Release v0.8.4

.github/CODEOWNERS

@@ -1,2 +1,2 @@
 # These owners will be requested for review when someone opens a pull request.
-*       @ASFHyP3/plugins
+*       @ASFHyP3/Tools @ASFHyP3/SciDev

.github/dependabot.yml

@@ -5,9 +5,23 @@
 
 version: 2
 updates:
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: weekly
+    labels:
+      - bumpless
+    groups:
+      pip-deps:
+        patterns:
+          - "*"
   - package-ecosystem: github-actions
     directory: /
     schedule:
       interval: weekly
     labels:
       - bumpless
+    groups:
+      github-actions-deps:
+        patterns:
+          - "*"

.github/workflows/changelog.yml

@@ -11,4 +11,4 @@
       - develop
 jobs:
   call-changelog-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.20.0

.github/workflows/create-jira-issue.yml

@@ -6,10 +6,10 @@
 
 jobs:
   call-create-jira-issue-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-create-jira-issue.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-create-jira-issue.yml@v0.20.0
     secrets:
       JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
       JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}
       JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }}
       JIRA_PROJECT: ${{ secrets.JIRA_PROJECT }}
       JIRA_FIELDS: ${{ secrets.JIRA_FIELDS }}

.github/workflows/distribute.yml

@@ -7,17 +7,17 @@
 
 jobs:
   call-version-info-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.20.0
     with:
       python_version: "3.11"
 
   distribute:
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -31,7 +31,7 @@
           python -m build
 
       - name: upload to PyPI.org
-        uses: pypa/gh-action-pypi-publish@v1.12.3
+        uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           user: __token__
           password: ${{ secrets.TOOLS_PYPI_PAK }}

.github/workflows/labeled-pr.yml

@@ -12,4 +12,4 @@
 
 jobs:
   call-labeled-pr-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.20.0

.github/workflows/release.yml

@@ -9,7 +9,7 @@ jobs:
   finish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           token: ${{ secrets.TOOLS_BOT_PAK }}

.github/workflows/static-analysis.yml

@@ -5,10 +5,10 @@
 jobs:
   # Docs: https://github.com/ASFHyP3/actions
   call-secrets-analysis-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.20.0
 
   call-ruff-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-ruff.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-ruff.yml@v0.20.0
 
   call-mypy-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-mypy.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-mypy.yml@v0.20.0

.github/workflows/tag-version.yml

@@ -7,6 +7,6 @@
 
 jobs:
   call-bump-version-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.20.0
     secrets:
       USER_TOKEN: ${{ secrets.TOOLS_BOT_PAK }}

.github/workflows/test-and-build.yml

@@ -3,30 +3,38 @@ name: Test and build
 on:
   push:
     branches:
-      - main
       - develop
+    tags:
+      - 'v*'
   pull_request:
     branches:
       - main
       - develop
 
 jobs:
   call-pytest-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-pytest.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-pytest.yml@v0.20.0
+    permissions:
+      contents: read
     with:
       local_package_name: asf_tools
       python_versions: >-  # Optional; default shown
         ["3.10", "3.11"]
 
   call-version-info-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.20.0
+    permissions:
+      contents: read
     with:
       python_version: "3.10"
 
   call-docker-ghcr-workflow:
     needs: call-version-info-workflow
-    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.15.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.20.0
+    permissions:
+      contents: read
+      packages: write
     with:
       version_tag: ${{ needs.call-version-info-workflow.outputs.version_tag }}
     secrets:
-      USER_TOKEN: ${{ secrets.TOOLS_BOT_PAK }}
+      USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}

CHANGELOG.md

@@ -6,6 +6,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [PEP 440](https://www.python.org/dev/peps/pep-0440/) 
 and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.8.4]
+
+### Changed
+- Various dependencies have been upgraded.
+
+### Fixed
+- Support rasters with `nan` nodata values in `read_as_masked_array`
+- Upgraded to [Actions v0.20.0](https://github.com/ASFHyP3/actions/releases/tag/v0.20.0) so that Docker image `latest` tag will correspond to the actual version tag. See https://github.com/ASFHyP3/actions/issues/278
+
 ## [0.8.3]
 
 ### Changed

environment.yml

@@ -9,16 +9,14 @@ dependencies:
   # For packaging, and testing
   # - arcpy  # windows only
   - python-build
-  - ruff
-  - mypy
   - setuptools>=61
   - setuptools_scm>=6.2
   - pytest
   - pytest-console-scripts
   - pytest-cov
   # For running
   - astropy
-  - boto3<1.36.0  # FIXME: remove top pin when tests no longer fail
+  - boto3>=1.36.0
   - fiona
   - gdal>=3.7
   - geopandas
@@ -33,5 +31,6 @@ dependencies:
   - shapely
   - tqdm
   - pip:
+    - -r requirements-static.txt
     # for testing
     - gdal-utils

pyproject.toml

@@ -22,6 +22,7 @@ classifiers=[
 ]
 dependencies = [
     "astropy",
+    "boto3>=1.36.0",
     "fiona",
     "gdal>=3.3",
     "geopandas",
@@ -105,6 +106,12 @@ convention = "google"
 case-sensitive = true
 lines-after-imports = 2
 
+[tool.ruff.lint.flake8-annotations]
+suppress-dummy-args = true
+
+[tool.ruff.lint.extend-per-file-ignores]
+"tests/*" = ["D1", "ANN"]
+
 [tool.mypy]
 python_version = "3.10"
 warn_redundant_casts = true

requirements-static.txt

@@ -0,0 +1,2 @@
+ruff==0.12.3
+mypy==1.16.1

src/asf_tools/dem.py

@@ -31,6 +31,7 @@ def prepare_dem_vrt(vrt: str | Path, geometry: ogr.Geometry | BaseGeometry):
         if isinstance(geometry, BaseGeometry):
             geometry = ogr.CreateGeometryFromWkb(geometry.wkb)
 
+        assert isinstance(geometry, ogr.Geometry)
         min_lon, max_lon, _, _ = geometry.GetEnvelope()
         if min_lon < -160.0 and max_lon > 160.0:
             raise ValueError(f'asf_tools does not currently support geometries that cross the antimeridian: {geometry}')

src/asf_tools/hydrosar/flood_map.py

@@ -16,7 +16,7 @@
 from collections.abc import Callable
 from pathlib import Path
 from shutil import make_archive
-from typing import Literal
+from typing import Any, Literal
 
 import numpy as np
 from osgeo import gdal
@@ -164,7 +164,7 @@ def estimate_flood_depth(
 
         if estimator.lower() == 'nmad':
             hand_mean = np.nanmean(hand[flood_labels == label])
-            hand_std = stats.median_abs_deviation(hand[flood_labels == label], scale='normal', nan_policy='omit')
+            hand_std: Any = stats.median_abs_deviation(hand[flood_labels == label], scale='normal', nan_policy='omit')
 
         if estimator.lower() == 'numpy':
             hand_mean = np.nanmean(hand[flood_labels == label])
@@ -260,7 +260,9 @@ def make_flood_map(
     padding_mask = vv_array.mask
     del vv_array
 
-    labeled_flood_mask, num_labels = ndimage.label(flood_mask)
+    # The return type annotation for ndimage.label is int, which seems incorrect,
+    # since the documentation shows an example of unpacking the return value, like we do here.
+    labeled_flood_mask, num_labels = ndimage.label(flood_mask)  # type: ignore[misc]
     object_slices = ndimage.find_objects(labeled_flood_mask)
     log.info(f'Detected {num_labels} waterbodies...')
     if estimator.lower() == 'iterative':

src/asf_tools/hydrosar/hand/prepare.py

@@ -36,6 +36,7 @@ def prepare_hand_vrt(vrt: str | Path, geometry: ogr.Geometry | BaseGeometry):
         if isinstance(geometry, BaseGeometry):
             geometry = ogr.CreateGeometryFromWkb(geometry.wkb)
 
+        assert isinstance(geometry, ogr.Geometry)
         min_lon, max_lon, _, _ = geometry.GetEnvelope()
         if min_lon < -160.0 and max_lon > 160.0:
             raise ValueError(f'asf_tools does not currently support geometries that cross the antimeridian: {geometry}')

src/asf_tools/hydrosar/threshold.py

@@ -10,7 +10,7 @@ def _make_histogram(image):
     del indices
     size = image.size
     maximum = int(np.ceil(np.amax(image)) + 1)
-    histogram = np.zeros((1, maximum))
+    histogram: np.ndarray = np.zeros((1, maximum))
     for i in range(0, size):
         floor_value = np.floor(image[i]).astype(np.uint8)
         if 0 < floor_value < maximum - 1: