Xli branch update

.Rbuildignore

@@ -1,2 +1,5 @@
 ^LICENSE\.md$
 ^README\.Rmd$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,53 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+

DESCRIPTION

@@ -11,7 +11,10 @@ Description: Implementation of univariate total variation denoising (aka
 License: MIT + file LICENSE
 Imports: 
     Rcpp (>= 1.0.10)
+Suggests: 
+    testthat (>= 3.0.0)
 LinkingTo: 
     Rcpp
+Config/testthat/edition: 3
 Encoding: UTF-8
 RoxygenNote: 7.3.2

README.Rmd

@@ -16,6 +16,7 @@ knitr::opts_chunk$set(
 # tvdenoising
 
 <!-- badges: start -->
+[![R-CMD-check](https://github.com/glmgen/tvdenoising/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/glmgen/tvdenoising/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 This package provides an `R` frontend to a `C` implementation of linear-time 

README.md

@@ -4,8 +4,11 @@
 # tvdenoising
 
 <!-- badges: start -->
+[![R-CMD-check](https://github.com/glmgen/tvdenoising/actions/workflows/R-CMD-check.yaml/badge.svg?branch=xli-branch)](https://github.com/glmgen/tvdenoising/actions/workflows/R-CMD-check.yaml?branch=xli-branch)
 <!-- badges: end -->
 
+
+
 This package provides an `R` frontend to a `C` implementation of
 linear-time univariate total variation denoising via dynamic programming
 (Johnson 2013).

src/RcppExports.cpp

@@ -1,6 +1,7 @@
 // Generated by using Rcpp::compileAttributes() -> do not edit by hand
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+#include "../inst/include/tvdenoising.h"
 #include <Rcpp.h>
 #include <string>
 #include <set>

tests/testthat.R

@@ -0,0 +1,15 @@
+# tests/testthat.R
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(tvdenoising)
+
+test_check("tvdenoising")
+
+

tests/testthat/_snaps/tvdenoising.md

@@ -0,0 +1,16 @@
+# tvdenoising handles incorrect input properly
+
+    Code
+      tvdenoising(y, lambda)
+    Condition
+      Error in `tvdenoising()`:
+      ! is.numeric(lambda) & (length(lambda) == 1) is not TRUE
+
+---
+
+    Code
+      tvdenoising(y, 1, weights)
+    Condition
+      Error in `tvdenoising()`:
+      ! length(weights) == length(y) is not TRUE
+

tests/testthat/test-tvdenoising.R

@@ -0,0 +1,59 @@
+# tests/testthat/test-tvdenoising.R
+
+test_that("tvdenoising works correctly with no weights", {
+  y <- c(1, 2, 3, 5, 8, 13, 21)
+  lambda <- 1
+  result <- tvdenoising(y, lambda)
+  expected_result <- c(2, 2, 3, 5, 8, 13, 20)
+  expect_type(result, "double")
+  expect_length(result, length(y))
+  expect_equal(result, expected_result, tolerance = 1e-6) 
+})
+
+
+test_that("tvdenoising works correctly with weights", {
+  y <- c(1, 2, 3, 5, 8, 13, 21)
+  lambda <- 1
+
+  weights <- c(1, 3, 3, 2, 5, 6, 2)
+  result <- tvdenoising(y, lambda, weights)
+  expect_type(result, "double")
+  expect_length(result, length(y))
+  expected_result <- c(2,2,3,5,8,13,20.5)
+  expect_equal(result, expected_result, tolerance = 1e-6) 
+})
+
+
+test_that("tvdenoising with uniform weights 1 matches unweighted version", {
+  y <- c(1, 2, 3, 5, 8, 13, 21)
+  lambda <- 1
+  uniform_weights1 <- rep(1, length(y))  
+  result_no_weights <- tvdenoising(y, lambda)
+  result_with_weights1 <- tvdenoising(y, lambda, uniform_weights1)
+  expect_equal(result_no_weights, result_with_weights1, tolerance = 1e-6)
+})
+
+test_that("tvdenoising with uniform weights 2", {
+  y <- c(1, 2, 3, 5, 8, 13, 21)
+  lambda <- 1
+  uniform_weights2 <- rep(2, length(y))  
+  expected_result <- c(1.5, 2, 3, 5, 8, 13, 20.5)
+  result_with_weights2 <- tvdenoising(y, lambda, uniform_weights2)
+  expect_equal(expected_result, result_with_weights2, tolerance = 1e-6)
+})
+
+
+
+test_that("tvdenoising handles incorrect input properly", {
+  y <- c(1, 2, 3, 5, 8, 13, 21)
+  lambda <- "not a number"
+
+  # when lambda is not numeric
+  expect_snapshot(error = TRUE, tvdenoising(y, lambda))
+
+  # when weights length does not match y
+  weights <- c(1, 2)
+  expect_snapshot(error = TRUE, tvdenoising(y, 1, weights))
+})
+
+

tvdenoising.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