actions test

USDA-ARS-GBRU · Sep 19, 2024 · 27096ac · 27096ac
1 parent f84bed0
commit 27096ac
Showing 1 changed file with 9 additions and 5 deletions.
diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
@@ -24,6 +24,7 @@ jobs:
       uses: conda-incubator/setup-miniconda@v3
       with:
         channels: conda-forge,bioconda,default
+        auto-activate-base: true
     - name: Initialize conda
       run: |
         conda info
@@ -39,14 +40,17 @@ jobs:
         pip install .
     - name: Test with pytest
       run: |
+        echo "begin: PATH=$PATH;"
         conda activate testenv
+        echo "after conda activate testenv: PATH=$PATH;"
         conda info
         ls $CONDA/bin
-        $CONDA/bin/pytest 
+        pytest -h
     - name: Test qiime install
       run: |
-        conda activate testenv
-        conda info
-        $CONDA/bin/qiime dev refresch-cache
-        $CONDA/bin/qiime itsxpress --help
+        ls
+        #conda activate testenv
+        #conda info
+        #$CONDA/bin/qiime dev refresch-cache
+        #$CONDA/bin/qiime itsxpress --help