fix: switch default provider to NSIDC_CPRD

.github/workflows/python-publish.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   deploy:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4

doc/environment.yml

@@ -2,7 +2,7 @@ name: icesat2-docs
 channels:
   - conda-forge
 dependencies:
-  - docutils<0.18
+  - docutils
   - fontconfig
   - freetype
   - future

doc/make.bat

@@ -10,8 +10,6 @@ if "%SPHINXBUILD%" == "" (
 set SOURCEDIR=source
 set BUILDDIR=build
 
-if "%1" == "" goto help
-
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
 	echo.
@@ -21,10 +19,12 @@ if errorlevel 9009 (
 	echo.may add the Sphinx directory to PATH.
 	echo.
 	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
+	echo.https://www.sphinx-doc.org/
 	exit /b 1
 )
 
+if "%1" == "" goto help
+
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 goto end
 

doc/source/_assets/ASAS_product_chart.tex

@@ -56,49 +56,51 @@
 		\node (ppd)[ext, below of=atl02, xshift=-1cm]{\textbf{PPD}};
 		\node (pod)[ext, below of=atl02, xshift=1cm]{\textbf{POD}};
 		% Level 2 products
-		\node (atl03)[l2, below of=ppd, xshift=1cm]{\textbf{ATL03}\\Geolocated\\Photons};
+		\node (atl03)[l2, below of=ppd, xshift=1cm]{\textbf{ATL03  (+QL)}\\Geolocated\\Photons};
 		\node (atl04)[l2, right of=atl02, xshift=3.5cm]{\textbf{ATL04}\\Normalized\\Backscatter\\Profiles};
 		% connection coordinates for single arrow out of ATL03
 		\node(A)[shape=coordinate, below=0.5cm of atl03] {};
 		\node (B)[shape=coordinate, left=1.375cm of A] {};
 		\node (C)[shape=coordinate, left=2.75cm of B] {};
 		\node (D)[shape=coordinate, left=2.75cm of C] {};
-		\node (E)[shape=coordinate, right=1.375cm of A] {};
-		\node (F)[shape=coordinate, right=2.75cm of E] {};
+		\node (E)[shape=coordinate, left=3.00cm of D] {};
+		\node (F)[shape=coordinate, right=1.375cm of A] {};
 		\node (G)[shape=coordinate, right=2.75cm of F] {};
 		\node (H)[shape=coordinate, right=2.75cm of G] {};
+		\node (I)[shape=coordinate, right=2.75cm of H] {};
 		% Level 3a products
-		\node (atl06)[l3a, below=0.5cm of D]{\textbf{ATL06}\\Land Ice\\Height};
-		\node (atl07)[l3a, below=0.5cm of C]{\textbf{ATL07}\\Sea Ice\\Height};
-		\node (atl10)[l3a, below=0.5cm of B]{\textbf{ATL10}\\Sea Ice\\Freeboard};
-		\node (atl08)[l3a, below=0.5cm of E]{\textbf{ATL08}\\Land/Vegetation\\Height};
+		\node (atl10)[l3a, below=0.5cm of E]{\textbf{ATL10 (+QL)}\\Sea Ice\\Freeboard};
+		\node (atl07)[l3a, below=0.5cm of D]{\textbf{ATL07 (+QL)}\\Sea Ice\\Height};
+		\node (atl06)[l3a, below=0.5cm of C]{\textbf{ATL06}\\Land Ice\\Height};
+		\node (atl08)[l3a, below=0.5cm of B]{\textbf{ATL08 (+QL)}\\Land/Vegetation\\Height};
 		\node (atl12)[l3a, below=0.5cm of F]{\textbf{ATL12}\\Ocean Surface\\Height};
-		\node (atl13)[l3a, below=0.5cm of G]{\textbf{ATL13}\\Inland Water\\Height};
+		\node (atl13)[l3a, below=0.5cm of G]{\textbf{ATL13 (+QL)}\\Inland Surface\\Water Data};
 		\node (atl24)[l3a, dashed, below=0.5cm of H]{\textbf{ATL24}\\Bathymetric\\Elevation};
-		\node (atl09)[l3a, right of=atl03, xshift=3.5cm]{\textbf{ATL09}\\Calibrated\\Backscatter\\Profiles};
+		\node (atl25)[l3a, dashed, below=0.5cm of I]{\textbf{ATL25}\\Lake Ice\\Height};
+		\node (atl09)[l3a, right of=atl03, xshift=3.5cm]{\textbf{ATL09 (+QL)}\\Calibrated\\Backscatter\\Profiles};
 		% connection coordinates for single arrow out of ATL09
-		\node (I)[shape=coordinate, below=0.5cm of atl09] {};
-		\node (J)[shape=coordinate, right=5.5cm of atl09] {};
+		\node (J)[shape=coordinate, below=0.5cm of atl09] {};
+		\node (K)[shape=coordinate, right=5.5cm of atl09] {};
 		% Level 3b products
 		\node (atl11)[l3b, below=0.5cm of atl06]{\textbf{ATL11}\\Land Ice Height\\Time Series};
-		\node (atl14)[l3b, below=0.5cm of atl11, xshift=-3cm]{\textbf{ATL14}\\Gridded Land\\ Ice Height};
-		\node (atl15)[l3b, below=0.5cm of atl11, xshift=0cm]{\textbf{ATL15}\\Gridded Land\\ Ice Height Change};
+		\node (atl14)[l3b, below=0.5cm of atl11, xshift=-1.5cm]{\textbf{ATL14}\\Gridded Land\\ Ice Height};
+		\node (atl15)[l3b, below=0.5cm of atl11, xshift=1.5cm]{\textbf{ATL15}\\Gridded Land\\ Ice Height Change};
 		\node (atl20)[l3b, below=0.5cm of atl10, xshift=-1.5cm]{\textbf{ATL20}\\Gridded Sea\\ Ice Freeboard};
-		\node (atl21)[l3b, below=0.5cm of atl20, xshift=0cm]{\textbf{ATL21}\\Gridded Polar Sea\\ Surface Height};
+		\node (atl21)[l3b, below=0.5cm of atl10, xshift=1.5cm]{\textbf{ATL21}\\Gridded Polar Sea\\ Surface Height};
 		\node (atl18)[l3b, dashed, below=0.5cm of atl08, xshift=0cm]{\textbf{ATL18}\\Gridded Land\\ and Vegetation\\Height};
 		\node (atl19)[l3b, below=0.5cm of atl12]{\textbf{ATL19}\\Gridded Ocean\\Topography};
-		\node (atl23)[l3b, dashed, below=0.5cm of atl19]{\textbf{ATL23}\\3-Month Gridded\\Ocean Topography};
-		\node (atl22)[l3b, below=0.5cm of atl13]{\textbf{ATL22}\\Mean Inland\\Water Height};
-		\node (atl16)[l3b, below=4.65cm of J]{\textbf{ATL16}\\Weekly Gridded\\Atmosphere};
+		\node (atl23)[l3b, below=0.5cm of atl19]{\textbf{ATL23}\\3-Month Gridded\\Ocean Topography};
+		\node (atl22)[l3b, below=0.5cm of atl13]{\textbf{ATL22}\\Mean Inland\\ Water Data};
+		\node (atl16)[l3b, below=4.65cm of K]{\textbf{ATL16}\\Weekly Gridded\\Atmosphere};
 		\node (atl17)[l3b, below=0.5cm of atl16]{\textbf{ATL17}\\Monthly Gridded\\Atmosphere};
 		% Legend
-		\node (legend)[right=16cm of atl00, yshift=1cm, minimum height=0cm, minimum width=2.75cm]{\textbf{Legend}};
-		\node (level0)[l0, below=-0.1cm of legend, minimum height=0.75cm, minimum width=2.75cm]{\textbf{Level 0}};
-		\node (level1)[l1, below=0.1cm of level0, minimum height=0.75cm, minimum width=2.75cm]{\textbf{Level 1}};
-		\node (level2)[l2, below=0.1cm of level1, minimum height=0.75cm, minimum width=2.75cm]{\textbf{Level 2}};
-		\node (level3a)[l3a, below=0.1cm of level2, minimum height=0.75cm, minimum width=2.75cm]{\textbf{Level 3a}};
-		\node (level3b)[l3b, below=0.1cm of level3a, minimum height=0.75cm, minimum width=2.75cm]{\textbf{Level 3b}};
-		\node (extern)[ext, below=0.1cm of level3b, minimum height=0.75cm, minimum width=2.75cm]{\textbf{External}};
+		\node (legend)[right=16cm of atl00, yshift=1cm, minimum height=0cm, minimum width=3cm]{\textbf{Legend}};
+		\node (level0)[l0, below=-0.1cm of legend, minimum height=0.75cm, minimum width=3cm]{\textbf{Level 0}};
+		\node (level1)[l1, below=0.1cm of level0, minimum height=0.75cm, minimum width=3cm]{\textbf{Level 1}};
+		\node (level2)[l2, below=0.1cm of level1, minimum height=0.75cm, minimum width=3cm]{\textbf{Level 2}};
+		\node (level3a)[l3a, below=0.1cm of level2, minimum height=0.75cm, minimum width=3cm]{\textbf{Level 3a}};
+		\node (level3b)[l3b, below=0.1cm of level3a, minimum height=0.75cm, minimum width=3cm]{\textbf{Level 3b}};
+		\node (extern)[ext, below=0.1cm of level3b, minimum height=0.75cm, minimum width=3cm]{\textbf{External}};
 		% draw arrows between nodes
 		\draw[line width=0.3mm,-Latex](atl00) -- (atl01);
 		\draw[line width=0.3mm,-Latex](atl01) -- (atl02);
@@ -110,24 +112,25 @@
 		\draw[line width=0.3mm,-Latex](atl02) -- (atl04);
 		\draw[line width=0.3mm,-Latex](atl04) -- (atl09);
 		\draw[line width=0.3mm,-](atl03.south) -- (A.north);
-		\draw[line width=0.3mm,-](atl09.south) -- (I.north);
-		\draw[line width=0.3mm,-](atl09.east) -- (J.west);
+		\draw[line width=0.3mm,-](atl09.south) -- (J.north);
+		\draw[line width=0.3mm,-](atl09.east) -- (K.west);
 		\draw[line width=0.3mm,-](A.west) -- (D.east);
-		\draw[line width=0.3mm,-](A.east) -- (H.west);
-		\draw[line width=0.3mm,-Latex](D.south) -- (atl06.north);
-		\draw[line width=0.3mm,-Latex](C.south) -- (atl07.north);
-		\draw[line width=0.3mm,-Latex](B.south) -- (atl10.north);
-		\draw[line width=0.3mm,-Latex](E.south) -- (atl08.north);
+		\draw[line width=0.3mm,-](A.east) -- (I.west);
+%		\draw[line width=0.3mm,-Latex](E.south) -- (atl10.north);
+		\draw[line width=0.3mm,-Latex](D.south) -- (atl07.north);
+		\draw[line width=0.3mm,-Latex](C.south) -- (atl06.north);
+		\draw[line width=0.3mm,-Latex](B.south) -- (atl08.north);
 		\draw[line width=0.3mm,-Latex](F.south) -- (atl12.north);
 		\draw[line width=0.3mm,-Latex](G.south) -- (atl13.north);
 		\draw[line width=0.3mm,-Latex](H.south) -- (atl24.north);
-		\draw[line width=0.3mm,-Latex](J.south) -- (atl16.north);
+		\draw[line width=0.3mm,-Latex](I.south) -- (atl25.north);
+		\draw[line width=0.3mm,-Latex](K.south) -- (atl16.north);
 		\draw[line width=0.3mm,-Latex](atl06) -- (atl11);
 		\draw[line width=0.3mm,-Latex](atl11) -- (atl14);
 		\draw[line width=0.3mm,-Latex](atl11) -- (atl15);
-		\draw[line width=0.3mm,-Latex](atl07) -- (atl20);
+		\draw[line width=0.3mm,-Latex](atl07) -- (atl10);
 		\draw[line width=0.3mm,-Latex](atl10) -- (atl20);
-		\draw[line width=0.3mm,-Latex](atl20) -- (atl21);
+		\draw[line width=0.3mm,-Latex](atl10) -- (atl21);
 		\draw[line width=0.3mm,-Latex](atl08) -- (atl18);
 		\draw[line width=0.3mm,-Latex](atl12) -- (atl19);
 		\draw[line width=0.3mm,-Latex](atl19) -- (atl23);

doc/source/api_reference/spatial.rst

@@ -4,7 +4,7 @@ spatial
 
 Utilities for reading and operating on spatial data
 
- - Can read netCDF4, HDF5 or geotiff files
+ - Can read netCDF4, HDF5, or (cloud optimized) geotiff files
 
 Calling Sequence
 ================

icesat2_toolkit/convert.py

@@ -570,7 +570,7 @@ def attributes_encoder(self, attr):
         if isinstance(attr, (np.int_, np.intc, np.intp, np.int8, np.int16, np.int32,
             np.int64, np.uint8, np.uint16, np.uint32, np.uint64)):
             return int(attr)
-        elif isinstance(attr, (np.float_, np.float16, np.float32, np.float64)):
+        elif isinstance(attr, (np.float16, np.float32, np.float64)):
             return float(attr)
         elif isinstance(attr, (np.ndarray)):
             if not isinstance(attr[0], (object)):

icesat2_toolkit/fit.py

@@ -30,7 +30,8 @@
 from icesat2_toolkit.utilities import import_dependency
 
 # attempt imports
-neighbors = import_dependency('sklearn.neighbors')
+sklearn = import_dependency('sklearn')
+sklearn.neighbors = import_dependency('sklearn.neighbors')
 
 # PURPOSE: compress complete list of valid indices into a set of ranges
 def compress_list(i,n):
@@ -526,7 +527,7 @@ def reduce_histogram_fit(x, y, z, ind, dt, FIT_TYPE='gaussian',
     # using kernel density functions from scikit-learn neighbors
     # gaussian kernels will reflect more accurate distributions of the data
     # with less sensitivity to sampling width than histograms (tophat kernels)
-    kde = neighbors.KernelDensity(bandwidth=dz, kernel='gaussian')
+    kde = sklearn.neighbors.KernelDensity(bandwidth=dz, kernel='gaussian')
     kde.fit(z[:,None])
     # kde score_samples outputs are normalized log density functions
     hist = np.exp(kde.score_samples(z_full[:,None]) + np.log(n_max*dz))
@@ -654,7 +655,7 @@ def reduce_histogram_fit(x, y, z, ind, dt, FIT_TYPE='gaussian',
             # using kernel density functions from scikit-learn neighbors
             # gaussian kernels will reflect more accurate distributions of the data
             # with less sensitivity to sampling width than histograms (tophat kernels)
-            kde = neighbors.KernelDensity(bandwidth=dz,kernel='gaussian')
+            kde = sklearn.neighbors.KernelDensity(bandwidth=dz, kernel='gaussian')
             kde.fit(z_filt[:,None])
             # kde score_samples outputs are normalized log density functions
             hist = np.exp(kde.score_samples(z_full[:,None]) + np.log(nz*dz))
@@ -989,7 +990,7 @@ def calc_first_photon_bias(temporal_residuals,n_pulses,n_pixels,dead_time,dt,
     # using kernel density functions from scikit-learn neighbors
     # gaussian kernels will reflect more accurate distributions of the data
     # with less sensitivity to sampling width than histograms (tophat kernels)
-    kde = neighbors.KernelDensity(bandwidth=dt,kernel='gaussian')
+    kde = sklearn.neighbors.KernelDensity(bandwidth=dt, kernel='gaussian')
     kde.fit(temporal_residuals[:,None])
     # kde score_samples outputs are normalized log density functions
     hist = np.exp(kde.score_samples(t_full[:,None]) + np.log(cnt*dt))

icesat2_toolkit/io/ATL03.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-ATL03.py (05/2024)
+ATL03.py (10/2025)
 Read ICESat-2 ATL03 and ATL09 data files to calculate average segment surfaces
     ATL03 datasets: Global Geolocated Photons
     ATL09 datasets: Atmospheric Characteristics
@@ -15,6 +15,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 10/2025: orbit_info group may now contain sub-groups
     Updated 05/2024: use wrapper to importlib for optional dependencies
         check if input filename is an open HDF5 file object
     Updated 03/2024: use pathlib to define and operate on paths
@@ -166,6 +167,12 @@ def read_granule(FILENAME, ATTRIBUTES=False, KEEP=False, **kwargs):
     IS2_atl03_attrs['orbit_info'] = {}
     for key,val in fileID['orbit_info'].items():
         IS2_atl03_mds['orbit_info'][key] = val[:]
+        if isinstance(val, h5py.Dataset):
+            IS2_atl03_mds['orbit_info'][key] = val[:]
+        elif isinstance(val, h5py.Group):
+            IS2_atl03_mds['orbit_info'][key] = {}
+            for k,v in val.items():
+                IS2_atl03_mds['orbit_info'][key][k] = v[:]
         # Getting attributes of group and included variables
         if ATTRIBUTES:
             # Global Group Attributes
@@ -463,7 +470,12 @@ def read_main(FILENAME, ATTRIBUTES=False, KEEP=False, **kwargs):
     IS2_atl03_mds['orbit_info'] = {}
     IS2_atl03_attrs['orbit_info'] = {}
     for key,val in fileID['orbit_info'].items():
-        IS2_atl03_mds['orbit_info'][key] = val[:]
+        if isinstance(val, h5py.Dataset):
+            IS2_atl03_mds['orbit_info'][key] = val[:]
+        elif isinstance(val, h5py.Group):
+            IS2_atl03_mds['orbit_info'][key] = {}
+            for k,v in val.items():
+                IS2_atl03_mds['orbit_info'][key][k] = v[:]
         # Getting attributes of group and included variables
         if ATTRIBUTES:
             # Global Group Attributes

icesat2_toolkit/io/ATL06.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-ATL06.py (05/2024)
+ATL06.py (10/2025)
 Read ICESat-2 ATL06 (Land Ice Along-Track Height Product) data files
 
 OPTIONS:
@@ -16,6 +16,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 10/2025: orbit_info group may now contain sub-groups
     Updated 05/2024: use wrapper to importlib for optional dependencies
         check if input filename is an open HDF5 file object
     Updated 03/2024: use pathlib to define and operate on paths
@@ -191,7 +192,12 @@ def read_granule(FILENAME, ATTRIBUTES=False, HISTOGRAM=False,
     # ICESat-2 orbit_info Group
     IS2_atl06_mds['orbit_info'] = {}
     for key,val in fileID['orbit_info'].items():
-        IS2_atl06_mds['orbit_info'][key] = val[:]
+        if isinstance(val, h5py.Dataset):
+            IS2_atl06_mds['orbit_info'][key] = val[:]
+        elif isinstance(val, h5py.Group):
+            IS2_atl06_mds['orbit_info'][key] = {}
+            for k,v in val.items():
+                IS2_atl06_mds['orbit_info'][key][k] = v[:]
     # ICESat-2 quality_assessment Group
     IS2_atl06_mds['quality_assessment'] = {}
     for key,val in fileID['quality_assessment'].items():

icesat2_toolkit/io/ATL07.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-ATL07.py (05/2024)
+ATL07.py (10/2025)
 Read ICESat-2 ATL07 (Sea Ice Height) data files
 
 PYTHON DEPENDENCIES:
@@ -11,6 +11,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 10/2025: orbit_info group may now contain sub-groups
     Updated 05/2024: use wrapper to importlib for optional dependencies
         check if input filename is an open HDF5 file object
     Updated 03/2024: use pathlib to define and operate on paths
@@ -135,7 +136,12 @@ def read_granule(FILENAME, ATTRIBUTES=False, KEEP=False, **kwargs):
     # ICESat-2 orbit_info Group
     IS2_atl07_mds['orbit_info'] = {}
     for key,val in fileID['orbit_info'].items():
-        IS2_atl07_mds['orbit_info'][key] = val[:]
+        if isinstance(val, h5py.Dataset):
+            IS2_atl07_mds['orbit_info'][key] = val[:]
+        elif isinstance(val, h5py.Group):
+            IS2_atl07_mds['orbit_info'][key] = {}
+            for k,v in val.items():
+                IS2_atl07_mds['orbit_info'][key][k] = v[:]
     # ICESat-2 quality_assessment Group
     IS2_atl07_mds['quality_assessment'] = {}
     for key,val in fileID['quality_assessment'].items():

icesat2_toolkit/io/ATL10.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-ATL10.py (05/2024)
+ATL10.py (10/2025)
 Read ICESat-2 ATL10 (Sea Ice Freeboard) data files
 
 PYTHON DEPENDENCIES:
@@ -11,6 +11,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 10/2025: orbit_info group may now contain sub-groups
     Updated 05/2024: use wrapper to importlib for optional dependencies
         check if input filename is an open HDF5 file object
     Updated 03/2024: use pathlib to define and operate on paths
@@ -133,7 +134,12 @@ def read_granule(FILENAME, ATTRIBUTES=False, KEEP=False, **kwargs):
     # ICESat-2 orbit_info Group
     IS2_atl10_mds['orbit_info'] = {}
     for key,val in fileID['orbit_info'].items():
-        IS2_atl10_mds['orbit_info'][key] = val[:]
+        if isinstance(val, h5py.Dataset):
+            IS2_atl10_mds['orbit_info'][key] = val[:]
+        elif isinstance(val, h5py.Group):
+            IS2_atl10_mds['orbit_info'][key] = {}
+            for k,v in val.items():
+                IS2_atl10_mds['orbit_info'][key][k] = v[:]
     # ICESat-2 quality_assessment Group
     IS2_atl10_mds['quality_assessment'] = {}
     for key,val in fileID['quality_assessment'].items():

icesat2_toolkit/io/ATL11.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-ATL11.py (05/2024)
+ATL11.py (10/2025)
 Read ICESat-2 ATL11 (Annual Land Ice Height) data files
 
 OPTIONS:
@@ -18,6 +18,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 10/2025: orbit_info group may now contain sub-groups
     Updated 05/2024: use wrapper to importlib for optional dependencies
         check if input filename is an open HDF5 file object
     Updated 03/2024: use pathlib to define and operate on paths
@@ -173,7 +174,12 @@ def read_granule(FILENAME, GROUPS=['cycle_stats'], ATTRIBUTES=False,
     # ICESat-2 orbit_info Group
     IS2_atl11_mds['orbit_info'] = {}
     for key,val in fileID['orbit_info'].items():
-        IS2_atl11_mds['orbit_info'][key] = val[:]
+        if isinstance(val, h5py.Dataset):
+            IS2_atl11_mds['orbit_info'][key] = val[:]
+        elif isinstance(val, h5py.Group):
+            IS2_atl11_mds['orbit_info'][key] = {}
+            for k,v in val.items():
+                IS2_atl11_mds['orbit_info'][key][k] = v[:]
 
     # ICESat-2 quality_assessment Group
     IS2_atl11_mds['quality_assessment'] = {}