setup miniconda

.github/workflows/main.yaml

@@ -23,17 +23,27 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10"]
-
+    # Set it to default use bash in interactive mode (required for miniconda setup)
+    defaults:
+      run:
+        shell: bash -el {0}
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+      - name: create environment with mamba
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          python-version:  ${{ matrix.python-version }}
+          channels: conda-forge,bioconda,defaults
+          auto-activate-base: false
+          environment-file: environment.yaml
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          conda install -c bioconda -c conda-forge "fastspar>=0.0.7" armadillo=8 "scipy<=1.10.1,>=1.8.0"
           pip install pytest
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           python setup.py install