From 23e7313e19018b9e388937c9974cd5ec5cea196b Mon Sep 17 00:00:00 2001
From: Emma Ai <emmaai@users.noreply.github.com>
Date: Thu, 16 Jan 2025 10:44:31 +1030
Subject: [PATCH] Mark geomad nodata in landcover level1 (#181)

* mark landcover level1 as nodata when geomad nodata

* pin datacube<1.9

* fix landcover level1 test

* fix failed action

* pin scipy<1.15 due to geomad

---------

Co-authored-by: Emma Ai <emma.ai@ga.gov.au>
---
 .github/workflows/statistician-dive.yml | 2 +-
 docker/env.yaml                         | 2 +-
 docker/requirements.txt                 | 2 +-
 odc/stats/plugins/lc_veg_class_a1.py    | 3 ++-
 setup.cfg                               | 2 +-
 tests/requirements.txt                  | 2 +-
 tests/test_landcover_plugin_a1.py       | 2 +-
 7 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/statistician-dive.yml b/.github/workflows/statistician-dive.yml
index 8c457f57..2fd5d3e9 100644
--- a/.github/workflows/statistician-dive.yml
+++ b/.github/workflows/statistician-dive.yml
@@ -47,7 +47,7 @@ jobs:
           wagoodman/dive:v0.12.0  --ci-config /.dive-ci ${ORG}/${IMAGE}:_build
 
       - name: Docker image size check
-        uses: wemake-services/docker-image-size-limit@master
+        uses: wemake-services/docker-image-size-limit@2.0.0
         with:
           image: ${{ env.ORG }}/${{ env.IMAGE}}:_build
           size: "3 GiB"
diff --git a/docker/env.yaml b/docker/env.yaml
index 3a3b64ef..23d1a808 100644
--- a/docker/env.yaml
+++ b/docker/env.yaml
@@ -112,7 +112,7 @@ dependencies:
   - s3fs
   - s3transfer
   - scikit-image
-  - scipy
+  - scipy<1.15
   - sentry-sdk
   - setuptools-scm
   - Shapely>=2.0
diff --git a/docker/requirements.txt b/docker/requirements.txt
index 53c6ce57..09575bc8 100644
--- a/docker/requirements.txt
+++ b/docker/requirements.txt
@@ -1,6 +1,6 @@
 
 --extra-index-url https://packages.dea.ga.gov.au/
-datacube[performance,s3]>=1.8.17
+datacube[performance,s3]<1.9
 hdstats==0.1.8.post1
 numexpr @ git+https://github.com/pydata/numexpr@a99412e
 odc-algo @ git+https://github.com/opendatacube/odc-algo@adb1856
diff --git a/odc/stats/plugins/lc_veg_class_a1.py b/odc/stats/plugins/lc_veg_class_a1.py
index 91074166..a0928b43 100644
--- a/odc/stats/plugins/lc_veg_class_a1.py
+++ b/odc/stats/plugins/lc_veg_class_a1.py
@@ -212,9 +212,10 @@ def l3_class(self, xx: xr.Dataset):
 
         # Mask nans and pixels where non of classes applicable
         l3_mask = expr_eval(
-            "where((e<=0)|(e==254), nodata, e)",
+            "where((e<=0)|(e==254)|(g!=g), nodata, e)",
             {
                 "e": l3_mask,
+                "g": si5.squeeze(0),
             },
             name="mark_nodata",
             dtype="uint8",
diff --git a/setup.cfg b/setup.cfg
index ba01f18d..7f7cd778 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,7 +22,7 @@ install_requires =
     botocore
     click>=8.0.0
     dask
-    datacube!=1.8.14
+    datacube<1.9
     distributed
     numpy
     odc-cloud[ASYNC]>=0.2.5
diff --git a/tests/requirements.txt b/tests/requirements.txt
index 8c4faafb..cf18641b 100644
--- a/tests/requirements.txt
+++ b/tests/requirements.txt
@@ -1,5 +1,5 @@
 --extra-index-url https://packages.dea.ga.gov.au/
-datacube>=1.8.17
+datacube<1.9
 # for pytest-depends
 deepdiff
 future_fstrings
diff --git a/tests/test_landcover_plugin_a1.py b/tests/test_landcover_plugin_a1.py
index 5c49083a..09244fa4 100644
--- a/tests/test_landcover_plugin_a1.py
+++ b/tests/test_landcover_plugin_a1.py
@@ -242,7 +242,7 @@ def test_l3_classes(dataset):
                 [223, 221, 210, 125],
                 [223, 223, 223, 210],
                 [223, 221, 223, 223],
-                [221, 223, 223, 223],
+                [221, 255, 223, 223],
             ]
         ],
         dtype="uint8",