Basic import

.Rbuildignore

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+^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

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+*.html

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

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+# 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
+
+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'}
+
+    # Shorter timeout to prevent mac builders hanging for 6 hours!
+    timeout-minutes: 30
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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

.github/workflows/pkgdown.yaml

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+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    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 }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

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+# 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

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

.lintr

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+linters: linters_with_defaults(
+    object_length_linter = NULL,
+    object_usage_linter = NULL,
+    cyclocomp_linter = NULL
+    )
+exclusions: list("tests/testthat.R", "R/cpp11.R")

DESCRIPTION

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+Package: mcstate2
+Title: Next Generation mcstate
+Version: 0.1.0
+Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
+                    email = "[email protected]"),
+             person("Imperial College of Science, Technology and Medicine",
+                    role = "cph"))
+Description: Experimental sources for the next generation of mcstate,
+    which will support much of the old mcstate functionality but new
+    things like better parameter interfaces, Hamiltonian Monte Carlo,
+    etc.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1
+URL: https://github.com/mrc-ide/mcstate2
+BugReports: https://github.com/mrc-ide/mcstate2/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

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+PACKAGE := $(shell grep '^Package:' DESCRIPTION | sed -E 's/^Package:[[:space:]]+//')
+RSCRIPT = Rscript --no-init-file
+
+all:
+	${RSCRIPT} -e 'pkgbuild::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

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+# Generated by roxygen2: do not edit by hand

R/util.R

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

README.md

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+# mcstate2
+
+<!-- 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/mcstate2/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/mcstate2/actions)
+[![codecov.io](https://codecov.io/github/mrc-ide/mcstate2/coverage.svg?branch=main)](https://codecov.io/github/mrc-ide/mcstate2?branch=main)
+<!-- badges: end -->
+
+## Installation
+
+To install `mcstate2`:
+
+```r
+remotes::install_github("mrc-ide/mcstate2", upgrade = FALSE)
+```
+
+## License
+
+MIT © Imperial College of Science, Technology and Medicine

tests/testthat.R

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+library(testthat)
+library(mcstate2)
+
+test_check("mcstate2")

tests/testthat/test-util.R

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+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)
+})