From 9d597ccc491f32a5e84bed70db6dcd241dd52fd3 Mon Sep 17 00:00:00 2001
From: ehwenk <ehwenk@gmail.com>
Date: Tue, 23 Apr 2024 12:42:44 +1000
Subject: [PATCH 1/2] Update align_taxa.R

Add message that indicates how many taxa have perfect matches to APC.
---
 R/align_taxa.R | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/R/align_taxa.R b/R/align_taxa.R
index 5a6d409b..83d32f6c 100644
--- a/R/align_taxa.R
+++ b/R/align_taxa.R
@@ -165,6 +165,7 @@ align_taxa <- function(original_name,
   # move all checked taxa to "checked"
   taxa <- redistribute(taxa)
   
+  # messages if there is an saved list being added to
   if (!is.null(output) && file.exists(output) && !all(taxa$tocheck$checked)) {
   # check unknown taxa
   message(
@@ -180,6 +181,23 @@ align_taxa <- function(original_name,
     " taxa yet to be checked"
   )
   }
+
+  # otherwise if there are taxa that require checking add 
+  # simple message that indicates number of perfect matches.
+  if (!all(taxa$tocheck$checked)) {
+
+  perfect_matches <- taxa$tocheck %>%
+    filter(original_name %in% resources$`APC list (accepted)`$canonical_name) %>%
+    distinct() %>%
+    nrow()
+
+  message(
+    "  -> of these ",
+    crayon::blue(perfect_matches),
+    " names have a perfect match to a scientific name in the APC. Alignments being sought for remaining names."
+  )
+  }
+
   # do the actual matching
   taxa <- 
     match_taxa(taxa, resources, fuzzy_abs_dist, fuzzy_rel_dist, fuzzy_matches, imprecise_fuzzy_matches, APNI_matches, identifier) %>%

From bc163920e6747a2918151746e9e05a11d77c9b70 Mon Sep 17 00:00:00 2001
From: ehwenk <ehwenk@gmail.com>
Date: Tue, 23 Apr 2024 14:04:59 +1000
Subject: [PATCH 2/2] update documentation

---
 man/download_taxonomic_resources_for_release.Rd | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 man/download_taxonomic_resources_for_release.Rd

diff --git a/man/download_taxonomic_resources_for_release.Rd b/man/download_taxonomic_resources_for_release.Rd
new file mode 100644
index 00000000..d4a94a65
--- /dev/null
+++ b/man/download_taxonomic_resources_for_release.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/release.R
+\name{download_taxonomic_resources_for_release}
+\alias{download_taxonomic_resources_for_release}
+\title{Download taxonomic resources for GitHub Release}
+\usage{
+download_taxonomic_resources_for_release(version_name = NULL, path = "ignore/")
+}
+\arguments{
+\item{version_name}{character string of version name, follow semantic versioning}
+
+\item{path}{to download parquets to upload}
+}
+\description{
+Download taxonomic resources for GitHub Release
+}
+\keyword{internal}