Minor fix in prepartion for CRAN resubmission

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

NEWS.md

@@ -2,8 +2,6 @@
 
 - Added `get_versions()`
 
-# APCalign 1.1.0
-
 - Create a genus->family lookup from the specified APC release 
 
 # APCalign 1.0.2

R/load_taxonomic_resources.R

@@ -411,8 +411,16 @@ default_version <- function() {
   # Pull out versions
   versions <- unique(release_data$tag_name)
 
-  # Exclude Taxonomy: first upload
-  dplyr::first(versions)
+  # Exclude rough semantic versions
+  cleaned_versions <- versions[!grepl("^\\d+\\.\\d+\\.\\d+(\\.\\d+)?$", versions)]
+
+  # Verify only dates left
+  if(! all(grepl("^\\d{4}-\\d{2}-\\d{2}$", cleaned_versions))) 
+    rlang::abort("Inconsistent date formats detected in versions!")
+
+  # Return latest version
+    sort(cleaned_versions, decreasing = TRUE) |> #Sort from most recent to oldest
+    dplyr::first() #  and take the first value after sorting
   }
 }
 

README.Rmd

@@ -95,13 +95,9 @@ get_apc_genus_family_lookup(c("Eucalyptus",
                             resources = tax_resources)
 ```
 
-## Shiny application ✨
-
-We also developed a shiny application for non-R users to update and align their taxonomic names. You can find the application here: https://unsw.shinyapps.io/APCalign-app
-
 ## Cheatsheet
 
-<a href="https://github.com/traitecoevo/APCalign/tree/master/inst/cheatsheet/APCalign-cheatsheet.pdf"><img src="man/figures/APCalign-cheatsheet.png" width="60%"/></a>
+<a href="https://github.com/traitecoevo/APCalign/blob/master/inst/cheatsheet/APCalign-cheatsheet.pdf"><img src="man/figures/APCalign-cheatsheet.png" width="60%"/></a>
 
 ## Learn more 📚
 

README.md

@@ -125,15 +125,9 @@ get_apc_genus_family_lookup(c("Eucalyptus",
 #> 6 Triodia    Poaceae
 ```
 
-## Shiny application ✨
-
-We also developed a shiny application for non-R users to update and
-align their taxonomic names. You can find the application here:
-<https://unsw.shinyapps.io/APCalign-app>
-
 ## Cheatsheet
 
-<a href="https://github.com/traitecoevo/APCalign/tree/master/inst/cheatsheet/APCalign-cheatsheet.pdf"><img src="man/figures/APCalign-cheatsheet.png" width="60%"/></a>
+<a href="https://github.com/traitecoevo/APCalign/blob/master/inst/cheatsheet/APCalign-cheatsheet.pdf"><img src="man/figures/APCalign-cheatsheet.png" width="60%"/></a>
 
 ## Learn more 📚
 
@@ -143,7 +137,7 @@ vignette to learn about how to use `APCalign`. You can also learn more
 about our [taxa matching
 algorithm](https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html).
 
-## Show us support 💚
+## Show us support 💛
 
 Please consider citing our work, we are really proud of it!
 

cran-comments.md

@@ -4,8 +4,6 @@
 
 
 * This is a resubmission
-* More gracefully handling edge cases involving parts of the internet being down
-* Better handling an error in the vignette specific to certain MacOS versions
+* Improved handling for release tag versions from Github API
 * Adding one user function for genus->family lookup
 
-