Merge pull request #311 from podaac/release/2.13.0

Release 2.13.0

.github/workflows/build-pipeline.yml

@@ -315,7 +315,7 @@ jobs:
         uses: softprops/action-gh-release@v2
         with:
           tag_name: "${{ env.software_version }}"  # Use the tag that triggered the action
-          release_name: Release v{{ env.software_version }}
+          name: Release v{{ env.software_version }}
           draft: false
           generate_release_notes: true
           token: ${{ secrets.GITHUB_TOKEN }}

CHANGELOG.md

@@ -13,6 +13,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Security
 
 
+## [2.13.0]
+### Added
+### Changed
+### Deprecated 
+### Removed
+- Removed the "time" dependency when doing spatial only subsetting.
+### Fixed
+- Updated xarray enhancement get_indexers_from_nd function for SMAP_RSS_L2_SSS_V6.
+- Fix minor bug in checking for empty indexers and same data bounds.
+### Security
+
+
 ## [2.12.0]
 ### Added
 - Added custom exception to progate error messages to harmony.

deployment/harmony_deploy.py

@@ -59,9 +59,6 @@ def bearer_token() -> str:
     }
 
     response = requests.put(url, headers=headers, json=data)
+    response.raise_for_status()
 
-    print(response.status_code)
-    try:
-        print(response.json())
-    except json.JSONDecodeError:
-        print("Response content is not in JSON format")
+    print(f"Response JSON: {response.json()}")

docs/conf.py

@@ -47,8 +47,7 @@
     'sphinx.ext.coverage',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
-    'sphinx_rtd_theme',
-    'm2r2'
+    'sphinx_rtd_theme'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -77,3 +76,4 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
+

podaac/subsetter/subset.py

@@ -560,11 +560,7 @@ def compute_time_variable_name(dataset: xr.Dataset, lat_var: xr.Variable, total_
         if var_name not in total_time_vars and 'time' in var_name_time.lower() and dataset[var_name].squeeze().dims[0] in lat_var.squeeze().dims:
             return var_name
 
-    # OB.DAAC data does not have a time variable. Returning the following field of a composite time value to avoid exceptions.
-    if '__scan_line_attributes__day' in dataset.data_vars:
-        return '__scan_line_attributes__day'
-
-    raise ValueError('Unable to determine time variable')
+    return None
 
 
 def compute_utc_name(dataset: xr.Dataset) -> Union[str, None]:
@@ -1296,6 +1292,9 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str,
             time_var_names=time_var_names
         )
 
+        if not time_var_names and (min_time or max_time):
+            raise ValueError('Could not determine time variable')
+
         start_date = None
         if hdf_type and (min_time or max_time):
             dataset, start_date = tc.convert_to_datetime(dataset, time_var_names, hdf_type)

podaac/subsetter/subset_harmony.py

@@ -24,6 +24,7 @@
 from tempfile import mkdtemp
 import traceback
 from typing import List, Union
+import sys
 
 import pystac
 from pystac import Asset
@@ -41,9 +42,16 @@
 
 
 class L2SSException(HarmonyException):
-    """Base class for exceptions in the Harmony GDAL Adapter."""
-
+    """L2SS Exception class for custom error messages to see in harmony api calls."""
     def __init__(self, original_exception):
+        # Ensure we can extract traceback information
+        if original_exception.__traceback__ is None:
+            # Capture the current traceback if not already present
+            try:
+                raise original_exception
+            except type(original_exception):
+                original_exception.__traceback__ = sys.exc_info()[2]
+
         # Extract the last traceback entry (most recent call) for the error location
         tb = traceback.extract_tb(original_exception.__traceback__)[-1]
 
@@ -57,7 +65,11 @@ def __init__(self, original_exception):
         readable_message = (f"Error in file '{filename}', line {lineno}, in function '{funcname}': "
                             f"{error_msg}")
 
-        super().__init__(readable_message, 'nasa/harmony-gdal-adapter')
+        # Call the parent class constructor with the formatted message and category
+        super().__init__(readable_message, 'podaac/l2-subsetter')
+
+        # Store the original exception for potential further investigation
+        self.original_exception = original_exception
 
 
 def podaac_to_harmony_bbox(bbox: np.ndarray) -> Union[np.ndarray, float]:

podaac/subsetter/xarray_enhancements.py

@@ -69,57 +69,50 @@ def get_indexers_from_nd(cond: xr.Dataset, cut: bool) -> dict:
         Indexer dictionary for the provided condition.
     """
     # check if the lat/lon coordinate numpy array has 2 or more dimensions
-    transpose = False
-    if cond.values.squeeze().ndim == 2:
-        x_axis = 1
-        y_axis = 0
+    transpose = dim_grid = False
+    ndim = cond.values.squeeze().ndim
+
+    # Determine axes and flags
+    if ndim == 2:
+        x_axis, y_axis = 1, 0
     else:
-        if any('xtrack' in dim for dim in list(cond.dims)) and\
-           any('atrack' in dim for dim in list(cond.dims)):
-            x_axis = list(cond.dims).index('xtrack')
-            y_axis = list(cond.dims).index('atrack')
+        if 'xtrack' in cond.dims and 'atrack' in cond.dims:
+            x_axis, y_axis = cond.dims.index('xtrack'), cond.dims.index('atrack')
             transpose = True
+        elif 'xdim_grid' in cond.dims and 'ydim_grid' in cond.dims:
+            x_axis, y_axis = cond.dims.index('xdim_grid'), cond.dims.index('ydim_grid')
+            dim_grid = x_axis == 1 and y_axis == 0
         else:
-            x_axis = 2
-            y_axis = 1
+            x_axis, y_axis = 2, 1
 
-    rows = np.any(cond.values.squeeze(), axis=x_axis)
-    if cut:
-        cols = np.any(cond.values.squeeze(), axis=y_axis)
-    else:
-        cols = np.ones(len(cond.values[0]))
+    # Compute rows and columns
+    squeezed_values = cond.values.squeeze()
+    rows = np.any(squeezed_values, axis=x_axis)
+    cols = np.any(squeezed_values, axis=y_axis) if cut else np.ones(len(squeezed_values[0]))
 
-    # If the subsetted area is equal to the original area
-    if np.all(rows) & np.all(cols):
+    # Log information about subsetted area
+    if np.all(rows) and np.all(cols):
         logging.info("Subsetted area equal to the original granule.")
-
-    # If the subsetted area is empty
-    if not np.any(rows) | np.any(cols):
+    if not np.any(rows) or not np.any(cols):
         logging.info("No data within the given bounding box.")
 
-    cond_shape_list = list(cond.shape)
-    cond_list = list(cond.dims)
-    output = [idx for idx, element in enumerate(cond_shape_list) if element == 1]
-    for i in output:
-        cond_list.pop(i)
-
-    if rows.ndim == 1:
-        indexers = {
-            cond_list[0]: np.where(rows)[0],
-            cond_list[1]: np.where(cols)[0]
-        }
-    else:
-        # if the lat/lon had 3 dimensions the conditional array was identical in the z direction - taking the first
+    # Determine dimensions and clean them up
+    cond_dims = list(cond.dims)
+    cond_shape = list(cond.shape)
+    cond_dims = [dim for dim, size in zip(cond_dims, cond_shape) if size > 1]
+
+    # Adjust for 3D data
+    if rows.ndim > 1:
         if transpose:
-            rows = rows.transpose()[0]
-            cols = cols.transpose()[0]
-        else:
-            rows = rows[0]
-            cols = cols[0]
-        indexers = {
-            cond_list[y_axis]: np.where(rows)[0],
-            cond_list[x_axis]: np.where(cols)[0]
-        }
+            rows, cols = rows.transpose()[0], cols.transpose()[0]
+        elif not dim_grid:
+            rows, cols = rows[0], cols[0]
+
+    # Generate indexers
+    indexers = {
+        cond_dims[y_axis]: np.where(rows)[0],
+        cond_dims[x_axis]: np.where(cols)[0]
+    }
 
     return indexers