fix exports

DESCRIPTION

@@ -32,6 +32,7 @@ Imports:
  MsBackendMsp (>= 1.6.0),
  msentropy (>= 0.1.4),
  pbapply (>= 1.7.2),
+ R.utils (>= 2.12.3),
  rlang (>= 1.1.4),
  rotl (>= 3.1.0),
  shiny (>= 1.9.0),
@@ -53,7 +54,8 @@ Suggests:
  pkgload,
  shinytest2,
  spelling,
- testthat (>= 3.0.0)
+ testthat (>= 3.0.0),
+ visNetwork
 VignetteBuilder:
  knitr
 biocViews: metabolite annotation, chemotaxonomy, scoring system, natural

NEWS.md

@@ -2,6 +2,8 @@
 
 # tima 2.10.1
 
+* Reduced dependencies
+* Reduced exports
 * Removed `CompoundDb` dependency as it was causing too many issues
 * Removed `pak` install and switched to `r-universe`
 * Replaced internal functions by `Spectra` equivalents (#166)

inst/app.R

@@ -1,5 +1,3 @@
-library(tima)
-
 # Check if runs in Docker environment or not
 i_am_a_whale <- file.exists("/.dockerenv")
 if (i_am_a_whale) {
@@ -1690,13 +1688,13 @@ ui <- shiny::fluidPage(
 
 # save the results to a file
 save_input <- function(input) {
- paths_data_source <- parse_yaml_paths()$data$source$path
+ paths_data_source <- tima:::parse_yaml_paths()$data$source$path
  paths_data_interim_annotations <-
- parse_yaml_paths()$data$interim$annotations$path
+ tima:::parse_yaml_paths()$data$interim$annotations$path
  ## safety
- create_dir(paths_data_source)
+ tima::create_dir(paths_data_source)
 
- list <- load_yaml_files()
+ list <- tima:::load_yaml_files()
 
  yamls_params <- list$yamls_params
  yaml_files <- list$yaml_files
@@ -1746,7 +1744,7 @@ save_input <- function(input) {
  if (!is.null(prefil_sir_raw)) {
  if (!file.exists(prefil_sir_raw_1)) {
  ## safety
- create_dir(paths_data_interim_annotations)
+ tima::create_dir(paths_data_interim_annotations)
  fs::file_copy(
  path = prefil_sir_raw[[4]],
  new_path = file.path(prefil_sir_raw_1),
@@ -1777,8 +1775,8 @@ save_input <- function(input) {
  ms_pol <- shiny::isolate(input$ms_pol)
  summarise <- shiny::isolate(input$summarise)
 
- log_debug(x = "Changing parameters ...")
- log_debug(x = "... Small")
+ message(x = "Changing parameters ...")
+ message(x = "... Small")
  yaml_small <- yamls_params[["inst/params/prepare_params"]]
  yaml_small$files$pattern <- fil_pat
  yaml_small$files$features$raw <- fil_fea_raw
@@ -1792,7 +1790,7 @@ save_input <- function(input) {
  create_dir("inst/params")
  yaml::write_yaml(x = yaml_small, file = parse_yaml_paths()$params$prepare_params)
 
- log_debug(x = "... Advanced")
+ message(x = "... Advanced")
  yaml_advanced <- yamls_params[["inst/params/prepare_params_advanced"]]
  yaml_advanced$annotations$candidates$final <-
  shiny::isolate(input$ann_can_fin)
@@ -1815,42 +1813,43 @@ save_input <- function(input) {
  yaml_advanced$files$pattern <- fil_pat
  yaml_advanced$files$annotations$raw$spectral$gnps <-
  yaml_advanced$files$annotations$raw$spectral$gnps |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$annotations$raw$spectral$spectral <-
  yaml_advanced$files$annotations$raw$spectral$spectral |>
- replace_id()
+ tima:::replace_id()
  # yaml_advanced$files$annotations$raw$sirius <-
  # yaml_advanced$files$annotations$raw$sirius |>
- # replace_id()
+ # tima:::replace_id()
  yaml_advanced$files$annotations$raw$sirius <- fil_sir_raw
  yaml_advanced$files$annotations$prepared$canopus <-
  yaml_advanced$files$annotations$prepared$canopus |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$annotations$prepared$formula <-
  yaml_advanced$files$annotations$prepared$formula |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$annotations$prepared$structural$gnps <-
  yaml_advanced$files$annotations$prepared$structural$gnps |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$annotations$prepared$structural$ms1 <-
  yaml_advanced$files$annotations$prepared$structural$ms1 |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$annotations$prepared$structural$sirius <-
  yaml_advanced$files$annotations$prepared$structural$sirius |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$annotations$prepared$structural$spectral <-
  yaml_advanced$files$annotations$prepared$structural$spectral |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$annotations$filtered <-
- yaml_advanced$files$annotations$filtered |> replace_id()
+ yaml_advanced$files$annotations$filtered |>
+ tima:::replace_id()
  # yaml_advanced$files$annotations$processed <-
  # yaml_advanced$files$annotations$processed |>
- # replace_id()
+ #  tima:::replace_id()
  yaml_advanced$files$features$raw <-
  fil_fea_raw
  yaml_advanced$files$features$prepared <-
  yaml_advanced$files$features$prepared |>
- replace_id()
+ tima:::replace_id()
  # TODO
  # yaml_advanced$files$libraries$sop$raw$closed <-
  # shiny::isolate(input$todo)
@@ -1901,23 +1900,23 @@ save_input <- function(input) {
  # shiny::isolate(input$todo)
  yaml_advanced$files$networks$spectral$edges$raw$ms1 <-
  yaml_advanced$files$networks$spectral$edges$raw$ms1 |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$networks$spectral$edges$raw$spectral <-
  yaml_advanced$files$networks$spectral$edges$raw$spectral |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$networks$spectral$edges$prepared <-
  yaml_advanced$files$networks$spectral$edges$prepared |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$networks$spectral$components$raw <-
  yaml_advanced$files$networks$spectral$components$raw |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$networks$spectral$components$prepared <-
  yaml_advanced$files$networks$spectral$components$prepared |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$metadata$raw <- fil_met_raw
  yaml_advanced$files$metadata$prepared <-
  yaml_advanced$files$metadata$prepared |>
- replace_id()
+ tima:::replace_id()
  yaml_advanced$files$spectral$raw <- fil_spe_raw
  yaml_advanced$gnps$id <- gnps_job_id
  yaml_advanced$gnps$workflow <-
@@ -2104,7 +2103,7 @@ save_input <- function(input) {
 
  yaml::write_yaml(
  x = yaml_advanced,
- file = parse_yaml_paths()$params$prepare_params_advanced
+ file = tima:::parse_yaml_paths()$params$prepare_params_advanced
  )
 }
 
@@ -2384,7 +2383,7 @@ server <- function(input, output, session) {
  })
 }
 url <- "<http://127.0.0.1:3838>"
-log_debug("Please, open:", url, "on your favorite browser, but not Edge.")
+message("Please, open:", url, "on your favorite browser, but not Edge.")
 shiny::shinyApp(
  ui = ui,
  server = server,
@@ -2393,7 +2392,7 @@ shiny::shinyApp(
  message("I'm inside the matrix ;(")
  setwd(dir = "..")
  } else {
- go_to_cache()
+ tima:::go_to_cache()
  }
  }
 )

tests/testthat/test-shinytest2.R

@@ -1,9 +1,8 @@
 library(shinytest2)
-library(tima)
 
 test_that("{shinytest2} recording: app", {
- get_file(url = "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_spectra_mini.mgf", export = "data/source/example_spectra.mgf")
- get_file(url = "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_features.csv", export = "data/source/example_features.csv")
+ tima:::get_file(url = "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_spectra_mini.mgf", export = "data/source/example_spectra.mgf")
+ tima:::get_file(url = "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_features.csv", export = "data/source/example_features.csv")
  app <- AppDriver$new(
  timeout = 100000,
  load_timeout = 100000,

vignettes/articles/I-gathering.Rmd

@@ -24,9 +24,9 @@ knitr::opts_chunk$set(
 knitr::opts_knit$set(root.dir = "../..")
 ```
 
-```{r tima, results="hide", message=FALSE, warning=FALSE, include = FALSE}
+```{r tima, include = FALSE}
 library("tima")
-copy_backbone()
+tima:::copy_backbone()
 ```
 This vignette describes...