conda's environment.yml: install pytorch gpu by pegging cudatoolkit to <= v11.5

.gitattributes

@@ -1,2 +1,4 @@
 # Do not change line endings on test data, it will change the MD5
-/tests/data/*/** binary
+/tests/data/*/** -text
+# Test data generation files are fine though
+/tests/data/**/data.py text

.github/workflows/release.yaml

@@ -16,11 +16,12 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install pip dependencies
       run: |
-        pip install cython numpy  # needed for pycocotools
+        pip install --pre 'rasterio>=1.0.16'
         pip install .[tests]
+        pip list
     - name: Run pytest checks
       run: pytest --cov=torchgeo --cov-report=xml
   integration:
@@ -32,9 +33,12 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install pip dependencies
-      run: pip install .[datasets,tests]
+      run: |
+        pip install --pre 'rasterio>=1.0.16'
+        pip install .[datasets,tests]
+        pip list
     - name: Run integration checks
       run: pytest -m slow
   notebooks:
@@ -46,11 +50,13 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install pip dependencies
       run: |
+        pip install --pre 'rasterio>=1.0.16'
         pip install .[datasets,tests]
         pip install -r docs/requirements.txt
+        pip list
     - name: Run notebook checks
       env:
         MLHUB_API_KEY: ${{ secrets.MLHUB_API_KEY }}

.github/workflows/style.yaml

@@ -18,9 +18,12 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install pip dependencies
-      run: pip install .[style]
+      run: |
+        pip install --pre 'rasterio>=1.0.16'
+        pip install .[style]
+        pip list
     - name: Run black checks
       run: black . --check --diff
   flake8:
@@ -32,9 +35,12 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install pip dependencies
-      run: pip install .[style]
+      run: |
+        pip install --pre 'rasterio>=1.0.16'
+        pip install .[style]
+        pip list
     - name: Run flake8 checks
       run: flake8
   isort:
@@ -46,9 +52,12 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install pip dependencies
-      run: pip install .[style]
+      run: |
+        pip install --pre 'rasterio>=1.0.16'
+        pip install .[style]
+        pip list
     - name: Run isort checks
       run: isort . --check --diff
   pydocstyle:
@@ -60,8 +69,28 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install pip dependencies
-      run: pip install .[style]
+      run: |
+        pip install --pre 'rasterio>=1.0.16'
+        pip install .[style]
+        pip list
     - name: Run pydocstyle checks
       run: pydocstyle
+  pyupgrade:
+    name: pyupgrade
+    runs-on: ubuntu-latest
+    steps:
+    - name: Clone repo
+      uses: actions/checkout@v2
+    - name: Set up python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install pip dependencies
+      run: |
+        pip install --pre 'rasterio>=1.0.16'
+        pip install .[style]
+        pip list
+    - name: Run pyupgrade checks
+      run: pyupgrade --py37-plus $(find . -name "*.py")

.github/workflows/tests.yaml

@@ -18,11 +18,12 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install pip dependencies
       run: |
-        pip install cython numpy  # needed for pycocotools
+        pip install --pre 'rasterio>=1.0.16'
         pip install .[datasets,tests]
+        pip list
     - name: Run mypy checks
       run: mypy .
   pytest:
@@ -33,10 +34,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.6, 3.7, 3.8, 3.9]
-        exclude:
-        - os: windows-latest
-          python-version: 3.6
+        python-version: ['3.7', '3.8', '3.9', '3.10']
     steps:
     - name: Clone repo
       uses: actions/checkout@v2
@@ -59,16 +57,15 @@ jobs:
       if: ${{ runner.os == 'Windows' }}
     - name: Install conda dependencies (Windows)
       run: |
-        # PyTorch isn't compatible with setuptools 59.6+, pin for now until new PyTorch release
-        # https://github.com/pytorch/pytorch/pull/69904
-        conda install 'fiona>=1.5' h5py 'rasterio>=1.0.16' 'setuptools<59.6'
+        conda install 'fiona>=1.5' 'rasterio>=1.0.16'
         conda list
         conda info
       if: ${{ runner.os == 'Windows' }}
     - name: Install pip dependencies
       run: |
-        pip install cython numpy  # needed for pycocotools
+        pip install --pre 'rasterio>=1.0.16'
         pip install .[datasets,tests]
+        pip list
     - name: Run pytest checks
       run: pytest --cov=torchgeo --cov-report=xml
     - name: Report coverage

.gitignore

@@ -2,7 +2,6 @@
 /data/
 /logs/
 /output/
-*.csv
 *.pdf
 
 # Spack

.pre-commit-config.yaml

@@ -1,12 +1,18 @@
 repos:
+    -   repo: https://github.com/asottile/pyupgrade
+        rev: v2.31.1
+        hooks:
+        -   id: pyupgrade
+            args: [--py37-plus]
+
     -   repo: https://github.com/pycqa/isort
         rev: 5.10.1
         hooks:
         -    id: isort
              additional_dependencies: ["colorama>=0.4.3"]
 
     -   repo: https://github.com/psf/black
-        rev: 22.1.0
+        rev: 22.3.0
         hooks:
         -   id: black
             args: [--skip-magic-trailing-comma]
@@ -24,9 +30,9 @@ repos:
             additional_dependencies: ["toml"]
 
     -   repo: https://github.com/pre-commit/mirrors-mypy
-        rev: v0.931
+        rev: v0.942
         hooks:
         -   id: mypy
             args: [--strict, --ignore-missing-imports, --show-error-codes]
-            additional_dependencies: [torch>=1.7, torchmetrics>=0.7, pytorch-lightning>=1.3, pytest>=6, omegaconf>=2.1, kornia>=0.6, numpy>=1.22.0]
+            additional_dependencies: [torch>=1.11, torchmetrics>=0.7, pytorch-lightning>=1.6, pytest>=6, omegaconf>=2.1, kornia>=0.6, numpy>=1.22.0]
             exclude: (build|data|dist|logo|logs|output)/

.readthedocs.yaml

@@ -4,6 +4,12 @@
 # Required
 version: 2
 
+# Set the version of Python
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
 # Configuration of the Python environment to be used
 python:
    install:

README.md

@@ -80,7 +80,7 @@ In this example, we show how easy it is to work with geospatial data and to samp
 
 ```python
 landsat7 = Landsat7(root="...")
-landsat8 = Landsat8(root="...", bands=["B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9"])
+landsat8 = Landsat8(root="...", bands=Landsat8.all_bands[1:-2])
 landsat = landsat7 | landsat8
 ```
 

benchmark.py

@@ -208,17 +208,15 @@ def main(args: argparse.Namespace) -> None:
     # Benchmark model
     model = resnet34()
     # Change number of input channels to match Landsat
-    model.conv1 = nn.Conv2d(  # type: ignore[attr-defined]
+    model.conv1 = nn.Conv2d(
         len(bands), 64, kernel_size=7, stride=2, padding=3, bias=False
     )
 
-    criterion = nn.CrossEntropyLoss()  # type: ignore[attr-defined]
+    criterion = nn.CrossEntropyLoss()
     params = model.parameters()
     optimizer = optim.SGD(params, lr=0.0001)
 
-    device = torch.device(  # type: ignore[attr-defined]
-        "cuda" if torch.cuda.is_available() else "cpu", args.device
-    )
+    device = torch.device("cuda" if torch.cuda.is_available() else "cpu", args.device)
     model = model.to(device)
 
     tic = time.time()
@@ -227,7 +225,7 @@ def main(args: argparse.Namespace) -> None:
         num_total_patches += args.batch_size
         x = torch.rand(args.batch_size, len(bands), args.patch_size, args.patch_size)
         # y = torch.randint(0, 256, (args.batch_size, args.patch_size, args.patch_size))
-        y = torch.randint(0, 256, (args.batch_size,))  # type: ignore[attr-defined]
+        y = torch.randint(0, 256, (args.batch_size,))
         x = x.to(device)
         y = y.to(device)
 

conf/inria.yaml

@@ -0,0 +1,30 @@
+program:
+  overwrite: True
+
+
+trainer:
+  gpus: 1
+  min_epochs: 5
+  max_epochs: 100
+  benchmark: True
+  log_every_n_steps: 2
+
+experiment:
+  task: "inria"
+  name: "inria_test"
+  module:
+    loss: "ce"
+    segmentation_model: "unet"
+    encoder_name: "resnet18"
+    encoder_weights: "imagenet"
+    learning_rate: 1e-3
+    learning_rate_schedule_patience: 6
+    in_channels: 3
+    num_classes: 2
+    ignore_zeros: True  # class 0 not used for scoring
+  datamodule:
+      root_dir: "data/inria"
+      batch_size: 2
+      num_workers: 32
+      patch_size: 512
+      num_patches_per_tile: 4

docs/api/datamodules.rst

@@ -44,6 +44,11 @@ FAIR1M (Fine-grAined object recognItion in high-Resolution imagery)
 
 .. autoclass:: FAIR1MDataModule
 
+Inria Aerial Image Labeling
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autoclass:: InriaAerialImageLabelingDataModule
+
 LandCover.ai (Land Cover from Aerial Imagery)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

docs/api/datasets.rst

@@ -52,6 +52,11 @@ Cropland Data Layer (CDL)
 
 .. autoclass:: CDL
 
+EDDMapS
+^^^^^^^
+
+.. autoclass:: EDDMapS
+
 EnviroAtlas
 ^^^^^^^^^^^
 
@@ -67,11 +72,21 @@ EU-DEM
 
 .. autoclass:: EUDEM
 
+GBIF
+^^^^
+
+.. autoclass:: GBIF
+
 GlobBiomass
 ^^^^^^^^^^^
 
 .. autoclass:: GlobBiomass
 
+iNaturalist
+^^^^^^^^^^^
+
+.. autoclass:: INaturalist
+
 Landsat
 ^^^^^^^
 
@@ -96,7 +111,7 @@ Open Buildings
 ^^^^^^^^^^^^^^
 
 .. autoclass:: OpenBuildings
-    
+
 Sentinel
 ^^^^^^^^
 
@@ -157,6 +172,11 @@ FAIR1M (Fine-grAined object recognItion in high-Resolution imagery)
 
 .. autoclass:: FAIR1M
 
+Forest Damage
+^^^^^^^^^^^^^
+
+.. autoclass:: ForestDamage
+
 GID-15 (Gaofen Image Dataset)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -233,6 +253,7 @@ SpaceNet
 .. autoclass:: SpaceNet
 .. autoclass:: SpaceNet1
 .. autoclass:: SpaceNet2
+.. autoclass:: SpaceNet3
 .. autoclass:: SpaceNet4
 .. autoclass:: SpaceNet5
 .. autoclass:: SpaceNet7

docs/api/samplers.rst

@@ -32,6 +32,11 @@ Grid Geo Sampler
 
 .. autoclass:: GridGeoSampler
 
+Pre-chipped Geo Sampler
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autoclass:: PreChippedGeoSampler
+
 Batch Samplers
 --------------