Merge branch 'main' into bigearthnnetv1brokenlink

.github/dependabot.yml

@@ -20,6 +20,10 @@ updates:
           - "torch"
           - "torchvision"
     ignore:
+      # lightning 2.3+ contains known bugs related to YAML parsing
+      # https://github.com/Lightning-AI/pytorch-lightning/issues/19977
+      - dependency-name: "lightning"
+        version: ">=2.3"
       # setuptools releases new versions almost daily
       - dependency-name: "setuptools"
         update-types: ["version-update:semver-patch"]

.github/workflows/labeler.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Add label
         uses: actions/[email protected]
         with:

.github/workflows/release.yaml

@@ -12,9 +12,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Set up python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: "3.12"
       - name: Cache dependencies
@@ -40,9 +40,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Set up python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: "3.12"
       - name: Cache dependencies

.github/workflows/style.yaml

@@ -14,9 +14,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Set up python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: "3.12"
       - name: Cache dependencies
@@ -39,9 +39,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Set up python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: "3.12"
       - name: Cache dependencies
@@ -66,9 +66,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Set up nodejs
-        uses: actions/[email protected].2
+        uses: actions/[email protected].3
         with:
           node-version: "20"
           cache: "npm"

.github/workflows/tests.yaml

@@ -20,9 +20,9 @@ jobs:
         python-version: ["3.10", "3.11", "3.12"]
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Set up python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache dependencies
@@ -57,7 +57,7 @@ jobs:
           pytest --cov=torchgeo --cov-report=xml --durations=10
           python3 -m torchgeo --help
       - name: Report coverage
-        uses: codecov/codecov-action@v4.4.1
+        uses: codecov/codecov-action@v4.5.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
   minimum:
@@ -67,9 +67,9 @@ jobs:
       MPLBACKEND: Agg
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Set up python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: "3.10"
       - name: Cache dependencies
@@ -96,7 +96,7 @@ jobs:
           pytest --cov=torchgeo --cov-report=xml --durations=10
           python3 -m torchgeo --help
       - name: Report coverage
-        uses: codecov/codecov-action@v4.4.1
+        uses: codecov/codecov-action@v4.5.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
   datasets:
@@ -106,9 +106,9 @@ jobs:
       MPLBACKEND: Agg
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Set up python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: "3.12"
       - name: Cache dependencies
@@ -129,7 +129,7 @@ jobs:
           pytest --cov=torchgeo --cov-report=xml --durations=10
           python3 -m torchgeo --help
       - name: Report coverage
-        uses: codecov/codecov-action@v4.4.1
+        uses: codecov/codecov-action@v4.5.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 concurrency:

.github/workflows/tutorials.yaml

@@ -16,9 +16,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Clone repo
-        uses: actions/[email protected].6
+        uses: actions/[email protected].7
       - name: Set up python
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           python-version: "3.12"
       - name: Cache dependencies

.pre-commit-config.yaml

@@ -26,7 +26,7 @@ repos:
           - lightning>=2.0.9
           - matplotlib>=3.8.1
           - numpy>=1.22
-          - pillow>=10.3.0
+          - pillow>=10.4.0
           - pytest>=6.1.2
           - pyvista>=0.34.2
           - scikit-image>=0.22.0

README.md

@@ -239,7 +239,7 @@ torchgeo fit --config config.yaml
 # Validate-only
 torchgeo validate --config config.yaml
 # Calculate and report test accuracy
-torchgeo test --config config.yaml ckpt_path=...
+torchgeo test --config config.yaml --ckpt_path=...
 ```
 
 It can also be imported and used in a Python script if you need to extend it to add new features:

docs/api/non_geo_datasets.csv

@@ -27,7 +27,7 @@ Dataset,Task,Source,License,# Samples,# Classes,Size (px),Resolution (m),Bands
 `NASA Marine Debris`_,OD,PlanetScope,"Apache-2.0",707,1,256x256,3,RGB
 `OSCD`_,CD,Sentinel-2,"CC-BY-4.0",24,2,"40--1,180",60,MSI
 `PASTIS`_,I,Sentinel-1/2,"CC-BY-4.0","2,433",19,128x128xT,10,MSI
-`PatternNet`_,C,Google Earth,-,"30,400",38,256x256,0.06--5,RGB
+`PatternNet`_,C,Google Earth,"CC-BY-4.0","30,400",38,256x256,0.06--5,RGB
 `Potsdam`_,S,Aerial,-,38,6,"6,000x6,000",0.05,MSI
 `QuakeSet`_,"C, R",Sentinel-1,"OpenRAIL","3,327",2,512x512,10,SAR
 `ReforesTree`_,"OD, R",Aerial,"CC-BY-4.0",100,6,"4,000x4,000",0.02,RGB

docs/conf.py

@@ -144,22 +144,6 @@
    :class: colabbadge
    :alt: Open in Colab
    :target: {{ host }}/github/{{ repo }}/blob/{{ branch }}/{{ urlpath }}
-
-{% set host = "https://pccompute.westeurope.cloudapp.azure.com" %}
-{% set host = host ~ "/compute/hub/user-redirect/git-pull" %}
-{% set repo = "https%3A%2F%2Fgithub.com%2Fmicrosoft%2Ftorchgeo" %}
-{% set urlpath = "tree%2Ftorchgeo%2Fdocs%2F" %}
-{% set urlpath = urlpath ~ env.docname | replace("/", "%2F") ~ ".ipynb" %}
-{% if "dev" in env.config.release %}
-    {% set branch = "main" %}
-{% else %}
-    {% set branch = "releases%2Fv" ~ env.config.version %}
-{% endif %}
-
-.. image:: https://img.shields.io/badge/-Open%20on%20Planetary%20Computer-blue
-   :class: colabbadge
-   :alt: Open on Planetary Computer
-   :target: {{ host }}?repo={{ repo }}&urlpath={{ urlpath }}&branch={{ branch }}
 """
 
 # Disables requirejs in nbsphinx to enable compatibility with the pytorch_sphinx_theme

experiments/ssl4eo/plot_example_predictions.py

@@ -63,13 +63,9 @@
             data = sample[key]
             if key == 'image':
                 data = data[[2, 1, 0]].permute(1, 2, 0).numpy().astype('uint8')
-                Image.fromarray(data, 'RGB').save(  # type: ignore[no-untyped-call]
-                    f'{path}/{key}.png'
-                )
+                Image.fromarray(data, 'RGB').save(f'{path}/{key}.png')
             else:
                 data = data * 255 / 4
                 data = data.numpy().astype('uint8').squeeze()
-                Image.fromarray(data, 'L').save(  # type: ignore[no-untyped-call]
-                    f'{path}/{key}.png'
-                )
+                Image.fromarray(data, 'L').save(f'{path}/{key}.png')
         i += 1

pyproject.toml

@@ -40,14 +40,16 @@ dependencies = [
     "einops>=0.3",
     # fiona 1.8.21+ required for Python 3.10 wheels
     "fiona>=1.8.21",
-    # kornia 0.7.2+ required for dict support in AugmentationSequential
-    "kornia>=0.7.2",
+    # kornia 0.7.3+ required for instance segmentation support in AugmentationSequential
+    "kornia>=0.7.3",
     # lightly 1.4.4+ required for MoCo v3 support
     # lightly 1.4.26 is incompatible with the version of timm required by smp
     # https://github.com/microsoft/torchgeo/issues/1824
     "lightly>=1.4.4,!=1.4.26",
     # lightning 2+ required for LightningCLI args + sys.argv support
-    "lightning[pytorch-extra]>=2",
+    # lightning 2.3+ contains known bugs related to YAML parsing
+    # https://github.com/Lightning-AI/pytorch-lightning/issues/19977
+    "lightning[pytorch-extra]>=2,<2.3",
     # matplotlib 3.5+ required for Python 3.10 wheels
     "matplotlib>=3.5",
     # numpy 1.21.2+ required by Python 3.10 wheels
@@ -266,7 +268,7 @@ quote-style = "single"
 skip-magic-trailing-comma = true
 
 [tool.ruff.lint]
-extend-select = ["D", "I", "UP"]
+extend-select = ["D", "I", "NPY201", "UP"]
 
 [tool.ruff.lint.per-file-ignores]
 "docs/**" = ["D"]

requirements/datasets.txt

@@ -1,11 +1,11 @@
 # datasets
 h5py==3.11.0
-laspy==2.5.3
-opencv-python==4.9.0.80
-pycocotools==2.0.7
-pyvista==0.43.8
+laspy==2.5.4
+opencv-python==4.10.0.84
+pycocotools==2.0.8
+pyvista==0.44.0
 radiant-mlhub==0.4.1
 rarfile==4.2
-scikit-image==0.23.2
-scipy==1.13.1
+scikit-image==0.24.0
+scipy==1.14.0
 zipfile-deflate64==0.2.0

requirements/min-reqs.old

@@ -4,7 +4,7 @@ setuptools==61.0.0
 # install
 einops==0.3.0
 fiona==1.8.21
-kornia==0.7.2
+kornia==0.7.3
 lightly==1.4.4
 lightning[pytorch-extra]==2.0.0
 matplotlib==3.5.0

requirements/package.json

@@ -2,6 +2,6 @@
   "name": "torchgeo",
   "private": "true",
   "dependencies": {
-    "prettier": ">=3.0.0"
+    "prettier": ">=3.3.3"
   }
 }

requirements/required.txt

@@ -1,22 +1,22 @@
 # setup
-setuptools==70.0.0
+setuptools==70.3.0
 
 # install
 einops==0.8.0
 fiona==1.9.6
-kornia==0.7.2
-lightly==1.5.4
+kornia==0.7.3
+lightly==1.5.9
 lightning[pytorch-extra]==2.2.5
 matplotlib==3.9.0
 numpy==1.26.4
 pandas==2.2.2
-pillow==10.3.0
+pillow==10.4.0
 pyproj==3.6.1
 rasterio==1.3.10
-rtree==1.2.0
+rtree==1.3.0
 segmentation-models-pytorch==0.3.3
-shapely==2.0.4
+shapely==2.0.5
 timm==0.9.2
-torch==2.3.0
+torch==2.3.1
 torchmetrics==1.4.0.post0
-torchvision==0.18.0
+torchvision==0.18.1

requirements/style.txt

@@ -1,3 +1,3 @@
 # style
-mypy==1.10.0
-ruff==0.4.6
+mypy==1.10.1
+ruff==0.5.2

requirements/tests.txt

@@ -1,4 +1,4 @@
 # tests
-nbmake==1.5.3
-pytest==8.2.1
+nbmake==1.5.4
+pytest==8.2.2
 pytest-cov==5.0.0

tests/data/README.md

@@ -20,7 +20,7 @@ with rio.open(os.path.join(ROOT, FILENAME), "r") as src:
     dtype = src.profile["dtype"]
     Z = np.random.randint(np.iinfo(dtype).max, size=(SIZE, SIZE), dtype=dtype)
     with rio.open(FILENAME, "w", **src.profile) as dst:
-        for i in dst.profile.indexes:
+        for i in dst.indexes:
             dst.write(Z, i)
 ```
 

tests/data/cv4a_kenya_crop_type/FieldIds.csv

@@ -0,0 +1,5 @@
+train,test
+1,2
+3,4
+5
+6