Create main.yml

.github/workflows/main.yml

@@ -0,0 +1,66 @@
+name: Testing Apple Silicon install
+
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: "0 0 */7 * *"
+
+jobs:
+  build-linux:
+    runs-on: macos-14
+    strategy:
+      max-parallel: 5
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+    - run:   |
+        #sudo apt update
+        #sudo apt install gcc-10 g++-10
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+        echo $CONDA_PREFIX
+        $CONDA/bin/conda list
+        $CONDA/bin/conda info --base
+        conda create --name testenv python=3.8.16
+        #CONDA_PREFIX=/usr/share/miniconda/envs/testenv
+        $CONDA/bin/conda info
+        $CONDA/bin/conda list
+        
+    - name: Initiate conda channels
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        channels: conda-forge,bioconda,default
+        activate-environment: testenv
+        auto-activate-base: false
+
+
+    - name: Set up environment
+      run: |
+        wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2023.9-py38-linux-conda.yml
+        $CONDA/bin/conda env update --file qiime2-amplicon-2023.9-py38-linux-conda.yml --name testenv
+    - name: Install Dependencies
+      run: |
+        echo $CONDA_PREFIX
+        source activate testenv
+        $CONDA/bin/conda install biopython
+        pip install pyzstd
+        pip install pytest
+        pip install .
+        qiime
+        #itsxpress
+        #qiime itsxpress
+        #ls
+    - name: Test with pytest
+      run: |
+        source activate testenv
+        pytest