Work on fixing CI

.lintr

@@ -0,0 +1,5 @@
+linters: linters_with_defaults(
+    line_length_linter(120),
+    object_name_linter(styles = c("snake_case", "symbols", "camelCase"))
+  )
+encoding: "UTF-8"

DESCRIPTION

@@ -2,7 +2,7 @@ Package: omopbundles
 Type: Package
 Title: Bundles of OMOP Concepts for Ease of Data Selection
 Version: 0.1.0
-Author: person('Stef', 'Piatek', email = '[email protected]', role = c('cre', 'aut'))
+Authors@R: person('Stef', 'Piatek', email = '[email protected]', role = c('cre', 'aut'))
 Description: Bundles of OMOP Concepts for Ease of Data Selection
 License: Apache License (>= 2)
 Encoding: UTF-8
@@ -14,5 +14,7 @@ Imports:
 Suggests:
   usethis,
   testthat (>= 3.0.0),
-  lintr
+  lintr,
+  pkgload
 Config/testthat/edition: 3
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1 +1,8 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(available_bundles)
+export(concept_by_bundle)
+importFrom(dplyr,mutate)
+importFrom(dplyr,tibble)
+importFrom(purrr,map_dfr)
+importFrom(readr,read_csv)

R/bundles.R

@@ -11,18 +11,19 @@
 #' @export
 available_bundles <- function(version = "latest") {
   raw_dir <- .get_raw_dir()
-  directories <- list.dirs(raw_dir, full.names=TRUE)
+  directories <- list.dirs(raw_dir, full.names = TRUE)
   domain_directories <- directories[directories != raw_dir]
 
   purrr::map_dfr(domain_directories, .build_concepts_from_directory)
 }
 
 .get_raw_dir <- function(...) {
-  system.file("data", "raw", ..., package = "omopbundles", mustWork=TRUE)
+  system.file("data", "raw", ..., package = "omopbundles", mustWork = TRUE)
 }
 
 .build_concepts_from_directory <- function(directory) {
   concept_files <- list.files(directory)
+  concept_name <- NULL
 
   dplyr::tibble(
     id = concept_files,
@@ -39,7 +40,7 @@ available_bundles <- function(version = "latest") {
 #' @param bundle_row Single row of a dataframe with a domain and id
 #' @return Dataframe with a concept_id and domain column
 #' @export
-concept_by_bundle <- function(bundle_row){
+concept_by_bundle <- function(bundle_row) {
   stopifnot(is.data.frame(bundle_row))
   stopifnot(nrow(bundle_row) == 1)
 

renv.lock

@@ -170,6 +170,11 @@
       ],
       "Hash": "b8552d117e1b808b09a832f589b79035"
     },
+    "lintr": {
+      "Package": "lintr",
+      "Version": "3.1.2",
+      "Source": "Repository"
+    },
     "magrittr": {
       "Package": "magrittr",
       "Version": "2.0.3",
@@ -207,6 +212,11 @@
       ],
       "Hash": "01f28d4278f15c76cddbea05899c5d6f"
     },
+    "pkgload": {
+      "Package": "pkgload",
+      "Version": "1.4.0",
+      "Source": "Repository"
+    },
     "prettyunits": {
       "Package": "prettyunits",
       "Version": "1.2.0",
@@ -290,6 +300,11 @@
       ],
       "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
     },
+    "roxygen2": {
+      "Package": "roxygen2",
+      "Version": "7.3.2",
+      "Source": "Repository"
+    },
     "tibble": {
       "Package": "tibble",
       "Version": "3.2.1",

tests/testthat/test-bundles.R

@@ -3,12 +3,12 @@ library(omopbundles)
 library(testthat)
 
 
-test_that("available_bundles is not empty",{
+test_that("available_bundles is not empty", {
   result <- available_bundles()
   expect_true(nrow(result) > 0, info = "The dataframe should not be empty")
 })
 
-test_that("Smoking exists as an observation",{
+test_that("Smoking exists as an observation", {
   result <- available_bundles() |>
     dplyr::filter(concept_name == "smoking")
 
@@ -17,7 +17,7 @@ test_that("Smoking exists as an observation",{
 })
 
 
-test_that("Avilable bundles and concept_by_bundle play nicely together",{
+test_that("Avilable bundles and concept_by_bundle play nicely together", {
   smoking_bundle <- available_bundles() |>
     dplyr::filter(concept_name == "smoking")