Rework list of required dependencies (#287)

* Rework list of required dependencies

* Update open3d import error msg

* Style fixes

* Remove extra empty line

* Increase test coverage

* Fix idtrees tests

.github/workflows/docs.yaml

@@ -37,7 +37,7 @@ jobs:
       run: sudo apt-get install pandoc
     - name: Install pip dependencies
       run: |
-        pip install .[train]
+        pip install .
         pip install -r docs/requirements.txt
     - name: Run sphinx checks
       run: cd docs && make html

.github/workflows/release.yaml

@@ -25,7 +25,7 @@ jobs:
     - name: Install pip dependencies
       run: |
         pip install gdal tqdm  # TODO: these deps shouldn't be needed
-        pip install .[datasets,tests,train]
+        pip install .[datasets,tests]
         pip install -r docs/requirements.txt
     - name: Run notebook checks
       env:
@@ -42,6 +42,6 @@ jobs:
       with:
         python-version: 3.9
     - name: Install pip dependencies
-      run: pip install .[datasets,tests,train]
+      run: pip install .[datasets,tests]
     - name: Run integration checks
       run: pytest -m slow

.github/workflows/tests.yaml

@@ -20,9 +20,25 @@ jobs:
     - name: Install pip dependencies
       run: |
         pip install cython numpy  # needed for pycocotools
-        pip install .[datasets,tests,train]
+        pip install .[datasets,tests]
     - name: Run mypy checks
       run: mypy .
+  datasets:
+    name: datasets
+    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 cython numpy  # needed for pycocotools
+        pip install .[tests]
+    - name: Run pytest checks
+      run: pytest --cov=torchgeo --cov-report=xml
   pytest:
     name: pytest
     runs-on: ${{ matrix.os }}
@@ -64,7 +80,7 @@ jobs:
     - name: Install pip dependencies
       run: |
         pip install cython numpy  # needed for pycocotools
-        pip install .[datasets,tests,train]
+        pip install .[datasets,tests]
     - name: Run pytest checks
       run: pytest --cov=torchgeo --cov-report=xml
     - name: Report coverage

setup.cfg

@@ -37,6 +37,8 @@ install_requires =
     kornia>=0.5.4
     matplotlib
     numpy
+    # omegaconf 2.1+ required for to_object method
+    omegaconf>=2.1
     # pillow 2.9+ required for height attribute
     pillow>=2.9
     # pyproj 2.2+ required for CRS object
@@ -51,8 +53,13 @@ install_requires =
     scikit-learn>=0.18
     # shapely 1.3+ required for Python 3 support
     shapely>=1.3
+    # segmentation-models-pytorch 0.2+ required for smp.losses module
+    segmentation-models-pytorch>=0.2
+    # timm 0.2.1+ required for `features_only` option in create_model
+    timm>=0.2.1
     # torch 1.7+ required for typing
     torch>=1.7
+    torchmetrics
     # torchvision 0.10+ required for torchvision.utils.draw_segmentation_masks
     torchvision>=0.10
 python_requires = >= 3.6
@@ -65,9 +72,9 @@ include = torchgeo*
 # Optional dataset requirements
 datasets =
     h5py
-    # loading .las point clouds (idtrees) laspy 2+ required for Python 3.6+ support
-    laspy>=2.0.0
-    # open3d v0.11.2 last version for tests to pass
+    # laspy 2+ required for Python 3.6+ support
+    laspy>=2
+    # open3d 0.11.2+ required to avoid GLFW error:
     # https://github.com/isl-org/Open3D/issues/1550
     open3d>=0.11.2
     opencv-python
@@ -81,15 +88,6 @@ datasets =
     rarfile>=3
     # scipy 0.9+ required for scipy.io.wavfile.read
     scipy>=0.9
-# Optional trainer requirements
-train =
-    # omegaconf 2.1+ required for to_object method
-    omegaconf>=2.1
-    # segmentation-models-pytorch 0.2+ required for smp.losses module
-    segmentation-models-pytorch>=0.2
-    # timm 0.2.1+ required for `features_only` option in create_model
-    timm>=0.2.1
-    torchmetrics
 # Optional developer requirements
 style =
     # black 21+ required for Python 3.9 support
@@ -101,6 +99,7 @@ style =
     isort[colors]>=5.8
     # pydocstyle 6.1+ required for pyproject.toml support
     pydocstyle[toml]>=6.1
+# Optional testing requirements
 tests =
     # mypy 0.900+ required for pyproject.toml support
     mypy>=0.900

tests/datasets/test_advance.py

@@ -25,7 +25,6 @@ class TestADVANCE:
     def dataset(
         self, monkeypatch: Generator[MonkeyPatch, None, None], tmp_path: Path
     ) -> ADVANCE:
-        pytest.importorskip("scipy", minversion="0.9.0")
         monkeypatch.setattr(  # type: ignore[attr-defined]
             torchgeo.datasets.utils, "download_url", download_url
         )
@@ -57,6 +56,7 @@ def mocked_import(name: str, *args: Any, **kwargs: Any) -> Any:
         )
 
     def test_getitem(self, dataset: ADVANCE) -> None:
+        pytest.importorskip("scipy", minversion="0.9.0")
         x = dataset[0]
         assert isinstance(x, dict)
         assert isinstance(x["image"], torch.Tensor)

tests/datasets/test_idtrees.py

@@ -19,6 +19,9 @@
 import torchgeo.datasets.utils
 from torchgeo.datasets import IDTReeS
 
+pytest.importorskip("pandas", minversion="0.19.1")
+pytest.importorskip("laspy", minversion="2")
+
 
 def download_url(url: str, root: str, *args: str, **kwargs: str) -> None:
     shutil.copy(url, root)
@@ -32,8 +35,6 @@ def dataset(
         tmp_path: Path,
         request: SubRequest,
     ) -> IDTReeS:
-        pytest.importorskip("pandas")
-        pytest.importorskip("laspy")
         monkeypatch.setattr(  # type: ignore[attr-defined]
             torchgeo.datasets.idtrees, "download_url", download_url
         )
@@ -124,11 +125,11 @@ def test_mock_missing_module(
                 ImportError,
                 match=f"{package} is not installed and is required to use this dataset",
             ):
-                IDTReeS(dataset.root, download=True, checksum=True)
-        else:
+                IDTReeS(dataset.root, dataset.split, dataset.task)
+        elif package in ["open3d"]:
             with pytest.raises(
                 ImportError,
-                match=f"{package} is not installed and is required to use this dataset",
+                match=f"{package} is not installed and is required to plot point cloud",
             ):
                 dataset.plot_las(0)
 
@@ -153,7 +154,7 @@ def test_plot(self, dataset: IDTReeS) -> None:
         reason="segmentation fault on macOS and windows",
     )
     def test_plot_las(self, dataset: IDTReeS) -> None:
-        pytest.importorskip("open3d")
+        pytest.importorskip("open3d", minversion="0.11.2")
         vis = dataset.plot_las(index=0, colormap="BrBG")
         vis.close()
         vis = dataset.plot_las(index=0, colormap=None)

tests/datasets/test_nwpu.py

@@ -1,11 +1,12 @@
 # Copyright (c) Microsoft Corporation. All rights reserved.
 # Licensed under the MIT License.
 
+import builtins
 import os
 import shutil
 import sys
 from pathlib import Path
-from typing import Generator
+from typing import Any, Generator
 
 import pytest
 import torch
@@ -17,7 +18,6 @@
 import torchgeo.datasets.utils
 from torchgeo.datasets import VHR10
 
-pytest.importorskip("rarfile")
 pytest.importorskip("pycocotools")
 
 
@@ -35,6 +35,7 @@ def dataset(
         tmp_path: Path,
         request: SubRequest,
     ) -> VHR10:
+        pytest.importorskip("rarfile", minversion="3")
         monkeypatch.setattr(  # type: ignore[attr-defined]
             torchgeo.datasets.nwpu, "download_url", download_url
         )
@@ -54,6 +55,21 @@ def dataset(
         transforms = nn.Identity()  # type: ignore[attr-defined]
         return VHR10(root, split, transforms, download=True, checksum=True)
 
+    @pytest.fixture
+    def mock_missing_module(
+        self, monkeypatch: Generator[MonkeyPatch, None, None]
+    ) -> None:
+        import_orig = builtins.__import__
+
+        def mocked_import(name: str, *args: Any, **kwargs: Any) -> Any:
+            if name == "pycocotools.coco":
+                raise ImportError()
+            return import_orig(name, *args, **kwargs)
+
+        monkeypatch.setattr(  # type: ignore[attr-defined]
+            builtins, "__import__", mocked_import
+        )
+
     def test_getitem(self, dataset: VHR10) -> None:
         x = dataset[0]
         assert isinstance(x, dict)
@@ -84,3 +100,13 @@ def test_invalid_split(self) -> None:
     def test_not_downloaded(self, tmp_path: Path) -> None:
         with pytest.raises(RuntimeError, match="Dataset not found or corrupted."):
             VHR10(str(tmp_path))
+
+    def test_mock_missing_module(
+        self, dataset: VHR10, mock_missing_module: None
+    ) -> None:
+        if dataset.split == "positive":
+            with pytest.raises(
+                ImportError,
+                match="pycocotools is not installed and is required to use this datase",
+            ):
+                VHR10(dataset.root, dataset.split)

tests/datasets/test_resisc45.py

@@ -17,8 +17,6 @@
 import torchgeo.datasets.utils
 from torchgeo.datasets import RESISC45, RESISC45DataModule
 
-pytest.importorskip("rarfile")
-
 
 def download_url(url: str, root: str, *args: str, **kwargs: str) -> None:
     shutil.copy(url, root)
@@ -33,6 +31,8 @@ def dataset(
         tmp_path: Path,
         request: SubRequest,
     ) -> RESISC45:
+        pytest.importorskip("rarfile", minversion="3")
+
         monkeypatch.setattr(  # type: ignore[attr-defined]
             torchgeo.datasets.resisc45, "download_url", download_url
         )

tests/datasets/test_so2sat.py

@@ -1,9 +1,10 @@
 # Copyright (c) Microsoft Corporation. All rights reserved.
 # Licensed under the MIT License.
 
+import builtins
 import os
 from pathlib import Path
-from typing import Generator
+from typing import Any, Generator
 
 import matplotlib.pyplot as plt
 import pytest
@@ -14,6 +15,8 @@
 
 from torchgeo.datasets import So2Sat, So2SatDataModule
 
+pytest.importorskip("h5py")
+
 
 class TestSo2Sat:
     @pytest.fixture(params=["train", "validation", "test"])
@@ -32,6 +35,21 @@ def dataset(
         transforms = nn.Identity()  # type: ignore[attr-defined]
         return So2Sat(root, split, transforms, checksum=True)
 
+    @pytest.fixture
+    def mock_missing_module(
+        self, monkeypatch: Generator[MonkeyPatch, None, None]
+    ) -> None:
+        import_orig = builtins.__import__
+
+        def mocked_import(name: str, *args: Any, **kwargs: Any) -> Any:
+            if name == "h5py":
+                raise ImportError()
+            return import_orig(name, *args, **kwargs)
+
+        monkeypatch.setattr(  # type: ignore[attr-defined]
+            builtins, "__import__", mocked_import
+        )
+
     def test_getitem(self, dataset: So2Sat) -> None:
         x = dataset[0]
         assert isinstance(x, dict)
@@ -65,6 +83,15 @@ def test_plot(self, dataset: So2Sat) -> None:
         dataset.plot(x)
         plt.close()
 
+    def test_mock_missing_module(
+        self, dataset: So2Sat, mock_missing_module: None
+    ) -> None:
+        with pytest.raises(
+            ImportError,
+            match="h5py is not installed and is required to use this dataset",
+        ):
+            So2Sat(dataset.root)
+
 
 class TestSo2SatDataModule:
     @pytest.fixture(scope="class", params=zip([True, False], ["rgb", "s2"]))

tests/datasets/test_utils.py

@@ -98,7 +98,7 @@ def test_mock_missing_module(mock_missing_module: None) -> None:
     ],
 )
 def test_extract_archive(src: str, tmp_path: Path) -> None:
-    pytest.importorskip("rarfile")
+    pytest.importorskip("rarfile", minversion="3")
     extract_archive(os.path.join("tests", "data", src), str(tmp_path))
 
 

torchgeo/datasets/idtrees.py

@@ -522,7 +522,7 @@ def plot_las(self, index: int, colormap: Optional[str] = None) -> Any:
             import open3d  # noqa: F401
         except ImportError:
             raise ImportError(
-                "open3d is not installed and is required to use this dataset"
+                "open3d is not installed and is required to plot point clouds"
             )
         import laspy
 

torchgeo/datasets/nwpu.py

@@ -117,7 +117,12 @@ def __init__(
 
         if split == "positive":
             # Must be installed to parse annotations file
-            from pycocotools.coco import COCO
+            try:
+                from pycocotools.coco import COCO  # noqa: F401
+            except ImportError:
+                raise ImportError(
+                    "pycocotools is not installed and is required to use this dataset"
+                )
 
             self.coco = COCO(
                 os.path.join(

torchgeo/datasets/so2sat.py

@@ -132,7 +132,12 @@ def __init__(
             AssertionError: if ``split`` argument is invalid
             RuntimeError: if data is not found in ``root``, or checksums don't match
         """
-        import h5py
+        try:
+            import h5py  # noqa: F401
+        except ImportError:
+            raise ImportError(
+                "h5py is not installed and is required to use this dataset"
+            )
 
         assert split in ["train", "validation", "test"]