Merge pull request #3 from nlmixr2/maintenance

Maintenance

.Rbuildignore

@@ -9,3 +9,4 @@
 ^pkgdown$
 \.o$
 ^\.github$
+^codecov\.yml$

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

@@ -1,18 +1,10 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
-#
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -26,83 +18,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
-            # We explicitly set the user agent for R devel to the current release version of R so RSPM serves the release binaries.
-          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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-pandoc@v1
-
-      - uses: r-lib/actions/setup-tinytex@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -1,48 +1,48 @@
+# 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
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -3,7 +3,7 @@
 doc
 Meta
 /vignettes/lbfgsb3c.R
-/vignettes/.Rhistory
 /src/lbfgsb3c.so
-/src/.Rhistory
-/.Rhistory
+.Rhistory
+docs
+inst/doc

DESCRIPTION

@@ -23,16 +23,25 @@ Description: Interfacing to Nocedal et al. L-BFGS-B.3.0
 License: GPL-2
 Depends: R (>= 3.6)
 Imports: Rcpp (>= 0.12.3), numDeriv, methods
-Suggests: optimx, microbenchmark, testthat, knitr, pkgbuild, rmarkdown, RcppArmadillo
+Suggests: 
+    knitr,
+    microbenchmark,
+    optimx,
+    pkgbuild,
+    RcppArmadillo,
+    rmarkdown,
+    testthat (>= 3.0.0)
 LinkingTo: Rcpp (>= 0.12.3), RcppArmadillo
 Encoding: UTF-8
 VignetteBuilder: knitr
 NeedsCompilation: yes
-RoxygenNote: 7.0.2
+RoxygenNote: 7.2.3
 Author: Matthew L Fidler [aut, cre],
   John C Nash [aut],
   Ciyou Zhu [aut],
   Richard Byrd [aut],
   Jorge Nocedal [aut],
   Jose Luis Morales [aut]
 Packaged: 2020-02-26 20:18:51 UTC; john
+URL: https://nlmixr2.github.io/lbfgsb3c/
+Config/testthat/edition: 3

README.md

@@ -1,6 +1,9 @@
-[![R-CMD-check](https://github.com/nlmixrdevelopment/lbfgsb3c/workflows/R-CMD-check/badge.svg)](https://github.com/nlmixrdevelopment/lbfgsb3c/actions)
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/nlmixr2/lbfgsb3c/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nlmixr2/lbfgsb3c/actions/workflows/R-CMD-check.yaml)
 [![CRAN total downloads](https://cranlogs.r-pkg.org/badges/grand-total/lbfgsb3c)](https://cran.r-project.org/package=lbfgsb3c)
 [![CRAN total downloads](https://cranlogs.r-pkg.org/badges/lbfgsb3c)](https://cran.r-project.org/package=lbfgsb3c)
+[![Codecov test coverage](https://codecov.io/gh/nlmixr2/lbfgsb3c/branch/main/graph/badge.svg)](https://app.codecov.io/gh/nlmixr2/lbfgsb3c?branch=main)
+<!-- badges: end -->
 
 # libfgsb3c interface from C
 This is the fork of the libfgsb3 from cran with the following differences:

_pkgdown.yml

@@ -1 +1,4 @@
-destination: docs
+url: https://nlmixr2.github.io/lbfgsb3c/
+template:
+  bootstrap: 5
+

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

tests/testthat.R

@@ -1,3 +1,11 @@
+# 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(lbfgsb3c)
 

tests/testthat/test-bounds.R

@@ -1,4 +1,3 @@
-context("Bounds")
 test_that("bounds test", {
     bt.f<-function(x){
         sum(x*x)

tests/testthat/test-cyq.R

@@ -82,7 +82,6 @@ nn <- c(2, 3, 5, 8)
 
 for (n in nn) {
     str <- paste0("Chebyquad in ", n, " parameters");
-    context(str)
     test_that(str, {
         lower <- rep(-10, n)
         upper <- rep(10, n)
@@ -109,5 +108,4 @@ for (n in nn) {
                          round(ans$value, 3))
         }
     })
-
 }

tests/testthat/test-genrose.R

@@ -28,7 +28,7 @@ genrose.g <- function(x, gs = NULL) {
   gg
 }
 
-context("Unconstrained Genrose test with gradient")
+# Unconstrained Genrose test with gradient
 
 nn <- 100
 xx <- rep(3, nn)
@@ -41,7 +41,7 @@ test_that("100u", {
 })
 
 
-context("Unconstrained Genrose test without gradient")
+# Unconstrained Genrose test without gradient
 ans100un <- lbfgsb3c(xx, genrose.f,
                      gr = NULL, gs = 10)
 

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

vignettes/lbfgsb3c.Rmd

@@ -5,13 +5,12 @@ author: "John C Nash
     University of Ottawa,
     nashjc@uottawa.ca"
 date: "October 22, 2019"
-output: 
-    pdf_document
+output: rmarkdown::html_vignette
 bibliography: lbfgsb3c.bib
 vignette: >
   %\VignetteIndexEntry{lbfgsb3c-nocompile}
   %\VignetteEngine{knitr::rmarkdown}
-  \usepackage[utf8]{inputenc}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r setup, include=FALSE}