Automate R docs build from roxygen comments (#205)

* Automate R docs build from roxygen comments

* Update docs on docs

.github/workflows/docs.yaml

@@ -49,12 +49,25 @@ jobs:
       - name: Set up Julia
         uses: julia-actions/setup-julia@v1
 
-      - name: Install package
+
+      - name: Install R
+        uses: r-lib/actions/setup-r@v2.6.5
+
+      - name: Install R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2.6.5
+        with:
+          packages: |
+            any::roxygen2
+            github::Genentech/rd2markdown
+
+      - name: Install packages
         run: |
           cd python/
           pip install .
           cd ../julia
           julia --project=./docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+          cd ../R/
+          Rscript -e "install.packages(getwd(), repos=NULL, type=\"source\")"
 
       - name: Calculate version
         if:

R/R/bridgestan.R

@@ -1,6 +1,6 @@
 #' StanModel
 #'
-#' R6 Class representing a compiled BridgeStan model.
+#' @description R6 Class representing a compiled BridgeStan model.
 #'
 #' This model exposes log density, gradient, and Hessian information
 #' as well as constraining and unconstraining transforms.

R/R/compile.R

@@ -2,16 +2,6 @@ IS_WINDOWS <- isTRUE(.Platform$OS.type == "windows")
 MAKE <- Sys.getenv("MAKE", ifelse(IS_WINDOWS, "mingw32-make", "make"))
 
 
-#' Get the path to BridgeStan.
-#'
-#' By default this is set to the value of the environment
-#' variable `BRIDGESTAN`.
-#'
-#' If there is no path set, this function will download
-#' a matching version of BridgeStan to a folder called
-#' `.bridgestan` in the user's home directory.
-#'
-#' See also `set_bridgestan_path`
 verify_bridgestan_path <- function(path) {
     suppressWarnings({
         folder <- normalizePath(path)
@@ -26,15 +16,25 @@ verify_bridgestan_path <- function(path) {
     }
 }
 
-#' Set the path to BridgeStan.
-#'
-#' This should point to the top-level folder of the repository.
+#' @title Function `set_bridgestan_path()`
+#' @description Set the path to BridgeStan.
+#' @details This should point to the top-level folder of the repository.
 #' @export
 set_bridgestan_path <- function(path) {
     verify_bridgestan_path(path)
     Sys.setenv(BRIDGESTAN = normalizePath(path))
 }
 
+#' Get the path to BridgeStan.
+#'
+#' By default this is set to the value of the environment
+#' variable `BRIDGESTAN`.
+#'
+#' If there is no path set, this function will download
+#' a matching version of BridgeStan to a folder called
+#' `.bridgestan` in the user's home directory.
+#'
+#' @seealso [set_bridgestan_path]
 get_bridgestan_path <- function() {
     # try to get from environment
     path <- Sys.getenv("BRIDGESTAN", unset = "")
@@ -54,8 +54,10 @@ get_bridgestan_path <- function() {
 }
 
 
-#' Run BridgeStan's Makefile on a `.stan` file, creating the `.so`
-#' used by the StanModel class.
+#' @title Function `compile_model()`
+#' @description Compiles a Stan model.
+#' @details Run BridgeStan's Makefile on a `.stan` file, creating
+#' the `.so` used by the StanModel class.
 #' This function checks that the path to BridgeStan is valid
 #' and will error if not. This can be set with `set_bridgestan_path`.
 #'
@@ -67,6 +69,8 @@ get_bridgestan_path <- function() {
 #' threading for the compiled model. If the same flags are defined
 #' in `make/local`, the versions passed here will take precedent.
 #' @return Path to the compiled model.
+#'
+#' @seealso [bridgestan::set_bridgestan_path()]
 #' @export
 compile_model <- function(stan_file, stanc_args = NULL, make_args = NULL) {
     verify_bridgestan_path(get_bridgestan_path())

R/convert_docs.R

@@ -0,0 +1,30 @@
+# Converts R documentation (.Rd) files to markdown (.md) files
+# for use in Sphinx.
+
+library(rd2markdown)
+library(roxygen2)
+
+roxygen2::roxygenize()
+
+files <- list.files("man", pattern="*.Rd")
+
+# we only want to doc exported functions, so we need
+# to read the NAMESPACE file
+namespace <- paste0(readLines("NAMESPACE"), collapse="\n")
+
+for (f in files){
+    name <- substr(f, 1, nchar(f)-3)
+
+    if (!grepl(name, namespace, fixed=TRUE)){
+        print(paste0("Skipping unexported ", name))
+        next
+    }
+
+    # read .Rd file and convert to markdown
+    rd <- rd2markdown::get_rd(file=file.path(".", "man", f))
+    md <- rd2markdown::rd2markdown(rd, fragments=c())
+
+    # write it to the docs folder
+    writeLines(md, file.path("..", "docs", "languages", "_r", paste0(name, ".md")))
+
+}

docs/conf.py

@@ -140,6 +140,30 @@
     else:
         print("Failed to build julia docs!\n", e)
 
+try:
+    print("Building R doc")
+    subprocess.run(
+        ["Rscript", "convert_docs.R"],
+        cwd=pathlib.Path(__file__).parent.parent / "R",
+        check=True,
+    )
+
+    # delete some broken links in the generated R docs
+    StanModel = (pathlib.Path(__file__).parent / "languages" / "_r" / "StanModel.md")
+    text = StanModel.read_text()
+    start = text.find("### Public methods")
+    end = text.find("### Method `")
+    text = text[:start] + text[end:]
+    StanModel.write_text(text)
+
+except Exception as e:
+    # fail loudly in Github Actions
+    if RUNNING_IN_CI:
+        raise e
+    else:
+        print("Failed to build R docs!\n", e)
+
+
 try:
     print("Checking C++ doc availability")
     import breathe

docs/internals/documentation.rst

@@ -6,8 +6,8 @@ Documenting a mixed-language project such as BridgeStan can be tricky.
 
 We attempt to keep documentation in the natural place for each language: C/C++
 code is documented with doxygen-style comments in the source, Python documentation
-appears in docstrings, etc. With the exception of the R interface, our documentation
-generation (powered by `Sphinx <https://www.sphinx-doc.org/en/master/>`__) automatically
+appears in docstrings, etc. Our documentation generation
+(powered by `Sphinx <https://www.sphinx-doc.org/en/master/>`__) automatically
 combines these together into the documentation you are reading now.
 
 To build the documentation, you can run ``make docs`` in the top-level directory.
@@ -31,3 +31,8 @@ Similarly, the Julia documentation will only update if Julia is installed. Julia
 documentation is written in :file:`julia/docs/src/julia.md`. We then build
 this with `DocumenterMarkdown.jl <https://github.com/JuliaDocs/DocumenterMarkdown.jl>`__,
 and the output is placed in :file:`docs/languages/julia.md`.
+
+Finally, the R documentation is primarily written in :file:`/docs/languages/r.md`.
+The API documentation for R is done by including files generated by
+`rd2markdown <https://github.com/Genentech/rd2markdown>`__, which runs
+on the results of the `roxygen2 package <https://roxygen2.r-lib.org/>`__.

docs/languages/_r/README

@@ -0,0 +1,3 @@
+These files are automatically generated in `conf.py` and should
+not be manually edited. They are built from the documentation
+comments in the R source code.