Merge pull request #7 from globalbioticinteractions/master

add indexing GloBI configuration

.github/workflows/review.yml

@@ -0,0 +1,41 @@
+# This workflow will review a GloBI indexed dataset.
+# For more information see: https://globalbioticinteractions.org
+
+name: GloBI review by Elton
+
+on:
+  push:
+    branches: [ '*' ]
+  pull_request:
+    branches: [ '*' ]
+  schedule:
+    - cron: "0 0 * * 1"
+
+jobs:
+  review:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '8'
+      - name: download review script
+        run: curl --silent -L "https://raw.githubusercontent.com/globalbioticinteractions/globinizer/master/check-dataset.sh" > check-dataset.sh
+      - name: download network compiler script
+        run: |
+          curl --silent -L "https://raw.githubusercontent.com/globalbioticinteractions/globinizer/master/compile-network.sh" > compile-network.sh
+          chmod +x compile-network.sh
+      - name: review dataset
+        run: bash check-dataset.sh "${GITHUB_REPOSITORY}"
+      - name: Share review report
+        uses: actions/upload-artifact@v4
+        with:
+          name: review-report
+          path: |
+            README.txt
+            datasets/
+            index.*
+            indexed-*
+            review*

.gitignore

@@ -1,30 +1,3 @@
-# History files
-.Rhistory
-.Rapp.history
-# Session Data files
-.RData
-# Example code in package build process
-*-Ex.R
-# Output files from R CMD build
-/*.tar.gz
-# Output files from R CMD check
-/*.Rcheck/
-# RStudio files
-.Rproj.user/
-# produced vignettes
-vignettes/*.html
-vignettes/*.pdf
-# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
-.httr-oauth
-# knitr and R markdown default cache directories
-/*_cache/
-/cache/
-# Temporary files created by R markdown
-*.utf8.md
-*.knit.md
-#Custom view
-.DS_Store
-Thumbs.db
-OBservData.Rproj
-#Embargo Folder
-Processing_files/Datasets_Processing/Embargo/
+.elton/
+add_travis_artifact_upload_keys.sh
+datasets/

README.md

@@ -41,3 +41,10 @@ Please let us know in an [issue](https://github.com/ibartomeus/OBservData/issues
 
 We started using livedat **Template Repo** designed to assist in setting up a repository for regularly-updated data. Details in [this PLOS Biology paper](https://doi.org/10.1371/journal.pbio.3000125). Instructions for creating an updating data workflow can be found at this companion website: [UpdatingData.org](https://www.updatingdata.org/).  
 
+## Indexing
+
+[![GloBI Review by Elton](../../actions/workflows/review.yml/badge.svg)](../../actions/workflows/review.yml) [![GloBI](https://api.globalbioticinteractions.org/interaction.svg?accordingTo=globi:ibartomeus/OBservData&refutes=true&refutes=false)](https://globalbioticinteractions.org/?accordingTo=globi:ibartomeus/OBservData)
+
+Configuration to help Global Biotic Interactions (GloBI, https://globalbioticinteractions.org) index: 
+
+Allen-Perkins, Alfonso, Magrach, Ainhoa, Dainese, Matteo, Garibaldi, Lucas A., Kleijn, David, Rader, Romina, Reilly, James R., et al. 2022. “ CropPol: A Dynamic, Open and Global Database on Crop Pollination.” Ecology 103(3): e3614. https://doi.org/10.1002/ecy.3614