Merge pull request #37 from NOAA-CEFI-Portal/hotfix-regiondir

Hotfix for data path

.github/workflows/gha_pytest_pr.yml

@@ -17,7 +17,7 @@ jobs:
       - name: Setup Micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: regional_mom6.yml
+          environment-file: environment.yml
           init-shell: bash
 
       - name: Setup package config file

.github/workflows/gha_pytest_push.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Setup Micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: regional_mom6.yml
+          environment-file: environment.yml
           init-shell: bash
 
       - name: Setup package config file

README.md

@@ -48,5 +48,5 @@ To use the module in the package at this stage
     }
     ```
 
-    current setup assuming the data directory structure is fixed (flexibility need to be considered)
+    current setup assuming the data directory structure is fixed (i.e. the historical run or forecast data subdirectory (ex: hist_run and forecast) need to be under this data_path )
 

regional_mom6.yml → environment.yml

@@ -1,4 +1,4 @@
-name: regional_mom6
+name: regional-mom6
 channels:
   - conda-forge
 dependencies:
@@ -9,4 +9,4 @@ dependencies:
   - xarray
   - xesmf
   - pytest
-  - beautifulsoup4
+  - beautifulsoup4

mom6/mom6_module/mom6_io.py

@@ -37,6 +37,7 @@ class OpenDapStore:
     """
     def __init__(
             self,
+            region : Literal['northwest_atlantic'] = 'northwest_atlantic',
             grid : Literal['raw','regrid'] = 'raw',
             data_type : Literal['forecast','historical'] = 'historical'
     ) -> None:
@@ -53,6 +54,7 @@ def __init__(
             to calculate the indexes, by default 'historical'
 
         """
+        self.region = region
         self.grid = grid
         self.data_type = data_type
 
@@ -86,13 +88,15 @@ def get_catalog(self)-> list:
         elif self.grid == 'regrid' :
             gridtype = 'regrid/'
 
+        regiontype = self.region
+
         catalog_url = (
             'https://psl.noaa.gov/thredds/catalog/'+
-            f'Projects/CEFI/regional_mom6/{datatype}/{gridtype}'
+            f'Projects/CEFI/regional_mom6/{regiontype}/{datatype}/{gridtype}'
         )
         opendap_url = (
             'https://psl.noaa.gov/thredds/dodsC/'+
-            f'Projects/CEFI/regional_mom6/{datatype}/{gridtype}'
+            f'Projects/CEFI/regional_mom6/{regiontype}/{datatype}/{gridtype}'
         )
 
         # Send a GET request to the URL

tests/conftest.py

@@ -1,3 +1,13 @@
+"""
+This is a pytest setting file to have the option of 
+pytesting under different location/platform
+
+To do pytest on the local machine
+`pytest` (will do the opendap option below)
+`pytest --location opendap` (testing mock index calculation)
+`pytest --location local` (testing real index calculation)
+
+"""
 import pytest
 
 def pytest_addoption(parser):

tests/test_mom6_io.py

@@ -12,7 +12,7 @@ def test_OpenDapStore():
     """Test OpenDap Connection
     """
 
-    opendap_raw = mom6_io.OpenDapStore('raw','historical')
+    opendap_raw = mom6_io.OpenDapStore(grid='raw',data_type='historical',region='northwest_atlantic')
     test_url = opendap_raw.get_catalog()[0]
     try:
         ds = xr.open_dataset(test_url)
@@ -21,7 +21,7 @@ def test_OpenDapStore():
         pytest.fail('OSError is raised OPeNDAP url not working')
 
 
-    opendap_regrid = mom6_io.OpenDapStore('regrid','historical')
+    opendap_regrid = mom6_io.OpenDapStore(grid='regrid',data_type='historical',region='northwest_atlantic')
     test_url = opendap_regrid.get_catalog()[0]
     try:
         ds = xr.open_dataset(test_url)
@@ -34,7 +34,7 @@ def test_OpenDapStore():
 def test_MOM6Forecast(location):
     """Test the forecast IO
 
-    only available local
+    currently only available local
 
     Parameters
     ----------