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Issue 127: Check Stan code is valid syntax #158

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Jul 15, 2024
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Issue 127: Check Stan code is valid syntax #158

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9 changes: 6 additions & 3 deletions tests/testthat/test-int-latent_individual.R
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
prep_obs <- as_latent_individual(sim_obs)
prep_obs_gamma <- as_latent_individual(sim_obs_gamma)

test_that("epidist.epidist_latent_individual Stan code compiles in the default case", { # nolint: line_length_linter.
test_that("epidist.epidist_latent_individual Stan code has no syntax errors and compiles in the default case", { # nolint: line_length_linter.
skip_on_cran()
stancode <- epidist(data = prep_obs, fn = brms::make_stancode)
mod <- cmdstan_model(stan_file = write_stan_file(stancode), compile = FALSE)
expect_true(mod$check_syntax())
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Are the comments here an issue : https://github.com/epinowcast/epinowcast/blob/d957b21af07c7708d8ae28fc248fffe39d453828/.github/workflows/check-cmdstan.yaml#L67

The concern would be that brms has pedantic problems at some point and this then breaks out testing.

expect_no_error(mod$compile())
})

Expand Down Expand Up @@ -50,7 +51,7 @@ test_that("epidist.epidist_latent_individual recovers the simulation settings fo
expect_equal(mean(lognormal_draws$sdlog), sdlog, tolerance = 0.1)
})

test_that("epidist.epidist_latent_individual Stan code compiles in the gamma delay case", { # nolint: line_length_linter.
test_that("epidist.epidist_latent_individual Stan code has no syntax errors and compiles in the gamma delay case", { # nolint: line_length_linter.
skip_on_cran()
stancode_gamma <- epidist(
data = prep_obs_gamma,
Expand All @@ -60,10 +61,11 @@ test_that("epidist.epidist_latent_individual Stan code compiles in the gamma del
mod_gamma <- cmdstan_model(
stan_file = write_stan_file(stancode_gamma), compile = FALSE
)
expect_true(mod_gamma$check_syntax())
expect_no_error(mod_gamma$compile())
})

test_that("epidist.epidist_latent_individual Stan code compiles for an alternative formula", { # nolint: line_length_linter.
test_that("epidist.epidist_latent_individual Stan code has no syntax errors and compiles for an alternative formula", { # nolint: line_length_linter.
skip_on_cran()
prep_obs$sex <- rbinom(n = nrow(prep_obs), size = 1, prob = 0.5)
formula_sex <- epidist_formula(prep_obs, delay_central = ~ 1 + sex,
Expand All @@ -73,6 +75,7 @@ test_that("epidist.epidist_latent_individual Stan code compiles for an alternati
mod_sex <- cmdstan_model(
stan_file = write_stan_file(stancode_sex), compile = FALSE
)
expect_true(mod_sex$check_syntax())
expect_no_error(mod_sex$compile())
})

Expand Down
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