fix: some small changes for glambie submission

.github/workflows/python-request.yml

@@ -24,7 +24,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up pixi environment
-      uses: prefix-dev/setup-pixi@v0.9.1
+      uses: prefix-dev/setup-pixi@v0.9.6
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

CITATION.cff

@@ -27,9 +27,9 @@ contributors:
     affiliation: University of Washington, Applied Physics Laboratory
 
 contact:
-- family-names: Sutterley
-  given-names: Tyler C.
-  orcid: "https://orcid.org/0000-0002-6964-1194"
+  - family-names: Sutterley
+    given-names: Tyler C.
+    orcid: "https://orcid.org/0000-0002-6964-1194"
 
 identifiers:
   - type: doi

IS2view/api.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 api.py
-Written by Tyler Sutterley (02/2026)
+Written by Tyler Sutterley (06/2026)
 Plotting tools for visualizing rioxarray variables on leaflet maps
 
 PYTHON DEPENDENCIES:
@@ -28,6 +28,7 @@
         https://xyzservices.readthedocs.io/en/stable/
 
 UPDATE HISTORY:
+    Updated 06/2026: verify that area is conserved between calls if using option
     Updated 02/2026: add conserve and all_touched options to extract function
     Updated 01/2025: added more zoom levels and update max_zoom
         deprecation update for writing the crs to the dataset object
@@ -1919,16 +1920,18 @@ def average(
             clipped = self._ds_selected.sel(time=t).where(mask, drop=False)
             # reduce cell area to time (for Release-02 and above)
             if (ice_area.ndim == 3) and ("time" in ice_area.dims):
-                area = ice_area.sel(time=t)
+                area = ice_area.sel(time=t).where(mask, drop=False)
             else:
-                area = ice_area.copy()
+                area = ice_area.where(mask, drop=False)
+            # multiply area by clipped mask
+            area *= np.isfinite(clipped).astype(float)
             # calculate regional average
             if self._variable in error_variables:
                 self._data[i] = np.sqrt(
-                    np.sum(area * clipped**2) / np.sum(area)
+                    np.nansum(area * clipped**2) / np.nansum(area)
                 )
             else:
-                self._data[i] = np.sum(area * clipped) / np.sum(area)
+                self._data[i] = np.nansum(area * clipped) / np.nansum(area)
             # output additional fields
             for field_name in fields:
                 # reduce data to time and clip to geometry
@@ -1937,14 +1940,14 @@ def average(
                 )
                 if field_name in error_variables:
                     self._fields[field_name][i] = np.sqrt(
-                        np.sum(area * clipped**2) / np.sum(area)
+                        np.nansum(area * clipped**2) / np.nansum(area)
                     )
                 else:
-                    self._fields[field_name][i] = np.sum(
+                    self._fields[field_name][i] = np.nansum(
                         area * clipped
-                    ) / np.sum(area)
+                    ) / np.nansum(area)
             # calculate total area for region
-            self._area[i] = np.sum(area)
+            self._area[i] = np.nansum(area)
         # only create plot if valid
         if np.all(np.isnan(self._data)):
             return

doc/source/api_reference/API-Reference.rst

@@ -0,0 +1,12 @@
+=============
+API Reference
+=============
+
+.. toctree::
+    :maxdepth: 1
+
+    ./api.rst
+    ./convert.rst
+    ./io.rst
+    ./tools.rst
+    ./utilities.rst

doc/source/api_reference/api.rst

@@ -1,6 +1,6 @@
-===
-api
-===
+=======
+``api``
+=======
 
 Plotting tools for visualizing `rioxarray <https://corteva.github.io/rioxarray/stable/>`_ variables on `ipyleaflet <https://ipyleaflet.readthedocs.io/en/latest/>`_ maps
 

doc/source/api_reference/convert.rst

@@ -1,6 +1,6 @@
-=======
-convert
-=======
+===========
+``convert``
+===========
 
 Utilities for converting gridded ICESat-2 files from native netCDF4
 

doc/source/api_reference/io.rst

@@ -1,6 +1,6 @@
-==
-io
-==
+======
+``io``
+======
 
 Utilities for reading gridded ICESat-2 files using rasterio and xarray
 

doc/source/api_reference/tools.rst

@@ -1,6 +1,6 @@
-=====
-tools
-=====
+=========
+``tools``
+=========
 
 `User interface <https://ipywidgets.readthedocs.io/en/latest/>`_ tools for `Jupyter notebook <https://jupyter.org/>`_
 

doc/source/api_reference/utilities.rst

@@ -1,6 +1,6 @@
-=========
-utilities
-=========
+=============
+``utilities``
+=============
 
 Download and management utilities
 

doc/source/conf.py

@@ -10,14 +10,20 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
+import os
+
 # import sys
+import logging
 import datetime
+import warnings
+
 # sys.path.insert(0, os.path.abspath('.'))
 import importlib.metadata
 
 
 # -- Project information -----------------------------------------------------
+on_rtd = os.environ.get('READTHEDOCS') == 'True'
+on_github = os.environ.get('GITHUB_ACTIONS') == 'true'
 
 # package metadata
 metadata = importlib.metadata.metadata("IS2view")
@@ -32,6 +38,10 @@
 # append "v" before the version
 release = f"v{version}"
 
+# suppress warnings in examples and documentation
+if on_rtd:
+    warnings.filterwarnings('ignore')
+
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
@@ -52,7 +62,21 @@
     ".rst": "restructuredtext",
     ".ipynb": "myst-nb",
 }
-nb_execution_mode = "off"
+# execute notebooks on build
+if on_rtd:
+    nb_execution_mode = 'auto'
+    nb_execution_excludepatterns = [
+        'notebooks/*.ipynb',
+    ]
+    nb_output_stderr = 'remove-warn'
+elif on_github:
+    nb_execution_mode = 'off'
+else:
+    nb_execution_mode = 'auto'
+    nb_execution_excludepatterns = [
+        'notebooks/*.ipynb',
+    ]
+    nb_output_stderr = 'remove-warn'
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -101,21 +125,27 @@
     name, _, url = project_url.partition(', ')
     project_urls[name.lower()] = url
 # fetch the repository url
-repository_url = project_urls.get('repository')
+github_url = project_urls.get("repository")
+*_, github_user, github_repo = github_url.split("/")
 # add html context
 html_context = {
+    "display_github": True,
+    "github_user": github_user,
+    "github_repo": github_repo,
+    "github_version": "main",
+    "conf_py_path": "/doc/source/",
     "menu_links": [
         (
             '<i class="fa fa-github fa-fw"></i> Source Code',
-            repository_url,
+            github_url,
         ),
         (
             '<i class="fa fa-book fa-fw"></i> License',
-            f"{repository_url}/blob/main/LICENSE",
+            f"{github_url}/blob/main/LICENSE",
         ),
         (
             '<i class="fa fa-comment fa-fw"></i> Discussions',
-            f"{repository_url}/discussions",
+            f"{github_url}/discussions",
         ),
     ],
 }

doc/source/getting_started/Install.ipynb

@@ -0,0 +1,164 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "2e01086c",
+   "metadata": {},
+   "source": [
+    "# Setup and Installation\n",
+    "\n",
+    "## Dependencies\n",
+    "\n",
+    "`IS2view` is dependent on several open source programs that can be installed using OS-specific package management systems (e.g. `apt` or `homebrew`), `conda` or from source:\n",
+    "\n",
+    "- [PROJ](https://proj.org/)\n",
+    "- [HDF5](https://www.hdfgroup.org/)\n",
+    "- [libxml2](http://xmlsoft.org/)\n",
+    "- [libxslt](http://xmlsoft.org/XSLT/)\n",
+    "\n",
+    "## Installation\n",
+    "\n",
+    "`IS2view` is available for download from the [GitHub repository](https://github.com/tsutterley/IS2view), the [Python Package Index (pypi)](https://pypi.org/project/IS2view/), and from [conda-forge](https://anaconda.org/conda-forge/IS2view).\n",
+    "\n",
+    "\n",
+    "The simplest installation for most users will likely be using `conda` or `mamba`:\n",
+    "\n",
+    "```bash\n",
+    "conda install -c conda-forge is2view\n",
+    "```\n",
+    "\n",
+    "`conda` installed versions of `IS2view` can be upgraded to the latest stable release:\n",
+    "\n",
+    "```bash\n",
+    "conda update is2view\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "af65ece3",
+   "metadata": {},
+   "source": [
+    "## Development Install\n",
+    "\n",
+    "To use the development repository, please fork `IS2view` into your own account and then clone onto your system:\n",
+    "\n",
+    "```bash\n",
+    "git clone https://github.com/tsutterley/IS2view.git\n",
+    "```\n",
+    "\n",
+    "`IS2view` can then be installed within the package directory using `pip`:\n",
+    "\n",
+    "```bash\n",
+    "python3 -m pip install --user .\n",
+    "```\n",
+    "\n",
+    "To include all optional dependencies:\n",
+    "\n",
+    "```bash\n",
+    "python3 -m pip install --user .[all]\n",
+    "```\n",
+    "\n",
+    "The development version of `IS2view` can also be installed directly from GitHub using `pip`:\n",
+    "\n",
+    "```bash\n",
+    "python3 -m pip install --user git+https://github.com/tsutterley/IS2view.git\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "14ae498c",
+   "metadata": {},
+   "source": [
+    "## Package Management with ``pixi``\n",
+    "\n",
+    "Alternatively `pixi` can be used to create a [streamlined environment](https://pixi.sh/) after cloning the repository:\n",
+    "\n",
+    "```bash\n",
+    "pixi install\n",
+    "```\n",
+    "\n",
+    "`pixi` maintains isolated environments for each project, allowing for different versions of `IS2view` and its dependencies to be used without conflict.\n",
+    "The `pixi.lock` file within the repository defines the required packages and versions for the environment.\n",
+    "\n",
+    "`pixi` can also create shells for running programs within the environment:\n",
+    "\n",
+    "```bash\n",
+    "pixi shell\n",
+    "```\n",
+    "\n",
+    "To see the available tasks within the `IS2view` workspace:\n",
+    "\n",
+    "```bash\n",
+    "pixi task list\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "15f4d37e",
+   "metadata": {
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "! pixi task list"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "158990b9",
+   "metadata": {},
+   "source": [
+    "```{note}\n",
+    "`pixi` is under active development and may change in future releases\n",
+    "```\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "286e9898",
+   "metadata": {},
+   "source": [
+    "## Verifying Installation"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dbeee9a1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import IS2view\n",
+    "\n",
+    "print(f\"IS2view version: {IS2view.__version__}\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}