Merge branch 'develop' into dev-define-engines-abc

Author: shaneahmed

.github/workflows/mypy-type-check.yml

@@ -0,0 +1,40 @@
+# This workflow will perform code type checking using mypy
+
+name: mypy type checking
+
+on:
+  push:
+    branches: [ develop, pre-release, master, main ]
+  pull_request:
+    branches: [ develop, pre-release, master, main ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - name: Setup mypy
+      run: |
+        pip install mypy
+
+    - name: Perform type checking
+      run: |
+        mypy --install-types --non-interactive --follow-imports=skip \
+          tiatoolbox/__init__.py \
+          tiatoolbox/__main__.py \
+          tiatoolbox/utils/exceptions.py

.pre-commit-config.yaml

@@ -59,7 +59,7 @@ repos:
       - id: rst-directive-colons    # Detect mistake of rst directive not ending with double colon.
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/psf/black
-    rev: 23.9.1 # Replace with any tag/version: https://github.com/psf/black/tags
+    rev: 23.10.0 # Replace with any tag/version: https://github.com/psf/black/tags
     hooks:
       - id: black
         language_version: python3 # Should be a command that runs python3.+
@@ -68,7 +68,7 @@ repos:
         language: python
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.0.292
+    rev: v0.1.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

requirements/requirements_dev.txt

@@ -4,6 +4,7 @@ black>=23.3.0
 coverage>=7.0.0
 docutils>=0.18.1
 jinja2>=3.0.3, <3.1.0
+mypy>=1.6.1
 pip>=22.3
 poetry-bumpversion>=0.3.1
 pre-commit>=2.20.0

tests/test_init.py

@@ -139,3 +139,14 @@ def test_lazy_import() -> None:
     )
 
     assert "exceptions" in sys.modules
+
+
+def test_lazy_import_module_not_found() -> None:
+    """'Test lazy import for ModuleNotFoundError."""
+    from tiatoolbox import _lazy_import
+
+    with pytest.raises(ModuleNotFoundError):
+        _lazy_import(
+            "nonexistent_module",
+            Path(__file__).parent.parent / "tiatoolbox",
+        )

tests/test_utils.py

@@ -1638,7 +1638,7 @@ def test_patch_pred_store() -> None:
         "other": "other",
     }
 
-    store = misc.patch_pred_store(patch_output, (1.0, 1.0))
+    store = misc.dict_to_store(patch_output, (1.0, 1.0))
 
     # Check that its an SQLiteStore containing the expected annotations
     assert isinstance(store, SQLiteStore)
@@ -1651,7 +1651,7 @@ def test_patch_pred_store() -> None:
     patch_output.pop("coordinates")
     # check correct error is raised if coordinates are missing
     with pytest.raises(ValueError, match="coordinates"):
-        misc.patch_pred_store(patch_output, (1.0, 1.0))
+        misc.dict_to_store(patch_output, (1.0, 1.0))
 
 
 def test_patch_pred_store_cdict() -> None:
@@ -1665,7 +1665,7 @@ def test_patch_pred_store_cdict() -> None:
         "other": "other",
     }
     class_dict = {0: "class0", 1: "class1"}
-    store = misc.patch_pred_store(patch_output, (1.0, 1.0), class_dict=class_dict)
+    store = misc.dict_to_store(patch_output, (1.0, 1.0), class_dict=class_dict)
 
     # Check that its an SQLiteStore containing the expected annotations
     assert isinstance(store, SQLiteStore)
@@ -1686,10 +1686,113 @@ def test_patch_pred_store_sf() -> None:
         "probabilities": [[0.1, 0.9], [0.9, 0.1], [0.4, 0.6]],
         "labels": [1, 0, 1],
     }
-    store = misc.patch_pred_store(patch_output, (2.0, 2.0))
+    store = misc.dict_to_store(patch_output, (2.0, 2.0))
 
     # Check that its an SQLiteStore containing the expected annotations
     assert isinstance(store, SQLiteStore)
     assert len(store) == 3
     for annotation in store.values():
         assert annotation.geometry.area == 4
+
+
+def test_patch_pred_store_zarr(tmp_path: pytest.TempPathFactory) -> None:
+    """Test patch_pred_store_zarr."""
+    # Define a mock patch_output
+    patch_output = {
+        "predictions": [1, 0, 1],
+        "coordinates": [(0, 0, 1, 1), (1, 1, 2, 2), (2, 2, 3, 3)],
+        "probabilities": [[0.1, 0.9], [0.9, 0.1], [0.4, 0.6]],
+        "labels": [1, 0, 1],
+    }
+
+    save_path = tmp_path / "patch_output" / "output.zarr"
+
+    store_path = misc.dict_to_zarr(patch_output, save_path=save_path)
+
+    print("Zarr path: ", store_path)
+    assert Path.exists(store_path), "Zarr output file does not exist"
+
+
+def test_patch_pred_store_zarr_ext(tmp_path: pytest.TempPathFactory) -> None:
+    """Test patch_pred_store_zarr and ensures the output file extension is `.zarr`."""
+    # Define a mock patch_output
+    patch_output = {
+        "predictions": [1, 0, 1],
+        "coordinates": [(0, 0, 1, 1), (1, 1, 2, 2), (2, 2, 3, 3)],
+        "probabilities": [[0.1, 0.9], [0.9, 0.1], [0.4, 0.6]],
+        "labels": [1, 0, 1],
+    }
+
+    # sends the path of a jpeg source image, expects .zarr file in the same directory
+    save_path = tmp_path / "patch_output" / "patch.jpeg"
+
+    store_path = misc.dict_to_zarr(patch_output, save_path=save_path)
+
+    print("Zarr path: ", store_path)
+    assert Path.exists(store_path), "Zarr output file does not exist"
+
+
+def test_patch_pred_store_persist(tmp_path: pytest.TempPathFactory) -> None:
+    """Test patch_pred_store. and persists store output to a .db file."""
+    # Define a mock patch_output
+    patch_output = {
+        "predictions": [1, 0, 1],
+        "coordinates": [(0, 0, 1, 1), (1, 1, 2, 2), (2, 2, 3, 3)],
+        "probabilities": [[0.1, 0.9], [0.9, 0.1], [0.4, 0.6]],
+        "labels": [1, 0, 1],
+    }
+    save_path = tmp_path / "patch_output" / "output.db"
+
+    store_path = misc.dict_to_store(patch_output, (1.0, 1.0), save_path=save_path)
+
+    print("Annotation store path: ", store_path)
+    assert Path.exists(store_path), "Annotation Store output file does not exist"
+
+    store = SQLiteStore(store_path)
+
+    # Check that its an SQLiteStore containing the expected annotations
+    assert isinstance(store, SQLiteStore)
+    assert len(store) == 3
+    for annotation in store.values():
+        assert annotation.geometry.area == 1
+        assert annotation.properties["type"] in [0, 1]
+        assert "other" not in annotation.properties
+
+    patch_output.pop("coordinates")
+    # check correct error is raised if coordinates are missing
+    with pytest.raises(ValueError, match="coordinates"):
+        misc.dict_to_store(patch_output, (1.0, 1.0))
+
+
+def test_patch_pred_store_persist_ext(tmp_path: pytest.TempPathFactory) -> None:
+    """Test patch_pred_store and ensures the output file extension is `.db`."""
+    # Define a mock patch_output
+    patch_output = {
+        "predictions": [1, 0, 1],
+        "coordinates": [(0, 0, 1, 1), (1, 1, 2, 2), (2, 2, 3, 3)],
+        "probabilities": [[0.1, 0.9], [0.9, 0.1], [0.4, 0.6]],
+        "labels": [1, 0, 1],
+    }
+
+    # sends the path of a jpeg source image, expects .db file in the same directory
+    save_path = tmp_path / "patch_output" / "output.jpeg"
+
+    store_path = misc.dict_to_store(patch_output, (1.0, 1.0), save_path=save_path)
+
+    print("Annotation store path: ", store_path)
+    assert Path.exists(store_path), "Annotation Store output file does not exist"
+
+    store = SQLiteStore(store_path)
+
+    # Check that its an SQLiteStore containing the expected annotations
+    assert isinstance(store, SQLiteStore)
+    assert len(store) == 3
+    for annotation in store.values():
+        assert annotation.geometry.area == 1
+        assert annotation.properties["type"] in [0, 1]
+        assert "other" not in annotation.properties
+
+    patch_output.pop("coordinates")
+    # check correct error is raised if coordinates are missing
+    with pytest.raises(ValueError, match="coordinates"):
+        misc.dict_to_store(patch_output, (1.0, 1.0))

tiatoolbox/__init__.py

@@ -9,12 +9,14 @@
 if sys.version_info >= (3, 9):  # pragma: no cover
     import importlib.resources as importlib_resources
 else:  # pragma: no cover
-    import importlib_resources  # To support Python 3.8
+    # To support Python 3.8
+    import importlib_resources  # type: ignore[import-not-found]
 
 import yaml
 
 if TYPE_CHECKING:  # pragma: no cover
     from logging import LogRecord
+    from types import ModuleType
 
 __author__ = """TIA Centre"""
 __email__ = "[email protected]"
@@ -71,6 +73,7 @@ def filter(self: DuplicateFilter, record: LogRecord) -> bool:
 
 
 # runtime context parameters
+rcParam: dict[str, str | Path | dict]  # noqa: N816
 rcParam = {  # noqa: N816
     "TIATOOLBOX_HOME": Path.home() / ".tiatoolbox",
 }
@@ -88,6 +91,7 @@ def read_registry_files(path_to_registry: str | Path) -> dict | str:
 
 
     """
+    path_to_registry = str(path_to_registry)  # To pass tests with Python 3.8
     pretrained_files_registry_path = importlib_resources.as_file(
         importlib_resources.files("tiatoolbox") / path_to_registry,
     )
@@ -101,8 +105,10 @@ def read_registry_files(path_to_registry: str | Path) -> dict | str:
 rcParam["pretrained_model_info"] = read_registry_files("data/pretrained_model.yaml")
 
 
-def _lazy_import(name: str, module_location: Path) -> sys.modules:
+def _lazy_import(name: str, module_location: Path) -> ModuleType:
     spec = importlib.util.spec_from_file_location(name, module_location)
+    if spec is None or spec.loader is None:
+        raise ModuleNotFoundError(name=name, path=str(module_location))
     loader = importlib.util.LazyLoader(spec.loader)
     spec.loader = loader
     module = importlib.util.module_from_spec(spec)

tiatoolbox/utils/exceptions.py

@@ -1,4 +1,5 @@
 """Custom Errors and Exceptions for TIAToolbox."""
+from __future__ import annotations
 
 
 class FileNotSupportedError(Exception):
@@ -10,7 +11,7 @@ class FileNotSupportedError(Exception):
     """
 
     def __init__(
-        self: Exception,
+        self: FileNotSupportedError,
         message: str = "File format is not supported",
     ) -> None:
         """Initialize :class:`FileNotSupportedError`."""
@@ -25,6 +26,9 @@ class MethodNotSupportedError(Exception):
 
     """
 
-    def __init__(self: Exception, message: str = "Method is not supported") -> None:
+    def __init__(
+        self: MethodNotSupportedError,
+        message: str = "Method is not supported",
+    ) -> None:
         """Initialize :class:`MethodNotSupportedError`."""
         super().__init__(message)