Add CI workflow

.Rprofile

@@ -0,0 +1,2 @@
+source("rv/scripts/rvr.R")
+source("rv/scripts/activate.R")

.github/workflows/r-tests.yml

@@ -0,0 +1,123 @@
+name: R CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: r-ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  R_VERSION: '4.5.2'
+  RV_VERSION: '0.22.2'
+  RV_SHA256: '9805dbad14eb049265c0052635873c9b7891bc7334d445662c13fbad61cb269c'
+
+jobs:
+  standard:
+    name: Standard checks
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ env.R_VERSION }}
+
+      - name: Install rv
+        shell: bash
+        run: |
+          mkdir -p "$HOME/.local/bin"
+          curl -fsSL \
+            "https://github.com/A2-ai/rv/releases/download/v${RV_VERSION}/rv-v${RV_VERSION}-x86_64-unknown-linux-gnu.tar.gz" \
+            -o "$RUNNER_TEMP/rv.tar.gz"
+          echo "$RV_SHA256  $RUNNER_TEMP/rv.tar.gz" | sha256sum --check
+          tar -xzf "$RUNNER_TEMP/rv.tar.gz" -C "$HOME/.local/bin"
+          echo "$HOME/.local/bin" >> "$GITHUB_PATH"
+
+      - name: Restore R package library
+        uses: actions/cache@v6
+        with:
+          path: rv/library
+          key: rv-${{ env.RV_VERSION }}-${{ runner.os }}-${{ runner.arch }}-r-${{ env.R_VERSION }}-${{ hashFiles('rproject.toml') }}
+
+      - name: Install system dependencies
+        shell: bash
+        run: |
+          sudo apt-get update
+          rv sysdeps --only-absent | xargs --no-run-if-empty sudo apt-get install -y
+
+      - name: Sync R dependencies
+        run: rv sync
+
+      - name: Validate minimal demo inputs
+        run: |
+          Rscript validate.R --data-root data/vqa-demo1-min
+          Rscript validate.R --data-root data/vqa-demo2-min
+
+      - name: Run standard tests
+        run: Rscript tests/testthat.R
+
+      - name: Run lintr
+        shell: Rscript {0}
+        run: |
+          files <- c(
+            "analyse.R",
+            "validate.R",
+            list.files(
+              c(
+                "analysis", "pipeline", "preprocessing", "validation",
+                "tests/testthat", "tests/refactor/testthat"
+              ),
+              pattern = "[.]R$", recursive = TRUE, full.names = TRUE
+            )
+          )
+          lints <- unlist(lapply(files, lintr::lint), recursive = FALSE)
+          print(lints)
+          quit(status = as.integer(length(lints) > 0L))
+
+  refactor:
+    name: Refactor parity
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ env.R_VERSION }}
+
+      - name: Install rv
+        shell: bash
+        run: |
+          mkdir -p "$HOME/.local/bin"
+          curl -fsSL \
+            "https://github.com/A2-ai/rv/releases/download/v${RV_VERSION}/rv-v${RV_VERSION}-x86_64-unknown-linux-gnu.tar.gz" \
+            -o "$RUNNER_TEMP/rv.tar.gz"
+          echo "$RV_SHA256  $RUNNER_TEMP/rv.tar.gz" | sha256sum --check
+          tar -xzf "$RUNNER_TEMP/rv.tar.gz" -C "$HOME/.local/bin"
+          echo "$HOME/.local/bin" >> "$GITHUB_PATH"
+
+      - name: Restore R package library
+        uses: actions/cache@v6
+        with:
+          path: rv/library
+          key: rv-${{ env.RV_VERSION }}-${{ runner.os }}-${{ runner.arch }}-r-${{ env.R_VERSION }}-${{ hashFiles('rproject.toml') }}
+
+      - name: Install system dependencies
+        shell: bash
+        run: |
+          sudo apt-get update
+          rv sysdeps --only-absent | xargs --no-run-if-empty sudo apt-get install -y
+
+      - name: Sync R dependencies
+        run: rv sync
+
+      - name: Run refactor parity tests
+        run: Rscript tests/refactor/testthat.R

.gitignore

@@ -11,11 +11,9 @@ CHANGELOG_ps.md
 
 # R project files
 ## rv
-rv/
 rv.lock
 
 ## R
-.Rprofile
 .Rhistory
 .Rapp.history
 

README.md

@@ -1,5 +1,7 @@
 # Vegetation Quality Assessment (VQA)
 
+[![R CI](https://github.com/OxfordRSE/OpenVQA/actions/workflows/r-tests.yml/badge.svg)](https://github.com/OxfordRSE/OpenVQA/actions/workflows/r-tests.yml)
+
 ***Warning: this is an outdated README. Will update soon for OpenVQA***
 
 VQA is a semi-automated R pipeline for estimating quality of reclaimed vegetation relative to undisturbed native vegetation.
@@ -84,6 +86,9 @@ You can read more about VQA in detail in this open access [publication](https://
 
 ## Developer Setup
 
+GitHub Actions validates both minimal demo projects, runs the standard and refactor parity
+test suites, and lints the actively refactored R code on pull requests and pushes to `main`.
+
 If you are working on the codebase itself, use the tracked `pre-commit` configuration to run formatting and linting automatically before commits.
 
 1. Install the R project dependencies.

rproject.toml

@@ -4,8 +4,10 @@ r_version = "4.5"
 
 # A list of repositories to fetch packages from. Order matters: we will try to get a package from each repository in order.
 # The alias is only used in this file if you want to specifically require a dependency to come from a certain repository.
-# Example: { alias = "PPM", url = "https://packagemanager.posit.co/cran/latest" },
-repositories = [{ alias = "CRAN", url = "https://cloud.r-project.org/" }]
+repositories = [
+  { alias = "PPM", url = "https://packagemanager.posit.co/cran/latest" },
+  { alias = "CRAN", url = "https://cloud.r-project.org/" },
+]
 
 # A list of packages to install and any additional configuration
 # Examples:

rv/.gitignore

@@ -0,0 +1 @@
+library

rv/scripts/activate.R

@@ -0,0 +1,94 @@
+local({
+	if (!nzchar(Sys.which("rv"))) {
+		warning(
+			"rv is not installed! Install rv, then restart your R session",
+			call. = FALSE
+		)
+		return()
+	}
+	rv_info <- system2(
+		"rv",
+		c("info", "--library", "--r-version", "--repositories"),
+		stdout = TRUE
+	)
+	if (!is.null(attr(rv_info, "status"))) {
+		# if system2 fails it'll add a status attribute with the error code
+		warning("failed to run rv info, check your console for messages")
+		return()
+	}
+	get_val <- function(prefix) {
+		line <- grep(paste0("^", prefix, ":"), rv_info, value = TRUE)
+		sub(paste0("^", prefix, ":\\s*"), "", line)
+	}
+
+	# Set repos option
+	repo_str <- get_val("repositories")
+
+	repo_parts <- strsplit(repo_str, "), ", fixed = TRUE)[[1]]
+	repo_parts <- gsub("[()]", "", repo_parts)
+
+	repo_urls <- character(length(repo_parts))
+	repo_names <- character(length(repo_parts))
+
+	for (i in seq_along(repo_parts)) {
+		parts <- strsplit(repo_parts[i], ",", fixed = TRUE)[[1]]
+		repo_names[i] <- trimws(parts[1])
+		repo_urls[i] <- trimws(parts[2])
+	}
+	names(repo_urls) <- repo_names
+	options(repos = repo_urls)
+
+	# Check R version and set library
+	rv_r_ver <- get_val("r-version")
+	sys_r <- sprintf("%s.%s", R.version$major, R.version$minor)
+	r_match <- grepl(paste0("^", rv_r_ver), sys_r)
+
+	rv_lib <- if (r_match) {
+		normalizePath(get_val("library"), mustWork = FALSE)
+	} else {
+		message(sprintf(
+			"WARNING: R version specified in config (%s) does not match session version (%s).
+rv library will not be activated until the issue is resolved. Entering safe mode...
+			",
+			rv_r_ver,
+			sys_r
+		))
+		file.path(tempdir(), "__rv_R_mismatch")
+	}
+
+	if (!dir.exists(rv_lib)) {
+		if (r_match) {
+			message("creating rv library: ", rv_lib, "\n")
+		} else {
+			message("creating temporary library: ", rv_lib, "\n")
+		}
+		dir.create(rv_lib, recursive = TRUE)
+	}
+
+	.libPaths(rv_lib, include.site = FALSE)
+	Sys.setenv("R_LIBS_USER" = rv_lib)
+	Sys.setenv("R_LIBS_SITE" = rv_lib)
+
+	# Results
+	if (interactive()) {
+		message(
+			"rv repositories active!\nrepositories: \n",
+			paste0(
+				"  ",
+				names(getOption("repos")),
+				": ",
+				getOption("repos"),
+				collapse = "\n"
+			),
+			"\n"
+		)
+		message(
+			if (r_match) {
+				"rv libpaths active!\nlibrary paths: \n"
+			} else {
+				"rv libpaths are not active due to R version mismatch. Using temp directory: \n"
+			},
+			paste0("  ", .libPaths(), collapse = "\n")
+		)
+	}
+})

rv/scripts/rvr.R

@@ -0,0 +1,26 @@
+.rv <- new.env()
+.rv$config_path <- file.path(normalizePath(getwd()), "rproject.toml")
+.rv$summary <- function(json = FALSE) {
+  command <- c("summary")
+  if (json) { command <- c(command, "--json") }
+  .rv$command(command)
+}
+.rv$plan <- function() { .rv$command("plan") }
+.rv$sync <- function() { .rv$command("sync") }
+.rv$add <- function(..., dry_run = FALSE) {
+  dots <- unlist(list(...))
+  command <- c("add", dots)
+  if (dry_run) { command <- c(command, "--dry-run") }
+  .rv$command(command)
+}
+
+.rv$command <- function(command) {
+  # underlying system calls to rv
+  args <- c(command, "-c", .rv$config_path)
+  res <- system2("rv", args, stdout = TRUE)
+  if (!is.null(attr(res, "status"))) {
+    warning(sprintf("failed to run `rv %s`, check your console for messages", paste(args, collapse = " ")))
+  } else {
+    message(paste(res, collapse = "\n"))
+  }
+}