Streamline and tighten lintr checks (#220)

* Replace lint.yaml by lint-changed-file.yaml

Copied from r-lib/actions with some extra bells and whistles copied from lint.yaml

- triggered on develop and can be triggered manually
- can be skipped with the [ci skip] instruction in the commit message

* Try to include all linters

* Fix some indents

Indents in function argument definition have not been changed because they are an explicit style choice

* Add fixed = TRUE to calls with fixed regexes

* Add leading zero to double

* Use toString() rather than paste(collapse = ", ")

* Use anyNA() rather than any(is.na())

* Remove unused variables

* Pass function directly to sapply instead of creating lambda

* Use dedicated lengths() function

* Remove unnecessary library() calls

* Use file.path() to construct file paths

* Replace unnecessary ifelse() by as.numeric()

* Remove unnecessary paste0() in warning() and stop()

* Remove unnecessary c()

* Use seq_len() rather than :

* Use sort() rather than order()

* Remove nested if

* Disable linters that generate too many false positive
or that flag explicit style choices that diverge from default

* Run devtools::document()

* Add NEWS items

* Increment version number

* Remove extra trailing whitespace

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

@@ -0,0 +1,54 @@
+# 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
+      - develop
+  pull_request:
+    branches:
+      - main
+      - master
+      - develop
+  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

.lintr

@@ -1,7 +1,15 @@
-linters: linters_with_defaults(
-    line_length_linter = line_length_linter(80),
-    cyclocomp_linter = cyclocomp_linter(complexity_limit = 20L),
-    object_usage_linter = NULL)
-exclusions: c(list.files(path = "tests/", recursive = T, full.names = T),
-    "vignettes/germany-age-stratified-nowcasting.Rmd.orig")
-exclude: "# nolint"
+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: c(
+    list.files("tests", recursive = TRUE, full.names = TRUE),
+    list.files("inst", recursive = TRUE, full.names = TRUE),
+    "vignettes/germany-age-stratified-nowcasting.Rmd.orig"
+  )

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: epinowcast
 Title: Flexible Hierarchical Nowcasting
-Version: 0.2.0.7000
+Version: 0.2.0.8000
 Authors@R:
   c(person(given = "Sam Abbott",
            role = c("aut", "cre"),

NEWS.md

@@ -1,4 +1,4 @@
-# epinowcast 0.2.0.7000
+# epinowcast 0.2.0.8000
 
 This is release is in development. It is not yet ready for production use. If you notice problems please report them on the [issue tracker](https://github.com/epinowcast/epinowcast/issues).
 
@@ -9,6 +9,8 @@ This is release is in development. It is not yet ready for production use. If yo
 
 ## Package
 
+- Added more non-default linters in `.lintr` configuration file. This file is used when `lintr::lint_package()` is run or in the new `lint-changed-files.yaml` GitHub Actions workflow. See #220 by @Bisaloo and reviewed by @pearsonca and @seeabs.
+- Switched to the `lint-changed-files.yaml` GitHub Actions workflow instead of the regular `lint.yaml` to avoid annotations unrelated to the changes made in the PR. See #220 by @Bisaloo and reviewed by @pearsonca and @seeabs.
 - Added tests for `summary.epinowcast()` and `plot.epinowcast()` methods. See #209 by @seabbs and reviewed by @pearsonca.
 - Added tests for `enw_plot_obs()` where not otherwise covered by `plot.epinowcast()` tests. See #209 by @seabbs and reviewed by @pearsonca.
 - Made the `.group` variable optional for all preprocessing functions using a new `add_group()` internal function. See #208 by @seabbs and reviewed by @pearsonca.

R/check.R

@@ -17,7 +17,7 @@ check_quantiles <- function(posterior, req_probs = c(0.5, 0.95, 0.2, 0.8)) {
   if (sum(cols %in% paste0("q", req_probs * 100)) != length(req_probs)) {
     stop(
       "Following quantiles must be present (set with probs): ",
-      paste(req_probs, collapse = ", ")
+      toString(req_probs)
     )
   }
   return(invisible(NULL))
@@ -88,16 +88,16 @@ check_group <- function(obs) {
 #' @return NULL
 #'
 #' @family check
-check_by <- function(obs, by = c()) {
+check_by <- function(obs, by = NULL) {
   if (length(by) > 0) {
     if (!is.character(by)) {
       stop("`by` must be a character vector")
     }
     if (!all(by %in% colnames(obs))) {
       stop(
         "`by` must be a subset of the columns in `obs`. \n",
-        paste0(paste(by[!(by %in% colnames(obs))], collapse = ", "),
-        " are not present in `obs`")
+        toString(by[!(by %in% colnames(obs))]),
+        " are not present in `obs`"
       )
     }
   }
@@ -151,15 +151,16 @@ check_modules_compatible <- function(modules) {
     modules[[4]]$data$model_miss &&
       !modules[[6]]$data$likelihood_aggregation
   ) {
-    warning(paste0(
+    warning(
       "Incompatible model specification: A missingness model has ",
       "been specified but likelihood aggregation is specified as ",
       "by snapshot. Switching to likelihood aggregation by group.",
       " This has no effect on the nowcast but limits the ",
       "number of threads per chain to the number of groups. To ",
       "silence this warning, set the `likelihood_aggregation` ",
-      "argument in `enw_fit_opts` to 'groups'."
-    ), immediate. = TRUE)
+      "argument in `enw_fit_opts` to 'groups'.",
+      immediate. = TRUE
+    )
   }
   return(invisible(NULL))
 }

R/epinowcast.R

@@ -115,9 +115,9 @@ epinowcast <- function(data,
                        ),
                        expectation = epinowcast::enw_expectation(
                          r = ~ 0 + (1 | day:.group),
-                         generation_time = c(1),
+                         generation_time = 1,
                          observation = ~1,
-                         latent_reporting_delay = c(1),
+                         latent_reporting_delay = 1,
                          data = data
                        ),
                        missing = epinowcast::enw_missing(