Merge branch 'datasets/fair1mv2' of github.com:isaaccorley/torchgeo i…

…nto datasets/fair1mv2

.github/workflows/release.yaml

@@ -14,7 +14,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies
@@ -37,7 +37,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies
@@ -60,7 +60,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies

.github/workflows/style.yaml

@@ -16,7 +16,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies
@@ -39,7 +39,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies
@@ -62,7 +62,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies
@@ -85,7 +85,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies
@@ -108,7 +108,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies

.github/workflows/tests.yaml

@@ -16,7 +16,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies
@@ -45,7 +45,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache dependencies
@@ -75,7 +75,7 @@ jobs:
     - name: Run pytest checks
       run: pytest --cov=torchgeo --cov-report=xml --durations=10
     - name: Report coverage
-      uses: codecov/codecov-action@v3.1.2
+      uses: codecov/codecov-action@v3.1.3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
   minimum:
@@ -87,7 +87,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.9'
     - name: Cache dependencies
@@ -96,6 +96,8 @@ jobs:
       with:
         path: ${{ env.pythonLocation }}
         key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/min-reqs.old') }}-${{ hashFiles('requirements/mins-cons.old') }}
+    - name: Setup headless display for pyvista
+      uses: pyvista/setup-headless-display-action@v2
     - name: Install apt dependencies (Linux)
       run: |
         sudo apt-get update
@@ -108,7 +110,7 @@ jobs:
     - name: Run pytest checks
       run: pytest --cov=torchgeo --cov-report=xml --durations=10
     - name: Report coverage
-      uses: codecov/codecov-action@v3.1.2
+      uses: codecov/codecov-action@v3.1.3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
 concurrency:

.github/workflows/tutorials.yaml

@@ -18,7 +18,7 @@ jobs:
     - name: Clone repo
       uses: actions/checkout@v3.5.2
     - name: Set up python
-      uses: actions/setup-python@v4.5.0
+      uses: actions/setup-python@v4.6.0
       with:
         python-version: '3.10'
     - name: Cache dependencies

.pre-commit-config.yaml

@@ -34,5 +34,5 @@ repos:
         hooks:
         -   id: mypy
             args: [--strict, --ignore-missing-imports, --show-error-codes]
-            additional_dependencies: [torch>=2, torchmetrics>=0.10, lightning>=1.8, pytest>=6, pyvista>=0.20, omegaconf>=2.1, kornia>=0.6, numpy>=1.22.0]
+            additional_dependencies: [torch>=2, torchmetrics>=0.10, lightning>=1.8, pytest>=6.1.2, pyvista>=0.29, omegaconf>=2.0.1, hydra-core>=1, kornia>=0.6.5, numpy>=1.22]
             exclude: (build|data|dist|logo|logs|output)/

SECURITY.md

@@ -38,4 +38,4 @@ We prefer all communications to be in English.
 
 Microsoft follows the principle of [Coordinated Vulnerability Disclosure](https://www.microsoft.com/en-us/msrc/cvd).
 
-<!-- END MICROSOFT SECURITY.MD BLOCK -->
+<!-- END MICROSOFT SECURITY.MD BLOCK -->

conf/bigearthnet.yaml

@@ -1,22 +1,24 @@
+module:
+  _target_: torchgeo.trainers.MultiLabelClassificationTask
+  loss: "bce"
+  model: "resnet18"
+  learning_rate: 1e-3
+  learning_rate_schedule_patience: 6
+  weights: null
+  in_channels: 14
+  num_classes: 19
+
+datamodule:
+  _target_: torchgeo.datamodules.BigEarthNetDataModule
+  root: "data/bigearthnet"
+  bands: "all"
+  num_classes: ${module.num_classes}
+  batch_size: 128
+  num_workers: 4
+
 trainer:
+  _target_: lightning.pytorch.Trainer
   accelerator: gpu
   devices: 1
-  min_epochs: 10
+  min_epochs: 15
   max_epochs: 40
-  benchmark: True
-experiment:
-  task: "bigearthnet"
-  module:
-    loss: "bce"
-    model: "resnet18"
-    learning_rate: 1e-3
-    learning_rate_schedule_patience: 6
-    weights: null
-    in_channels: 14
-    num_classes: 19
-  datamodule:
-    root: "data/bigearthnet"
-    bands: "all"
-    num_classes: ${experiment.module.num_classes}
-    batch_size: 128
-    num_workers: 4

conf/chesapeake_cvpr.yaml

@@ -1,33 +1,34 @@
+module:
+  _target_: torchgeo.trainers.SemanticSegmentationTask
+  loss: "ce"
+  model: "unet"
+  backbone: "resnet18"
+  weights: null
+  learning_rate: 1e-3
+  learning_rate_schedule_patience: 6
+  in_channels: 4
+  num_classes: 7
+  num_filters: 256
+  ignore_index: null
+
+datamodule:
+  _target_: torchgeo.datamodules.ChesapeakeCVPRDataModule
+  root: "data/chesapeake/cvpr"
+  train_splits:
+    - "de-train"
+  val_splits:
+    - "de-val"
+  test_splits:
+    - "de-test"
+  batch_size: 200
+  patch_size: 256
+  num_workers: 4
+  class_set: ${module.num_classes}
+  use_prior_labels: False
+
 trainer:
+  _target_: lightning.pytorch.Trainer
   accelerator: gpu
   devices: 1
-  min_epochs: 20
-  max_epochs: 100
-  benchmark: True
-experiment:
-  task: "chesapeake_cvpr"
-  name: "chesapeake_cvpr_example"
-  module:
-    loss: "ce"
-    model: "unet"
-    backbone: "resnet18"
-    weights: null
-    learning_rate: 1e-3
-    learning_rate_schedule_patience: 6
-    in_channels: 4
-    num_classes: 7
-    num_filters: 256
-    ignore_index: null
-  datamodule:
-    root: "data/chesapeake/cvpr"
-    train_splits:
-      - "de-train"
-    val_splits:
-      - "de-val"
-    test_splits:
-      - "de-test"
-    batch_size: 200
-    patch_size: 256
-    num_workers: 4
-    class_set: ${experiment.module.num_classes}
-    use_prior_labels: False
+  min_epochs: 15
+  max_epochs: 40

conf/cowc_counting.yaml

@@ -1,18 +1,21 @@
+module:
+  _target_: torchgeo.trainers.RegressionTask
+  model: resnet18
+  weights: null
+  num_outputs: 1
+  in_channels: 3
+  learning_rate: 1e-3
+  learning_rate_schedule_patience: 2
+
+datamodule:
+  _target_: torchgeo.datamodules.COWCCountingDataModule
+  root: "data/cowc_counting"
+  batch_size: 64
+  num_workers: 4
+
 trainer:
+  _target_: lightning.pytorch.Trainer
   accelerator: gpu
   devices: 1
   min_epochs: 15
-experiment:
-  task: cowc_counting
-  name: cowc_counting_test
-  module:
-    model: resnet18
-    weights: null
-    num_outputs: 1
-    in_channels: 3
-    learning_rate: 1e-3
-    learning_rate_schedule_patience: 2
-  datamodule:
-    root: "data/cowc_counting"
-    batch_size: 64
-    num_workers: 4
+  max_epochs: 40

conf/cyclone.yaml

@@ -1,18 +1,21 @@
+module:
+  _target_: torchgeo.trainers.RegressionTask
+  model: "resnet18"
+  weights: null
+  num_outputs: 1
+  in_channels: 3
+  learning_rate: 1e-3
+  learning_rate_schedule_patience: 2
+
+datamodule:
+  _target_: torchgeo.datamodules.TropicalCycloneDataModule
+  root: "data/cyclone"
+  batch_size: 32
+  num_workers: 4
+
 trainer:
+  _target_: lightning.pytorch.Trainer
   accelerator: gpu
   devices: 1
   min_epochs: 15
-experiment:
-  task: "cyclone"
-  name: "cyclone_test"
-  module:
-    model: "resnet18"
-    weights: null
-    num_outputs: 1
-    in_channels: 3
-    learning_rate: 1e-3
-    learning_rate_schedule_patience: 2
-  datamodule:
-    root: "data/cyclone"
-    batch_size: 32
-    num_workers: 4
+  max_epochs: 40