Basic r setup

.github/workflows/run_preflight.yml

@@ -14,6 +14,9 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
       - name: Set up Rust
         uses: actions-rs/toolchain@v1
         with:
@@ -24,6 +27,9 @@ jobs:
         working-directory: rust
         run: rustup component add clippy rustfmt
 
+      - name: Set R_HOME env var
+        run: echo "R_HOME=$(R RHOME)" >> $GITHUB_ENV
+
       - name: Format check
         working-directory: rust
         run: cargo fmt --all -- --check

.github/workflows/run_rust_unit_tests.yml

@@ -17,6 +17,9 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v3
 
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
       - name: Set up Rust
         uses: actions-rs/toolchain@v1
         with:
@@ -27,7 +30,9 @@ jobs:
         run: sudo apt-get update && sudo apt-get install -y libssl-dev pkg-config
 
       - name: Run tests
-        working-directory: rust
-        run: cargo test
+        run: |
+          export LD_LIBRARY_PATH=$(R RHOME)/lib:$LD_LIBRARY_PATH
+          cargo test
+
 
 

.gitignore

@@ -33,4 +33,17 @@ venv/
 .codegpt
 
 # prettier node
-node_modules/
+node_modules/
+
+# R specific
+.Rhistory
+.RData
+bindings/r/src/rust/vendor
+bindings/r/src/Makevars
+bindings/r/src/Makevars.win
+*.o
+*.so
+*.dll
+target
+.cargo
+.Rproj.user

Cargo.toml

@@ -2,5 +2,6 @@
 members = [
     "rust/codelist-rs",
     "rust/codelist-validator-rs",
-    "bindings/python"
+    "bindings/python",
+    "bindings/r/src/rust"
 ]

bindings/r/.Rbuildignore

@@ -0,0 +1,8 @@
+^\.vscode$
+^src/\.cargo$
+^src/rust/vendor$
+^src/rust/target$
+^src/Makevars$
+^src/Makevars\.win$
+^.*\.Rproj$
+^\.Rproj\.user$

bindings/r/DESCRIPTION

@@ -10,4 +10,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Imports:
     rextendr
-Config/rextendr/version: 0.3.1
+Config/rextendr/version: 0.4.0.9000
+SystemRequirements: Cargo (Rust's package manager), rustc
+Depends: 
+    R (>= 4.2)

bindings/r/NAMESPACE

@@ -1,2 +1,5 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method("$",Codelist)
+S3method("[[",Codelist)
 useDynLib(codelist, .registration = TRUE)
-export(hello)

bindings/r/R/extendr-wrappers.R

@@ -12,5 +12,19 @@ NULL
 
 hello <- function() .Call(wrap__hello)
 
+Codelist <- new.env(parent = emptyenv())
+
+Codelist$new <- function(name) .Call(wrap__Codelist__new, name)
+
+Codelist$set_name <- function(new_name) .Call(wrap__Codelist__set_name, self, new_name)
+
+Codelist$get_entries <- function() .Call(wrap__Codelist__get_entries, self)
+
+#' @export
+`$.Codelist` <- function (self, name) { func <- Codelist[[name]]; environment(func) <- environment(); func }
+
+#' @export
+`[[.Codelist` <- `$.Codelist`
+
 
 # nolint end

bindings/r/README.md

@@ -1,8 +1,6 @@
 # R Bindings
 
-This package demonstrates how to call Rust functions from R using extendr. I
-(@CarolineMorton) have not yet implemented this with our Codelist library but
-rather with a simple "hello world" function.
+This package demonstrates how to call Rust functions from R using extendr.
 
 ## Prerequisites
 
@@ -35,19 +33,15 @@ which i said no to.
 
 ## Building and Installing
 
-1. First build the Rust library:
+1. First go into R folder and build the package.
 
 ```bash
-cd r
-cargo build --release
+cd bindings/r
 ```
 
-This will create a shared library in `target/release/libcodelist.dylib` (macOS)
-or `target/release/libcodelist.so` (Linux).
-
-2. Open R with the terminal command `R` and install required packages. If you
-   get an error message when running this, you may also need to install package
-   dependencies for `devtools` first if not already installed:
+You will need to go into R at this point and install required packages of
+`rextendr`. If you get an error message when running this, you may also need to
+install package dependencies for `devtools` first if not already installed:
 
 ```r
 install.packages("devtools")
@@ -60,8 +54,6 @@ I picked `64` as the mirror I wanted to use.
 
 ```r
 rextendr::document()
-devtools::document()
-devtools::load_all()
 ```
 
 4. Test that it works:
@@ -70,18 +62,22 @@ devtools::load_all()
 hello()
 ```
 
-## Installing Permanently
-
-To install the package permanently:
+Everytime you make changes to the Rust code, you will need to run the following
+commands in R:
 
 ```r
-devtools::build()
-devtools::install()
+rextendr::document()
+library(codelist)
 ```
 
-After installation, you can use it like any other R package:
+The `library(codelist)` command loads the package, so you can use the functions
+and structs within in so it is important to run this after you have made changes
+to the Rust code.
 
-```r
-library(codelist)
-hello()
-```
+#### Tips for non-R users
+
+- You can create R scripts by making a file that ends with `.R` and then running
+  it in R. It is probably easier at this point to opne in RStudio and run in the
+  console or by clicking at the script. Remember to save.
+- Exit the R console with `q()` and then type `n` to not save the workspace
+  image.

bindings/r/configure

@@ -0,0 +1,3 @@
+#!/usr/bin/env sh
+: "${R_HOME=`R RHOME`}"
+"${R_HOME}/bin/Rscript" tools/config.R 

bindings/r/configure.win

@@ -0,0 +1,2 @@
+#!/usr/bin/env sh
+"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" tools/config.R

bindings/r/r.Rproj

@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

bindings/r/scripts/scratch.R

@@ -0,0 +1,8 @@
+library(codelist)
+
+c <- Codelist$new('test')
+c$set_name('new_test')
+e <- c$get_entries()
+
+first <- e[[1]]$code
+

bindings/r/src/Makevars

@@ -1,13 +1,42 @@
-LIBDIR = ../target/release
+TARGET_DIR = ./rust/target
+LIBDIR = $(TARGET_DIR)/debug
 STATLIB = $(LIBDIR)/libcodelist.a
 PKG_LIBS = -L$(LIBDIR) -lcodelist
 
-all: C_clean
+all: $(SHLIB) rust_clean
+
+.PHONY: $(STATLIB)
 
 $(SHLIB): $(STATLIB)
 
+CARGOTMP = $(CURDIR)/.cargo
+VENDOR_DIR = $(CURDIR)/vendor
+
+
+# RUSTFLAGS appends --print=native-static-libs to ensure that 
+# the correct linkers are used. Use this for debugging if need. 
+#
+# CRAN note: Cargo and Rustc versions are reported during
+# configure via tools/msrv.R.
+#
+# vendor.tar.xz, if present, is unzipped and used for offline compilation.
 $(STATLIB):
-	cargo build --lib --release
 
-C_clean:
-	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS)
+	if [ -f ./rust/vendor.tar.xz ]; then \
+		tar xf rust/vendor.tar.xz && \
+		mkdir -p $(CARGOTMP) && \
+		cp rust/vendor-config.toml $(CARGOTMP)/config.toml; \
+	fi
+
+	export CARGO_HOME=$(CARGOTMP) && \
+	export PATH="$(PATH):$(HOME)/.cargo/bin" && \
+	RUSTFLAGS="$(RUSTFLAGS) --print=native-static-libs" cargo build  --lib  --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR) 
+
+	# Always clean up CARGOTMP
+	rm -Rf $(CARGOTMP);
+
+rust_clean: $(SHLIB)
+	rm -Rf $(CARGOTMP) $(VENDOR_DIR) 
+
+clean:
+	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(TARGET_DIR) $(VENDOR_DIR)

bindings/r/src/Makevars.in

@@ -0,0 +1,42 @@
+TARGET_DIR = ./rust/target
+LIBDIR = $(TARGET_DIR)/@LIBDIR@
+STATLIB = $(LIBDIR)/libcodelist.a
+PKG_LIBS = -L$(LIBDIR) -lcodelist
+
+all: $(SHLIB) rust_clean
+
+.PHONY: $(STATLIB)
+
+$(SHLIB): $(STATLIB)
+
+CARGOTMP = $(CURDIR)/.cargo
+VENDOR_DIR = $(CURDIR)/vendor
+
+
+# RUSTFLAGS appends --print=native-static-libs to ensure that 
+# the correct linkers are used. Use this for debugging if need. 
+#
+# CRAN note: Cargo and Rustc versions are reported during
+# configure via tools/msrv.R.
+#
+# vendor.tar.xz, if present, is unzipped and used for offline compilation.
+$(STATLIB):
+
+	if [ -f ./rust/vendor.tar.xz ]; then \
+		tar xf rust/vendor.tar.xz && \
+		mkdir -p $(CARGOTMP) && \
+		cp rust/vendor-config.toml $(CARGOTMP)/config.toml; \
+	fi
+
+	export CARGO_HOME=$(CARGOTMP) && \
+	export PATH="$(PATH):$(HOME)/.cargo/bin" && \
+	RUSTFLAGS="$(RUSTFLAGS) --print=native-static-libs" cargo build @CRAN_FLAGS@ --lib @PROFILE@ --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR) @TARGET@
+
+	# Always clean up CARGOTMP
+	rm -Rf $(CARGOTMP);
+
+rust_clean: $(SHLIB)
+	rm -Rf $(CARGOTMP) $(VENDOR_DIR) @CLEAN_TARGET@
+
+clean:
+	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(TARGET_DIR) $(VENDOR_DIR)

bindings/r/src/Makevars.win.in

@@ -0,0 +1,39 @@
+TARGET = $(subst 64,x86_64,$(subst 32,i686,$(WIN)))-pc-windows-gnu
+
+TARGET_DIR = ./rust/target
+LIBDIR = $(TARGET_DIR)/$(TARGET)/@LIBDIR@
+STATLIB = $(LIBDIR)/libcodelist.a
+PKG_LIBS = -L$(LIBDIR) -lcodelist -lws2_32 -ladvapi32 -luserenv -lbcrypt -lntdll
+
+all: $(SHLIB) rust_clean
+
+.PHONY: $(STATLIB)
+
+$(SHLIB): $(STATLIB)
+
+CARGOTMP = $(CURDIR)/.cargo
+VENDOR_DIR = vendor
+
+$(STATLIB):
+	mkdir -p $(TARGET_DIR)/libgcc_mock
+	touch $(TARGET_DIR)/libgcc_mock/libgcc_eh.a
+
+	if [ -f ./rust/vendor.tar.xz ]; then \
+		tar xf rust/vendor.tar.xz && \
+		mkdir -p $(CARGOTMP) && \
+		cp rust/vendor-config.toml $(CARGOTMP)/config.toml; \
+	fi
+
+	# Build the project using Cargo with additional flags
+	export CARGO_HOME=$(CARGOTMP) && \
+	export LIBRARY_PATH="$(LIBRARY_PATH);$(CURDIR)/$(TARGET_DIR)/libgcc_mock" && \
+	RUSTFLAGS="$(RUSTFLAGS) --print=native-static-libs" cargo build @CRAN_FLAGS@ --target=$(TARGET) --lib @PROFILE@ --manifest-path=rust/Cargo.toml --target-dir=$(TARGET_DIR)
+
+	# Always clean up CARGOTMP
+	rm -Rf $(CARGOTMP);
+
+rust_clean: $(SHLIB)
+	rm -Rf $(CARGOTMP) $(VENDOR_DIR) @CLEAN_TARGET@
+
+clean:
+	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(TARGET_DIR) $(VENDOR_DIR)