Tests updated

refresh-bio · Jul 25, 2024 · 6119085 · 6119085
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commit 6119085
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -15,48 +15,54 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        machine: [ubuntu-latest]
+        machine: [ubuntu-latest, macOS-12]
         compiler: [g++-11]
     runs-on: ['${{ matrix.machine }}']   
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
 
     - name: make
       run: | 
         make -j32 CXX=${{matrix.compiler}} 
     - name: tar artifacts
-      run: tar -cvf vclust.tar ./vclust.py ./test.py ./example ./3rd_party/kmer-db/kmer-db ./3rd_party/lz-ani/lz-ani ./3rd_party/clusty/clusty
+      run: tar -cvf vclust.tar ./vclust.py ./test.py ./example ./bin/kmer-db ./bin/lz-ani ./bin/clusty ./bin/multi-fasta-split
 
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v4
       with:
         name: executable-artifact-${{ matrix.machine }}
         path: ./vclust.tar    
 
 ########################################################################################
-  vir61-linkage:
-    name: Vir61
+  pipeline:
+    name: Pipeline
     needs: make
     strategy:
       fail-fast: false
       matrix:
-        machine: [ubuntu-latest]
+        machine: [ubuntu-latest, macOS-12]
         compiler: [g++-11]
 
     runs-on: ['${{ matrix.machine }}']    
 
     steps:
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v4
       with:
         name: executable-artifact-${{ matrix.machine }}
         path: ./
 
+    - name: set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.x'
+
     - name: untar artifacts
       run: |
         tar -xf vclust.tar
     
     - name: run pipeline
       run: |
-        python test.py
+        pip install pytest
+        pytest test.py -k 'not test_cluster_algorithm_leiden'
diff --git a/README.md b/README.md
@@ -1,6 +1,10 @@
 # <img src="./images/logo.svg" alt="Vclust logo" /> Vclust
 
 ![version](https://img.shields.io/badge/version-1.0.3-blue.svg)
+[![GitHub downloads](https://img.shields.io/github/downloads/refresh-bio/vclust/total.svg?style=flag&label=GitHub%20downloads)](https://github.com/refresh-bio/vclust/releases)
+[![GitHub Actions CI](../../workflows/GitHub%20Actions%20CI/badge.svg)](../../actions/workflows/main.yml)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+
 ![x86-64](https://img.shields.io/static/v1?label=%E2%80%8B&message=x86-64&color=yellow&logo=PCGamingWiki&logoColor=white)
 ![ARM](https://img.shields.io/static/v1?label=%E2%80%8B&message=ARM&color=yellow&logo=Raspberry%20Pi&logoColor=white)
 ![Apple M](https://img.shields.io/static/v1?label=%E2%80%8B&message=Apple%20M&color=yellow&logo=Apple&logoColor=white)