first commit

.Rbuildignore

@@ -0,0 +1,23 @@
+^scripts$
+^Makefile$
+^README\.Rmd$
+^\.travis\.yml$
+^docs$
+^\.lintr$
+^tests/testthat/.*\.o$
+^tests/testthat/.*\.so$
+^tests/testthat/.*\.dll$
+\.dylib$
+^appveyor\.yml$
+^docker$
+^\.hadolint\.yaml$
+\.valgrind_ignore$
+^scripts$
+\.gcda$
+\.gcno$
+^pkgdown$
+^LICENSE\.md$
+^buildkite$
+^\.covrignore$
+^\.github$
+\.*gcov$

.github/.gitignore

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

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

@@ -0,0 +1,86 @@
+# 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
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@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", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@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 dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          install.packages("pkgdown", type = "binary")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,48 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@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 dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -0,0 +1,17 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
+TODO.md
+docs
+*.o
+*.so
+*.dll
+*.dylib
+*.gcda
+*.gcno
+*.gcov
+.valgrind_ignore
+inst/doc
+pkgdown

.lintr

@@ -0,0 +1,7 @@
+linters: with_defaults(
+    object_length_linter = NULL,
+    object_usage_linter = NULL,
+    todo_comment_linter = NULL,
+    cyclocomp_linter = NULL
+    )
+exclusions: list("tests/testthat.R", "R/cpp11.R")

DESCRIPTION

@@ -0,0 +1,17 @@
+Package: threemc
+Title: Package Title Here
+Version: 0.1.0
+Authors@R: c(person("First", "Last", role = c("aut", "cre"),
+                    email = "[email protected]"),
+             person("Imperial College of Science, Technology and Medicine",
+                    role = "cph"))
+Description: Description of the pacakge in more than one full sentence.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1
+URL: https://github.com/mrc-ide/threemc
+BugReports: https://github.com/mrc-ide/threemc/issues
+Suggests:
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2021
+COPYRIGHT HOLDER: Imperial College of Science, Technology and Medicine

Makefile

@@ -0,0 +1,34 @@
+PACKAGE := $(shell grep '^Package:' DESCRIPTION | sed -E 's/^Package:[[:space:]]+//')
+RSCRIPT = Rscript --no-init-file
+
+all:
+	${RSCRIPT} -e 'devtools::compile_dll()'
+
+test:
+	${RSCRIPT} -e 'devtools::test()'
+
+roxygen:
+	@mkdir -p man
+	${RSCRIPT} -e "devtools::document()"
+
+install:
+	R CMD INSTALL .
+
+build:
+	R CMD build .
+
+README.md: README.Rmd
+	Rscript -e 'devtools::load_all(); knitr::knit("README.Rmd")'
+	sed -i.bak 's/[[:space:]]*$$//' README.md
+	rm -f $@.bak
+
+check:
+	_R_CHECK_CRAN_INCOMING_=FALSE make check_all
+
+check_all:
+	${RSCRIPT} -e "rcmdcheck::rcmdcheck(args = c('--as-cran', '--no-manual'))"
+
+clean:
+	rm -f src/*.o src/*.so src/*.gcda src/*.gcno src/*.gcov
+
+.PHONY: clean all test document install

NAMESPACE

@@ -0,0 +1 @@
+# Generated by roxygen2: do not edit by hand

R/R/test.R

@@ -0,0 +1,4 @@
+# test function for R
+sum <- function(x, y) {
+    return(x, y)
+}

R/R/util.R

@@ -0,0 +1,3 @@
+`%||%` <- function(x, y) { # nolint
+  if (is.null(x)) y else x
+}

R/util.R

@@ -0,0 +1,3 @@
+`%||%` <- function(x, y) { # nolint
+  if (is.null(x)) y else x
+}

README.md

@@ -0,0 +1,20 @@
+# threemc
+
+<!-- badges: start -->
+[![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
+[![R build status](https://github.com/mrc-ide/threemc/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/threemc/actions)
+[![Build status]()](https://buildkite.com/mrc-ide/mrcide/threemc?branch=main)
+[![codecov.io](https://codecov.io/github/mrc-ide/threemc/coverage.svg?branch=main)](https://codecov.io/github/mrc-ide/threemc?branch=main)
+<!-- badges: end -->
+
+## Installation
+
+To install `threemc`:
+
+```r
+remotes::install_github("mrc-ide/threemc", upgrade = FALSE)
+```
+
+## License
+
+MIT © Imperial College of Science, Technology and Medicine

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(threemc)
+
+test_check("threemc")

tests/testthat/test-util.R

@@ -0,0 +1,6 @@
+test_that("null-or-value works", {
+  expect_equal(1 %||% NULL, 1)
+  expect_equal(1 %||% 2, 1)
+  expect_equal(NULL %||% NULL, NULL)
+  expect_equal(NULL %||% 2, 2)
+})