chore: upgrade actions/upload-artifact to v3 (#391)

Author: alldoami

.github/workflows/short-read-mngs-viral-benchmarks.yml

@@ -71,7 +71,7 @@ jobs:
           taxadb create -i taxadb --dbname taxadb.sqlite || true  # exits nonzero w/o accessions
           workflows/short-read-mngs/auto_benchmark/harvest.py ${{ matrix.sample }}=testrun/${{ matrix.sample }} \
             --taxadb taxadb.sqlite > ${{ matrix.sample }}.${{ matrix.settings }}_viral.json
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: ${{ matrix.sample }}.${{ matrix.settings }}_viral.json
           path: ${{ matrix.sample }}.${{ matrix.settings }}_viral.json
@@ -120,11 +120,11 @@ jobs:
           cp -r workflows/short-read-mngs/auto_benchmark/ref_libs/${{ matrix.settings }}_viral ref_libs/
       - name: test harvest2.py
         run: workflows/short-read-mngs/auto_benchmark/harvest2.py *_viral.json --version "$(git describe --long --tags --always --dirty)" --index-version 2021-01-22 --wall 999
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: short-read-mngs-benchmarks.${{ matrix.settings }}_viral.html
           path: short-read-mngs-benchmarks.${{ matrix.settings }}_viral.html
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: short-read-mngs-benchmarks.${{ matrix.settings }}_viral.ipynb
           path: |