integrate dev branch and update software environments

.github/workflows/benchmark.yml

@@ -18,7 +18,6 @@ jobs:
   run-benchmark:
     name: Run Benchmark
     runs-on: ubuntu-latest
-    ## runs-on: self-hosted
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
@@ -49,27 +48,26 @@ jobs:
         shell: bash -l {0}
         run: |
           mamba install -y pip
-          pip install git+https://github.com/omnibenchmark/omnibenchmark.git@reduce_install_scope
+          pip install git+https://github.com/omnibenchmark/omnibenchmark.git@main
 
       - name: Load benchmark cache
         id: cache-benchmark
         uses: actions/cache@v3
         with:
           path: out/
-          key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}
+          key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering_conda_short.yml') }}
 
       - name: Run benchmark
         shell: bash -l {0}
-        continue-on-error: true
+        continue-on-error: false
         run: |
-          echo "y" | ob run benchmark -b Clustering.yaml --local --cores 3 --continue-on-error
+          ob run benchmark -b Clustering_conda_short.yml --local --cores 3 --continue-on-error --yes
 
   upload-artifact:
     name: Benchmark Artifact
     runs-on: ubuntu-latest
-    ## runs-on: self-hosted
     needs: run-benchmark
-    if: always()
+    if: github.ref == 'refs/heads/main' && github.repository_owner == 'omnibenchmark'
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
@@ -100,12 +98,11 @@ jobs:
 
       - name: Deploy to GitHub Pages
         uses: actions/deploy-pages@v4
-          
+
       - name: Create Job Summary
         if: always()
         run: |
           echo "### Reports" >> $GITHUB_STEP_SUMMARY
           echo "- [Plotting Report](https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }})" >> $GITHUB_STEP_SUMMARY
           echo "### All Outputs" >> $GITHUB_STEP_SUMMARY
           echo "- [Complete Benchmark Output](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}#artifacts)" >> $GITHUB_STEP_SUMMARY
-

.gitignore

@@ -0,0 +1,10 @@
+# image build artifacts
+envs/*.sif
+
+# snakemake
+snakemake.log
+.snakemake/
+
+# vim swaps
+*.swp
+*.swo