Merge pull request #140 from GeoscienceAustralia/upgrade_dev

Use latest DEA Tools in dev requirements, make `postgres` optional extra

Author: vnewey

.github/workflows/dea-intertidal-image-dev.yml

@@ -31,6 +31,11 @@ on:
   release:
     types: [edited, published]
 
+# Ensure only one test workflow runs per branch/PR at a time
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}  # Group by workflow and branch/PR ref
+  cancel-in-progress: true # Cancel any in-progress runs if a new one starts
+
 permissions:
   id-token: write  # Required for requesting Json web token
   contents: write  # Required for actions/checkout

.github/workflows/dea-intertidal-image.yml

@@ -34,6 +34,11 @@ on:
   release:
     types: [edited, published]
 
+# Ensure only one test workflow runs per branch/PR at a time
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}  # Group by workflow and branch/PR ref
+  cancel-in-progress: true # Cancel any in-progress runs if a new one starts
+
 permissions:
   id-token: write  # Required for requesting Json web token
   contents: write  # Required for actions/checkout

Dockerfile

@@ -36,7 +36,7 @@ RUN pip install uv && \
 # Now copy the rest of the files
 COPY . /app
 
-# Install DEA Intertidal and verify installation
-RUN uv pip install . --system && \
+# Install DEA Intertidal with postgres extra and verify installation
+RUN uv pip install .[postgres] --system && \
     uv pip check && \
     dea-intertidal --help

dev-requirements.in

@@ -3,18 +3,18 @@ aiohttp==3.10.10
 awscli==1.38.1
 botocore==1.37.1
 Bottleneck==1.4.2
-click==8.1.7
+click==8.2.1
 dask==2024.3.1
-datacube[s3,performance]==1.9.3
-dea-tools==0.3.6
+datacube[s3,performance]==1.9.6
+dea-tools==0.4.0
 eodatasets3
 eo-tides==0.8.0
 hdstats==0.1.8.post1
 geopandas==0.14.4
 matplotlib==3.9.2
 mdutils==1.6.0
 numpy==1.26.4
-odc-algo==0.2.3
+odc-algo==1.0.1
 odc-geo==0.4.10
 odc-ui==0.2.1
 pandas==2.2.3

intertidal/io.py

@@ -31,6 +31,7 @@
 from eodatasets3.verify import PackageChecksum
 from eodatasets3.stac import to_stac_item, validate_item
 from datacube.utils.masking import mask_invalid_data
+from datacube.utils.geometry import Geometry as Geometry_datacube18
 
 from intertidal.utils import configure_logging
 
@@ -120,7 +121,7 @@ def extract_geobox(
     """
 
     # List of valid input geometry types (from `odc-geo` or `datacube-core`)
-    GEOM_TYPES = (odc.geo.geom.Geometry, datacube.utils.geometry._base.Geometry)
+    GEOM_TYPES = (odc.geo.geom.Geometry, Geometry_datacube18)
 
     # Either `study_area` or `geom` must be provided
     if study_area is None and geom is None:

setup.py

@@ -44,6 +44,11 @@
     "xarray",
 ]
 
+# Optional dependencies
+EXTRAS = {
+    "postgres": ["psycopg2"],
+}
+
 # Package metadata
 NAME = "dea_intertidal"
 DESCRIPTION = "Tools for running Digital Earth Australia Intertidal"
@@ -63,6 +68,7 @@
     "python_requires": REQUIRES_PYTHON,
     "url": URL,
     "install_requires": REQUIRED,
+    "extras_require": EXTRAS,
     "packages": find_packages(),
     "include_package_data": True,
     "license": "Apache License 2.0",

tests/README.md

@@ -10,7 +10,7 @@ Integration tests
 
 This directory contains tests that are run to verify that DEA Intertidal code runs correctly. The ``test_intertidal.py`` file runs a small-scale full workflow analysis over an intertidal flat in the Gulf of Carpentaria using the DEA Intertidal [Command Line Interface (CLI) tools](../notebooks/Intertidal_CLI.ipynb), and compares these results against a LiDAR validation DEM to produce some simple accuracy metrics.
 
-The latest integration test completed at **2025-07-14 14:20**. Compared to the previous run, it had an:
+The latest integration test completed at **2025-07-16 17:07**. Compared to the previous run, it had an:
 - RMSE accuracy of **0.14 m ( :heavy_minus_sign: no change)**
 - MAE accuracy of **0.12 m ( :heavy_minus_sign: no change)**
 - Bias of **0.12 m ( :heavy_minus_sign: no change)**

tests/validation.csv

@@ -120,3 +120,7 @@ time,Correlation,RMSE,MAE,R-squared,Bias,Regression slope
 2025-07-08 04:33:10.752555+00:00,0.975,0.145,0.123,0.95,0.117,1.119
 2025-07-09 06:39:54.701598+00:00,0.975,0.145,0.123,0.95,0.117,1.119
 2025-07-14 04:20:42.968376+00:00,0.975,0.145,0.123,0.95,0.117,1.119
+2025-07-16 05:28:52.268887+00:00,0.975,0.145,0.123,0.95,0.117,1.119
+2025-07-16 06:18:39.433814+00:00,0.975,0.145,0.123,0.95,0.117,1.119
+2025-07-16 06:35:53.694461+00:00,0.975,0.145,0.123,0.95,0.117,1.119
+2025-07-16 07:07:43.740627+00:00,0.975,0.145,0.123,0.95,0.117,1.119