Staging version 2.4.0

.github/workflows/build.yml

@@ -26,7 +26,7 @@ jobs:
         - name: Install dependencies
           run: |
             python -m pip install --upgrade pip
-            python setup.py install
+            python -m pip install .
             python -c 'import cerf; cerf.install_package_data()'
 
         - name: Test and generate coverage report on Linux
@@ -35,8 +35,3 @@ jobs:
             pip install pytest-cov
             pytest --cov=./ --cov-report=xml
 
-        - name: Upload coverage to Codecov
-          uses: codecov/codecov-action@v1
-          with:
-            file: ./coverage.xml
-            fail_ci_if_error: true

README.md

@@ -1,5 +1,4 @@
 [![build](https://github.com/IMMM-SFA/cerf/actions/workflows/build.yml/badge.svg)](https://github.com/IMMM-SFA/cerf/actions/workflows/build.yml)
-[![codecov](https://codecov.io/gh/IMMM-SFA/cerf/branch/main/graph/badge.svg?token=9jbGJv8XCJ)](https://codecov.io/gh/IMMM-SFA/cerf)
 [![DOI](https://zenodo.org/badge/115649750.svg)](https://zenodo.org/badge/latestdoi/115649750)
 [![status](https://joss.theoj.org/papers/28fee3407bbbef020fb4bb19bd451407/status.svg)](https://joss.theoj.org/papers/28fee3407bbbef020fb4bb19bd451407)
 

cerf/__init__.py

@@ -8,4 +8,4 @@
 from .install_supplement import install_package_data
 
 
-__version__ = "2.3.2"
+__version__ = "2.4.0"

cerf/install_supplement.py

@@ -23,23 +23,27 @@ class InstallSupplement:
     """
 
     # URL for DOI minted example data hosted on Zenodo
-    DATA_VERSION_URLS = {'2.0.0': 'https://zenodo.org/record/5218436/files/cerf_package_data.zip?download=1',
-                         '2.0.1': 'https://zenodo.org/record/5218436/files/cerf_package_data.zip?download=1',
-                         '2.0.2': 'https://zenodo.org/record/5218436/files/cerf_package_data.zip?download=1',
-                         '2.0.3': 'https://zenodo.org/record/5218436/files/cerf_package_data.zip?download=1',
-                         '2.0.4': 'https://zenodo.org/record/5247690/files/cerf_package_data.zip?download=1',
-                         '2.0.5': 'https://zenodo.org/record/5247690/files/cerf_package_data.zip?download=1',
-                         '2.0.6': 'https://zenodo.org/record/5247690/files/cerf_package_data.zip?download=1',
-                         '2.0.7': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
-                         '2.0.8': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
-                         '2.0.9': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
-                         '2.1.0': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
-                         '2.1.1': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
-                         '2.2.0': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
-                         '2.2.1': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
-                         '2.3': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
-                         '2.3.1': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
-                         '2.3.2': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1'}
+    DATA_VERSION_URLS = {
+        '2.0.0': 'https://zenodo.org/record/5218436/files/cerf_package_data.zip?download=1',
+        '2.0.1': 'https://zenodo.org/record/5218436/files/cerf_package_data.zip?download=1',
+        '2.0.2': 'https://zenodo.org/record/5218436/files/cerf_package_data.zip?download=1',
+        '2.0.3': 'https://zenodo.org/record/5218436/files/cerf_package_data.zip?download=1',
+        '2.0.4': 'https://zenodo.org/record/5247690/files/cerf_package_data.zip?download=1',
+        '2.0.5': 'https://zenodo.org/record/5247690/files/cerf_package_data.zip?download=1',
+        '2.0.6': 'https://zenodo.org/record/5247690/files/cerf_package_data.zip?download=1',
+        '2.0.7': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
+        '2.0.8': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
+        '2.0.9': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
+        '2.1.0': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
+        '2.1.1': 'https://zenodo.org/record/5514010/files/cerf_package_data.zip?download=1',
+        '2.2.0': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
+        '2.2.1': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
+        '2.3': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
+        '2.3.1': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
+        '2.3.2': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
+        '2.3.3': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
+        '2.4.0': 'https://zenodo.org/record/6998151/files/cerf_package_data.zip?download=1',
+    }
 
     def __init__(self, data_dir=None):
 

cerf/interconnect.py

@@ -2,22 +2,16 @@
 import logging
 import tempfile
 
+import geopandas as gpd
+import numpy as np
 import rasterio
-import whitebox
+from rasterio import features
+from scipy.ndimage import distance_transform_edt
 import yaml
 
-import numpy as np
-import geopandas as gpd
-
 import cerf.package_data as pkg
-
-from rasterio import features
-
 from cerf.utils import suppress_callback
 
-# instantiate whitebox toolset
-wbt = whitebox.WhiteboxTools()
-
 
 class Interconnection:
     """Calculate interconnection costs per grid cell in $ / yr using:
@@ -263,19 +257,17 @@ def process_pipelines(self):
 
             return gdf
 
+
     def transmission_to_cost_raster(self, setting):
         """Create a cost per grid cell in $/km from the input GeoDataFrame of transmission infrastructure having a cost
-        designation field as '_rval_'
+        designation field as '_rval_'.
 
         :param setting:                         Either 'substations' or 'pipelines'
         :type setting:                          str
 
         :return:                                Array of transmission interconnection cost per grid cell
 
         """
-        # conversion factor for meters to km
-        m_to_km_factor = 0.001
-
         if setting == 'substations':
             infrastructure_gdf = self.process_substations()
 
@@ -335,27 +327,36 @@ def transmission_to_cost_raster(self, setting):
                 # write the outputs to file
                 dataset.write_band(1, burned)
 
-            # calculate Euclidean distance and write raster; result just stores the return value 0
-            dist_result = wbt.euclidean_distance(out_rast, out_dist, callback=suppress_callback)
+            # create a mask of target (non-zero) cells
+            target_cells = burned != 0
+
+            # calculate the Euclidean distance and the indices of the nearest target cell
+            distance_array, nearest_indices = distance_transform_edt(
+                ~target_cells, 
+                return_distances=True, 
+                return_indices=True
+            )
 
-            # calculate Euclidean allocation and write raster
-            alloc_result = wbt.euclidean_allocation(out_rast, out_alloc, callback=suppress_callback)
+            # use the nearest indices to map the value of the nearest target to each cell (allocation map)
+            nearest_row_indices, nearest_col_indices = nearest_indices
+            allocation_array = burned[nearest_row_indices, nearest_col_indices]
 
-            with rasterio.open(out_dist) as dist:
-                dist_arr = dist.read(1)
+            with rasterio.open(out_dist, 'w', **metadata) as dist_ds:
+                dist_ds.write(distance_array.astype(rasterio.float64), 1)
 
-            with rasterio.open(out_alloc) as alloc:
-                alloc_arr = alloc.read(1)
+            with rasterio.open(out_alloc, 'w', **metadata) as alloc_ds:
+                alloc_ds.write(allocation_array.astype(rasterio.float64), 1)
 
             with rasterio.open(out_costs, 'w', **metadata) as out:
 
                 # distance in km * the cost of the nearest substation; outputs thous$/km
-                cost_arr = (dist_arr * m_to_km_factor) * alloc_arr
+                cost_arr = distance_array * allocation_array
 
                 out.write(cost_arr, 1)
 
         return cost_arr
 
+
     def generate_interconnection_costs_array(self):
         """Calculate the costs of interconnection for each technology."""
 

cerf/utils.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pandas as pd
 import rasterio
-import xarray as xr
+import rioxarray
 import geopandas as gpd
 from shapely.geometry import Point
 
@@ -253,7 +253,7 @@ def raster_to_coord_arrays(template_raster):
     """
 
     # Read the data
-    da = xr.open_rasterio(template_raster)
+    da = rioxarray.open_rasterio(template_raster)
 
     # Compute the lon/lat coordinates with rasterio.warp.transform
     x, y = np.meshgrid(da['x'], da['y'])

docs/source/conf.py

@@ -16,7 +16,7 @@
 import sphinx_rtd_theme
 
 # import cerf
-version = "2.3.2" #str(cerf.__version__)
+version = "2.4.0" #str(cerf.__version__)
 
 
 sys.path.insert(0, os.path.abspath('../../'))

docs/source/release_notes.rst

@@ -4,6 +4,14 @@ Release notes
 This is the list of changes to **cerf** between each release. For full details,
 see the `commit logs <https://github.com/IMMM-SFA/cerf/commits>`_.
 
+Version 2.4.0
+_____________
+
+- Replaced whitebox dependency used in Euclidean distance calculations with SciPy https://github.com/IMMM-SFA/cerf/pull/107 
+- Limited NumPy version to less than 2 due Fiona dependency https://github.com/IMMM-SFA/cerf/pull/105
+- Updated depreciated calls to xarray https://github.com/IMMM-SFA/cerf/pull/105 
+
+
 Version 2.2.1
 _____________
 

environment.yml

@@ -6,7 +6,8 @@ dependencies:
     - pip
     - pip:
         - cerf
-        - numpy>=1.19.4
+        - numpy>=1.19.4,<2
+        - scipy>=1.12
         - pandas>=1.1.4
         - rasterio>=1.2.3
         - xarray>=0.16.1
@@ -15,7 +16,6 @@ dependencies:
         - joblib>=1.0.1
         - matplotlib>=3.3.3
         - seaborn>=0.11.1
-        - whitebox>=1.5.1
         - fiona>=1.8.19
         - pyproj>=3.0.1
         - rtree>=0.9.7