build: Add a GHA Linter

.Rbuildignore

@@ -4,3 +4,5 @@
 .git
 .github
 misc
+^\.github$
+.lintr

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/lint-project.yaml

@@ -0,0 +1,32 @@
+# 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]
+  pull_request:
+
+name: lint-project.yaml
+
+permissions: read-all
+
+jobs:
+  lint-project:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install lintr
+        run: install.packages("lintr")
+        shell: Rscript {0}
+
+      - name: Lint root directory
+        run: lintr::lint_dir()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.lintr

@@ -0,0 +1,6 @@
+linters: linters_with_defaults(
+    line_length_linter(120),
+    commented_code_linter = NULL,
+    object_usage_linter = NULL
+  )
+

R/cmd.R

@@ -10,12 +10,11 @@
 #'
 #' @noRd
 louper_create_cloupe <- function(
-  h5path,
-  output_dir = NULL,
-  output_name = NULL, 
-  executable_path = NULL,
-  force = FALSE
-) {
+    h5path,
+    output_dir = NULL,
+    output_name = NULL,
+    executable_path = NULL,
+    force = FALSE) {
   # default loupe name to `converted.cloupe`
   if (is.null(output_name)) {
     output_name <- "converted"
@@ -54,10 +53,10 @@ louper_create_cloupe <- function(
     return(err(sprintf("cannot find Louper executable at path: '%s'", executable_path)))
   }
 
-  cmd_msg <- sprintf('running command: "%s"', paste(c(executable_path, args), collapse=" "))
-  logMsg(cmd_msg)
+  cmd_msg <- sprintf('running command: "%s"', paste(c(executable_path, args), collapse = " "))
+  log_msg(cmd_msg)
 
-  status <- system2(command=executable_path, args=args)
+  status <- system2(command = executable_path, args = args)
 
   if (status == 0) {
     return(SUCCESS)

R/err.R

@@ -9,18 +9,32 @@ err <- function(msg) {
 
 #' The non-error variant of above
 #' @noRd
-SUCCESS <- list(success = TRUE, msg = NULL)
+SUCCESS <- list(success = TRUE, msg = NULL) # nolint
 
 #' validation error with link to 10x support
 #' @noRd
 validation_err <- function(msg, name) {
-  sprintf("\nIt looks like the formatting of your %s does not match the required formatting for LoupeR. For further information, please see the documentation: 10xgen.com/louper\n\n%s", name, msg)
+  sprintf(
+    paste(
+      "\nIt looks like the formatting of your %s does not match the required formatting for LoupeR.",
+      "For further information, please see the documentation: 10xgen.com/louper\n\n%s"
+    ),
+    name,
+    msg
+  )
 }
 
 #' general error with link to 10x support
 #' @noRd
 general_err <- function(msg, name) {
-  sprintf("\nIt looks like there was an issue with %s. For further information, please see the documentation: 10xgen.com/louper\n\n%s", name, msg)
+  sprintf(
+    paste(
+      "\nIt looks like there was an issue with %s. For further information,",
+      "please see the documentation: 10xgen.com/louper\n\n%s",
+    ),
+    name,
+    msg
+  )
 }
 
 #' Create a Bugreport from a Seurat Object
@@ -49,15 +63,15 @@ create_bugreport_from_seurat <- function(obj) {
   }
 
   # overview
-  namedAssay <- select_assay(obj)
-  if (is.null(namedAssay)) {
+  named_assay <- select_assay(obj)
+  if (is.null(named_assay)) {
     cat("\nSeurat:\n\n")
     cat("No assay found\n")
     return(invisible())
   }
 
-  assay_name <- names(namedAssay)
-  assay <- namedAssay[[1]]
+  assay_name <- names(named_assay)
+  assay <- named_assay[[1]]
   clusters <- select_clusters(obj)
   projections <- select_projections(obj)
   counts <- counts_matrix_from_assay(assay)
@@ -78,24 +92,25 @@ create_bugreport_from_seurat <- function(obj) {
 #' This bugreport can then be included when reaching out to 10xGenomics Support or when filing
 #' a Github ticket.  This information should be included along with any other output when creating a Loupe file.
 #'
-#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.  Rows are features, Columns are barcodes.
+#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.
+#'   Rows are features, Columns are barcodes.
 #' @param clusters list of factors that hold information for each barcode
 #' @param projections list of matrices, all with dimensions (barcodeCount x 2)
 #' @param assay_name optional string that holds the Seurat Object assay name.
-#' @param seurat_obj_version optional string that holds the Seurat Object version.  It is useful for debugging compatibility issues.
+#' @param seurat_obj_version optional string that holds the Seurat Object version.
+#'   It is useful for debugging compatibility issues.
 #' @param skip_metadata optional logical which skips printing metadata
 #'
 #' @importFrom methods is
 #'
 #' @export
 create_bugreport <- function(
-  count_mat,
-  clusters,
-  projections,
-  assay_name = NULL,
-  seurat_obj_version = NULL,
-  skip_metadata = FALSE
-) {
+    count_mat,
+    clusters,
+    projections,
+    assay_name = NULL,
+    seurat_obj_version = NULL,
+    skip_metadata = FALSE) {
   # metadata
   if (!skip_metadata) {
     cat("\nMetadata:\n\n")
@@ -118,8 +133,8 @@ create_bugreport <- function(
   cat("\nMatrix Sampling:\n\n")
   all_features <- rownames(count_mat)
   all_barcodes <- colnames(count_mat)
-  features <- sample(rownames(count_mat), size=min(10, length(all_features)))
-  barcodes <- sample(colnames(count_mat), size=min(10, length(all_barcodes)))
+  features <- sample(rownames(count_mat), size = min(10, length(all_features)))
+  barcodes <- sample(colnames(count_mat), size = min(10, length(all_barcodes)))
   cat(sprintf("feature count: %d\n", length(all_features)))
   cat(sprintf("barcode count: %d\n", length(all_barcodes)))
   cat(sprintf("feature sampling:\n"))

R/eula.R

@@ -1,4 +1,4 @@
-AUTO_ACCEPT_ENV_VAR <- "AUTO_ACCEPT_EULA"
+AUTO_ACCEPT_ENV_VAR <- "AUTO_ACCEPT_EULA" # nolint
 
 #' Present EULA and Record agreement
 #'

R/hdf5.R

@@ -1,31 +1,33 @@
 #' Create an hdf5 interchange file
 #'
-#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.  Rows are features, Columns are barcodes.
+#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.
+#'   Rows are features, Columns are barcodes.
 #' @param clusters list of factors that hold information for each barcode
 #' @param projections list of matrices, all with dimensions (barcodeCount x 2)
 #' @param h5path path to h5 file
-#' @param feature_ids optional character vector that specifies the feature ids of the count matrix.  Typically, these are the ensemble ids.
-#' @param seurat_obj_version optional string that holds the Seurat Object version.  It is useful for debugging compatibility issues.
+#' @param feature_ids optional character vector that specifies the feature ids of the count matrix.
+#'   Typically, these are the ensemble ids.
+#' @param seurat_obj_version optional string that holds the Seurat Object version.
+#'   It is useful for debugging compatibility issues.
 #'
 #' @importFrom hdf5r H5File
 #'
 #' @return TRUE on success, FALSE on error
 #'
 #' @noRd
 create_hdf5 <- function(
-  count_mat,
-  clusters,
-  projections,
-  h5path,
-  feature_ids,
-  seurat_obj_version
-) {
+    count_mat,
+    clusters,
+    projections,
+    h5path,
+    feature_ids,
+    seurat_obj_version) {
   if (file.exists(h5path)) {
     return(err(sprintf("cannot create h5 file %s", h5path)))
   }
 
   # create hdf5 file and matrix groups
-  f <- hdf5r::H5File$new(h5path, mode="w")
+  f <- hdf5r::H5File$new(h5path, mode = "w")
 
   write_mat(f, count_mat, feature_ids)
   write_clusters(f, clusters)
@@ -40,8 +42,10 @@ create_hdf5 <- function(
 #' Writes the matrix to the H5 file
 #'
 #' @param f An open H5File
-#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.  Rows are features, Columns are barcodes.
-#' @param feature_ids optional character vector that specifies the feature ids of the count matrix.  Typically, these are the ensemble ids.
+#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.
+#'   Rows are features, Columns are barcodes.
+#' @param feature_ids optional character vector that specifies the feature ids of the count matrix.
+#'   Typically, these are the ensemble ids.
 #'
 #' @noRd
 write_mat <- function(f, count_mat, feature_ids) {
@@ -62,14 +66,16 @@ write_mat <- function(f, count_mat, feature_ids) {
   matrix_group$close()
 
   if (is.null(feature_ids)) {
-    feature_ids <- lapply(1:length(features), function(x) {return(sprintf("feature_%d", x))})
+    feature_ids <- lapply(seq_along(features), function(x) {
+      return(sprintf("feature_%d", x))
+    })
   }
 
   create_str_dataset(features_group, "name", features)
-  create_str_dataset(features_group, "id", as.character(feature_ids)) 
+  create_str_dataset(features_group, "id", as.character(feature_ids))
   create_str_dataset(features_group, "feature_type", rep("Gene Expression", length(features)))
   create_str_dataset(features_group, "_all_tag_keys", as.character()) # required features
-  
+
   features_group$close()
 }
 
@@ -79,7 +85,7 @@ write_mat <- function(f, count_mat, feature_ids) {
 #' @param prefix What to prefix each line
 #'
 #' @noRd
-print_metadata <- function(metadata, prefix="") {
+print_metadata <- function(metadata, prefix = "") {
   for (name in names(metadata)) {
     val <- metadata[[name]]
 
@@ -179,27 +185,28 @@ create_metadata <- function(seurat_obj_version = NULL) {
   }
 
   meta <- list()
-  meta["tool"]             <- "loupeR"
-  meta["tool_version"]     <- as.character(utils::packageVersion("loupeR"))
-  meta["os"]               <- ifelse(is.null(sinfo$running), "Unknown", sinfo$running)
-  meta["system"]           <- sinfo$platform
-  meta["language"]         <- rversion$language
+  meta["tool"] <- "loupeR"
+  meta["tool_version"] <- as.character(utils::packageVersion("loupeR"))
+  meta["os"] <- ifelse(is.null(sinfo$running), "Unknown", sinfo$running)
+  meta["system"] <- sinfo$platform
+  meta["language"] <- rversion$language
   meta["language_version"] <- language_version
 
-  extra = list()
-  extra["loupeR_seurat_version"]        <- as.character(utils::packageVersion("Seurat"))
+  extra <- list()
+  extra["loupeR_seurat_version"] <- as.character(utils::packageVersion("Seurat"))
   extra["loupeR_seurat_object_version"] <- ifelse(is.null(seurat_obj_version), "n/a", seurat_obj_version)
-  extra["loupeR_hdf5r_version"]         <- as.character(utils::packageVersion("hdf5r"))
-  extra["loupeR_hdf5_version"]          <- hdf5r::h5version(FALSE)
-  meta[["extra"]]                       <- extra
+  extra["loupeR_hdf5r_version"] <- as.character(utils::packageVersion("hdf5r"))
+  extra["loupeR_hdf5_version"] <- hdf5r::h5version(FALSE)
+  meta[["extra"]] <- extra
 
   meta
 }
 
 #' Writes the metadata
 #'
 #' @param f An open H5File
-#' @param seurat_obj_version optional string that holds the Seurat Object version.  It is useful for debugging compatibility issues.
+#' @param seurat_obj_version optional string that holds the Seurat Object version.
+#'   It is useful for debugging compatibility issues.
 #'
 #' @noRd
 write_metadata <- function(f, seurat_obj_version) {
@@ -254,8 +261,7 @@ create_str_dataset <- function(obj, key, strs, ...) {
     max_len <- max(as.numeric(lapply(strs, nchar)))
   }
 
-  dtype <- hdf5r::H5T_STRING$new(size=max_len)
+  dtype <- hdf5r::H5T_STRING$new(size = max_len)
 
-  create_dataset(obj, key, strs, dtype=dtype, ...)
+  create_dataset(obj, key, strs, dtype = dtype, ...)
 }
-