fixes

.github/prehooks/pre-commit

@@ -23,7 +23,7 @@ echo ""
 
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-echo ">> Updating semantic versioning and date..."
+echo "Updating semantic versioning and date..."
 
 # get tags from remote, and remove tags not on remote:
 git fetch origin --prune --prune-tags --quiet
@@ -31,7 +31,7 @@ currenttagfull=`git describe --tags --abbrev=0`
 currenttag=`git describe --tags --abbrev=0 | sed 's/v//'`
 if [ "$currenttag" = "" ]; then
   # there is no tag, so set tag to 0.0.1 and commit index to current count
-  echo ">>  - no git tags found, create one in this format: 'v(x).(y).(z)'!"
+  echo "- no git tags found, create one in this format: 'v(x).(y).(z)'!"
   currenttag="0.0.1"
   currentcommit=`git rev-list --count HEAD`
 else
@@ -41,18 +41,18 @@ else
     # tag is new, so this must become the version number
     currentversion="$currenttag"
   fi
-  echo ">>  - latest tag is '${currenttagfull}', with ${currentcommit} previous commits"
+  echo "- latest tag is '${currenttagfull}', with ${currentcommit} previous commits"
 fi
 if [ "$currentversion" = "" ]; then
   # combine tag (e.g. 1.2.3) and commit number (like 5) increased by 9000 to indicate beta version
   currentversion="$currenttag.$((currentcommit + 9001))" # results in e.g. 1.2.3.9005
 fi
-echo ">>  - ${currentpkg} pkg version set to ${currentversion}"
+echo "- ${currentpkg} pkg version set to ${currentversion}"
 
 # set version number and date to DESCRIPTION file
 sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
 sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
-echo ">>  - updated DESCRIPTION"
+echo "- updated DESCRIPTION"
 # remove leftover on macOS
 rm -f DESCRIPTION--
 # add to commit
@@ -64,12 +64,12 @@ if [ -e "NEWS.md" ]; then
     currentpkg=""
   fi
   sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
-  echo ">>  - updated NEWS.md"
+  echo "- updated NEWS.md"
   # remove leftover on macOS
   rm -f NEWS.md--
   # add to commit
   git add NEWS.md
 else
-  echo ">>  - no NEWS.md found!"
+  echo "- no NEWS.md found!"
 fi
-echo ">>  "
+echo ""

.github/workflows/check-pr.yaml

@@ -33,7 +33,7 @@ name: R-code-check-PR
 jobs:
   R-code-check-PR:
     # do not run if we are the authors - the other checks will already run
-    if: ${{ github.event.comment.author_association != 'MEMBER' && github.event.comment.author_association != 'OWNER' }}
+    if: ${{ github.event.comment.author_association }} != 'MEMBER' && ${{ github.event.comment.author_association }} != 'OWNER'
     
     runs-on: ${{ matrix.config.os }}
 

.github/workflows/check.yaml

@@ -159,15 +159,7 @@ jobs:
           echo "---"
           ls ${GITHUB_WORKSPACE}
           echo "---"
-          ls ../${GITHUB_WORKSPACE}
+          ls ${GITHUB_WORKSPACE}.Rcheck
-          echo "---"
-          ls ../${GITHUB_WORKSPACE}/AMR
-          echo "---"
-          ls ../${GITHUB_WORKSPACE}/AMR.Rcheck
-          echo "---"
-          ls ${GITHUB_WORKSPACE}/AMR
-          echo "---"
-          ls ${GITHUB_WORKSPACE}/AMR.Rcheck
 
       - name: Upload artifacts
         if: always()

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9063
+Version: 1.8.1.9064
 Date: 2022-09-23
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.1.9063
+# AMR 1.8.1.9064
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 

data-raw/microorganisms.md5

@@ -1 +1 @@
-004b36b27ef78bc03cd12cca3794126e
+5ac1152c166d5d4f5763547d948fce79

inst/tinytest/test-mo_property.R

@@ -103,9 +103,13 @@ expect_identical(
   mo_species("Escherichia coli")
 )
 expect_identical(
-  mo_property("Escherichia coli", property = "species_id"),
+  mo_property("Escherichia coli", property = "lpsn"),
   mo_lpsn("Escherichia coli")
 )
+expect_identical(
+  mo_property("Escherichia coli", property = "gbif"),
+  mo_gbif("Escherichia coli")
+)
 
 expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
 expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")

tests/tinytest.R

@@ -36,7 +36,10 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
     library(AMR)
     # set language
     set_AMR_locale("English")
-    # get trimws() and strrep() if on old R
+    # get dir.exists(), trimws() and strrep() if on old R
+    if (getRversion() < "3.2.0") {
+      dir.exists <- AMR:::dir.exists
+    }
     if (getRversion() < "3.3.0") {
       trimws <- AMR:::trimws
       strrep <- AMR:::strrep