Update conda-env-create-and-pytest.yml

ahhhhh the pytest, conda installations brought in with the python environment pointed to by github actions "setup-python" take precedence over the conda env python etc. not my favorite thing- but it does seem at least to work consistently. i hope to see most steps work after this commit.
NOAA-GFDL · Jul 23, 2024 · 1c29cc0 · 1c29cc0
1 parent 984ec95
commit 1c29cc0
Showing 1 changed file with 12 additions and 11 deletions.
diff --git a/.github/workflows/conda-env-create-and-pytest.yml b/.github/workflows/conda-env-create-and-pytest.yml
@@ -29,25 +29,26 @@ jobs:
 
     - name: Run pytest in catalogbuilder environment
       run: |
-        # $CONDA/envs/catalogbuilder/bin/pytest
         which python
         python --version
+        $CONDA/envs/catalogbuilder/bin/python --version
         which pytest
-        pytest
+        $CONDA/envs/catalogbuilder/bin/pytest
 
     - name: Make sample data
       run: |
-        python tests/make_sample_data.py
+        # python tests/make_sample_data.py
+        $CONDA/envs/catalogbuilder/bin/python tests/make_sample_data.py
 
     - name: Generate catalog
       run: |
-        # $CONDA/envs/catalogbuilder/bin/python catalogbuilder/scripts/gen_intake_gfdl.py archive/am5/am5/am5f3b1r0/c96L65_am5f3b1r0_pdclim1850F/gfdl.ncrc5-deploy-prod-openmp/pp gfdl_autotest
-        python catalogbuilder/scripts/gen_intake_gfdl.py archive/am5/am5/am5f3b1r0/c96L65_am5f3b1r0_pdclim1850F/gfdl.ncrc5-deploy-prod-openmp/pp gfdl_autotest
+        $CONDA/envs/catalogbuilder/bin/python catalogbuilder/scripts/gen_intake_gfdl.py archive/am5/am5/am5f3b1r0/c96L65_am5f3b1r0_pdclim1850F/gfdl.ncrc5-deploy-prod-openmp/pp gfdl_autotest
+        # python catalogbuilder/scripts/gen_intake_gfdl.py archive/am5/am5/am5f3b1r0/c96L65_am5f3b1r0_pdclim1850F/gfdl.ncrc5-deploy-prod-openmp/pp gfdl_autotest
   
     - name: Generate catalog with yaml
       run: |
-        # $CONDA/envs/catalogbuilder/bin/python catalogbuilder/scripts/gen_intake_gfdl.py --config tests/test_config.yaml
-        python catalogbuilder/scripts/gen_intake_gfdl.py --config tests/test_config.yaml
+        $CONDA/envs/catalogbuilder/bin/python catalogbuilder/scripts/gen_intake_gfdl.py --config tests/test_config.yaml
+        # python catalogbuilder/scripts/gen_intake_gfdl.py --config tests/test_config.yaml
 
     - name: upload-artifacts
       uses: actions/upload-artifact@v4
@@ -71,7 +72,7 @@ jobs:
 
     - name: Test for completeness
       run: | 
-        # $CONDA/envs/catalogbuilder/bin/python catalogbuilder/scripts/test_catalog.py -tf gfdl_autotest.json catalogbuilder/cats/gfdl_template.json
-        # $CONDA/envs/catalogbuilder/bin/python catalogbuilder/scripts/test_catalog.py -tf catalogbuilder/cats/gfdl_autotest_from_yaml.json
-        python catalogbuilder/scripts/test_catalog.py -tf gfdl_autotest.json catalogbuilder/cats/gfdl_template.json
-        python catalogbuilder/scripts/test_catalog.py -tf catalogbuilder/cats/gfdl_autotest_from_yaml.json 
+        $CONDA/envs/catalogbuilder/bin/python catalogbuilder/scripts/test_catalog.py -tf gfdl_autotest.json catalogbuilder/cats/gfdl_template.json
+        $CONDA/envs/catalogbuilder/bin/python catalogbuilder/scripts/test_catalog.py -tf catalogbuilder/cats/gfdl_autotest_from_yaml.json
+        # python catalogbuilder/scripts/test_catalog.py -tf gfdl_autotest.json catalogbuilder/cats/gfdl_template.json
+        # python catalogbuilder/scripts/test_catalog.py -tf catalogbuilder/cats/gfdl_autotest_from_yaml.json