workflow updates

.github/workflows/python-package-conda.yml

@@ -12,52 +12,56 @@ jobs:
     strategy:
       max-parallel: 5
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - 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_PREFIX=/usr/share/miniconda/envs/testenv
-
-        
+    - uses: actions/checkout@v4
+    - name: Check out Repo
+  #    uses: actions/setup-python@v5
+  #    with:
+  #      python-version: 3.9
+  #  - 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/bin/conda info --envs
+  #      #CONDA_PREFIX=/usr/share/miniconda/envs/testenv
+
     - name: Initiate conda channels
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         channels: conda-forge,bioconda,default
-        activate-environment: testenv
-        auto-activate-base: false
+   #     activate-environment: testenv
+        auto-activate-base: true
 
 
     - name: Set up environment
       run: |
-        $CONDA/bin/conda env create -n testenv --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
+        ls 
+        pwd
+        conda env create -n testenv --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
     - name: Install Dependencies
       run: |
-        echo $CONDA_PREFIX
-        source activate testenv
-        $CONDA/bin/conda install biopython
+        ls
+        pwd
+        conda activate testenv
+        conda install biopython=1.84
         pip install pyzstd
         pip install pytest
         pip install .
-        qiime
-        #itsxpress
-        #qiime itsxpress
-        #ls
 
     - name: Test with pytest
       run: |
-        source activate testenv
+        conda activate activate testenv
         pytest
+    - name: Test qiime install
+      run: |
+        qiime dev refresch-cache
+        qiime itsxpress --help
+