stan-dev · hsbadr · Jun 15, 2021 · Nov 15, 2020 · Nov 16, 2020 · Dec 18, 2020
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,5 +15,5 @@
 Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):
 
 By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:
-- Code: GPLv3 (http://opensource.org/licenses/GPL-3.0)
+- Code: GPLv3 (https://opensource.org/licenses/GPL-3.0)
 - Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -70,6 +70,14 @@ jobs:
       - name: Install dependencies
         run: |
           remotes::install_deps(pkg = "./rstan/rstan", dependencies = TRUE)
+          try(system("git submodule update --init --recursive --remote --force"))
+          try(system("rm -Rf StanHeaders/inst/include/upstream StanHeaders/inst/include/src StanHeaders/inst/include/mathlib StanHeaders/inst/include/stan StanHeaders/inst/include/libsundials"))
+          try(system("cp -Rpv --remove-destination stan/ StanHeaders/inst/include/upstream"))
+          try(system("cp -Rpv --remove-destination stan/src StanHeaders/inst/include/src"))
+          try(system("cp -Rpv --remove-destination stan/lib/stan_math StanHeaders/inst/include/mathlib"))
+          try(system("cp -Rpv --remove-destination stan/lib/stan_math/stan StanHeaders/inst/include/stan"))
+          try(system("cp -Rpv --remove-destination stan/lib/stan_math/lib/sundials_5.5.0 StanHeaders/inst/include/libsundials"))
+          remotes::install_local('StanHeaders', dependencies = TRUE, type = "source")
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 

diff --git a/.gitmodules b/.gitmodules
@@ -1,9 +1,5 @@
 [submodule "stan"]
-	path = StanHeaders/inst/include/upstream
+	path = stan
 	url = https://github.com/stan-dev/stan.git
 	ignore = dirty
 	branch = develop
-[submodule "StanHeaders/inst/include/mathlib"]
-	path = StanHeaders/inst/include/mathlib
-	url = https://github.com/stan-dev/math.git
-	branch = develop
diff --git a/README.md b/README.md
@@ -1,19 +1,19 @@
 # RStan <img src="rstan/rstan/man/figures/stanlogo.png" align="right" width="120" />
 
 <!-- badges: start -->
-[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/rstan?color=blue)](http://cran.r-project.org/package=rstan)
-[![Downloads](http://cranlogs.r-pkg.org/badges/rstan?color=blue)](http://cran.rstudio.com/package=rstan)
-[![Research software impact](http://depsy.org/api/package/cran/rstan/badge.svg)](http://depsy.org/package/r/rstan)
+[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/rstan?color=blue)](https://cran.r-project.org/package=rstan)
+[![Downloads](https://cranlogs.r-pkg.org/badges/rstan?color=blue)](https://cran.rstudio.com/package=rstan)
+[![Research software impact](http://depsy.org/api/package/cran/rstan/badge.svg)](https://depsy.org/package/r/rstan)
 [![R-CMD-check](https://github.com/stan-dev/rstan/workflows/R-CMD-check/badge.svg)](https://github.com/stan-dev/rstan/actions)
 <!-- badges: end -->
 
-**RStan** is the R interface to [Stan](http://mc-stan.org). 
+**RStan** is the R interface to [Stan](https://mc-stan.org).
 
 ### Quick links
 
-* [mc-stan.org/rstan](http://mc-stan.org/rstan) (online RStan documentation, vignettes)
-* [Stan documentation](http://mc-stan.org/users/documentation/) (language manual, case studies, and more)
-* [Ask a question](http://discourse.mc-stan.org) (Stan Forums on Discourse)
+* [mc-stan.org/rstan](https://mc-stan.org/rstan/) (online RStan documentation, vignettes)
+* [Stan documentation](https://mc-stan.org/users/documentation/) (language manual, case studies, and more)
+* [Ask a question](https://discourse.mc-stan.org) (Stan Forums on Discourse)
 * [Open an issue](https://github.com/stan-dev/rstan/issues) (GitHub issues for bug reports, feature requests)
 
 

diff --git a/StanHeaders/DESCRIPTION b/StanHeaders/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: StanHeaders
-Date: 2020-12-09
+Date: 2020-12-20
 Title: C++ Header Files for Stan
 Authors@R: c(person("Ben",family="Goodrich", email="[email protected]", role=c('cre','aut')),
              person("Joshua", "Pritikin", role = "ctb"),
@@ -24,6 +24,9 @@ Authors@R: c(person("Ben",family="Goodrich", email="[email protected]
              person("Dustin", "Tran", role = "aut"),
              person("Michael", "Malecki", role = "aut"),
              person("Yuanjun", "Gao", role = "aut"),
+             person("Hamada S.", "Badr", role = c("ctb"),
+                    email = "[email protected]",
+                    comment = c(ORCID = "0000-0002-9808-2344")),
              person("Trustees of", "Columbia University", role = "cph"),
              person("Lawrence Livermore", "National Security", role = "cph", comment = "CVODES"),
              person("The Regents of the", "University of California", role = "cph", comment = "CVODES"),
@@ -36,5 +39,7 @@ LinkingTo: RcppEigen, RcppParallel (>= 5.0.1)
 VignetteBuilder: knitr
 SystemRequirements: pandoc
 Depends: R (>= 3.4.0)
-Version: 2.21.0-7
+Version: 2.25.0.9000
 License: BSD_3_clause + file LICENSE
+Encoding: UTF-8
+RoxygenNote: 7.1.1
diff --git a/StanHeaders/R/Flags.R b/StanHeaders/R/Flags.R
@@ -1,14 +1,30 @@
 CxxFlags <- function(as_character = FALSE) {
-  TBB <- system.file("include", package = "RcppParallel", mustWork = TRUE)
-  CXXFLAGS <- paste0("-I", shQuote(TBB), " -D_REENTRANT -DSTAN_THREADS")
+  if (dir.exists(Sys.getenv("TBB_INC"))) {
+    TBB_INC <- normalizePath(Sys.getenv("TBB_INC"))
+  } else {
+    TBB_INC <- system.file("include", package = "RcppParallel", mustWork = TRUE)
+  }
+
+  if (file.exists(file.path(TBB_INC, "tbb", "version.h"))) {
+    CXXFLAGS <- paste0("-I", shQuote(TBB_INC), " -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW")
+  } else {
+    CXXFLAGS <- paste0("-I", shQuote(TBB_INC), " -D_REENTRANT -DSTAN_THREADS")
+  }
+
   if (isTRUE(as_character)) return(CXXFLAGS)
   cat(CXXFLAGS, " ")
   return(invisible(NULL))
 }
 
 LdFlags <- function(as_character = FALSE) {
-  TBB <- system.file("lib", .Platform$r_arch, package = "RcppParallel", mustWork = TRUE)
-  PKG_LIBS <- paste0("-L", shQuote(TBB), " -Wl,-rpath,", TBB, " -ltbb -ltbbmalloc")
+  if (dir.exists(Sys.getenv("TBB_LIB"))) {
+    TBB_LIB <- normalizePath(Sys.getenv("TBB_LIB"))
+  } else {
+    TBB_LIB <- system.file("lib", .Platform$r_arch, package = "RcppParallel", mustWork = TRUE)
+  }
+
+  PKG_LIBS <- paste0("-L", shQuote(TBB_LIB), " -Wl,-rpath,", TBB_LIB, " -ltbb -ltbbmalloc")
+
   if (isTRUE(as_character)) return(PKG_LIBS)
   cat(PKG_LIBS, " ")
   return(invisible(NULL))

diff --git a/StanHeaders/inst/include/libsundials b/StanHeaders/inst/include/libsundials
@@ -1 +1 @@
-mathlib/lib/sundials_4.1.0/
+../../../stan/lib/stan_math/lib/sundials_5.5.0/
diff --git a/StanHeaders/inst/include/mathlib b/StanHeaders/inst/include/mathlib
diff --git a/StanHeaders/inst/include/mathlib b/StanHeaders/inst/include/mathlib
@@ -0,0 +1 @@
+../../../stan/lib/stan_math/
diff --git a/StanHeaders/inst/include/src b/StanHeaders/inst/include/src
@@ -1 +1 @@
-upstream/src/
+../../../stan/src/
diff --git a/StanHeaders/inst/include/stan b/StanHeaders/inst/include/stan
@@ -1 +1 @@
-mathlib/stan/
+../../../stan/lib/stan_math/stan/
diff --git a/StanHeaders/inst/include/upstream b/StanHeaders/inst/include/upstream
diff --git a/StanHeaders/inst/include/upstream b/StanHeaders/inst/include/upstream
@@ -0,0 +1 @@
+../../../stan/
diff --git a/StanHeaders/install-github.R b/StanHeaders/install-github.R
@@ -6,11 +6,11 @@ install_StanHeaders <- function(rstan_branch = "develop",
                                 math_branch = "master",
                                 library_branch = "master") {
   path_rstan <- tempfile(pattern = "git2r-")
-  git2r::clone("http://github.com/stan-dev/rstan", path_rstan, branch = rstan_branch)
-  git2r::clone("http://github.com/stan-dev/stan",
+  git2r::clone("https://github.com/stan-dev/rstan", path_rstan, branch = rstan_branch)
+  git2r::clone("https://github.com/stan-dev/stan",
                file.path(path_rstan, "StanHeaders", "inst", "include", "upstream"), 
                branch = library_branch)
-  git2r::clone("http://github.com/stan-dev/math",
+  git2r::clone("https://github.com/stan-dev/math",
                file.path(path_rstan, "StanHeaders", "inst", "include", "mathlib"), 
                branch = math_branch)
   # writeLines(c(".PHONY: static", readLines(file.path(path_rstan, "StanHeaders", "src", "Makevars.win")),

diff --git a/licenses/rstan-license.txt b/licenses/rstan-license.txt
@@ -4,7 +4,7 @@ All rights reserved.
 
 
 RStan is licensed under the GPLv3 license. 
-http://opensource.org/licenses/GPL-3.0
+https://opensource.org/licenses/GPL-3.0
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -17,5 +17,5 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
diff --git a/rstan/install.R b/rstan/install.R
@@ -21,7 +21,7 @@ install_rstan <- function() {
   if(inherits(test, "try-error")) stop("hello world failed; ask for help on Rcpp list")
 
   options(repos = c(getOption("repos"), 
-          rstan = "http://rstan.org/repo/"))
+          rstan = "https://rstan.org/repo/"))
   install.packages("rstan", type = 'source')
   library(rstan)
   set_cppo("fast")

diff --git a/rstan/makefile b/rstan/makefile
@@ -55,7 +55,7 @@ help:
 .PHONY: build check install clean clean-all install_pre_rpkg test-R example_csv
 
 install_pre_rpkg:
-	@R -q -e "options(repos=structure(c(CRAN = 'http://cran.rstudio.com'))); for (pkg in c('inline', 'Rcpp', 'RcppEigen', 'RUnit', 'BH', 'StanHeaders', 'RInside')) if (!require(pkg, character.only = TRUE))  install.packages(pkg, dep = TRUE); sessionInfo()" 
+	@R -q -e "options(repos=structure(c(CRAN = 'https://cran.rstudio.com'))); for (pkg in c('inline', 'Rcpp', 'RcppEigen', 'RUnit', 'BH', 'StanHeaders', 'RInside')) if (!require(pkg, character.only = TRUE))  install.packages(pkg, dep = TRUE); sessionInfo()"
 
 build $(STANPKG): ./rstan/DESCRIPTION
 ifeq ($(GIT),)

diff --git a/rstan/rstan/DESCRIPTION b/rstan/rstan/DESCRIPTION
@@ -1,16 +1,18 @@
 Package: rstan
-Encoding: UTF-8
 Type: Package
 Title: R Interface to Stan
-Version: 2.21.3
-Date: 2020-09-01
+Version: 2.25.0.9000
+Date: 2020-12-20
 Authors@R: c(person("Jiqiang", "Guo", email = "[email protected]", role = "aut"),
              person("Jonah", "Gabry", email = "[email protected]", role = "aut"),
              person("Ben", "Goodrich", email = "[email protected]", role = c("cre", "aut")),
              person("Sebastian", "Weber", email = "[email protected]", role = "aut"),
              person("Daniel", "Lee", role = "ctb"),
              person("Krzysztof", "Sakrejda", role = "ctb"),
              person("Modrak", "Martin", role = "ctb"),
+             person("Hamada S.", "Badr", role = c("ctb"),
+                    email = "[email protected]",
+                    comment = c(ORCID = "0000-0002-9808-2344")),
              person("Trustees of", "Columbia University", role = "cph"),
              person("Oleg", "Sklyar", role = "cph", comment = "R/cxxfunplus.R"),
              person("The R", "Core Team", role = "cph", comment = "R/pairs.R, R/dynGet.R"),
@@ -40,15 +42,15 @@ Imports:
     RcppParallel (>= 5.0.1),
     loo (>= 2.3.0),
     pkgbuild,
-    V8
+    V8 (>= 3.4.0),
+    ggplot2 (>= 3.0.0)
 Depends:
     R (>= 3.4.0),
-    StanHeaders (>= 2.21.0),
-    ggplot2 (>= 3.0.0)
+    StanHeaders (>= 2.25.0)
 LinkingTo: Rcpp (>= 0.12.0),
     RcppEigen (>= 0.3.3.3.0),
     BH (>= 1.72.0-2),
-    StanHeaders (>= 2.21.0),
+    StanHeaders (>= 2.25.0),
     RcppParallel
 Suggests:
     RUnit,
@@ -62,10 +64,10 @@ Suggests:
     rstantools,
     rstudioapi,
     Matrix,
-    knitr (>= 1.15.1),
-    V8
-URL: https://mc-stan.org/rstan, https://discourse.mc-stan.org
+    knitr (>= 1.15.1)
+URL: https://mc-stan.org/rstan/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/rstan/issues/
 VignetteBuilder: knitr
 SystemRequirements: GNU make, pandoc
-RoxygenNote: 5.0.1
+Encoding: UTF-8
+RoxygenNote: 7.1.1
diff --git a/rstan/rstan/R/AllClass.R b/rstan/rstan/R/AllClass.R
@@ -30,7 +30,7 @@ setClass(Class = "cxxdso",
                                  #  3. The binary dso with name dso_bin, which is a raw vector.  
                                  #     We put it here since the environment is not copied 
                                  #     when assigned to another 
-                                 #     http://cran.r-project.org/doc/manuals/R-lang.html#Environment-objects
+                                 #     https://cran.r-project.org/doc/manuals/R-lang.html#Environment-objects
          ),
          validity = function(object) {
            length(object@sig) > 0 && identical(object@system, R.version$system)

diff --git a/rstan/rstan/R/Rcpp_module_def.R b/rstan/rstan/R/Rcpp_module_def.R
@@ -18,40 +18,62 @@
 get_Rcpp_module_def_code <- function(model_name) {
   RCPP_MODULE <-
 '
-#include <rstan_next/stan_fit.hpp>
+RCPP_MODULE(stan_fit4%model_name%_mod) {
+  class_<rstan::stan_fit<stan_model, boost::random::ecuyer1988> >(
+      "stan_fit4%model_name%")
 
-struct stan_model_holder {
-    stan_model_holder(rstan::io::rlist_ref_var_context rcontext,
-                      unsigned int random_seed)
-    : rcontext_(rcontext), random_seed_(random_seed)
-     {
-     }
+      .constructor<SEXP, SEXP, SEXP>()
 
-   //stan::math::ChainableStack ad_stack;
-   rstan::io::rlist_ref_var_context rcontext_;
-   unsigned int random_seed_;
-};
-
-Rcpp::XPtr<stan::model::model_base> model_ptr(stan_model_holder* smh) {
-  Rcpp::XPtr<stan::model::model_base> model_instance(new stan_model(smh->rcontext_, smh->random_seed_), true);
-  return model_instance;
-}
-
-Rcpp::XPtr<rstan::stan_fit_base> fit_ptr(stan_model_holder* smh) {
-  return Rcpp::XPtr<rstan::stan_fit_base>(new rstan::stan_fit(model_ptr(smh), smh->random_seed_), true);
-}
-
-std::string model_name(stan_model_holder* smh) {
-  return model_ptr(smh).get()->model_name();
-}
-
-RCPP_MODULE(stan_fit4%model_name%_mod){
-  Rcpp::class_<stan_model_holder>("stan_fit4%model_name%")
-  .constructor<rstan::io::rlist_ref_var_context, unsigned int>()
-  .method("model_ptr", &model_ptr)
-  .method("fit_ptr", &fit_ptr)
-  .method("model_name", &model_name)
-  ;
+      .method(
+          "call_sampler",
+          &rstan::stan_fit<stan_model, boost::random::ecuyer1988>::call_sampler)
+      .method(
+          "param_names",
+          &rstan::stan_fit<stan_model, boost::random::ecuyer1988>::param_names)
+      .method("param_names_oi",
+              &rstan::stan_fit<stan_model,
+                               boost::random::ecuyer1988>::param_names_oi)
+      .method("param_fnames_oi",
+              &rstan::stan_fit<stan_model,
+                               boost::random::ecuyer1988>::param_fnames_oi)
+      .method(
+          "param_dims",
+          &rstan::stan_fit<stan_model, boost::random::ecuyer1988>::param_dims)
+      .method("param_dims_oi",
+              &rstan::stan_fit<stan_model,
+                               boost::random::ecuyer1988>::param_dims_oi)
+      .method("update_param_oi",
+              &rstan::stan_fit<stan_model,
+                               boost::random::ecuyer1988>::update_param_oi)
+      .method("param_oi_tidx",
+              &rstan::stan_fit<stan_model,
+                               boost::random::ecuyer1988>::param_oi_tidx)
+      .method("grad_log_prob",
+              &rstan::stan_fit<stan_model,
+                               boost::random::ecuyer1988>::grad_log_prob)
+      .method("log_prob",
+              &rstan::stan_fit<stan_model, boost::random::ecuyer1988>::log_prob)
+      .method("unconstrain_pars",
+              &rstan::stan_fit<stan_model,
+                               boost::random::ecuyer1988>::unconstrain_pars)
+      .method("constrain_pars",
+              &rstan::stan_fit<stan_model,
+                               boost::random::ecuyer1988>::constrain_pars)
+      .method(
+          "num_pars_unconstrained",
+          &rstan::stan_fit<stan_model,
+                           boost::random::ecuyer1988>::num_pars_unconstrained)
+      .method(
+          "unconstrained_param_names",
+          &rstan::stan_fit<
+              stan_model, boost::random::ecuyer1988>::unconstrained_param_names)
+      .method(
+          "constrained_param_names",
+          &rstan::stan_fit<stan_model,
+                           boost::random::ecuyer1988>::constrained_param_names)
+      .method("standalone_gqs",
+              &rstan::stan_fit<stan_model,
+                               boost::random::ecuyer1988>::standalone_gqs);
 }
 '
 gsub("%model_name%", model_name, RCPP_MODULE)
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		mathlib/lib/sundials_4.1.0/
		../../../stan/lib/stan_math/lib/sundials_5.5.0/