2/stagnant/stagnant.stan
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example-models/bugs_examples/vol2/t_df/simt4.stan
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example-models/bugs_examples/vol3/fire/fire.stan
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example-models/bugs_examples/vol3/hepatitis/hepatitisME.stan
39+
example-models/regressions/matrix_indexing.stan
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example-models/bugs_examples/vol1/blocker/blocker.stan, 20000
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example-models/bugs_examples/vol1/bones/bones.stan, 20000
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example-models/bugs_examples/vol1/dyes/dyes.stan, 20000
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example-models/bugs_examples/vol1/equiv/equiv.stan, 20000
44+
example-models/bugs_examples/vol1/leuk/leuk.stan, 20000
45+
example-models/bugs_examples/vol1/leukfr/leukfr.stan, 20000
46+
example-models/bugs_examples/vol1/litter/litter.stan, 20000
47+
example-models/bugs_examples/vol1/magnesium/magnesium.stan, 20000
48+
example-models/bugs_examples/vol1/mice/mice.stan, 20000
49+
example-models/bugs_examples/vol1/pump/pump.stan, 20000
50+
example-models/bugs_examples/vol1/rats/rats.stan, 20000
51+
example-models/bugs_examples/vol1/rats/rats_vec.stan, 20000
52+
example-models/bugs_examples/vol1/rats/rats_vec_unit.stan, 20000
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example-models/bugs_examples/vol1/salm/salm.stan, 20000
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example-models/bugs_examples/vol1/salm/salm2.stan, 20000
55+
example-models/bugs_examples/vol1/seeds/seeds.stan, 20000
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example-models/bugs_examples/vol1/seeds/seeds_centered.stan, 20000
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example-models/bugs_examples/vol1/seeds/seeds_stanified.stan, 20000
58+
example-models/bugs_examples/vol1/stacks/stacks_a_normal.stan, 20000
59+
example-models/bugs_examples/vol1/stacks/stacks_b_dexp.stan, 20000
60+
example-models/bugs_examples/vol1/stacks/stacks_c_t4.stan, 20000
61+
example-models/bugs_examples/vol1/stacks/stacks_d_normal_ridge.stan, 20000
62+
example-models/bugs_examples/vol1/stacks/stacks_e_dexp_ridge.stan, 20000
63+
example-models/bugs_examples/vol1/stacks/stacks_f_t4_ridge.stan, 20000
64+
example-models/bugs_examples/vol1/surgical/surgical.stan, 20000
65+
example-models/bugs_examples/vol1/surgical/surgical_stanified.stan, 20000
66+
example-models/bugs_examples/vol2/air/air.stan, 20000
67+
example-models/bugs_examples/vol2/alli/alli2.stan, 20000
68+
example-models/bugs_examples/vol2/beetles/beetles_cloglog.stan, 20000
69+
example-models/bugs_examples/vol2/beetles/beetles_logit.stan, 20000
70+
example-models/bugs_examples/vol2/beetles/beetles_probit.stan, 20000
71+
example-models/bugs_examples/vol2/dugongs/dugongs.stan, 20000
72+
example-models/bugs_examples/vol2/endo/endo1.stan, 20000
73+
example-models/bugs_examples/vol2/endo/endo2.stan, 20000
74+
example-models/bugs_examples/vol2/endo/endo3.stan, 20000
75+
example-models/bugs_examples/vol2/eyes/eyes.stan, 20000
76+
example-models/bugs_examples/vol2/hearts/hearts.stan, 20000
77+
example-models/bugs_examples/vol2/ice/ice.stan, 20000
78+
example-models/bugs_examples/vol2/orange/orange.stan, 20000
79+
example-models/bugs_examples/vol2/pines/pines-2.stan, 20000
80+
example-models/bugs_examples/vol2/pines/pines.stan, 20000
81+
example-models/bugs_examples/vol2/stagnant/stagnant2.stan, 20000
82+
example-models/bugs_examples/vol2/t_df/estdof.stan, 20000
83+
example-models/bugs_examples/vol3/camel/camel.stan, 20000
84+
example-models/bugs_examples/vol3/camel/camel2.stan, 20000
85+
example-models/bugs_examples/vol3/data_cloning/seeds.stan, 20000
86+
example-models/bugs_examples/vol3/funshapes/circle.stan, 20000
87+
example-models/bugs_examples/vol3/funshapes/hsquare.stan, 20000
88+
example-models/bugs_examples/vol3/funshapes/parallelogram.stan, 20000
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example-models/bugs_examples/vol3/funshapes/ring.stan, 20000
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example-models/bugs_examples/vol3/funshapes/squaremc.stan, 20000
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example-models/bugs_examples/vol3/hepatitis/hepatitis.stan, 20000

‎compare-git-hashes.sh

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@@ -74,14 +74,14 @@ fi
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7575
set -e -x
7676

77-
# First checkout the first arg cmdstan hash, assuming stan and math are as specified
78-
# by that cmdstan commit
79-
clean_checkout "$2" "false" "false"
80-
./runPerformanceTests.py --overwrite-golds $1
81-
82-
for i in performance.*; do
83-
mv $i "${2}_${i}"
84-
done
85-
86-
clean_checkout "$3" "$4" "$5"
77+
#First checkout the first arg cmdstan hash, assuming stan and math are as specified
78+
#by that cmdstan commit
79+
# clean_checkout "$2" "false" "false"
80+
# ./runPerformanceTests.py --overwrite-golds $1
81+
#
82+
# for i in performance.*; do
83+
# mv $i "${2}_${i}"
84+
# done
85+
#
86+
# clean_checkout "$3" "$4" "$5"
8787
./runPerformanceTests.py --check-golds-exact 1e-8 $1 && ./comparePerformance.py "${2}_performance.csv" performance.csv

‎golds/example-models_ARM_Ch.17_flight_simulator_17.3.gold

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sigma_gamma 0.05024669883 0.100764633534
2+
gamma.2 -0.0205074653445 0.0573680096447
3+
gamma.3 0.00580261440449 0.0580097403328
4+
gamma.1 0.0251204697346 0.0587431048261
5+
sigma 0.393390753 0.00904819652672
6+
gamma.4 -0.0081227442617 0.0472391342104
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gamma.5 -0.0141873322623 0.0579827390012
8+
mu 0.45751961 1.06337558104
9+
sigma_delta 0.411155739 1.13193826713
10+
delta.8 0.43660481518 1.08350927365
11+
delta.7 -0.33147951126 1.13316414792
12+
delta.6 -0.024697946216 1.12461747455
13+
delta.5 -0.24019045814 1.14883114678
14+
delta.4 -0.117611167707 1.13144812417
15+
delta.3 -0.010093004112 1.1518963726
16+
delta.2 0.49846102176 1.1093358902
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delta.1 -0.32579000634 1.1411114229

‎golds/example-models_ARM_Ch.17_multilevel_logistic_17.4.gold

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b_v_prev 5.83691828 1.91746926027
2+
b_edu.4 -0.009595316526 0.9515609988
3+
b_edu.2 -0.035192119811 1.02728391771
4+
b_edu.3 0.155966649788 0.743070204419
5+
b_edu.1 -0.199386999807 1.35589783444
6+
b_age_edu.1.3 0.050125307711 0.475395344178
7+
b_age_edu.1.2 0.050088990039 0.438569183239
8+
b_age_edu.1.1 -0.062530232538 0.782656430058
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b_age_edu.1.4 -0.0089981007477 0.31355998207
10+
b_age.3 0.0263734928532 0.288244048636
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b_age.2 -0.0635046603634 0.235476827804
12+
b_age.1 0.0597233043297 0.228325067133
13+
b_age.4 -0.090839179603 0.801760867035
14+
b_age_edu.2.4 -0.0421513526644 0.564167867207
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b_age_edu.2.1 0.0847049049435 0.36651665395
16+
b_age_edu.2.2 -0.106852127149 0.462858088647
17+
b_age_edu.2.3 -0.0138333866494 0.28300268272
18+
b_female -0.090022899633 0.305682329179
19+
b_hat.9 0.75920652832 6.6775502014
20+
b_hat.8 2.82276244 1.18881673813
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b_hat.1 3.57324862 1.00798011398
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b_hat.3 3.45051533 1.21838430564
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b_hat.2 3.55424718 2.1466779217
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b_hat.5 2.9439995 0.559435766953
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b_hat.4 3.27649133 1.22323721579
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b_hat.7 3.13891632 1.36671317237
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b_hat.6 3.18924419 1.21487095752
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b_age_edu.4.2 -0.005890781669 0.607952995544
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b_age_edu.4.3 0.0500247779847 0.419945352422
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b_age_edu.4.1 -0.130802052059 0.566615717531
31+
b_hat.28 3.70923033 1.41634602467
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b_hat.29 3.36484825 1.4257593111
33+
b_age_edu.4.4 0.044137593595 0.534123346414
34+
b_region.5 -0.11249879028 7.07655343152
35+
b_hat.25 3.70101863 1.33825432038
36+
b_hat.26 2.85613098 0.872307945971
37+
b_hat.27 3.15340955 1.98663398714
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b_hat.20 2.92808883 1.92028456759
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b_hat.21 2.54791586 1.58343833668
40+
b_region.3 0.4656678902 0.954328902773
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b_region.2 -0.1994601733 1.28693518873
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sigma_region 0.529011576 2.60618675419
43+
b_hat.39 2.86800457 0.952602779556
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b_hat.38 2.77484242 1.11317466853
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b_hat.37 3.94670836 1.68198028813
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b_hat.36 3.17043559 1.11530247401
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b_hat.35 3.41022015 1.27975916132
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b_hat.34 3.58529311 1.35295597689
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b_hat.33 2.72752718 0.622076918765
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b_hat.32 3.01431606 2.13578203516
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b_hat.31 3.07717809 0.683684193019
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b_hat.30 3.53867675 1.05469550632
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b_hat.24 2.54205199 1.08864131931
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b_region.4 -0.334683041225 1.11744971479
55+
sigma_age 0.1363198558 0.478764817726
56+
b_region.1 -0.214406737183 0.912287292895
57+
b_hat.22 2.60327032 1.65220251308
58+
b_hat.23 3.02893867 0.981643771634
59+
sigma_edu 0.2690752181 0.519683352868
60+
b_0 -2.6978884 1.14404682407
61+
b_hat.15 3.25490692 0.973290228069
62+
b_hat.14 2.85203692 1.27570381006
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b_hat.17 3.48073125 2.18458930557
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b_hat.16 2.75325074 1.56293075764
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b_hat.11 3.20584359 1.51951556972
66+
b_hat.10 3.60589901 1.07835206097
67+
b_hat.13 3.61848453 1.62838811143
68+
b_hat.12 2.63366159 2.18334320507
69+
b_hat.19 3.59228769 0.888328628876
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b_hat.18 3.59189907 1.11741405915
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b_hat.51 3.58430724 1.8880982681
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b_hat.50 2.79865904 1.28686687308
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b_hat.46 3.0606445 0.818223317806
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b_hat.47 3.74913719 0.705535786986
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b_hat.44 3.57060868 1.16372174085
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b_hat.45 3.98931163 1.89499461395
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b_hat.42 3.32113157 1.57886742989
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b_hat.43 3.54329557 1.84020331911
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b_hat.40 2.43047973 1.66529263401
80+
b_hat.41 3.62650136 1.41045233054
81+
b_hat.48 2.91391046 1.28083442247
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b_hat.49 2.71692043 1.38578907708
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b_black -1.559126233 2.88893696705
84+
b_female_black -0.358876978166 4.49130421589
85+
b_age_edu.3.1 0.0455205865548 0.38202510695
86+
b_age_edu.3.3 0.02982004782 0.46346063537
87+
b_age_edu.3.2 0.0176704999258 0.342675436918
88+
b_age_edu.3.4 -0.001420538337 0.379736322791
89+
sigma_state 0.1630793845 0.290508664418
90+
sigma_age_edu 0.1321262858 0.0973056418228
91+
sigma inf inf

‎golds/example-models_basic_estimators_bernoulli.gold

+1
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theta 0.251875169 0.144799800121

‎golds/example-models_basic_estimators_negative_binomial.gold

+2
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alpha 15.95244755 3253.87214015
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beta 10.5987227 2154.50870793

‎golds/example-models_basic_estimators_negative_binomial2.gold

+3
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p_success 1.0 0.0
2+
beta 6.71148640726e+14 6.23494360026e+31
3+
alpha 1.22517819766e+15 2.20901483736e+32

‎golds/example-models_basic_estimators_normal_censored.gold

+1
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mu 0.999557047 0.112991591691

‎golds/example-models_basic_estimators_normal_loc.gold

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mu 1.228300794 1.44310992396

‎golds/example-models_basic_estimators_normal_mixture.gold

+5
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log_one_minus_theta -0.34401738 0.00350077696628
2+
theta 0.29095987 0.00176269637598
3+
log_theta -1.2356125 0.0210342642801
4+
mu.1 -10.0014216 0.040067770695
5+
mu.2 10.0287581 0.0172041955059

‎golds/example-models_basic_estimators_normal_truncated.gold

+2
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mu 0.0936545383117 2.37940761007
2+
sigma 1.075774305 0.369658284372

‎golds/example-models_bugs_examples_vol1_blocker_blocker.gold

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mu.11 -2.341214 0.02184887288
2+
delta.22 -0.34318607 0.0625178044231
3+
delta.20 -0.26132702 0.0756781839323
4+
delta.21 -0.37815901 0.213896414042
5+
mu.6 -2.606458 0.408919806253
6+
mu.7 -1.685979 0.02698916703
7+
mu.17 -2.088836 0.12722159248
8+
delta.9 -0.36524951 0.110483420581
9+
delta.8 -0.04909331 0.248306696603
10+
delta.7 -0.445341 0.0161933787347
11+
mu.22 -2.869779 0.0495046046967
12+
mu.21 -2.071826 0.105574494413
13+
mu.20 -1.511934 0.0918160652133
14+
delta.3 -0.32719548 0.193332829445
15+
delta.2 -0.3721356 0.0736363968088
16+
delta.1 0.18165044 0.481629973899
17+
delta.6 -0.16347365 0.172062868481
18+
delta.13 -0.27364838 0.0627006196739
19+
delta.12 -0.13232099 0.16315926257
20+
delta.11 -0.21051635 0.074751011501
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sigmasq_delta 0.04976731 0.0015060854355
22+
delta.17 -0.07764378 0.0700671363847
23+
sigma_delta 0.2181603 0.00724463941603
24+
delta.15 -0.28633021 0.108883570223
25+
delta.14 0.11940578 0.202478756774
26+
mu.4 -2.417468 0.0112093508533
27+
mu.5 -2.470361 0.0591603093633
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delta.19 -0.26056455 0.0803287557114
29+
delta.18 -0.20073715 0.345194512034
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mu.1 -3.149121 0.63749161063
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mu.2 -2.160707 0.198371547603
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mu.3 -1.966437 0.31322781987
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delta.5 -0.084619981 0.0865350022511
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mu.9 -1.974826 0.188584853813
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delta.4 -0.20088918 0.0169232746496
36+
d -0.2232335 0.0250128529988
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delta_new -0.2691232 0.0433242944245
38+
delta.10 -0.2619267 0.0178675942827
39+
mu.18 -2.942733 0.29338987787
40+
mu.19 -3.352599 0.26974768963
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mu.16 -1.398626 0.08994340068
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mu.8 -2.222448 0.185951271187
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mu.14 -2.804006 0.0825822933467
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mu.15 -1.348127 0.0792998704033
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mu.12 -1.465258 0.08999178572
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mu.13 -2.958549 0.123465606963
47+
mu.10 -2.278517 0.0299906236033
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delta.16 -0.23805173 0.220872884389

‎golds/example-models_bugs_examples_vol1_bones_bones.gold

+13
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1+
theta.11 11.52029 0.468060229667
2+
theta.10 12.15684 1.19263562133
3+
theta.13 17.16314 0.864451394667
4+
theta.12 15.7166 0.621532606667
5+
theta.9 8.897703 0.36978159627
6+
theta.8 9.302029 1.7225546515
7+
theta.1 0.2530312 0.139781236285
8+
theta.3 2.401623 0.22209862367
9+
theta.2 1.4500885 0.431071076334
10+
theta.5 5.748232 0.448794160187
11+
theta.4 2.873985 0.184239630017
12+
theta.7 6.504797 0.297190838737
13+
theta.6 6.670146 0.354996705347

‎golds/example-models_bugs_examples_vol1_dyes_dyes.gold

+13
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1+
tau_within 0.0021362358 3.237190443e-05
2+
sigma_within 36.389354 1059.46116836
3+
sigmasq_within 1642.02369 6478598.78243
4+
sigma_between 0.3685142 5.1155572e-06
5+
sigmasq_between 0.1358042 2.79428653333e-06
6+
theta 1.98528 5.22823333333e-05
7+
mu.4 -1.30879 0.000221768266667
8+
mu.5 -0.04972923 0.000116622101847
9+
mu.6 1.623479 0.000160952496667
10+
tau_between 7.36387 0.008047473
11+
mu.1 -1.894749 4.77683633333e-05
12+
mu.2 0.3596954 3.09505594667e-05
13+
mu.3 0.2070739 3.98603469667e-05

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