fix targets

R/tima-package.R

@@ -8,3 +8,11 @@
 ## usethis namespace: end
 NULL
 .datatable.aware <- TRUE
+.onLoad <- function(libname, pkgname) {
+ Sys.setenv(TAR_CONFIG = system.file("pipelines/_targets.yaml", package = "tima"))
+ invisible()
+}
+
+.onAttach <- function(libname, pkgname) {
+ packageStartupMessage("Welcome to Taxonomically Informed Metabolite Annotation")
+}

inst/app.R

@@ -2364,7 +2364,6 @@ server <- function(input, output, session) {
  )
  targets::tar_make(
  names = targets::matches("^ann_pre$"),
- script = system.file("pipelines/_targets.R", package = "tima"),
  garbage_collection = TRUE,
  reporter = "verbose_positives"
  )

inst/pipelines/_targets.yaml

@@ -0,0 +1,3 @@
+---
+main:
+ script: inst/pipelines/_targets.R

inst/scripts/annotate_masses.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ", crayon::blue("CH"), crayon::cyan("MS"), "\n")
 
-targets::tar_make(names = matches("^ann_ms1_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("^ann_ms1_pre"))
 
 end <- Sys.time()
 

inst/scripts/annotate_spectra.R

@@ -15,7 +15,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("^ann_spe_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("^ann_spe_pre"))
 
 end <- Sys.time()
 

inst/scripts/create_components.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("fea_com"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("fea_com"))
 
 end <- Sys.time()
 

inst/scripts/create_edges_spectra.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ", crayon::blue("CH"), crayon::cyan("MS"), "\n")
 
-targets::tar_make(names = matches("fea_edg_spe"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("fea_edg_spe"))
 
 end <- Sys.time()
 

inst/scripts/filter_annotations.R

@@ -14,7 +14,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("^ann_fil"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("^ann_fil"))
 
 end <- Sys.time()
 

inst/scripts/get_gnps_tables.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("gnps_tables"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("gnps_tables"))
 
 end <- Sys.time()
 

inst/scripts/get_isdb_lotus.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_spe_is_lot"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_spe_is_lot"))
 
 end <- Sys.time()
 

inst/scripts/get_lotus.R

@@ -13,7 +13,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_sop_lot$"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_lot$"))
 
 end <- Sys.time()
 

inst/scripts/get_massbank_spectra.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_spe_exp_mb_raw"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_spe_exp_mb_raw"))
 
 end <- Sys.time()
 

inst/scripts/prepare_annotations_gnps.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("^ann_spe_exp_gnp_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("^ann_spe_exp_gnp_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_annotations_sirius.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("^ann_sir_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("^ann_sir_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_annotations_spectra.R

@@ -13,7 +13,7 @@ log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
 ## Not ann_spe because of `ann_spe_int` (see #69)
-targets::tar_make(names = c(matches("^ann_spe_is"), script = system.file("pipelines/_targets.R", package = "tima")))
+targets::tar_make(names = c(matches("^ann_spe_is")))
 
 end <- Sys.time()
 

inst/scripts/prepare_features_components.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("fea_com_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("fea_com_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_features_edges.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("fea_edg_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("fea_edg_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_features_tables.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("fea_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("fea_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_libraries_rt.R

@@ -15,7 +15,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_rt"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_rt"))
 
 end <- Sys.time()
 

inst/scripts/prepare_libraries_sop_closed.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_sop_clo_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_clo_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_libraries_sop_ecmdb.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_sop_ecm_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_ecm_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_libraries_sop_hmdb.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_sop_hmd_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_hmd_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_libraries_sop_lotus.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_sop_lot_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_lot_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_libraries_sop_merged.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_sop_mer"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_mer"))
 
 end <- Sys.time()
 

inst/scripts/prepare_libraries_spectra.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_spe_exp_int_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_spe_exp_int_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_libraries_spectra_is_lotus.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("lib_spe_is_lot_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_spe_is_lot_pre"))
 
 end <- Sys.time()
 

inst/scripts/prepare_params.R

@@ -12,7 +12,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"))
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("par_"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("par_"))
 
 end <- Sys.time()
 

inst/scripts/prepare_taxa.R

@@ -18,7 +18,7 @@ log_debug(
 )
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("tax_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("tax_pre"))
 
 end <- Sys.time()
 

inst/scripts/tima_full.R

@@ -9,7 +9,7 @@ log_debug(
 log_debug("Authors: ", crayon::green("AR"), "\n")
 log_debug("Contributors: ", crayon::blue("PMA"), "\n")
 
-targets::tar_make(names = matches("^ann_pre$"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("^ann_pre$"))
 
 end <- Sys.time()
 

inst/scripts/weight_annotations.R

@@ -20,7 +20,7 @@ log_debug(
 )
 log_debug("Contributors: ...")
 
-targets::tar_make(names = matches("ann_pre$"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("ann_pre$"))
 
 end <- Sys.time()
 

vignettes/articles/I-gathering.Rmd

@@ -107,7 +107,7 @@ tima::get_file(
 MassBank is downloaded and used by default.
 
 ```{r spectra-mb, results="hide", message=FALSE, warning=FALSE, include = FALSE}
-targets::tar_make(names = matches("lib_spe_exp_mb_raw"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_spe_exp_mb_raw"))
 ```
 
 We are currently working to get all MONA and GNPS experimental spectra easily available.
@@ -129,11 +129,11 @@ For more info, see <https://doi.org/10.5281/zenodo.5607185>.
 It is made available in both polarities.
 
 ```{r get-isdb-lotus, results="hide", message=FALSE, warning=FALSE, include = FALSE}
-targets::tar_make(names = matches("lib_spe_is_lot"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_spe_is_lot"))
 ```
 
 ```{r prepare-isdb-lotus-1, results="hide", message=FALSE, warning=FALSE, include = FALSE}
-targets::tar_make(names = matches("lib_spe_is_lot_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_spe_is_lot_pre"))
 ```
 
 You can also complement with the in silico spectra from HMDB (not running by default as quite long):
@@ -156,7 +156,7 @@ It could also be a library of in silico predicted retention times.
 If you want to prepare you own library, have a look at `inst/params/user/prepare_libraries_rt.yaml`, and then:
 
 ```{r rts-2, results="hide", message=FALSE, warning=FALSE}
-targets::tar_make(names = matches("lib_rt"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_rt"))
 ```
 
 #### Structure-Organism Pairs
@@ -171,11 +171,11 @@ As we developed [LOTUS](https://lotusnprod.github.io/lotus-manuscript)^[For more
 we provide it here as a starting point for your structure-organism pairs library.
 
 ```{r get-lotus, results="hide", message=FALSE, warning=FALSE, include = FALSE}
-targets::tar_make(names = matches("lib_sop_lot$"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_lot$"))
 ```
 
 ```{r prepare-lotus-2, results="hide", message=FALSE, warning=FALSE, include = FALSE}
-targets::tar_make(names = matches("lib_sop_lot_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_lot_pre"))
 ```
 
 The process to download LOTUS looks like this:
@@ -186,7 +186,6 @@ targets::tar_visnetwork(
  exclude = c(
  contains("benchmark"),
  ),
- script = system.file("pipelines/_targets.R", package = "tima"),
  targets_only = TRUE,
  degree_from = 8
 )
@@ -201,15 +200,15 @@ If a newer version exists, it will fetch it and re-run needed steps accordingly.
 By default, we also complement LOTUS pairs with the ones coming from [ECMDB](https://ecmdb.ca/).
 
 ```{r prepare-ecmdb-1, results="hide", message=FALSE, warning=FALSE, include = FALSE}
-targets::tar_make(names = matches("lib_sop_ecm_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_ecm_pre"))
 ```
 
 ##### HMDB
 
 And we do the same with the ones coming from [HMDB](https://hmdb.ca/).
 
 ```{r prepare-hmdb, results="hide", message=FALSE, warning=FALSE, include = FALSE}
-targets::tar_make(names = matches("lib_sop_hmd_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_hmd_pre"))
 ```
 
 For these first steps, you do not need to change any parameters as they are implemented *by default*.
@@ -224,15 +223,15 @@ If you need help formatting your library or would like to share it with us for i
 Before running the corresponding code, do not forget to modify `inst/params/user/prepare_libraries_sop_closed.yaml`
 
 ```{r prepare-closed, results="hide", message=FALSE, warning=FALSE}
-targets::tar_make(names = matches("lib_sop_clo_pre"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_clo_pre"))
 ```
 
 ##### Merging
 
 Once all sub-libraries are ready, they are then merged in a single file that will be used for the next steps.
 
 ```{r libraries-sop-1, results="hide", message=FALSE, warning=FALSE, include = FALSE}
-targets::tar_make(names = matches("lib_sop_mer"), script = system.file("pipelines/_targets.R", package = "tima"))
+targets::tar_make(names = matches("lib_sop_mer"))
 ```
 
 ```{r libraries-sop-2, echo=FALSE, message=FALSE, warning=FALSE, out.width="100%"}
@@ -243,7 +242,6 @@ targets::tar_visnetwork(
  contains("par_"),
  contains("paths")
  ),
- script = system.file("pipelines/_targets.R", package = "tima"),
  targets_only = TRUE,
  degree_from = 8
 )