fix

R/parse_yaml_params.R

@@ -17,7 +17,7 @@ parse_yaml_params <- function(def = get("default_path",
  envir = parent.frame()
  )) {
  ## Read the default YAML fil
- params <- yaml::read_yaml(file = def))
+ params <- yaml::read_yaml(file = def)
 
  ## If a user-specified YAML file exists,
  ## read it and overwrite the default values with the user-specified ones

tests/testthat/test-functions.R

@@ -37,14 +37,18 @@ test_that(desc = "Test functions", code = {
  prepare_params()
 
  ## replace id
- replace_id(x = "example/123456_features.tsv",
- user_gnps = "",
- user_filename = "Foo")
+ replace_id(
+ x = "example/123456_features.tsv",
+ user_gnps = "",
+ user_filename = "Foo"
+ )
 
  ## Get all files
  ### Features table
- get_file(url = paths$urls$examples$features,
- export = paths$data$source$features)
+ get_file(
+ url = paths$urls$examples$features,
+ export = paths$data$source$features
+ )
  get_gnps_tables(
  filename = "example",
  path_features = paths$data$source$features,
@@ -53,8 +57,10 @@ test_that(desc = "Test functions", code = {
  gnps_job_id = params$gnps$id
  )
  ### Metadata table
- get_file(url = paths$urls$examples$metadata,
- export = paths$data$source$metadata)
+ get_file(
+ url = paths$urls$examples$metadata,
+ export = paths$data$source$metadata
+ )
  get_file(
  url = paths$urls$examples$metadata |>
  gsub(
@@ -294,9 +300,11 @@ test_that(desc = "Test functions", code = {
  )
  )
  #### If does not exist
- prepare_libraries_spectra(input = "doesNotExists.txt",
- output_pos = "data/interim/libraries/spectra/exp/nope_pos.rds",
- output_neg = "data/interim/libraries/spectra/exp/nope_neg.rds",)
+ prepare_libraries_spectra(
+ input = "doesNotExists.txt",
+ output_pos = "data/interim/libraries/spectra/exp/nope_pos.rds",
+ output_neg = "data/interim/libraries/spectra/exp/nope_neg.rds",
+ )
  #### Classical
  prepare_libraries_spectra()
  #### Again
@@ -322,9 +330,11 @@ test_that(desc = "Test functions", code = {
  temp_exp = paths$data$source$libraries$rt$example_mini
  )
  ## Check wrong SMILES
- tidytable::tidytable("rt" = 0.1,
- "smiles" = "wrongSMILES",
- "inchikey" = NA) |>
+ tidytable::tidytable(
+ "rt" = 0.1,
+ "smiles" = "wrongSMILES",
+ "inchikey" = NA
+ ) |>
  tidytable::fwrite("data/source/libraries/rt/example_bad.tsv")
  prepare_libraries_rt(temp_exp = "data/source/libraries/rt/example_bad.tsv")
  expect_warning(object = prepare_libraries_rt(temp_exp = "data/source/libraries/rt/example_bad.tsv"))
@@ -424,13 +434,16 @@ test_that(desc = "Test functions", code = {
  )
 
  ## Create MS2 based edges
- create_edges_spectra(## shallow tolerance to speed up tests
- ppm = 1, dalton = 0.001)
+ create_edges_spectra( ## shallow tolerance to speed up tests
+ ppm = 1, dalton = 0.001
+ )
  ## if MS1 only
- create_edges_spectra(input = "data/source/example_spectra_ms1.mgf",
- ## shallow tolerance to speed up tests
- ppm = 1,
- dalton = 0.001)
+ create_edges_spectra(
+ input = "data/source/example_spectra_ms1.mgf",
+ ## shallow tolerance to speed up tests
+ ppm = 1,
+ dalton = 0.001
+ )
 
  ### GNPS results
  prepare_annotations_gnps(input = "fileDoesNotExist")