Merge remote-tracking branch 'origin/main' into hayes-dev

.github/workflows/ci.yml

@@ -30,9 +30,6 @@ jobs:
       - uses: pre-commit/[email protected]
         with:
           extra_args: --hook-stage manual --all-files
-      - name: Run PyLint
-        continue-on-error: true
-        run: pipx run nox -s pylint -- --output-format=github
 
   checks:
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
@@ -68,7 +65,8 @@ jobs:
           python -m pytest -ra --cov --cov-report=xml --cov-report=term
           --durations=20
 
-      - name: Upload coverage report
-        uses: codecov/[email protected]
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+      # NOTE: need an account for this...
+      # - name: Upload coverage report
+      #   uses: codecov/[email protected]
+      #   with:
+      #     token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pixi.yml

@@ -15,16 +15,24 @@ jobs:
 
       - uses: prefix-dev/[email protected]
         with:
+          pixi-version: v0.34.0
           environments: dev
-          cache: true
-          cache-write:
-            ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+          manifest-path: pyproject.toml
+          cache: false
+          locked: false
+          #cache-write:
+          #  ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
       # NOTE: https://github.com/prefix-dev/setup-pixi/issues/136
       - name: Ensure Dynamic version
         run: |
           pip install -e .
 
+      - name: Run Pylint
+        continue-on-error: true
+        run: |
+          pixi run lint
+
       - name: Run Pytest
         env:
           MAXAR_API_KEY: ${{ secrets.MAXAR_API_KEY}}

.github/workflows/upstream.yml

@@ -0,0 +1,48 @@
+# Test against the latest versions of Python and other libraries
+name: Upstream versions
+
+on:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  checks:
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.13", "3.14"]
+        # windows-latest,
+        runs-on: [ubuntu-latest, macos-14]
+        #include:
+        #  - python-version: "pypy-3.10"
+        #    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Install package
+        run: python -m pip install .[dev]
+
+      - name: Test package
+        env:
+          MAXAR_API_KEY: ${{ secrets.MAXAR_API_KEY}}
+        run: >-
+          python -m pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20

.pre-commit-config.yaml

@@ -87,3 +87,13 @@ repos:
       - id: check-dependabot
       - id: check-github-workflows
       - id: check-readthedocs
+
+  # https://pylint.pycqa.org/en/latest/user_guide/installation/pre-commit-integration.html#pre-commit-integration
+  # - repo: local
+  #   hooks:
+  #     - id: pylint
+  #       name: pylint
+  #       entry: pylint
+  #       language: system
+  #       types: [python]
+  #       require_serial: true

README.md

@@ -2,6 +2,7 @@
 
 [![Actions Status][actions-badge]][actions-link]
 [![Documentation Status][rtd-badge]][rtd-link]
+
 [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/uw-cryo/coincident)
 
 <!-- SPHINX-START -->
@@ -27,39 +28,14 @@ Such datasets are intended to be used by the NASA STV community for
 calibration/validation, fusion algorithm development, and discipline-specific
 scientific analysis.
 
-**This tool is under active development, there are no stable releases yet!**
-https://science.nasa.gov/earth-science/decadal-surveys/decadal-stv/coincident-datasets/
-
-## Development
-
-Use [pixi](https://pixi.sh) for environment management
-
-```bash
-git clone https://github.com/uw-cryo/coincident.git
-cd coincident
-git checkout -b newfeature
-pixi shell --environment dev # type `exit` to deactivate
-pre-commit install
+See here for more information:
+<https://science.nasa.gov/earth-science/decadal-surveys/decadal-stv/coincident-datasets>
 
-# Or run pre-configured environments and commands
-pixi run test
-pixi run lint
-pixi run docs
-```
-
-## Authentication
-
-Some datasets require authentication to _search_ (Maxar) others only require
-authentication to _download_ data (NASA). `coincident` assumes you have the
-following Environment Variables defined:
-
-```bash
-export EARTHDATA_USERNAME=xxxxx
-export EARTHDATA_PASSWORD=yyyyy
-export MAXAR_API_KEY=zzzzz
-```
+**This tool is under active development, there are no stable releases yet!**
 
-### Acknowledgements
+## Acknowledgements
 
 - Python packaging template provided by
-  https://github.com/scientific-python/cookie
+  <https://github.com/scientific-python/cookie>
+
+- Funding for this effort was provided by NASA Grant 80NSSC22K1094

docs/_static/custom.css

@@ -0,0 +1,4 @@
+/* Make default pandas table font smaller */
+div.cell_output table {
+  font-size: 0.8em;
+}

docs/api.rst

@@ -19,7 +19,6 @@ Search
    wesm.get_swath_polygons
 
 
-
 Overlaps
 --------
 
@@ -29,6 +28,7 @@ Overlaps
    :toctree: generated/
 
    geographic_area
+   subset_by_minimum_area
    subset_by_temporal_overlap
 
 

docs/conf.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import importlib.metadata
-from typing import Any
 
 project = "coincident"
 copyright = "2024, Scott Henderson"
@@ -34,25 +33,39 @@
     ".venv",
 ]
 
-html_theme = "furo"
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme_options: dict[str, Any] = {
-    "footer_icons": [
+html_theme = "pydata_sphinx_theme"
+html_theme_options = {
+    "use_edit_page_button": True,
+    "icon_links": [
         {
             "name": "GitHub",
             "url": "https://github.com/uw-cryo/coincident",
-            "html": """
-                <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
-                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
-                </svg>
-            """,
-            "class": "",
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
         },
     ],
-    "source_repository": "https://github.com/uw-cryo/coincident",
-    "source_branch": "main",
-    "source_directory": "docs/",
 }
+html_title = "Coincident"
+html_context = {
+    "github_user": "uw-cryo",
+    "github_repo": "coincident",
+    "github_version": "main",
+    "doc_path": "docs",
+}
+
+# remove sidebar, see GH issue #82
+html_css_files = [
+    "custom.css",
+]
+
+html_static_path = ["_static"]
+
+# NOTE: consider adding back in once for distinct sections (user guide, examples, API reference)
+# https://pydata-sphinx-theme.readthedocs.io/en/stable/user_guide/layout.html#primary-sidebar-left
+# html_sidebars = {"**": []}
 
 myst_enable_extensions = [
     "colon_fence",