Linting

.github/workflows/lint-only-changed-files.yaml

@@ -0,0 +1,47 @@
+# 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
+  workflow_dispatch:
+
+name: lint-changed-files
+
+jobs:
+  lint-changed-files:
+    runs-on: ubuntu-latest
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::gh
+            any::lintr
+            any::purrr
+          needs: check
+
+      - name: Add lintr options
+        run: |
+          cat('\noptions(lintr.linter_file = ".lintr")\n', file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Extract and lint files changed by this PR
+        run: |
+          files <- gh::gh("GET https://api.github.com/repos/${{ 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/render-readme.yaml

@@ -0,0 +1,36 @@
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'README.Rmd'
+
+jobs:
+  render-readme:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - 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::.
+
+      - 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 man/figures/
+          git diff-index --quiet HEAD || git commit -m "Automatic readme update"
+          git push origin || echo "No changes to push"

.lintr

@@ -1,31 +1,15 @@
-linters: with_defaults(
-    line_length_linter = line_length_linter(120)
+linters: linters_with_tags(
+    tags = NULL, # include all linters
+    implicit_integer_linter = NULL,
+    extraction_operator_linter = NULL,
+    undesirable_function_linter = NULL,
+    function_argument_linter = NULL,
+    indentation_linter = NULL,
+    object_name_linter = NULL,
+    cyclocomp_linter(25L)
   )
-exclusions: list(
-    "inst/dev/load-stan-functions.R",
-    "inst/dev/recover-synthetic.R",
-    "inst/dev/test-secondary.R",
-    "inst/pkg-structure/generate-pkgstructure-report.R",
-    "R/stanmodels.R",
-    "tests/spelling.R",
-    "tests/testthat.R",
-    "tests/testthat/test-calc_CrI.R",
-    "tests/testthat/test-calc_CrIs.R",
-    "tests/testthat/test-calc_summary_measures.R",
-    "tests/testthat/test-calc_summary_stats.R",
-    "tests/testthat/test-create_future-rt.R",
-    "tests/testthat/test-create_stan_args.R",
-    "tests/testthat/test-epinow.R",
-    "tests/testthat/test-estimate_infections.R",
-    "tests/testthat/test-extract_CrIs.R",
-    "tests/testthat/test-get_dist.R",
-    "tests/testthat/test-set_dt_single_thread.R",
-    "tests/testthat/test-match_output_arguments.R",
-    "tests/testthat/test-regional_epinow.R",
-    "tests/testthat/test-regional_runtimes.R",
-    "tests/testthat/test-setup_future.R",
-    "tests/testthat/test-simulate_infections.R",
-    "tests/testthat/test-stan-infections.R",
-    "tests/testthat/test-stan-rt.R",
-    "tests/testthat/test-stan-secondary.R"
+exclusions: c(
+    list.files("tests", recursive = TRUE, full.names = TRUE),
+    list.files("inst", recursive = TRUE, full.names = TRUE),
+    "R/stanmodels.R"
   )

DESCRIPTION

@@ -2,7 +2,7 @@ Type: Package
 Package: EpiNow2
 Title: Estimate Real-Time Case Counts and Time-Varying
     Epidemiological Parameters
-Version: 1.3.6.1000
+Version: 1.3.6.2000
 Authors@R: 
     c(person(given = "Sam",
              family = "Abbott",

NEWS.md

@@ -1,10 +1,13 @@
-# EpiNow2 1.3.6.1000
+# EpiNow2 1.3.6.2000
 
 This release is in development. For a stable release install 1.3.5 from CRAN.
 
 ## Package
 
 * Model description has been expanded to include more detail.
+* Moved to a GitHub Action to only lint changed files.
+* Linted the package with a wider range of default linters.
+* Added a GitHub Action to build the README when it is altered.
 
 # EpiNow2 1.3.5
 

R/adjust.R

@@ -3,19 +3,24 @@
 #' @description  `r lifecycle::badge("stable")`
 #' Maps from cases by date of infection to date of report via date of
 #' onset.
-#' @param infections `data.table` containing a `date` variable and a numeric `cases` variable.
+#' @param infections `data.table` containing a `date` variable and a numeric
+#' `cases` variable.
 #'
-#' @param delay_defs A list of single row data.tables that each  defines a delay distribution (model, parameters and maximum delay for each model).
+#' @param delay_defs A list of single row data.tables that each  defines a
+#' delay distribution (model, parameters and maximum delay for each model).
 #' See `lognorm_dist_def` for an example of the structure.
 #'
-#' @param reporting_effect A numeric vector of length 7 that allows the scaling of reported cases
-#' by the day on which they report (1 = Monday, 7 = Sunday). By default no scaling occurs.
+#' @param reporting_effect A numeric vector of length 7 that allows the scaling
+#' of reported cases by the day on which they report (1 = Monday, 7 = Sunday).
+#' By default no scaling occurs.
 #'
-#' @param reporting_model A function that takes a single numeric vector as an argument and returns a
-#' single numeric vector. Can be used to apply stochastic reporting effects. See the examples for details.
+#' @param reporting_model A function that takes a single numeric vector as an
+#' argument and returns a single numeric vector. Can be used to apply stochastic
+#' reporting effects. See the examples for details.
 #'
-#' @return A `data.table` containing a `date` variable (date of report) and a `cases` variable. If `return_onset = TRUE` there will be
-#' a third variable `reference` which indicates what the date variable refers to.
+#' @return A `data.table` containing a `date` variable (date of report) and a
+#' `cases` variable. If `return_onset = TRUE` there will be a third variable
+#' `reference` which indicates what the date variable refers to.
 #' @export
 #' @inheritParams sample_approx_dist
 #' @importFrom data.table setorder data.table data.table
@@ -42,7 +47,9 @@
 #' )
 #'
 #' # simple mapping
-#' report <- adjust_infection_to_report(cases, delay_defs = list(incubation_def, delay_def))
+#' report <- adjust_infection_to_report(
+#'  cases, delay_defs = list(incubation_def, delay_def)
+#' )
 #' print(report)
 #'
 #' # mapping with a weekly reporting effect