Merge pull request #32 from IBM/feature/dependabot

Feature/refactor + dependabot

.github/workflows/test.yaml

@@ -1,17 +1,24 @@
 name: terratorch tuning toolkit
 
-on: [pull_request]
+on: 
+  push:
+    branches:
+      - main
+
+  pull_request:
+    branches:
+      - main
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ["3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Clone repo
+        uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
@@ -20,8 +27,9 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest
-          pip install -e .
+          pip install -r requirements/required.txt -r requirements/test.txt
+      - name: List pip dependencies
+        run: pip list
       - name: Test with pytest
         run: |
           pytest -s tests

README.md

@@ -24,7 +24,7 @@ a common CLI tool, with no need of installing dependencies or activating environ
 
 TerraTorch requires gdal to be installed, which can be quite a complex process. If you don't have GDAL set up on your system, we reccomend using a conda environment and installing it with `conda install -c conda-forge gdal`.
 
-To install as a developer (e.g. to extend the library) clone this repo, install dependencies using `pip install -r requirements.txt` and run `pip install -e .`
+To install as a developer (e.g. to extend the library) clone this repo, install dependencies using `pip install -r requirements/required.txt -r requirements/dev.txt` and run `pip install -e .`
 
 ## Quick start
 

pyproject.toml

@@ -26,8 +26,6 @@ classifiers = [
   "Programming Language :: Python :: Implementation :: PyPy",
 ]
 dependencies = [
-  "coverage",
-  "pytest",
   "torch>=2.1.0",
   "torchvision>=0.16.0",
   "torchgeo>=0.5.1",
@@ -50,6 +48,11 @@ dev = [
   "mkdocstrings[python]"
 ]
 
+test = [
+  "coverage",
+  "pytest"
+]
+
 [project.urls]
 Documentation = "https://github.com/IBM/terratorch#readme"
 Issues = "https://github.com/IBM/terratorch/issues"

requirements-dev.txt → requirements/dev.txt

@@ -1,6 +1,3 @@
-coverage[toml]>=6.5
-pytest-cov==4.1.0
-pytest==7.4.3
 mkdocs-material==9.4.14
 mkdocstrings[python]
 h5py==3.10.0

requirements/test.txt

@@ -0,0 +1,3 @@
+coverage[toml]>=6.5
+pytest-cov==4.1.0
+pytest==7.4.3

src/terratorch/__init__.py → terratorch/__init__.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 # register models with timm
 import terratorch.models
 from terratorch.models.backbones import *  # noqa: F403

src/terratorch/__main__.py → terratorch/__main__.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 """Command-line interface to TerraTorch."""
 
 from terratorch.cli_tools import build_lightning_cli

src/terratorch/cli_tools.py → terratorch/cli_tools.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 import logging  # noqa: I001
 import os
 import warnings

src/terratorch/datamodules/__init__.py → terratorch/datamodules/__init__.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 from terratorch.datamodules.fire_scars import FireScarsNonGeoDataModule
 from terratorch.datamodules.generic_pixel_wise_data_module import (
     GenericNonGeoPixelwiseRegressionDataModule,
@@ -6,26 +8,26 @@
 from terratorch.datamodules.generic_scalar_label_data_module import (
     GenericNonGeoClassificationDataModule,
 )
-
-# GenericNonGeoRegressionDataModule,
-from terratorch.datamodules.sen1floods11 import Sen1Floods11NonGeoDataModule
-from terratorch.datamodules.torchgeo_data_module import TorchGeoDataModule, TorchNonGeoDataModule
-
-# geobench classification datamodules
-from terratorch.datamodules.m_eurosat import MEuroSATNonGeoDataModule
 from terratorch.datamodules.m_bigearthnet import MBigEarthNonGeoDataModule
 from terratorch.datamodules.m_brick_kiln import MBrickKilnNonGeoDataModule
-from terratorch.datamodules.m_forestnet import MForestNetNonGeoDataModule
-from terratorch.datamodules.m_so2sat import MSo2SatNonGeoDataModule
-from terratorch.datamodules.m_pv4ger import MPv4gerNonGeoDataModule
 
 # geobench segmentation datamodules
 from terratorch.datamodules.m_cashew_plantation import MBeninSmallHolderCashewsNonGeoDataModule
-from terratorch.datamodules.m_nz_cattle import MNzCattleNonGeoDataModule
 from terratorch.datamodules.m_chesapeake_landcover import MChesapeakeLandcoverNonGeoDataModule
+
+# geobench classification datamodules
+from terratorch.datamodules.m_eurosat import MEuroSATNonGeoDataModule
+from terratorch.datamodules.m_forestnet import MForestNetNonGeoDataModule
+from terratorch.datamodules.m_neontree import MNeonTreeNonGeoDataModule
+from terratorch.datamodules.m_nz_cattle import MNzCattleNonGeoDataModule
+from terratorch.datamodules.m_pv4ger import MPv4gerNonGeoDataModule
 from terratorch.datamodules.m_pv4ger_seg import MPv4gerSegNonGeoDataModule
 from terratorch.datamodules.m_SA_crop_type import MSACropTypeNonGeoDataModule
-from terratorch.datamodules.m_neontree import MNeonTreeNonGeoDataModule
+from terratorch.datamodules.m_so2sat import MSo2SatNonGeoDataModule
+
+# GenericNonGeoRegressionDataModule,
+from terratorch.datamodules.sen1floods11 import Sen1Floods11NonGeoDataModule
+from terratorch.datamodules.torchgeo_data_module import TorchGeoDataModule, TorchNonGeoDataModule
 
 __all__ = (
     "GenericNonGeoSegmentationDataModule",

src/terratorch/datamodules/fire_scars.py → terratorch/datamodules/fire_scars.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 from typing import Any
 
 import kornia.augmentation as K  # noqa: N812

src/terratorch/datamodules/generic_pixel_wise_data_module.py → terratorch/datamodules/generic_pixel_wise_data_module.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 """
 This module contains generic data modules for instantiation at runtime.
 """

src/terratorch/datamodules/generic_scalar_label_data_module.py → terratorch/datamodules/generic_scalar_label_data_module.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 """
 This module contains generic data modules for instantiation at runtime.
 """

src/terratorch/datamodules/sen1floods11.py → terratorch/datamodules/sen1floods11.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 from pathlib import Path
 from typing import Any
 

src/terratorch/datamodules/torchgeo_data_module.py → terratorch/datamodules/torchgeo_data_module.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 """Ugly proxy objects so parsing config file works with transforms.
 
     These are necessary since, for LightningCLI to instantiate arguments as

src/terratorch/datamodules/utils.py → terratorch/datamodules/utils.py

@@ -1,6 +1,9 @@
-import albumentations as A
+# Copyright contributors to the Terratorch project
+
 from typing import Iterable
 
+import albumentations as A
+
 
 def wrap_in_compose_is_list(transform_list):
     # set check shapes to false because of the multitemporal case

src/terratorch/datasets/__init__.py → terratorch/datasets/__init__.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 from terratorch.datasets.fire_scars import FireScarsHLS, FireScarsNonGeo, FireScarsSegmentationMask
 from terratorch.datasets.generic_pixel_wise_dataset import (
     GenericNonGeoPixelwiseRegressionDataset,
@@ -6,30 +8,30 @@
 from terratorch.datasets.generic_scalar_label_dataset import (
     GenericNonGeoClassificationDataset,
 )
-
-# GenericNonGeoRegressionDataset,
-from terratorch.datasets.sen1floods11 import Sen1Floods11NonGeo
-from terratorch.datasets.utils import HLSBands
-
-# TorchGeo RasterDatasets
-from terratorch.datasets.wsf import WSF2019, WSFEvolution
 from terratorch.datasets.hls import HLSL30, HLSS30
-
-# geobench datasets classification
-from terratorch.datasets.m_eurosat import MEuroSATNonGeo
 from terratorch.datasets.m_bigearthnet import MBigEarthNonGeo
 from terratorch.datasets.m_brick_kiln import MBrickKilnNonGeo
-from terratorch.datasets.m_forestnet import MForestNetNonGeo
-from terratorch.datasets.m_so2sat import MSo2SatNonGeo
-from terratorch.datasets.m_pv4ger import MPv4gerNonGeo
 
 # geobench datasets segmentation
 from terratorch.datasets.m_cashew_plantation import MBeninSmallHolderCashewsNonGeo
-from terratorch.datasets.m_nz_cattle import MNzCattleNonGeo
 from terratorch.datasets.m_chesapeake_landcover import MChesapeakeLandcoverNonGeo
+
+# geobench datasets classification
+from terratorch.datasets.m_eurosat import MEuroSATNonGeo
+from terratorch.datasets.m_forestnet import MForestNetNonGeo
+from terratorch.datasets.m_neontree import MNeonTreeNonGeo
+from terratorch.datasets.m_nz_cattle import MNzCattleNonGeo
+from terratorch.datasets.m_pv4ger import MPv4gerNonGeo
 from terratorch.datasets.m_pv4ger_seg import MPv4gerSegNonGeo
 from terratorch.datasets.m_SA_crop_type import MSACropTypeNonGeo
-from terratorch.datasets.m_neontree import MNeonTreeNonGeo
+from terratorch.datasets.m_so2sat import MSo2SatNonGeo
+
+# GenericNonGeoRegressionDataset,
+from terratorch.datasets.sen1floods11 import Sen1Floods11NonGeo
+from terratorch.datasets.utils import HLSBands
+
+# TorchGeo RasterDatasets
+from terratorch.datasets.wsf import WSF2019, WSFEvolution
 
 __all__ = (
     "GenericNonGeoSegmentationDataset",

src/terratorch/datasets/fire_scars.py → terratorch/datasets/fire_scars.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 import dataclasses
 import glob
 import os

src/terratorch/datasets/generic_pixel_wise_dataset.py → terratorch/datasets/generic_pixel_wise_dataset.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 """Module containing generic dataset classes
 """
 import glob

src/terratorch/datasets/generic_scalar_label_dataset.py → terratorch/datasets/generic_scalar_label_dataset.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 """Module containing generic dataset classes
 """
 import glob

src/terratorch/datasets/hls.py → terratorch/datasets/hls.py

@@ -1,13 +1,14 @@
-# Copyright (c) IBM Corp. All rights reserved.
-# Licensed under the MIT License.
+# Copyright contributors to the Terratorch project
+
 
 """Harmonized Landsat and Sentinel-2 datasets."""
 
 import abc
 from collections.abc import Iterable, Sequence
+from typing import Any, Callable, Optional, Union
+
 from rasterio.crs import CRS
 from torchgeo.datasets import Landsat
-from typing import Any, Callable, Optional, Union
 
 
 class HLS(Landsat, abc.ABC):

src/terratorch/datasets/sen1floods11.py → terratorch/datasets/sen1floods11.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 import dataclasses
 import glob
 import os

src/terratorch/datasets/transforms.py → terratorch/datasets/transforms.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 from albumentations import BasicTransform, Compose, ImageOnlyTransform
 from einops import rearrange
 from torch import Tensor

src/terratorch/datasets/utils.py → terratorch/datasets/utils.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 import os
 from collections.abc import Iterator
 from enum import Enum

src/terratorch/datasets/wsf.py → terratorch/datasets/wsf.py

@@ -1,16 +1,16 @@
-# Copyright (c) IBM Corp. All rights reserved.
-# Licensed under the MIT License.
+# Copyright contributors to the Terratorch project
+
 
 """World Settlement Footprint datasets."""
 
 import abc
+from collections.abc import Iterable, Sequence
+from typing import Any, Callable, Optional, Union
+
 import matplotlib.pyplot as plt
 import numpy as np
-
-from collections.abc import Iterable, Sequence
 from rasterio.crs import CRS
 from torchgeo.datasets import RasterDataset
-from typing import Any, Callable, Optional, Union
 
 
 class WSF(RasterDataset, abc.ABC):

src/terratorch/models/__init__.py → terratorch/models/__init__.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 from terratorch.models.prithvi_model_factory import PrithviModelFactory
 from terratorch.models.satmae_model_factory import SatMAEModelFactory
 from terratorch.models.scalemae_model_factory import ScaleMAEModelFactory

terratorch/models/backbones/__init__.py

@@ -0,0 +1,5 @@
+# Copyright contributors to the Terratorch project
+
+# import so they get registered
+import terratorch.models.backbones.prithvi_swin
+import terratorch.models.backbones.prithvi_vit

src/terratorch/models/backbones/prithvi_select_patch_embed_weights.py → terratorch/models/backbones/prithvi_select_patch_embed_weights.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 import logging
 
 import torch

src/terratorch/models/backbones/prithvi_swin.py → terratorch/models/backbones/prithvi_swin.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 """This module handles registering prithvi_swin models into timm.
 """
 

src/terratorch/models/backbones/prithvi_vit.py → terratorch/models/backbones/prithvi_vit.py

@@ -1,5 +1,5 @@
-# Copyright (c) IBM Corp. All rights reserved.
-# Licensed under the MIT License.
+# Copyright contributors to the Terratorch project
+
 
 import logging
 from functools import partial

src/terratorch/models/backbones/swin_encoder_decoder.py → terratorch/models/backbones/swin_encoder_decoder.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 """Swin transformer implementation. Mix of MMSegmentation implementation and timm implementation.
 
 We use this implementation instead of the original implementation or timm's.

src/terratorch/models/backbones/vit_encoder_decoder.py → terratorch/models/backbones/vit_encoder_decoder.py

@@ -6,6 +6,9 @@
 # DeiT: https://github.com/facebookresearch/deit
 # --------------------------------------------------------
 
+# Copyright contributors to the Terratorch project
+
+
 from functools import lru_cache
 
 import numpy as np

src/terratorch/models/decoders/__init__.py → terratorch/models/decoders/__init__.py

@@ -1,6 +1,8 @@
+# Copyright contributors to the Terratorch project
+
 from terratorch.models.decoders.fcn_decoder import FCNDecoder
 from terratorch.models.decoders.identity_decoder import IdentityDecoder
-from terratorch.models.decoders.upernet_decoder import UperNetDecoder
 from terratorch.models.decoders.satmae_head import SatMAEHead, SatMAEHeadViT
+from terratorch.models.decoders.upernet_decoder import UperNetDecoder
 
 __all__ = ["FCNDecoder", "UperNetDecoder", "IdentityDecoder", "SatMAEHead", "SatMAEHeadViT"]

src/terratorch/models/decoders/fcn_decoder.py → terratorch/models/decoders/fcn_decoder.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 from torch import Tensor, nn
 
 

src/terratorch/models/decoders/identity_decoder.py → terratorch/models/decoders/identity_decoder.py

@@ -1,3 +1,5 @@
+# Copyright contributors to the Terratorch project
+
 """Pass the features straight through
 """