Update ASReview Makita from 0.10.x to 1.0.x

.github/workflows/ci-workflow.yml

@@ -27,33 +27,20 @@ jobs:
     - name: Lint python with ruff
       run: |
         ruff check .
-    - name: Create directories using Python
-      run: python -c "import os; [os.makedirs(path, exist_ok=True) for path in ['./tmp/basic/data-test', './tmp/arfi/data', './tmp/prior/data', './tmp/multimodel/data', './tmp/scripts', './tmp/synergy/data']]"
-    - name: set up environment
-      run: |
-        cp .github/workflows/test_data/labels.csv ./tmp/basic/data-test/labels.csv
-        cp .github/workflows/test_data/labels.csv ./tmp/arfi/data/labels.csv
-        cp .github/workflows/test_data/labels.csv ./tmp/prior/data/labels.csv
-        cp .github/workflows/test_data/labels.csv ./tmp/prior/data/prior_labels.csv
-        cp .github/workflows/test_data/labels.csv ./tmp/multimodel/data/labels.csv
     - name: Render makita templates
       run: |
-        cd tmp/basic
-        asreview makita template basic --classifier nb --feature_extractor tfidf --query_strategy max --n_runs 1 -s data-test -o output-test --init_seed 1 --model_seed 2 --skip_wordclouds --overwrite --instances_per_query 2 --stop_if min --balance_strategy double | tee output.txt
-        grep -q "ERROR" output.txt && exit 1 || true
-        cd ../arfi
-        asreview makita template arfi | tee output.txt
-        grep -q "ERROR" output.txt && exit 1 || true
-        cd ../prior
-        asreview makita template prior | tee output.txt
-        grep -q "ERROR" output.txt && exit 1 || true
-        cd ../multimodel
-        asreview makita template multimodel | tee output.txt
-        grep -q "ERROR" output.txt && exit 1 || true
+        asreview makita template basic -p basic -d .github/workflows/test_data/ --classifier nb --feature_extractor tfidf --query_strategy max --n_runs 1 --init_seed 1 --model_seed 2 --skip_wordclouds --overwrite --instances_per_query 2 --stop_if min --balance_strategy double | tee output_basic.txt
+        grep -q "ERROR" output_basic.txt && exit 1 || true
+        asreview makita template arfi -p arfi -d .github/workflows/test_data/ | tee output_arfi.txt
+        grep -q "ERROR" output_arfi.txt && exit 1 || true
+        asreview makita template prior -p prior -d .github/workflows/test_data/ | tee output_prior.txt
+        grep -q "ERROR" output_prior.txt && exit 1 || true
+        asreview makita template multimodel -p multimodel -d .github/workflows/test_data/ | tee output_multimodel.txt
+        grep -q "ERROR" output_multimodel.txt && exit 1 || true
     - name: Render makita scripts
       run: |
-        asreview makita add-script --all -o ./tmp/scripts | tee output.txt
-        grep -q "ERROR" output.txt && exit 1 || true
+        asreview makita add-script --all -o ./tmp/scripts | tee output_scripts.txt
+        grep -q "ERROR" output_scripts.txt && exit 1 || true
     - name: Run SciTree
       if: ${{ matrix.os != 'windows-latest' }}
       run: |
@@ -62,8 +49,20 @@ jobs:
     - name: Execute basic template jobs file
       if: ${{ matrix.os != 'windows-latest' }}
       run: |
-        cd tmp/synergy
-        synergy_dataset get -d van_de_Schoot_2018 -o ./data -l
-        asreview makita template basic --instances_per_query 100 --skip_wordclouds --overwrite --n_runs 2
+        mkdir basic_run
+        cd basic_run
+        asreview makita template basic -d ../.github/workflows/test_data/ --instances_per_query 100 --skip_wordclouds --overwrite --n_runs 1
+        scitree
         sh jobs.sh
         scitree
+    - name: Upload output files
+      if: always()
+      uses: actions/upload-artifact@v3
+      with:
+        name: output-files
+        path: |
+          output_basic.txt
+          output_arfi.txt
+          output_prior.txt
+          output_multimodel.txt
+          output_scripts.txt

.github/workflows/create-examples.yml

@@ -0,0 +1,56 @@
+name: Update Examples
+
+on:
+  push:
+    branches:
+      - v.1.0.x
+      - main
+
+jobs:
+  update-examples:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Set up Python environment
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          pip install .
+
+      # Generate examples
+      - name: Generate examples
+        run: |
+          synergy_dataset get -d van_de_Schoot_2018 Smid_2020 -o examples/data -l
+          mv ./examples/data/Smid_2020.csv ./examples/data/prior_Smid_2020.csv
+          ls ./examples/data
+          asreview makita template arfi -d ./examples/data -p ./examples/arfi_example --overwrite --platform linux
+          asreview makita template basic -d ./examples/data -p ./examples/basic_example --overwrite --platform linux
+          asreview makita template multimodel -d./examples/data -p ./examples/multimodel_example --overwrite --platform linux
+          asreview makita template prior -d./examples/data -p ./examples/prior_example --overwrite --platform linux
+
+      # Clean up data files (e.g., CSV, XLSX) to avoid committing them
+      - name: Clean up data files
+        run: |
+          find ./examples -type f -name "*.csv" -delete
+
+      # Check for changes, commit, and push
+      - name: Commit and push changes if any
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          if ! git diff --quiet; then
+            echo "Changes detected. Committing and pushing."
+            git add -A
+            git commit -m "Update examples"
+            git push
+          else
+            echo "No changes detected. Skipping commit and push."
+          fi

.github/workflows/test_data/labels.csv

@@ -1,5 +1,9 @@
 Unnamed: 0,abstract,alternate_title2,alternate_title3,file_attachments2,authors,id,issn,keywords,note,number,place_published,title,publication_year,publisher,secondary_authors,start_page,type_of_reference,label_included,url,volume
 0,"BACKGROUND: Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.  RESULTS: Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. CONCLUSIONS: Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium.",lorem,Lorem,http://example.com,"['Marx, Karl', 'Lindgren, Astrid']",12345,1932-6208,"['Pippi', 'Nordwind', 'Piraten']",1008150341,3,United States,Title of reference,2014//,Fun Factory,"['Glattauer, Daniel']",e0815,JOUR,1,http://example_url.com,9
+0,"BACKGROUND: Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.  RESULTS: Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. CONCLUSIONS: Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium.",lorem,Lorem,http://example.com,"['Marx, Karl', 'Lindgren, Astrid']",12345,1932-6208,"['Pippi', 'Nordwind', 'Piraten']",1008150341,3,United States,Title of reference,2014//,Fun Factory,"['Glattauer, Daniel']",e0815,JOUR,1,http://example_url.com,9
+0,"BACKGROUND: Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.  RESULTS: Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. CONCLUSIONS: Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium.",lorem,Lorem,http://example.com,"['Marx, Karl', 'Lindgren, Astrid']",12345,1932-6208,"['Pippi', 'Nordwind', 'Piraten']",1008150341,3,United States,Title of reference,2014//,Fun Factory,"['Glattauer, Daniel']",e0815,JOUR,1,http://example_url.com,9
+0,"BACKGROUND: Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.  RESULTS: Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. CONCLUSIONS: Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium.",lorem,Lorem,http://example.com,"['Marx, Karl', 'Lindgren, Astrid']",12345,1932-6208,"['Pippi', 'Nordwind', 'Piraten']",1008150341,3,United States,Title of reference,2014//,Fun Factory,"['Glattauer, Daniel']",e0815,JOUR,1,http://example_url.com,9
+0,"BACKGROUND: Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.  RESULTS: Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. CONCLUSIONS: Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium.",lorem,Lorem,http://example.com,"['Marx, Karl', 'Lindgren, Astrid']",12345,1932-6208,"['Pippi', 'Nordwind', 'Piraten']",1008150341,3,United States,Title of reference,2014//,Fun Factory,"['Glattauer, Daniel']",e0815,JOUR,1,http://example_url.com,9
 1,"BACKGROUND: Lorem dammed ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.  RESULTS: Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. CONCLUSIONS: Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium.",lorem,Lorem,http://example2.com,"['Marxus, Karlus', 'Lindgren, Astrid']",12345,1732-4208,"['Pippi Langstrumpf', 'Nordwind', 'Piraten']",1228150341,3,Germany,The title of the reference,2006//,Dark Factory,"['Glattauer, Daniel']",e0815341,JOUR,0,http://example_url.com,6
 1,"BACKGROUND: Lorem dammed ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.  RESULTS: Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. CONCLUSIONS: Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium.",lorem,Lorem,http://example2.com,"['Marxus, Karlus', 'Lindgren, Astrid']",12345,1732-4208,"['Pippi Langstrumpf', 'Nordwind', 'Piraten']",1228150341,3,Germany,The title of the reference,2006//,Dark Factory,"['Glattauer, Daniel']",e0815341,JOUR,0,http://example_url.com,6
 1,"BACKGROUND: Lorem dammed ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.  RESULTS: Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. CONCLUSIONS: Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium.",lorem,Lorem,http://example2.com,"['Marxus, Karlus', 'Lindgren, Astrid']",12345,1732-4208,"['Pippi Langstrumpf', 'Nordwind', 'Piraten']",1228150341,3,Germany,The title of the reference,2006//,Dark Factory,"['Glattauer, Daniel']",e0815341,JOUR,0,http://example_url.com,6