GeoscienceAustralia · danielb-ga · Mar 11, 2026 · Mar 11, 2026 · Mar 11, 2026 · Mar 11, 2026
diff --git a/environment.yml b/environment.yml
@@ -15,23 +15,23 @@ dependencies:
   - minizip=4.0.10
   - muparser=2.3.5
   - mpi4py=4.0.3
-  - numpy<1.23.0
+  - numpy=1.26.4
   - openmpi>=4.1.6
-  - openssl=3.5.0
+  - openssl=3.5.5
   - pcre2=10.45
   - pip=25.1.1
   - proj=9.6.0
-  - python=3.10.4
+  - python=3.12.13
   - setuptools=80.8.0
   - six=1.17.0
   - snappy=1.2.1
-  - sqlite=3.49.2
+  - sqlite=3.51.2
   - tk=8.6.13
   - uriparser=0.9.8
   - wheel=0.45.1
   - xerces-c=3.2.5
-  - xz=5.8.1
-  - xz-tools=5.8.1
+  - xz=5.8.2
+  - xz-tools=5.8.2
   - zlib=1.3.1
   - zstd=1.5.7
   - pip:
@@ -41,7 +41,7 @@ dependencies:
       - blosc2==2.7.1
       - boto3==1.34.67
       - botocore==1.34.162
-      - catboost==1.0.3
+      - catboost==1.2.10
       - certifi==2025.4.26
       - charset-normalizer==3.4.2
       - click==8.2.1
@@ -66,7 +66,7 @@ dependencies:
       - greenlet==3.2.2
       - hyperopt==0.2.5
       - idna==3.10
-      - imageio==2.9.0
+      - imageio==2.27
       - iniconfig==2.1.0
       - Jinja2==3.1.6
       - jmespath==1.0.1
@@ -80,14 +80,14 @@ dependencies:
       - msgpack==1.1.0
       - narwhals==1.41.0
       - ndindex==1.10.0
-      - networkx==2.5.1
+      - networkx==2.8
       - numba==0.61.2
       - numexpr==2.10.2
       - nvidia-nccl-cu12==2.26.5
       - optuna==3.2.0
       - packaging==25.0
       - pandas==2.2.3
-      - pillow==11.2.1
+      - pillow==12.1.1
       - plotly==6.1.2
       - pluggy==1.6.0
       - py-cpuinfo==9.0.0
@@ -104,11 +104,11 @@ dependencies:
       - pytz==2025.2
       - PyWavelets==1.2.0
       - PyYAML==6.0.2
-      - rasterio==1.3.7
+      - rasterio==1.4.3
       - requests==2.32.2
       - revrand==1.0.0
       - s3transfer==0.10.4
-      - scikit-image==0.19.1
+      - scikit-image==0.22.0
       - scikit-learn==1.2.2
       - scikit-optimize==0.9.0
       - scipy==1.15.3

diff --git a/pbs/README.md b/pbs/README.md
@@ -24,8 +24,8 @@ $ module load python3/3.10.4 gdal/3.5.0 openmpi/4.1.5
 2. Now add the following lines to the end of your `~/.bashrc`:
 ```bash
 export PATH=$HOME/.local/bin:$PATH
-export PYTHONPATH=$HOME/.local/lib/python3.10/site-packages:$PYTHONPATH
-export VIRTUALENVWRAPPER_PYTHON=/apps/python3/3.10.4/bin/python3
+export PYTHONPATH=$HOME/.local/lib/python3.12/site-packages:$PYTHONPATH
+export VIRTUALENVWRAPPER_PYTHON=/apps/python3/3.12.13/bin/python3
 export LC_ALL=en_AU.UTF-8
 export LANG=en_AU.UTF-8
 source $HOME/.local/bin/virtualenvwrapper.sh 

diff --git a/requirements.txt b/requirements.txt
@@ -4,7 +4,7 @@ attrs==25.3.0
 blosc2==2.5.1
 boto3==1.34.67
 botocore==1.34.162
-catboost==1.0.3
+catboost==1.2.10
 certifi==2025.4.26
 charset-normalizer==3.4.2
 click==8.1.8
@@ -28,7 +28,7 @@ graphviz==0.20.3
 greenlet==3.2.2
 hyperopt==0.2.5
 idna==3.10
-imageio==2.9.0
+imageio==2.27
 importlib_metadata==8.7.0
 importlib_resources==6.5.2
 iniconfig==2.1.0
@@ -46,10 +46,10 @@ mpi4py==4.0.3
 msgpack==1.1.0
 narwhals==1.40.0
 ndindex==1.10.0
-networkx==2.5.1
+networkx==2.8.0
 numba==0.60.0
 numexpr==2.10.2
-numpy==1.25.1
+numpy==1.26.4
 nvidia-nccl-cu12==2.26.5
 optuna==3.2.0
 packaging==25.0
@@ -71,11 +71,11 @@ python-dateutil==2.9.0.post0
 pytz==2025.2
 PyWavelets==1.2.0
 PyYAML==6.0.2
-rasterio==1.3.7
+rasterio==1.4.3
 requests==2.32.4
 revrand==1.0.0
 s3transfer==0.10.4
-scikit-image==0.19.1
+scikit-image==0.22.0
 scikit-learn==1.2.2
 scikit-optimize==0.9.0
 scipy==1.13.1
@@ -86,7 +86,7 @@ six==1.17.0
 slicer==0.0.7
 snuggs==1.4.7
 SQLAlchemy==2.0.41
-tables==3.9.2
+tables==3.10.1
 tabulate==0.9.0
 threadpoolctl==3.6.0
 tifffile==2024.8.30

diff --git a/setup.cfg b/setup.cfg
@@ -13,7 +13,6 @@ filterwarnings =
     ignore:.*U.*mode is deprecated:DeprecationWarning
     ignore::rasterio.errors.NotGeoreferencedWarning
     ignore::sklearn.exceptions.ConvergenceWarning
-    ignore::pandas.errors.SettingWithCopyWarning
     ignore::UserWarning
 addopts =
     --cov=uncoverml

diff --git a/setup.py b/setup.py
@@ -80,20 +80,20 @@ def run(self):
         'cython >= 0.29.22',
     ],
     install_requires=[
-        'numpy == 1.25.1',
+        'numpy == 1.26.4',
         'cython >= 0.29.22',
         'pycontracts == 1.7.9',
         'tables >= 3.2.2',
-        'rasterio == 1.3.7',
-        'catboost == 1.0.3',
+        'rasterio == 1.3.10',
+        'catboost == 1.2.10',
         'affine >= 2.2.1',
         'pyshp == 2.1.0',
         'click >= 6.6',
         'revrand >= 0.9.10',
         'mpi4py >= 3.1.3',
         'scipy >= 1.6.2',
         'scikit-learn == 1.2.2',
-        'scikit-image==0.19.1',
+        'scikit-image==0.22.0',
         'scikit-optimize == 0.9.0',
         'wheel >= 0.29.0',
         'PyYAML >= 3.11',
@@ -103,12 +103,12 @@ def run(self):
         'xgboost>=1.4.2',
         'setuptools>=30.0.0',
         'eli5>=0.8.2',
-        'networkx==2.5.1',
+        'networkx==2.8.0',
         'geopandas >= 0.9.0',
         'hyperopt==0.2.5',
-        'Pillow >= 8.1.2',
+        'Pillow >= 12.1.1',
         "PyWavelets==1.2.0",
-        "imageio==2.9.0",
+        "imageio==2.27.0",
         "optuna==3.2.0",
         "seaborn==0.13.0",
         'colorama==0.4.6',

diff --git a/tests/_run-tests.sh b/tests/_run-tests.sh
@@ -28,7 +28,7 @@ conda activate uncover-ml-env
 
 echo "Patching mlens..."
 sed -i 's|from collections import Sequence|from collections.abc import Sequence|g' \
-    ../miniconda/envs/uncover-ml-env/lib/python3.10/site-packages/mlens/externals/sklearn/type_of_target.py
+    ../miniconda/envs/uncover-ml-env/lib/python3.12/site-packages/mlens/externals/sklearn/type_of_target.py
 
 echo "Running tests…"
 mkdir -p test-results