catalog builder pkg usage updates

.github/workflows/ci-analysis.yml

@@ -9,24 +9,34 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9']
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
-        python3 -m pip install --upgrade pip
-        cd analysis-scripts; pip install .; cd ..
-        cd figure_tools; pip install .; cd ..
-        cd freanalysis; pip install .; cd ..
-        cd freanalysis_clouds; pip install .; cd ..
-        git clone https://github.com/aradhakrishnanGFDL/CatalogBuilder catalogbuilder
-        cd catalogbuilder; pip install .; cd ..
-        pip install pytest
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+        conda config --add channels noaa-gfdl
+        conda config --append channels conda-forge
+        conda create --name analysis-script-testing
+        conda install -n analysis-script-testing catalogbuilder -c noaa-gfdl
+        #conda activate analysis-script-testing
+        conda install pip
+        cd analysis-scripts
+        $CONDA/envs/analysis-script-testing/bin/python -m pip install .; cd ..
+        cd figure_tools
+        $CONDA/envs/analysis-script-testing/bin/python -m pip install .; cd ..
+        cd freanalysis
+        $CONDA/envs/analysis-script-testing/bin/python -m pip install .; cd ..
+        cd freanalysis_clouds
+        $CONDA/envs/analysis-script-testing/bin/python -m pip install .; cd ..
+
     - name: Test freanalysis_clouds
       run: |
-        python3 -m pytest tests
+         $CONDA/envs/analysis-script-testing/bin/pytest tests

tests/test_freanalysis_clouds.py

@@ -5,8 +5,8 @@
 from tempfile import TemporaryDirectory
 
 from freanalysis.plugins import list_plugins, plugin_requirements, run_plugin
-from scripts import gen_intake_gfdl
-
+import catalogbuilder
+from catalogbuilder.scripts import gen_intake_gfdl
 
 def download_test_data(stem):
     """Downloads test datasets from a FTP server.
@@ -47,7 +47,8 @@ def create_data_catalog(path, output="data-catalog"):
     yaml_path = Path(__file__).resolve().parent / "mdtf_timeslice_catalog.yaml"
 
     # Hack to stop click from exiting.
-    command = ["python3", "-m", "scripts.gen_intake_gfdl", str(path), output,
+    # TODO we have to move create catalog as its own pytest in the conda environment perhaps, and avoid this hardcoding
+    command = ["/usr/share/miniconda/envs/analysis-script-testing/bin/python", "-m", "catalogbuilder.scripts.gen_intake_gfdl", str(path), output,
                "--config", str(yaml_path)]
     run(command, check=True)
     return Path(f"{output}.json").resolve(), Path(f"{output}.csv").resolve()