Full package review for {bpmodels} CRAN release

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^\.github$
+^codecov\.yml$
+^README\.Rmd$
+^\.lintr$
+^\.gitattributes$
+^\_pkgdown.yml$
+^cran-comments\.md$
+^doc$
+^docs$
+^Meta$
+^pkgdown$
+^data-raw$
+^CITATION\.cff$
+^_pkgdown\.yml$

.github/.gitignore

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+*.html

.github/CONTRIBUTING.md

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+# Contributing to bpmodels
+
+This outlines how to propose a change to bpmodels.
+
+## Making changes
+
+If you want to make a change, it's a good idea to first file an issue and make 
+sure someone from the team agrees that it’s needed.
+If you’ve found a bug, please file an issue that illustrates the bug with 
+a minimal [reprex](https://www.tidyverse.org/help/#reprex) (this will also 
+help you write a unit test, if needed). See [bug report template](../.github/ISSUE_TEMPLATE/bug_report.md). If you have a 
+feature request see [feature request](../.github/ISSUE_TEMPLATE/feature_request.md).
+
+### Pull request process
+
+See [pull request template](../.github/PULL_REQUEST_TEMPLATE/pull_request_template.md)
+
+*   Fork the package and clone onto your computer. If you haven't done 
+this before, we recommend using `usethis::create_from_github("epiverse-trace/bpmodels", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, 
+and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for 
+    help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just 
+below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) 
+    package to apply these styles, but please don't restyle code that has 
+    nothing to do with your PR.  
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for 
+unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that `bpmodels` is released with a
+[Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Please place an "x" in all the boxes that apply
+---------------------------------------------
+
+- [ ] I have the most recent version of bpmodels and R
+- [ ] I have found a bug
+- [ ] I have a [reproducible example](http://reprex.tidyverse.org/articles/reprex-dos-and-donts.html)
+- [ ] I want to request a new feature
+
+--------
+
+Please include a brief description of the problem with a code example:
+
+```r
+# insert reprex here
+```
+
+---------

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. E.g., I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

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+* **Please check if the PR fulfils these requirements**
+
+- [ ] I have read the CONTRIBUTING guidelines 
+- [ ] The commit message follows our guidelines
+- [ ] Tests for the changes have been added (for bug fixes / features)
+- [ ] Docs have been added / updated (for bug fixes / features)
+
+
+* **What kind of change does this PR introduce?** (Bug fix, feature, docs update, ...)
+
+
+
+* **What is the current behaviour?** (You can also link to an open issue here)
+
+
+
+* **What is the new behaviour (if this is a feature change)?**
+
+
+
+* **Does this PR introduce a breaking change?** (What changes might users need to make in their application due to this PR?)
+
+
+
+* **Other information**:

.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'}
+
+    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/lint_changed_files.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:
+  pull_request:
+    branches: [main, master]
+
+name: lint-changed-files
+
+jobs:
+  lint-changed-files:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::gh
+            any::lintr
+            any::purrr
+            epiverse-trace/etdev
+          needs: check
+
+      - name: Add lintr options
+        run: |
+          cat('\noptions(lintr.linter_file = ".lintr")\n', file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Extract and lint files changed by this PR
+        run: |
+          files <- gh::gh("GET https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
+          changed_files <- purrr::map_chr(files, "filename")
+          all_files <- list.files(recursive = TRUE)
+          exclusions_list <- as.list(setdiff(all_files, changed_files))
+          lintr::lint_package(exclusions = exclusions_list)
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: 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/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/render_readme.yml

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+# Name of the workflow
+name: render-readme
+
+# Controls when the action will run. Triggers include:
+#
+# - button trigger from github action page
+# - on changes to readme.Rmd
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'README.Rmd'
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  render-readme:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repos
+        uses: actions/checkout@v2
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, local::.
+
+      - name: Compile the readme
+        run: |
+          rmarkdown::render("README.Rmd")
+        shell: Rscript {0}
+
+      - name: Commit files
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add README.md
+          # Also add README figures if they exist
+          if [ -d man/figures ]
+          then
+            git add man/figures/
+          fi
+          git diff-index --quiet HEAD || git commit -m "Automatic readme update"
+          git push origin || echo "No changes to push"

.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