BESS-JPL 1.13.0__tar.gz → 1.15.0__tar.gz

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout repository

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/BESS_JPL/BESS_JPL.py

@@ -6,7 +6,7 @@ import numpy as np
 import rasters as rt
 from rasters import Raster, RasterGeometry
 
-from check_distribution import check_distribution
+from .check_distribution import check_distribution
 
 from sun_angles import calculate_SZA_from_DOY_and_hour
 from solar_apparent_time import solar_day_of_year_for_area, solar_hour_of_day_for_area

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/BESS_JPL/canopy_shortwave_radiation.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from check_distribution import check_distribution
+from .check_distribution import check_distribution
 
 
 def canopy_shortwave_radiation(

bess_jpl-1.15.0/BESS_JPL/check_distribution.py

@@ -0,0 +1,118 @@
+"""
+Replacement for check_distribution package to avoid pycksum dependency.
+
+This module provides data validation functionality that was previously
+provided by the check-distribution package, which depends on pycksum
+that doesn't compile on Python 3.12.
+"""
+
+import logging
+from typing import Union, Optional
+from datetime import datetime
+
+# Try to import numpy, but make it optional
+try:
+    import numpy as np
+    HAS_NUMPY = True
+except ImportError:
+    np = None
+    HAS_NUMPY = False
+
+
+logger = logging.getLogger(__name__)
+
+
+def check_distribution(
+    data: Union["np.ndarray", float, int, None], 
+    name: str, 
+    time_UTC: Optional[datetime] = None
+) -> None:
+    """
+    Check and validate data distribution, logging warnings for invalid values.
+    
+    This function validates input data and logs information about the distribution,
+    including warnings for NaN values, infinite values, and basic statistics.
+    
+    Args:
+        data: The data to validate (numpy array, scalar, or None)
+        name: Name of the variable for logging purposes
+        time_UTC: Optional timestamp for logging context
+        
+    Returns:
+        None
+        
+    Raises:
+        Nothing - this function only logs warnings and information
+    """
+    
+    # Create log prefix with time if provided
+    time_prefix = f"[{time_UTC}] " if time_UTC else ""
+    
+    if data is None:
+        logger.warning(f"{time_prefix}{name}: data is None")
+        return
+    
+    # Handle numpy arrays or array-like objects
+    if hasattr(data, 'shape') and hasattr(data, 'dtype'):
+        # This is likely a numpy array or array-like object
+        
+        if hasattr(data, 'size') and data.size == 0:
+            logger.warning(f"{time_prefix}{name}: array is empty")
+            return
+        
+        if HAS_NUMPY:
+            # Use numpy functions if available
+            # Check for NaN values
+            if np.any(np.isnan(data)):
+                nan_count = np.sum(np.isnan(data))
+                nan_percentage = (nan_count / data.size) * 100
+                logger.warning(f"{time_prefix}{name}: contains {nan_count} NaN values ({nan_percentage:.1f}%)")
+            
+            # Check for infinite values  
+            if np.any(np.isinf(data)):
+                inf_count = np.sum(np.isinf(data))
+                inf_percentage = (inf_count / data.size) * 100
+                logger.warning(f"{time_prefix}{name}: contains {inf_count} infinite values ({inf_percentage:.1f}%)")
+                
+            # Calculate statistics for finite values only
+            finite_data = data[np.isfinite(data)]
+            if len(finite_data) > 0:
+                min_val = np.min(finite_data)
+                max_val = np.max(finite_data)
+                mean_val = np.mean(finite_data)
+                std_val = np.std(finite_data)
+                
+                logger.debug(f"{time_prefix}{name}: shape={data.shape}, "
+                            f"min={min_val:.6f}, max={max_val:.6f}, "
+                            f"mean={mean_val:.6f}, std={std_val:.6f}")
+            else:
+                logger.warning(f"{time_prefix}{name}: no finite values found")
+        else:
+            # Fallback when numpy is not available
+            logger.debug(f"{time_prefix}{name}: array-like data validated (numpy not available for detailed analysis)")
+            
+    else:
+        # Handle scalar values
+        try:
+            # Convert to float to check for NaN/inf
+            float_val = float(data)
+            
+            if HAS_NUMPY:
+                if np.isnan(float_val):
+                    logger.warning(f"{time_prefix}{name}: scalar value is NaN")
+                elif np.isinf(float_val):
+                    logger.warning(f"{time_prefix}{name}: scalar value is infinite")
+                else:
+                    logger.debug(f"{time_prefix}{name}: scalar value = {float_val:.6f}")
+            else:
+                # Basic validation without numpy
+                import math
+                if math.isnan(float_val):
+                    logger.warning(f"{time_prefix}{name}: scalar value is NaN")
+                elif math.isinf(float_val):
+                    logger.warning(f"{time_prefix}{name}: scalar value is infinite")
+                else:
+                    logger.debug(f"{time_prefix}{name}: scalar value = {float_val:.6f}")
+                
+        except (ValueError, TypeError) as e:
+            logger.warning(f"{time_prefix}{name}: cannot convert to float for validation: {e}")

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/BESS_JPL/model.py

@@ -6,7 +6,7 @@ import numpy as np
 import rasters as rt
 from rasters import Raster, RasterGeometry
 
-from check_distribution import check_distribution
+from .check_distribution import check_distribution
 
 from sun_angles import calculate_SZA_from_DOY_and_hour
 from solar_apparent_time import solar_day_of_year_for_area, solar_hour_of_day_for_area
@@ -16,7 +16,7 @@ from gedi_canopy_height import load_canopy_height, GEDI_DOWNLOAD_DIRECTORY
 from FLiESANN import FLiESANN
 from GEOS5FP import GEOS5FP
 from MODISCI import MODISCI
-from NASADEM import NASADEM
+from NASADEM import NASADEMConnection
 
 from .constants import *
 from .C3_photosynthesis import *
@@ -87,6 +87,8 @@ def BESS_JPL(
         peakVCmax_C3: np.ndarray = None,  # peak maximum carboxylation rate for C3 plants
         peakVCmax_C4: np.ndarray = None,  # peak maximum carboxylation rate for C4 plants
         CI: Union[Raster, np.ndarray] = None,
+        MODISCI_connection: MODISCI = None,
+        NASADEM_connection: NASADEMConnection = None,
         resampling: str = RESAMPLING,
         GEDI_download_directory: str = GEDI_DOWNLOAD_DIRECTORY):  # clumping index
     if geometry is None and isinstance(ST_C, Raster):
@@ -103,7 +105,11 @@ def BESS_JPL(
         raise ValueError("no time given between time_UTC, day_of_year, and hour_of_day")
 
     if elevation_km is None and geometry is not None:
-        elevation_km = NASADEM.elevation_km(geometry=geometry)
+        if NASADEM_connection is None:
+            from NASADEM import NASADEMConnection
+            NASADEM_connection = NASADEMConnection()
+
+        elevation_km = NASADEM_connection.elevation_km(geometry=geometry)
 
     # load air temperature in Celsius if not provided
     if Ta_C is None:
@@ -269,9 +275,11 @@ def BESS_JPL(
     if SZA is None:
         SZA = calculate_SZA_from_DOY_and_hour(geometry.lat, geometry.lon, day_of_year, hour_of_day)
 
+    if MODISCI_connection is None:
+        MODISCI_connection = MODISCI()
+
     if CI is None and geometry is not None:
-        modisci = MODISCI()
-        CI = modisci.CI(geometry=geometry, resampling=resampling)
+        CI = MODISCI_connection.CI(geometry=geometry, resampling=resampling)
 
     # canopy height defaults to zero
     canopy_height_meters = np.where(np.isnan(canopy_height_meters), 0, canopy_height_meters)

bess_jpl-1.15.0/BESS_JPL/version.txt

@@ -0,0 +1 @@
+1.15.0

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/BESS_JPL.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: BESS-JPL
-Version: 1.13.0
+Version: 1.15.0
 Summary: Breathing Earth System Simulator (BESS) Gross Primary Production (GPP) and Evapotranspiration (ET) Model Python
 Author-email: Gregory Halverson <gregory.h.halverson@jpl.nasa.gov>
 Project-URL: Homepage, https://github.com/JPL-Evapotranspiration-Algorithms/BESS-JPL
@@ -9,13 +9,12 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: check-distribution
 Requires-Dist: FLiESANN>=1.5.0
 Requires-Dist: gedi-canopy-height>=1.1.0
 Requires-Dist: GEOS5FP>=1.1.1
 Requires-Dist: koppengeiger>=1.0.4
 Requires-Dist: MODISCI>=1.3.0
-Requires-Dist: NASADEM
+Requires-Dist: NASADEM>=1.3.0
 Requires-Dist: numpy
 Requires-Dist: rasters
 Requires-Dist: solar-apparent-time>=1.3.2

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/BESS_JPL.egg-info/SOURCES.txt

@@ -38,6 +38,7 @@ BESS_JPL/canopy_shortwave_radiation.py
 BESS_JPL/carbon_uptake_efficiency.jpeg
 BESS_JPL/carbon_uptake_efficiency.tif
 BESS_JPL/carbon_water_fluxes.py
+BESS_JPL/check_distribution.py
 BESS_JPL/constants.py
 BESS_JPL/interpolate_C3_C4.py
 BESS_JPL/kn.jpeg

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/BESS_JPL.egg-info/requires.txt

@@ -1,10 +1,9 @@
-check-distribution
 FLiESANN>=1.5.0
 gedi-canopy-height>=1.1.0
 GEOS5FP>=1.1.1
 koppengeiger>=1.0.4
 MODISCI>=1.3.0
-NASADEM
+NASADEM>=1.3.0
 numpy
 rasters
 solar-apparent-time>=1.3.2

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: BESS-JPL
-Version: 1.13.0
+Version: 1.15.0
 Summary: Breathing Earth System Simulator (BESS) Gross Primary Production (GPP) and Evapotranspiration (ET) Model Python
 Author-email: Gregory Halverson <gregory.h.halverson@jpl.nasa.gov>
 Project-URL: Homepage, https://github.com/JPL-Evapotranspiration-Algorithms/BESS-JPL
@@ -9,13 +9,12 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: check-distribution
 Requires-Dist: FLiESANN>=1.5.0
 Requires-Dist: gedi-canopy-height>=1.1.0
 Requires-Dist: GEOS5FP>=1.1.1
 Requires-Dist: koppengeiger>=1.0.4
 Requires-Dist: MODISCI>=1.3.0
-Requires-Dist: NASADEM
+Requires-Dist: NASADEM>=1.3.0
 Requires-Dist: numpy
 Requires-Dist: rasters
 Requires-Dist: solar-apparent-time>=1.3.2

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=60", "setuptools-scm>=8.0", "wheel"]
 
 [project]
 name = "BESS-JPL"
-version = "1.13.0"
+version = "1.15.0"
 description = "Breathing Earth System Simulator (BESS) Gross Primary Production (GPP) and Evapotranspiration (ET) Model Python"
 readme = "README.md"
 authors = [
@@ -14,13 +14,12 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "check-distribution",
     "FLiESANN>=1.5.0",
     "gedi-canopy-height>=1.1.0",
     "GEOS5FP>=1.1.1",
     "koppengeiger>=1.0.4",
     "MODISCI>=1.3.0",
-    "NASADEM",
+    "NASADEM>=1.3.0",
     "numpy",
     "rasters",
     "solar-apparent-time>=1.3.2"

{bess_jpl-1.13.0 → bess_jpl-1.15.0}/tests/test_import_dependencies.py

@@ -2,7 +2,6 @@ import pytest
 
 # List of dependencies
 dependencies = [
-    "check_distribution",
     "FLiESANN",
     "gedi_canopy_height",
     "GEOS5FP",

bess_jpl-1.13.0/BESS_JPL/version.txt

@@ -1 +0,0 @@
-1.13.0