Replace use of conditionz with lifecycle for depreciation warnings

resolves #908
ropensci · Mar 9, 2023 · b996e9c · b996e9c
1 parent 05b6056
commit b996e9c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -96,7 +96,7 @@ Imports:
     crayon,
     cli,
     phangorn,
-    conditionz
+    lifecycle
 Suggests:
     testthat,
     vegan,

diff --git a/NAMESPACE b/NAMESPACE
@@ -346,7 +346,6 @@ importFrom(bold,bold_tax_name)
 importFrom(cli,cat_line)
 importFrom(cli,rule)
 importFrom(cli,symbol)
-importFrom(conditionz,ConditionKeeper)
 importFrom(crayon,style)
 importFrom(crul,AsyncVaried)
 importFrom(crul,HttpClient)

diff --git a/R/bold_search.R b/R/bold_search.R
@@ -65,8 +65,11 @@
 bold_search <- function(sci = NULL, id = NULL, fuzzy = FALSE,
   dataTypes = 'basic', includeTree=FALSE, response=FALSE, name = NULL, ...) {
 
-  pchk(name, "sci")
-  if (!is.null(name)) sci <- name
+  if (!is.null(name)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "bold_search(name)", with = "bold_search(sci)")
+    sci <- name
+  }
+
   stopifnot(!is.null(sci) | !is.null(id))
   type <- if (is.null(sci)) "id" else "sci"
   tmp <- switch(type,

diff --git a/R/children.R b/R/children.R
@@ -81,8 +81,11 @@ children <- function(...){
 #' @rdname children
 children.default <- function(sci_id, db = NULL, rows = NA, x = NULL, ...) {
   nstop(db)
-  pchk(x, "sci_id")
-  if (!is.null(x)) sci_id <- x
+  if (!is.null(x)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "children(x)", with = "children(sci_id)")
+    sci_id <- x
+  }
+
   results <- switch(
     db,
     itis = {

diff --git a/R/classification.R b/R/classification.R
@@ -228,7 +228,11 @@ classification <- function(...){
 classification.default <- function(sci_id, db = NULL, callopts = list(),
                                    return_id = TRUE, rows = NA, x = NULL, ...) {
   nstop(db)
-  pchk(x, "sci_id")
+  if (!is.null(x)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "classification(x)", with = "classification(sci_id)")
+    sci_id <- x
+  }
+
   switch(
     db,
     itis = {

diff --git a/R/comm2sci.R b/R/comm2sci.R
@@ -63,8 +63,11 @@ comm2sci <- function(...) {
 #' @rdname comm2sci
 comm2sci.default <- function(com, db='ncbi', itisby='search',
                              simplify=TRUE, commnames = NULL, ...) {
-  pchk(commnames, "com")
-  if (!is.null(commnames)) com <- commnames
+  if (!is.null(commnames)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "comm2sci(commnames)", with = "comm2sci(com)")
+    com <- commnames
+  }
+
   assert(com, "character")
   assert(simplify, "logical")
   temp <- lapply(com, sci_from_comm, db = db, simplify = simplify,

diff --git a/R/downstream.R b/R/downstream.R
@@ -115,7 +115,10 @@ downstream.default <- function(sci_id, db=NULL, downto=NULL,
                                intermediate=FALSE, rows=NA, x=NULL, ...) {
   nstop(downto, "downto")
   nstop(db)
-  pchk(x, "sci_id")
+  if (!is.null(x)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "downstream(x)", with = "downstream(sci_id)")
+    sci_id <- x
+  }
   if (!is.null(x)) sci_id <- x
   switch(
     db,

diff --git a/R/eol_search.R b/R/eol_search.R
@@ -40,7 +40,11 @@
 eol_search <- function(sci, page=1, exact=NULL, filter_tid=NULL,
   filter_heid=NULL, filter_by_string=NULL, cache_ttl=NULL, terms = NULL, ...) {
 
-  pchk(terms, "sci")
+  if (!is.null(terms)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "eol_search(terms)", with = "eol_search(sci)")
+    sci = terms
+  }
+
 	query <- gsub("\\s", "+", sci)
   args <- tc(list(q = query, page = page, exact = exact,
                   filter_by_taxon_concept_id = filter_tid,

diff --git a/R/gbif_downstream.R b/R/gbif_downstream.R
@@ -66,9 +66,11 @@
 gbif_downstream <- function(id, downto, intermediate = FALSE, limit = 100,
   start = NULL, key = NULL, ...) {
 
-  pchk(key, "id")
-  if (!is.null(key)) id <- key
-
+  if (!is.null(key)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "gbif_downstream(key)", with = "gbif_downstream(id)")
+    id <- key
+  }
+
   should_be('intermediate', intermediate, 'logical')
 
   downto <- tolower(downto)

diff --git a/R/get_boldid.R b/R/get_boldid.R
@@ -123,7 +123,11 @@ get_boldid <- function(sci, fuzzy = FALSE, dataTypes = 'basic',
   assert(division, "character")
   assert(parent, "character")
   assert_rows(rows)
-  pchk(searchterm, "sci")
+  if (!is.null(searchterm)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_boldid(searchterm)", with = "get_boldid(sci)")
+    sci <- searchterm
+  }
+
 
   if (inherits(sci, "character")) {
     tstate <- taxon_state$new(class = "boldid", names = sci)
@@ -352,7 +356,10 @@ check_boldid <- function(x){
 get_boldid_ <- function(sci, messages = TRUE, fuzzy = FALSE,
   dataTypes='basic', includeTree=FALSE, rows = NA, searchterm = NULL, ...) {
 
-  pchk(searchterm, "sci")
+  if (!is.null(searchterm)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_boldid_(searchterm)", with = "get_boldid_(sci)")
+    sci <- searchterm
+  }
   stats::setNames(lapply(sci, get_boldid_help, messages = messages,
     fuzzy = fuzzy, dataTypes=dataTypes, includeTree=includeTree,
     rows = rows, ...), sci)

diff --git a/R/get_eolid.R b/R/get_eolid.R
@@ -120,7 +120,11 @@ get_eolid <- function(sci_com, ask = TRUE, messages = TRUE,
   assert(rank, "character")
   assert(data_source, "character")
   assert_rows(rows)
-  pchk(sciname, "sci_com")
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_eolid(sciname)", with = "get_eolid(sci_com)")
+    sci_com <- sciname
+  }
+
 
   if (inherits(sci_com, "character")) {
     tstate <- taxon_state$new(class = "eolid", names = sci_com)
@@ -391,7 +395,11 @@ get_eol_pageid <- function(x) {
 #' @rdname get_eolid
 get_eolid_ <- function(sci_com, messages = TRUE, rows = NA, sciname = NULL,
   ...) {
-  pchk(sciname, "sci_com")
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_eolid_(sciname)", with = "get_eolid_(sci_com)")
+    sci_com <- sciname
+  }
+
   stats::setNames(lapply(sci_com, get_eolid_help, messages = messages,
                   rows = rows, ...), sci_com)
 }

diff --git a/R/get_gbifid.R b/R/get_gbifid.R
@@ -140,8 +140,11 @@ get_gbifid <- function(sci, ask = TRUE, messages = TRUE, rows = NA,
   assert(rank, "character")
   assert(method, "character")
   assert_rows(rows)
-  pchk(sciname, "sci")
-
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_gbifid(sciname)", with = "get_gbifid(sci)")
+    sci <- sciname
+  }
+
   if (inherits(sci, "character")) {
     tstate <- taxon_state$new(class = "gbifid", names = sci)
     items <- sci
@@ -323,7 +326,10 @@ check_gbifid <- function(x){
 get_gbifid_ <- function(sci, messages = TRUE, rows = NA, method = "backbone",
   sciname = NULL) {
 
-  pchk(sciname, "sci")
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_gbifid_(sciname)", with = "get_gbifid_(sci)")
+    sci <- sciname
+  }
   stats::setNames(lapply(sci, get_gbifd_help, messages = messages,
     rows = rows, method = method), sci)
 }

diff --git a/R/get_iucn.R b/R/get_iucn.R
@@ -56,7 +56,11 @@ get_iucn <- function(sci, messages = TRUE, key = NULL, x = NULL, ...) {
 
   assert(sci, c("character", "taxon_state"))
   assert(messages, "logical")
-  pchk(x, "sci")
+  if (!is.null(x)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_iucn(x)", with = "get_iucn(sci)")
+    sci <- x
+  }
+
 
   if (inherits(sci, "character")) {
     tstate <- taxon_state$new(class = "iucn", names = sci)

diff --git a/R/get_natservid.R b/R/get_natservid.R
@@ -80,7 +80,11 @@ get_natservid <- function(sci_com, searchtype = "scientific", ask = TRUE,
   assert(ask, "logical")
   assert(messages, "logical")
   assert_rows(rows)
-  pchk(query, "sci_com")
+  if (!is.null(commnames)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_natservid(query)", with = "get_natservid(sci_com)")
+    sci_com <- query
+  }
+
 
   if (inherits(sci_com, "character")) {
     tstate <- taxon_state$new(class = "natservid", names = sci_com)
@@ -266,7 +270,10 @@ check_natservid <- function(x){
 get_natservid_ <- function(sci_com, searchtype = "scientific", messages = TRUE,
   rows = NA, query = NULL, ...) {
 
-  pchk(query, "sci_com")
+  if (!is.null(query)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_natservid_(query)", with = "get_natservid_(sci_com)")
+    sci_com <- query
+  }
   stats::setNames(
     lapply(sci_com, get_natservid_help, searchtype = searchtype,
       messages = messages, rows = rows, ...),

diff --git a/R/get_nbnid.R b/R/get_nbnid.R
@@ -93,8 +93,11 @@ get_nbnid <- function(sci_com, ask = TRUE, messages = TRUE, rec_only = FALSE,
   assert(rank, "character")
   assert(messages, "logical")
   assert_rows(rows)
-  pchk(name, "sci_com")
-
+  if (!is.null(name)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_nbnid(name)", with = "get_nbnid(sci_com)")
+    sci_com <- name
+  }
+
   if (inherits(sci_com, "character")) {
     tstate <- taxon_state$new(class = "nbnid", names = sci_com)
     items <- sci_com
@@ -283,7 +286,10 @@ check_nbnid <- function(x){
 #' @rdname get_nbnid
 get_nbnid_ <- function(sci_com, messages = TRUE, rec_only = FALSE, rank = NULL,
                        rows = NA, name = NULL, ...) {
-  pchk(name, "sci_com")
+  if (!is.null(name)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_nbnid_(name)", with = "get_nbnid_(sci_com)")
+    sci_com <- name
+  }
   stats::setNames(lapply(sci_com, get_nbnid_help, messages = messages,
                   rec_only = rec_only, rank = rank, rows = rows, ...), sci_com)
 }

diff --git a/R/get_pow.R b/R/get_pow.R
@@ -104,8 +104,11 @@ get_pow <- function(sci_com, accepted = FALSE, ask = TRUE, messages = TRUE,
   assert(family_filter, "character")
   assert(rank_filter, "character")
   assert_rows(rows)
-  pchk(x, "sci_com")
-
+  if (!is.null(x)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_pow(x)", with = "get_pow(sci_com)")
+    sci_com <- x
+  }
+
   if (inherits(sci_com, "character")) {
     tstate <- taxon_state$new(class = "pow", names = sci_com)
     items <- sci_com
@@ -286,7 +289,11 @@ check_pow <- function(x){
 #' @export
 #' @rdname get_pow
 get_pow_ <- function(sci_com, messages = TRUE, rows = NA, x = NULL, ...) {
-  pchk(x, "sci_com")
+  if (!is.null(x)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_pow_(x)", with = "get_pow_(sci_com)")
+    sci_com <- x
+  }
+
   stats::setNames(lapply(sci_com, get_pow_help, messages = messages,
     rows = rows, ...), sci_com)
 }

diff --git a/R/get_tolid.R b/R/get_tolid.R
@@ -73,7 +73,11 @@ get_tolid <- function(sci, ask = TRUE, messages = TRUE, rows = NA,
   assert(sci, c("character", "taxon_state"))
   assert(ask, "logical")
   assert(messages, "logical")
-  pchk(sciname, "sci")
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tolid(sciname)", with = "get_tolid(sci)")
+    sci <- sciname
+  }
+
   if (!all(is.na(rows))) {
     assert(rows, c("numeric", "integer"))
     stopifnot(rows > 0)
@@ -254,7 +258,10 @@ check_tolid <- function(x){
 #' @export
 #' @rdname get_tolid
 get_tolid_ <- function(sci, messages = TRUE, rows = NA, sciname = NULL) {
-  pchk(sciname, "sci")
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tolid_(sciname)", with = "get_tolid_(sci)")
+    sci <- sciname
+  }
   stats::setNames(
     lapply(sci, get_tolid_help, messages = messages, rows = rows),
     sci

diff --git a/R/get_tpsid.R b/R/get_tpsid.R
@@ -106,11 +106,14 @@ get_tpsid <- function(sci, ask = TRUE, messages = TRUE, key = NULL,
 
   assert(sci, c("character", "taxon_state"))
   assert(ask, "logical")
-  assert(messages, "logical")
   assert(family, "character")
   assert(rank, "character")
   assert_rows(rows)
-  pchk(sciname, "sci")
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tpsid(sciname)", with = "get_tpsid(sci)")
+    sci <- sciname
+  }
+
 
   if (inherits(sci, "character")) {
     tstate <- taxon_state$new(class = "tpsid", names = sci)
@@ -283,7 +286,10 @@ check_tpsid <- function(x){
 get_tpsid_ <- function(sci, messages = TRUE, key = NULL, rows = NA,
   sciname = NULL, ...) {
 
-  pchk(sciname, "sci")
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tpsid_(sciname)", with = "get_tpsid_(sci)")
+    sci <- sciname
+  }
   stats::setNames(lapply(sci, get_tpsid_help, messages = messages, key=key,
     rows = rows, ...), sci)
 }

diff --git a/R/get_tsn.R b/R/get_tsn.R
@@ -83,7 +83,11 @@ get_tsn <- function(sci_com, searchtype = "scientific", accepted = FALSE,
   assert(searchtype, "character")
   assert(accepted, "logical")
   assert_rows(rows)
-  pchk(searchterm, "sci_com")
+  if (!is.null(searchterm)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tsn(searchterm)", with = "get_tsn(sci_com)")
+    sci_com <- searchterm
+  }
+
 
   if (inherits(sci_com, "character")) {
     tstate <- taxon_state$new(class = "tsn", names = sci_com)
@@ -269,7 +273,11 @@ check_tsn <- function(x){
 #' @rdname get_tsn
 get_tsn_ <- function(sci_com, messages = TRUE, searchtype = "scientific",
                      accepted = TRUE, rows = NA, searchterm = NULL, ...) {
-  pchk(searchterm, "sci_com")
+  if (!is.null(searchterm)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tsn_(searchterm)", with = "get_tsn_(sci_com)")
+    sci_com <- searchterm
+  }
+
   stats::setNames(
     lapply(sci_com, get_tsn_help, messages = messages,
            searchtype = searchtype, accepted = accepted, rows = rows, ...),

diff --git a/R/get_uid.R b/R/get_uid.R
@@ -174,7 +174,11 @@ get_uid <- function(sci_com, ask = TRUE, messages = TRUE, rows = NA,
   assert(rank_filter, "character")
   assert_rows(rows)
   key <- getkey(key, service = "entrez")
-  pchk(sciname, "sci_com")
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_uid(sciname)", with = "get_uid(sci_com)")
+    sci_com <- sciname
+  }
+
 
   if (inherits(sci_com, "character")) {
     tstate <- taxon_state$new(class = "uid", names = sci_com)
@@ -406,7 +410,11 @@ get_uid_ <- function(sci_com, messages = TRUE, rows = NA, key = NULL,
   sciname = NULL, ...) {
 
   key <- getkey(key, "ENTREZ_KEY")
-  pchk(sciname, "sci_com")
+  if (!is.null(sciname)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_uid_(sciname)", with = "get_uid_(sci_com)")
+    sci_com <- sciname
+  }
+
   stats::setNames(lapply(sci_com, get_uid_help, messages = messages,
     rows = rows, key = key, ...), sci_com)
 }

diff --git a/R/get_wiki.R b/R/get_wiki.R
@@ -56,7 +56,11 @@ get_wiki <- function(sci_com, wiki_site = "species", wiki = "en", ask = TRUE,
   assert(wiki, "character")
   assert(messages, "logical")
   assert_rows(rows)
-  pchk(x, "sci_com")
+  if (!is.null(x)) {
+    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_wiki(x)", with = "get_wiki(sci_com)")
+    sci_com <- x
+  }
+
 
   if (inherits(sci_com, "character")) {
     tstate <- taxon_state$new(class = "wiki", names = sci_com)