Version 1.0.0 (#227)

First major release of APCalign. A preprint is available at https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1. Article has been accepted for publication at Australian Journal of Botany. Following review, a number of changes have been implemented. These have sped & streamlined the package. * Update function documentation * Speed up `extract_genus` * Write a replacement function for `stringr::word` that is much faster. * Additional speed up and accuracy of `fuzzy_match` function by - Restricting reference list to names with the same first letter as input string. - Switch from using `utils::adist` to `stringdist:stringdist(method = "dl")` * Rework `standardise_names` to remove punctuation from the start of the string * Rework `strip_names_extra` (previously `strip_names_2`) to just perform additional functions to `strip_names`, rather than repeating those performed by `strip_names`. * Avoid importing entire packages by using package::function format throughout and removing functions from @import * Add fuzzy match arguments to `create_taxonomic_update_lookup` * Add 3 additional family-level APC matches to `match_taxa`. * Refine tests * Make messages to console optional * Fix issue with fails when github is down (#205) --------- Co-authored-by: Elizabeth Wenk <ehwenk@gmail.com> Co-authored-by: Fonti Kar <f.kar@unsw.edu.au> Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au> Co-authored-by: Will Cornwell <w.cornwell@unsw.edu.au>
traitecoevo · May 6, 2024 · 6bc7e1f · 6bc7e1f
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, develop]
   pull_request:
     branches: [main, master, develop]
 
@@ -18,17 +18,16 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -45,4 +44,5 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          upload-snapshots: true
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, develop]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, develop]
 
 name: test-coverage
 
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -27,5 +27,24 @@ jobs:
           needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
         shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: APCalign
 Title: Resolving Plant Taxon Names Using the Australian Plant Census
-Version: 0.1.4
+Version: 1.0.0
 Authors@R: c(
   person(given = "Daniel", family = "Falster", role = c("aut", "cre", "cph"), email = "daniel.falster@unsw.edu.au", comment = c(ORCID = "0000-0002-9814-092X")),
   person(given = "Elizabeth", family = "Wenk", role = c("aut", "ctb"), email = "e.wenk@unsw.edu.au", comment = c(ORCID = "0000-0001-5640-5910")),
@@ -18,11 +18,10 @@ Depends:
 Imports:
     readr,
     purrr,
-    forcats,
-    tibble,
     dplyr,
     stringr,
     stringi,
+    stringdist,
     crayon,
     httr,
     jsonlite,
@@ -38,9 +37,8 @@ Suggests:
     kableExtra,
     here,
     testthat (>= 3.0.0)
-Remotes: apache/arrow/r
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 URL: https://traitecoevo.github.io/APCalign/, https://github.com/traitecoevo/APCalign

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,23 +3,13 @@
 export(align_taxa)
 export(create_species_state_origin_matrix)
 export(create_taxonomic_update_lookup)
+export(default_version)
 export(load_taxonomic_resources)
 export(native_anywhere_in_australia)
 export(standardise_names)
+export(standardise_taxon_rank)
 export(state_diversity_counts)
 export(strip_names)
-export(strip_names_2)
+export(strip_names_extra)
 export(update_taxonomy)
-import(dplyr)
-import(stringr)
-importFrom(crayon,red)
-importFrom(dplyr,arrange)
-importFrom(dplyr,distinct)
-importFrom(dplyr,filter)
-importFrom(dplyr,mutate)
-importFrom(dplyr,select)
-importFrom(readr,col_character)
-importFrom(readr,col_logical)
-importFrom(readr,cols)
-importFrom(readr,read_csv)
-importFrom(tibble,tibble)
+importFrom(dplyr,"%>%")
diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,37 @@
-# APCalign 0.1.4
+# APCalign 1.0.0
 
+First major release of APCalign.  A preprint is available at 
+https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1. 
+Article has been accepted for publication at Australian journal of Botany.
 
-* Better handling of errors when API/network connection is down for `load_taxonomic_resources` 
+Following review, a number of changes have been implemented. These have sped & 
+streamlined the package.
 
-* Refined testing for `load_taxonomic_resources` 
+* Update function documentation
+* Speed up `extract_genus`
+* Write a replacement function for `stringr::word` that is much faster.
+* Additional speed up and accuracy of fuzzy_match function by
+  - Restricting reference list to names with the same first letter as input string.
+  - Switch from using `utils::adist` to `stringdist:stringdist(method = "dl")`
+* Rework `standardise_names` to remove punctuation from the start of the string
+* Rework `strip_names_extra` (previously `strip_names_2`) to just perform 
+additional functions to `strip_names`, rather than repeating those performed by `strip_names`.
+* Avoid importing entire packages by using package::function format throughout 
+and removing functions from @import
+* Add fuzzy match arguments to `create_taxonomic_update_lookup`
+* Add 3 additional family-level APC matches to `match_taxa`.
+* Refine tests
+* Make messages to console optional
+* Fix issue with fails when github is down (https://github.com/traitecoevo/APCalign/issues/205)
 
+# APCalign 0.1.5
 
 
+* Update installation instructions 
+* Added how to cite and version APCalign as an article
+* Exported `default_version`
+* Add citing method for R package
+* Update GitHub Actions
+* Improved family alignments 
+* Added `standardise_taxon_rank`
+* Improved messaging during alignment
diff --git a/R/APCalign-package.R b/R/APCalign-package.R
@@ -10,7 +10,8 @@
 #' @name APCalign
 #' @docType package
 #' @references If you have any questions, comments or suggestions, please
-#' submit an issue at our [GitHub repository](https://github.com/traitecoevo/APCalign/issues)
+#' submit an issue at our 
+#' [GitHub repository](https://github.com/traitecoevo/APCalign/issues)
 #' @keywords internal
 #' @section Functions:
 #' **Standarise taxon names**
@@ -51,9 +52,12 @@ utils::globalVariables(
     "checked",
     "cleaned_name",
     "family",
+    "family_accepted",
     "fuzzy_match_genus",
     "fuzzy_match_genus_APNI",
     "fuzzy_match_genus_synonym",
+    "fuzzy_match_family",
+    "fuzzy_match_family_synonym",
     "genus",
     "genus_accepted",
     "known",
@@ -75,6 +79,8 @@ utils::globalVariables(
     "taxon_ID",
     "taxon_ID_aligned",
     "taxon_rank",
+    "txtProgressBar",
+    "setTxtProgressBar",
     "taxonomic_status",
     "taxonomic_status_aligned",
     "taxonomic_status_genus",