Add R linting (#927)

.github/workflows/viash-test.yml

@@ -27,7 +27,26 @@ jobs:
           pip install ruff
       - name: Run Ruff
         run: ruff check --output-format=github .
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: any::lintr, any::styler, any::roxygen2
+          needs: lint, styler
+
+      - name: Lint
+        run: lintr::lint_dir(path = ".")
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
+
+      - name: Style
+        run: styler::style_dir(dry = "off")
+        shell: Rscript {0}
+
 
   # phase 1
   list:

.pre-commit-config.yaml

@@ -1,7 +1,23 @@
+
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
   rev: v0.8.1
   hooks:
     - id: ruff
-    - id: ruff-format
+    - id: ruff-format
+- repo: local
+  hooks:
+  - id: run_styler
+    name: run_styler
+    language: r
+    description: style files with {styler}
+    entry: "Rscript -e 'styler::style_file(commandArgs(TRUE))'"
+    files: '(\.[rR]profile|\.[rR]|\.[rR]md|\.[rR]nw|\.[qQ]md)$'
+    additional_dependencies: 
+      - styler
+      - knitr
+- repo: https://github.com/lorenzwalthert/precommit
+  rev: v0.4.3 
+  hooks:
+    - id: lintr

src/convert/from_h5mu_to_seurat/run_test.R

@@ -10,7 +10,10 @@ meta <- list(
 
 cat("> Checking whether output is correct\n")
 
-in_h5mu <- paste0(meta[["resources_dir"]], "/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect_mms.h5mu")
+in_h5mu <- paste0(
+  meta[["resources_dir"]],
+  "/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect_mms.h5mu"
+)
 out_rds <- "output.rds"
 
 cat("> Running ", meta[["name"]], "\n", sep = "")
@@ -36,4 +39,4 @@ expect_equal(sort(names(slot(obj, "assays"))), sort(c("prot", "rna")))
 obj_rna <- slot(obj, "assays")$rna
 obj_prot <- slot(obj, "assays")$prot
 
-# todo: check whether obj_rna and obj_prot have correct properties
+# todo: check whether obj_rna and obj_prot have correct properties

src/convert/from_h5mu_to_seurat/script.R

@@ -3,65 +3,78 @@ library(hdf5r)
 
 ## VIASH START
 par <- list(
-  input = "resources_test/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect_mms.h5mu",
+  input = paste0(
+    "resources_test/10x_5k_anticmv/",
+    "5k_human_antiCMV_T_TBNK_connect_mms.h5mu"
+  ),
   output = "output.rds"
 )
 ## VIASH END
 
 
-tempfile <- tempfile(fileext=".h5mu")
-file.copy(par$input, tempfile)
+temp_h5mu <- tempfile(fileext = ".h5mu")
+file.copy(par$input, temp_h5mu)
 
 delete_modality <- function(open_h5, modality_path) {
   open_h5$link_delete(modality_path)
   mod_name <- sub("/mod/", "", modality_path)
-  if ("mod-order" %in% names(h5attributes(open_h5[["mod"]]))) {
-    current_attributes <- h5attributes(open_h5[["mod"]])$`mod-order`
-    current_attributes <- current_attributes[current_attributes != mod_name] 
-    h5attr(open_h5[["mod"]], "mod-order") <- current_attributes
+  if ("mod-order" %in% names(hdf5r::h5attributes(open_h5[["mod"]]))) {
+    current_attributes <- hdf5r::h5attributes(open_h5[["mod"]])$`mod-order`
+    current_attributes <- current_attributes[current_attributes != mod_name]
+    hdf5r::h5attr(open_h5[["mod"]], "mod-order") <- current_attributes
   }
   for (obj_prefix in c("obsm/", "varm/", "varmap/", "obsmap/")) {
-    obj_path = paste0(obj_prefix, mod_name)
-    if (existsGroup(open_h5, obj_path)) {
-      open_h5$link_delete(obj_path) 
+    obj_path <- paste0(obj_prefix, mod_name)
+    if (hdf5r::existsGroup(open_h5, obj_path)) {
+      open_h5$link_delete(obj_path)
     }
   }
-
-} 
+}
+
+open_file <- H5File$new(temp_h5mu, mode = "r+")
+modalities <- list.groups(open_file[["mod"]],
+  full.names = TRUE, recursive = FALSE
+)
+to_delete <- c()
 
-open_file <- H5File$new(tempfile, mode="r+")
-modalities <- list.groups(open_file[["mod"]], full.names =  TRUE, recursive = FALSE)
-to_delete = c()
+determine_matrix_dims <- function(dataset, indexpointers, indices, rowwise) {
+  if ("shape" %in% hdf5r::h5attr_names(dataset)) {
+    x_dims <- hdf5r::h5attr(dataset, "shape")
+  } else {
+    x_dims <- c(length(indexpointers) - 1, max(indices) + 1)
+    if (rowwise) {
+      x_dims <- rev(x_dims)
+    }
+  }
+  return(x_dims)
+}
 for (modality_path in modalities) {
   dataset <- open_file[[modality_path]][["X"]]
   dataset_names <- names(dataset)
-  if ("data" %in% dataset_names  && "indices" %in% dataset_names && "indptr" %in% dataset_names) {
+  if (
+    "data" %in% dataset_names &&
+      "indices" %in% dataset_names &&
+      "indptr" %in% dataset_names
+  ) {
     indexpointers <- dataset[["indptr"]]$read()
     indices <- dataset[["indices"]]$read()
     rowwise <- FALSE
     if ("encoding-type" %in% h5attr_names(dataset)) {
       rowwise <- h5attr(dataset, "encoding-type") == "csr_matrix"
     }
-    if ("shape" %in% h5attr_names(dataset)) {
-      X_dims <- h5attr(dataset, "shape")
-    } else {
-      X_dims <- c(length(indexpointers) - 1, max(indices) + 1)
-      if (rowwise) {
-        X_dims <- rev(X_dims)
-      }
-    }
-    if (X_dims[2] < 1) {
+    x_dims <- determine_matrix_dims(dataset, indexpointers, indices, rowwise)
+    if (x_dims[2] < 1) {
       delete_modality(open_file, modality_path)
     }
-  } else if (dataset$dims[1] < 1){
+  } else if (dataset$dims[1] < 1) {
     delete_modality(open_file, modality_path)
   }
 }
 
 open_file$close_all()
 
 cat("Reading input file\n")
-obj <- ReadH5MU(tempfile)
+obj <- ReadH5MU(temp_h5mu)
 
 cat("Writing output file\n")
-saveRDS(obj, file = par$output, compress = TRUE)
+saveRDS(obj, file = par$output, compress = TRUE)

src/files/make_params/script.R

@@ -32,7 +32,9 @@ paths <- gsub("^/viash_automount", "", paths)
 
 cat("> Checking whether basenames are unique\n")
 i <- par$n_basename_id
-maxi <- strsplit(paths, "/") %>% map_int(length) %>% max
+maxi <- strsplit(paths, "/") %>%
+  map_int(length) %>%
+  max()
 
 regex <- paste0(".*/(", paste(rep("[^/]+/", i), collapse = ""), "[^/]*)$")
 ids <- gsub("/", "_", gsub(regex, "\\1", paths))
@@ -43,10 +45,13 @@ cat("\n")
 
 while (i < maxi && any(duplicated(ids))) {
   i <- i + 1
-  cat("Duplicated ids detected, combining with ", i, " dirnames in an attempt to get unique ids.\n")
+  cat(
+    "Duplicated ids detected, combining with ", i,
+    " dirnames in an attempt to get unique ids.\n"
+  )
   regex <- paste0(".*/(", paste(rep("[^/]+/", i), collapse = ""), "[^/]*)$")
   ids <- gsub("/", "_", gsub(regex, "\\1", paths))
-  
+
   cat("> Printing first five rows\n")
   print(tibble(id = ids, path = paths) %>% head(5))
   cat("\n")

src/genetic_demux/freemuxlet/script.R

@@ -45,10 +45,14 @@ argmap <- c(
 
 for (arg in names(argmap)) {
   if (!is.null(par[[arg]])) {
-    if (arg %in% c("aux_files", "keep_init_missing", "randomize_singlet_score")) {
-      if (toupper(par[[arg]]) == TRUE)
+    if (arg %in% c(
+      "aux_files", "keep_init_missing",
+      "randomize_singlet_score"
+    )) {
+      if (toupper(par[[arg]]) == TRUE) {
         cmd <- c(cmd, argmap[[arg]])
-    }else {
+      }
+    } else {
       cmd <- c(cmd, argmap[[arg]], par[[arg]])
     }
   }
@@ -87,4 +91,4 @@ freemuxlet_assign <- res2 %>% select(cell = BARCODE, donor_id)
 readr::write_csv(
   freemuxlet_assign,
   paste0(par$output, "/cell_annotation.csv")
-)
+)

src/integrate/harmony/script.R

@@ -34,4 +34,4 @@ harmony_embedding <- HarmonyMatrix(
 rna_data$obsm[[par$obsm_output]] <- harmony_embedding
 
 ## Save as h5mu
-data$write(par$output, compression=par$output_compression)
+data$write(par$output, compression = par$output_compression)