Second round of various extensions and fixes to support nimble2

.github/workflows/test-all.yaml

@@ -39,14 +39,10 @@ jobs:
       - uses: actions/checkout@v4
       - name: SessionInfo
         run: R -q -e 'sessionInfo()'
-      - name: Install nimbleModel
-        run: R -q -e 'remotes::install_github("https://github.com/perrydv/nimbleModel", subdir="nimbleModel", auth_token=Sys.getenv("GITHUB_TOKEN_NIMBLEMODEL"))'
-        env:
-          GITHUB_TOKEN_NIMBLEMODEL: ${{ secrets.GH_NM_PAT }}
       - name: Package Dependencies
         run: R -q -e 'remotes::install_deps("nCompiler", dependencies=TRUE)'
       - name: Install inline
-        run: R -q -e 'remotes::install_cran(c("inline", "nimble"))'
+        run: R -q -e 'remotes::install_cran(c("inline"))'
       - name: Build Package
         run: |
             R CMD build nCompiler
@@ -95,22 +91,17 @@ jobs:
       #- name: System Dependencies
       #  # can be used to install e.g. cmake or other build dependencies
       #  run: apt update -qq && apt install --yes --no-install-recommends cmake git
-      - name: Install nimbleModel
-        run: R -q -e 'remotes::install_github("https://github.com/perrydv/nimbleModel", subdir="nimbleModel", auth_token=Sys.getenv("GITHUB_TOKEN_NIMBLEMODEL"))'
-        env:
-          GITHUB_TOKEN_NIMBLEMODEL: ${{ secrets.GH_NM_PAT }}
       - name: Package Dependencies
         run: R -q -e 'remotes::install_deps("nCompiler", dependencies=TRUE)'
       - name: Install inline
-        run: R -q -e 'remotes::install_cran(c("inline", "nimble"))'
+        run: R -q -e 'remotes::install_cran(c("inline"))'
       - name: Build Package
         run: |
             R CMD build nCompiler
             R CMD INSTALL --install-tests nCompiler_*.tar.gz
       - name: Run nCompile and other tests
         run: |
           library(nCompiler)
-          # testthat::test_dir("nCompiler/tests/testthat/nimble_tests", reporter = "summary")
           testthat::test_dir("nCompiler/tests/testthat/nClass_tests", reporter = "summary")
           testthat::test_dir("nCompiler/tests/testthat/types_tests", reporter = "summary")
           testthat::test_dir("nCompiler/tests/testthat/serialization_tests", reporter = "summary")
@@ -157,7 +148,7 @@ jobs:
       - name: Package Dependencies
         run: R -q -e 'remotes::install_deps("nCompiler", dependencies=TRUE)'
       - name: Install inline
-        run: R -q -e 'remotes::install_cran(c("inline", "nimble"))'
+        run: R -q -e 'remotes::install_cran(c("inline"))'
       - name: Build Package
         run: |
             R CMD build nCompiler

.gitignore

@@ -37,3 +37,5 @@ sketches/
 .positai
 # devtools::load_all() convenience symlink (inst/include -> include)
 nCompiler/include
+# macOS Finder metadata
+.DS_Store

nCompiler/DESCRIPTION

@@ -35,7 +35,6 @@ Collate:
     compile_simpleIntermediates.R
     compile_simpleTransformations.R
     compile_finalTransformations.R
-    compileNimble.R
     cppDefs_core.R
     cppDefs_utils.R
     cppDefs_ADutils.R

nCompiler/NAMESPACE

@@ -19,7 +19,6 @@ export(NFinternals)
 export(OptimControlList)
 export(OptimResultList)
 export(SVDDecomp)
-export(type2cpp)
 export(asDense)
 export(asSparse)
 export(build_compiled_nClass)
@@ -34,15 +33,14 @@ export(createBlockRefInfoIntoC)
 export(createRef)
 export(createRefInfoIntoC)
 export(cube)
-export(deregisterOpDef)
-export(documentNClass)
-export(documentNFunction)
 export(dcar_normal)
 export(dcar_proper)
 export(dcat)
 export(dconstraint)
 export(ddexp)
 export(ddirch)
+export(deregisterOpDef)
+export(deregisterTypeDeclaration)
 export(dexp_nimble)
 export(dinvwish_chol)
 export(dflat)
@@ -55,6 +53,8 @@ export(dmnorm_chol)
 export(dmnorm_inv_ld)
 export(dmulti)
 export(dmvt_chol)
+export(documentNClass)
+export(documentNFunction)
 export(dt_nonstandard)
 export(dwish_chol)
 export(erasePackage)
@@ -64,6 +64,7 @@ export(get_nCompile_types)
 export(get_nOption)
 export(icloglog)
 export(ilogit)
+export(interface_names)
 export(iprobit)
 export(is.loadedObjectEnv)
 export(isCNC)
@@ -143,6 +144,7 @@ export(rconstraint)
 export(rdexp)
 export(rdirch)
 export(registerOpDef)
+export(registerTypeDeclaration)
 export(rexp_nimble)
 export(rflat)
 export(rhalfflat)
@@ -165,6 +167,8 @@ export(square)
 export(test_predefined)
 export(to_full_interface)
 export(to_generic_interface)
+export(type2cpp)
+export(type2symbol)
 export(value)
 export(writeCode)
 export(writeCpp_nCompiler)

nCompiler/R/NC.R

@@ -110,6 +110,7 @@ nClass <- function(classname,
   #   accessor specifier, typically "public", e.g. "public some_class".
   #   Similarly, template arguments (include CRTP) should be in the text explicitly.
   # needed_units: list of needed nClasses and nFunctions to include, by name or object
+  # createFromR: Default TRUE, whether to enable creation of objects from R.
   #
   # packageNames: can be a vector or list of two names, possibly named by "uncompiled" and "compiled",
   #  and taken in that order if unnamed. 
@@ -184,7 +185,7 @@ nClass <- function(classname,
     init_body_text <- deparse(body(Rpublic[['initialize']]))
     has_super_init    <- any(grepl("super\\$initialize",  init_body_text))
     has_init_cpublic  <- any(grepl("initialize_Cpublic", init_body_text))
-    if(!has_super_init && !has_init_cpublic)
+    if(!has_super_init && !has_init_cpublic && isTRUE(get_nOption("NCwarn")))
       warning(
         "The Rpublic 'initialize' function does not call 'super$initialize()' or ",
         "'initialize_Cpublic()'. Without one of these, the Cpublic component will not ",

nCompiler/R/NC_FullCompiledInterface.R

@@ -237,9 +237,15 @@ make_compiled_Cpub_class_code <- function(NCgenerator,
         if(is.null(newCobjFun))
           stop("Cannot create a nClass full interface object without a newCobjFun or a CppObj argument.")
         CppObj <- newCobjFun()
+      } else {
+        if(isCNC(CppObj)) {
+          CppObj <- CppObj$private$Cpublic_obj$private$CppObj
+        }
       }
+      if(!nCompiler:::is.loadedObjectEnv(CppObj))
+        stop("in initializeCpp: CppObj should be a loadedObjectEnv")
       private$CppObj <- CppObj
-      private$DLLenv <- `:::`("nCompiler", "get_DLLenv")(CppObj) # workaround static code scanning for nCompiler:::get_DLLenv(CppObj)
+      private$DLLenv <- nCompiler:::get_DLLenv(CppObj)
     },
     list(
       NEWCOBJFUN = if(package) as.name(newCobjFun)