Add a few improvements from the removals PR

src/middle/Stan_math_signatures.ml

@@ -252,6 +252,7 @@ let distributions =
   ; ([Lpdf; Log], "inv_wishart", [DMatrix; DReal; DMatrix], SoA)
   ; ([Lpdf; Log], "lkj_corr", [DMatrix; DReal], AoS)
   ; ([Lpdf; Log], "lkj_corr_cholesky", [DMatrix; DReal], AoS)
+  ; ([Lpdf; Log], "lkj_cov", [DMatrix; DVector; DVector; DReal], AoS)
   ; (full_lpdf_depr, "logistic", [DVReal; DVReal; DVReal], SoA)
   ; ([Lpdf; Rng; Cdf; Log], "loglogistic", [DVReal; DVReal; DVReal], SoA)
   ; (full_lpdf_depr, "lognormal", [DVReal; DVReal; DVReal], SoA)
@@ -1606,8 +1607,6 @@ let () =
   add_unqualified
     ("lkj_corr_cholesky_rng", ReturnType UMatrix, [UInt; UReal], AoS) ;
   add_unqualified ("lkj_corr_rng", ReturnType UMatrix, [UInt; UReal], AoS) ;
-  add_unqualified
-    ("lkj_cov_log", ReturnType UReal, [UMatrix; UVector; UVector; UReal], AoS) ;
   add_binary_vec_int_real "lmgamma" AoS ;
   add_binary_vec "lmultiply" SoA ;
   add_unqualified ("log", ReturnType UComplex, [UComplex], AoS) ;
@@ -2718,5 +2717,4 @@ let%expect_test "declarative distributions" =
   |> print_endline ;
   [%expect {|
     binomial_coefficient_log
-    multiply_log
-    lkj_cov_log |}]
+    multiply_log |}]

src/stancjs/stancjs.ml

@@ -55,6 +55,10 @@ let stan2cpp model_name model_string is_flag_set flag_val =
           flag_val "max-line-length"
           |> Option.map ~f:int_of_string
           |> Option.value ~default:78 in
+        let deprecation_warnings =
+          if canonicalizer_settings.deprecations then []
+          else Deprecation_analysis.collect_warnings typed_ast in
+        let warnings = warnings @ deprecation_warnings in
         let mir = Ast_to_Mir.trans_prog model_name typed_ast in
         let tx_mir = Transform_Mir.trans_prog mir in
         if is_flag_set "auto-format" || is_flag_set "print-canonical" then

test/integration/good/function-signatures/distributions/multivariate/continuous/lkj_cov_log.stan

@@ -7,8 +7,8 @@ data {
 }
 transformed data {
   real transformed_data_real;
-  transformed_data_real = lkj_cov_log(d_matrix, d_vector, d_vector, d_real);
-  transformed_data_real = lkj_cov_log(d_matrix, d_vector, d_vector, d_int);
+  transformed_data_real = lkj_cov_lpdf(d_matrix | d_vector, d_vector, d_real);
+  transformed_data_real = lkj_cov_lpdf(d_matrix | d_vector, d_vector, d_int);
 }
 parameters {
   matrix[d_int, d_int] p_matrix;
@@ -19,32 +19,31 @@ parameters {
 }
 transformed parameters {
   real transformed_param_real;
-  transformed_param_real = lkj_cov_log(d_matrix, d_vector, d_vector, d_real);
-  transformed_param_real = lkj_cov_log(d_matrix, d_vector, d_vector, p_real);
-  transformed_param_real = lkj_cov_log(d_matrix, d_vector, p_vector, d_real);
-  transformed_param_real = lkj_cov_log(d_matrix, d_vector, p_vector, p_real);
-  transformed_param_real = lkj_cov_log(d_matrix, p_vector, d_vector, d_real);
-  transformed_param_real = lkj_cov_log(d_matrix, p_vector, d_vector, p_real);
-  transformed_param_real = lkj_cov_log(d_matrix, p_vector, p_vector, d_real);
-  transformed_param_real = lkj_cov_log(d_matrix, p_vector, p_vector, p_real);
-  transformed_param_real = lkj_cov_log(p_matrix, d_vector, d_vector, d_real);
-  transformed_param_real = lkj_cov_log(p_matrix, d_vector, d_vector, p_real);
-  transformed_param_real = lkj_cov_log(p_matrix, d_vector, p_vector, d_real);
-  transformed_param_real = lkj_cov_log(p_matrix, d_vector, p_vector, p_real);
-  transformed_param_real = lkj_cov_log(p_matrix, p_vector, d_vector, d_real);
-  transformed_param_real = lkj_cov_log(p_matrix, p_vector, d_vector, p_real);
-  transformed_param_real = lkj_cov_log(p_matrix, p_vector, p_vector, d_real);
-  transformed_param_real = lkj_cov_log(p_matrix, p_vector, p_vector, p_real);
-  transformed_param_real = lkj_cov_log(d_matrix, d_vector, d_vector, d_int);
-  transformed_param_real = lkj_cov_log(d_matrix, d_vector, p_vector, d_int);
-  transformed_param_real = lkj_cov_log(d_matrix, p_vector, d_vector, d_int);
-  transformed_param_real = lkj_cov_log(d_matrix, p_vector, p_vector, d_int);
-  transformed_param_real = lkj_cov_log(p_matrix, d_vector, d_vector, d_int);
-  transformed_param_real = lkj_cov_log(p_matrix, d_vector, p_vector, d_int);
-  transformed_param_real = lkj_cov_log(p_matrix, p_vector, d_vector, d_int);
-  transformed_param_real = lkj_cov_log(p_matrix, p_vector, p_vector, d_int);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | d_vector, d_vector, d_real);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | d_vector, d_vector, p_real);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | d_vector, p_vector, d_real);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | d_vector, p_vector, p_real);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | p_vector, d_vector, d_real);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | p_vector, d_vector, p_real);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | p_vector, p_vector, d_real);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | p_vector, p_vector, p_real);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | d_vector, d_vector, d_real);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | d_vector, d_vector, p_real);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | d_vector, p_vector, d_real);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | d_vector, p_vector, p_real);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | p_vector, d_vector, d_real);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | p_vector, d_vector, p_real);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | p_vector, p_vector, d_real);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | p_vector, p_vector, p_real);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | d_vector, d_vector, d_int);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | d_vector, p_vector, d_int);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | p_vector, d_vector, d_int);
+  transformed_param_real = lkj_cov_lpdf(d_matrix | p_vector, p_vector, d_int);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | d_vector, d_vector, d_int);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | d_vector, p_vector, d_int);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | p_vector, d_vector, d_int);
+  transformed_param_real = lkj_cov_lpdf(p_matrix | p_vector, p_vector, d_int);
 }
 model {
   y_p ~ normal(0, 1);
 }
-

test/integration/good/warning/pretty.expected

@@ -2465,6 +2465,9 @@ Warning in 'lkj_cov_deprecation2.stan', line 8, column 2: increment_log_prob(...
     is deprecated and will be removed in Stan 2.33.0. Use target += ...;
     instead. This can be done automatically with the canonicalize flag for
     stanc
+Warning in 'lkj_cov_deprecation2.stan', line 8, column 21: lkj_cov_log is
+    deprecated and will be removed in Stan 2.33.0. Use lkj_cov_lpdf instead.
+    This can be automatically changed using the canonicalize flag for stanc
   $ ../../../../../install/default/bin/stanc --auto-format lvalue_multiindex.stan
 data {
   array[5] matrix[5, 5] x;

test/integration/signatures/stan_math_distributions.t

@@ -30,6 +30,7 @@ Display all Stan math distributions exposed in the language
   inv_wishart: lpdf, log (deprecated)
   lkj_corr: lpdf, log (deprecated)
   lkj_corr_cholesky: lpdf, log (deprecated)
+  lkj_cov: lpdf, log (deprecated)
   logistic: lpdf, rng, ccdf, cdf, log (deprecated)
   loglogistic: lpdf, rng, cdf, log (deprecated)
   lognormal: lpdf, rng, ccdf, cdf, log (deprecated)

test/integration/signatures/stan_math_signatures.t

@@ -11518,6 +11518,7 @@ Display all Stan math signatures exposed in the language
   lkj_corr_lpdf(matrix, real) => real
   lkj_corr_rng(int, real) => matrix
   lkj_cov_log(matrix, vector, vector, real) => real
+  lkj_cov_lpdf(matrix, vector, vector, real) => real
   lmgamma(int, real) => real
   lmgamma(int, vector) => vector
   lmgamma(array[] int, vector) => vector