subsurface-terra 2026.1.1rc1__tar.gz → 2026.1.2rc1__tar.gz

{subsurface_terra-2026.1.1rc1 → subsurface_terra-2026.1.2rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2026.1.1rc1
+Version: 2026.1.2rc1
 Summary: Subsurface data types and utilities. This version is the one used by Terranigma Solutions. Please feel free to take anything in this repository for the original one.
 Home-page: https://softwareunderground.github.io/subsurface
 Author: Software Underground

{subsurface_terra-2026.1.1rc1 → subsurface_terra-2026.1.2rc1}/subsurface/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '2026.1.1rc1'
-__version_tuple__ = version_tuple = (2026, 1, 1, 'rc1')
+__version__ = version = '2026.1.2rc1'
+__version_tuple__ = version_tuple = (2026, 1, 2, 'rc1')
 
-__commit_id__ = commit_id = 'gb37eb9192'
+__commit_id__ = commit_id = 'g7216f7b42'

{subsurface_terra-2026.1.1rc1 → subsurface_terra-2026.1.2rc1}/subsurface/core/geological_formats/boreholes/_survey_to_unstruct.py

@@ -47,7 +47,10 @@ def data_frame_to_unstructured_data(survey_df: 'pd.DataFrame', number_nodes: int
 
         this_well_vertex = np.vstack([pos.easting, pos.northing, pos.depth]).T
         cum_vertex = np.vstack([cum_vertex, this_well_vertex])
-        measured_depths = _calculate_distances(array_of_vertices=this_well_vertex)
+        measured_depths = _calculate_distances(
+            array_of_vertices=this_well_vertex,
+            start_md = depths[0]
+        )
 
         n_vertex_shift_0 = np.arange(0, len(pos.depth) - 1, dtype=np.int_)
         n_vertex_shift_1 = np.arange(1, len(pos.depth), dtype=np.int_)
@@ -152,12 +155,12 @@ def _grab_depths_from_attr(
     return attr_depths
 
 
-def _calculate_distances(array_of_vertices: np.ndarray) -> np.ndarray:
+def _calculate_distances(array_of_vertices: np.ndarray, start_md: float = 0) -> np.ndarray:
     # Calculate the differences between consecutive points
     differences = np.diff(array_of_vertices, axis=0)
 
     # Calculate the Euclidean distance for each pair of consecutive points
     distances = np.linalg.norm(differences, axis=1)
-    # Insert a 0 at the beginning to represent the starting point at the surface
-    measured_depths = np.insert(np.cumsum(distances), 0, 0)
+    # Start from start_md instead of 0
+    measured_depths = np.insert(np.cumsum(distances) + start_md, 0, start_md)
     return measured_depths

{subsurface_terra-2026.1.1rc1 → subsurface_terra-2026.1.2rc1}/subsurface/modules/reader/topography/topo_core.py

@@ -11,7 +11,7 @@ from ....core.reader_helpers.reader_unstruct import ReaderUnstructuredHelper
 from ..mesh.surfaces_api import read_2d_mesh_to_unstruct
 
 
-def read_structured_topography(path, crop_to_extent: Optional[Sequence]=None) -> StructuredData:
+def read_structured_topography(path, crop_to_extent: Optional[Sequence] = None) -> StructuredData:
     rasterio = require_rasterio()
 
     extension = get_extension(path)
@@ -31,8 +31,34 @@ def read_structured_topography_to_unstructured(path) -> UnstructuredData:
     return topography_to_unstructured_data(structured_data)
 
 
-def rasterio_dataset_to_structured_data(dataset, crop_to_extent: Optional[Sequence]=None):
-    if crop_to_extent is not None: 
+def rasterio_dataset_to_structured_data(dataset, crop_to_extent: Optional[Sequence] = None):
+    rasterio = require_rasterio()
+
+    if crop_to_extent is not None:
+        window = _get_raster_window(crop_to_extent, dataset)
+    else:
+        window = None
+
+    data = dataset.read(1, window=window)
+    data = np.fliplr(data.T)
+    shape = data.shape
+
+    # Use window bounds if cropping, otherwise use full dataset bounds
+    if window is not None:
+        left, bottom, right, top = rasterio.windows.bounds(window, dataset.transform)
+    else:
+        left, bottom, right, top = dataset.bounds.left, dataset.bounds.bottom, dataset.bounds.right, dataset.bounds.top
+
+    coords = {
+            'x': np.linspace(left, right, shape[0]),
+            'y': np.linspace(bottom, top, shape[1])
+    }
+    structured_data = StructuredData.from_numpy(data, data_array_name='topography', coords=coords)
+    return structured_data
+
+
+def rasterio_dataset_to_structured_data_(dataset, crop_to_extent: Optional[Sequence] = None):
+    if crop_to_extent is not None:
         window = _get_raster_window(crop_to_extent, dataset)
     else:
         window = None
@@ -40,30 +66,30 @@ def rasterio_dataset_to_structured_data(dataset, crop_to_extent: Optional[Sequen
     data = dataset.read(1, window=window)
     data = np.fliplr(data.T)
     shape = data.shape
-    
+
     # TODO: ===================
     # TODO: Add the option to crop
     # TODO: Resample
-    
+
     coords = {
-        'x': np.linspace(
-            dataset.bounds.left,
-            dataset.bounds.right,
-            shape[0]
-        ),
-        'y': np.linspace(
-            dataset.bounds.bottom,
-            dataset.bounds.top,
-            shape[1]
-        )
+            'x': np.linspace(
+                dataset.bounds.left,
+                dataset.bounds.right,
+                shape[0]
+            ),
+            'y': np.linspace(
+                dataset.bounds.bottom,
+                dataset.bounds.top,
+                shape[1]
+            )
     }
     structured_data = StructuredData.from_numpy(data, data_array_name='topography', coords=coords)
     return structured_data
 
 
-def read_unstructured_topography(path, additional_reader_kwargs: Optional[dict]=None) -> UnstructuredData:
+def read_unstructured_topography(path, additional_reader_kwargs: Optional[dict] = None) -> UnstructuredData:
     """For example, a dxf file"""
-    
+
     additional_reader_kwargs = additional_reader_kwargs or {}
     helper = GenericReaderFilesHelper(
         file_or_buffer=path,

{subsurface_terra-2026.1.1rc1 → subsurface_terra-2026.1.2rc1}/subsurface/modules/reader/wells/_read_to_df.py

@@ -21,7 +21,12 @@ def check_format_and_read_to_df(reader_helper: GenericReaderFilesHelper) -> pd.D
             )
         case (bytes() | io.BytesIO() | io.StringIO() | io.TextIOWrapper()), _:
             reader = _get_reader(reader_helper.format)
-            d = reader(reader_helper.file_or_buffer, **reader_helper.pandas_reader_kwargs)
+            d = reader(
+                filepath_or_buffer=reader_helper.file_or_buffer,
+                sep=reader_helper.separator,
+                engine='python',
+                **reader_helper.pandas_reader_kwargs
+            )
         case dict(), _:
             reader = _get_reader('dict')
             d = reader(reader_helper.file_or_buffer)

{subsurface_terra-2026.1.1rc1 → subsurface_terra-2026.1.2rc1}/subsurface_terra.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2026.1.1rc1
+Version: 2026.1.2rc1
 Summary: Subsurface data types and utilities. This version is the one used by Terranigma Solutions. Please feel free to take anything in this repository for the original one.
 Home-page: https://softwareunderground.github.io/subsurface
 Author: Software Underground