Merge branch 'develop' into enhance-torch-compile

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.4.10 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.5.1 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.10
+    rev: v0.5.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

benchmarks/annotation_store_alloc.py

@@ -306,8 +306,8 @@ def main(
             # Skip memray if not installed
             return
         regex = re.compile(r"Total memory allocated:\s*([\d.]+)MB")
-        pipe = subprocess.Popen(
-            [  # noqa: S603
+        pipe = subprocess.Popen(  # noqa: S603
+            [
                 sys.executable,
                 "-m",
                 "memray",

examples/full-pipelines/slide-graph.ipynb

@@ -1577,7 +1577,6 @@
     "        loss.backward()\n",
     "        optimizer.step()\n",
     "\n",
-    "        #\n",
     "        loss = loss.detach().cpu().numpy()\n",
     "        assert not np.isnan(loss)  # noqa: S101\n",
     "        wsi_labels = wsi_labels.cpu().numpy()\n",

examples/inference-pipelines/slide-graph.ipynb

@@ -1171,7 +1171,6 @@
     "        loss.backward()\n",
     "        optimizer.step()\n",
     "\n",
-    "        #\n",
     "        loss = loss.detach().cpu().numpy()\n",
     "        assert not np.isnan(loss)  # noqa: S101\n",
     "        wsi_labels = wsi_labels.cpu().numpy()\n",

pre-commit/notebook_urls.py

@@ -14,8 +14,8 @@
 def git_branch_name() -> str:
     """Get the current branch name."""
     return (
-        subprocess.check_output(
-            ["/usr/bin/git", "rev-parse", "--abbrev-ref", "HEAD"],  # noqa: S603
+        subprocess.check_output(  # noqa: S603
+            ["/usr/bin/git", "rev-parse", "--abbrev-ref", "HEAD"],
         )
         .decode()
         .strip()
@@ -27,8 +27,8 @@ def git_branch_modified_paths(from_ref: str, to_ref: str) -> set[Path]:
     from_to = f"{from_ref}...{to_ref}"
     return {
         Path(p)
-        for p in subprocess.check_output(
-            [  # noqa: S603
+        for p in subprocess.check_output(  # noqa: S603
+            [
                 "/usr/bin/git",
                 "diff",
                 "--name-only",
@@ -45,8 +45,8 @@ def git_previous_commit_modified_paths() -> set[Path]:
     """Get a set of file paths modified in the previous commit."""
     return {
         Path(p)
-        for p in subprocess.check_output(
-            ["/usr/bin/git", "diff", "--name-only", "HEAD~"],  # noqa: S603
+        for p in subprocess.check_output(  # noqa: S603
+            ["/usr/bin/git", "diff", "--name-only", "HEAD~"],
         )
         .decode()
         .strip()

pre-commit/requirements_consistency.py

@@ -88,8 +88,8 @@ def parse_conda(file_path: Path) -> dict[str, Requirement]:
         # pip-style dependency
         if isinstance(dependency, dict):
             pip = parse_pip(lines=dependency["pip"])
-            for package_name, requirement in pip.items():
-                packages[package_name] = requirement
+            packages = dict(pip.items())
+
             continue
         requirement = Requirement.parse(dependency)
         # Check for duplicate packages

requirements/requirements_dev.txt

@@ -11,7 +11,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.4.10  # This will be updated by pre-commit bot to latest version
+ruff==0.5.1  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tests/conftest.py

@@ -119,7 +119,17 @@ def sample_ome_tiff(remote_sample: Callable) -> Path:
     Download ome-tiff image for pytest.
 
     """
-    return remote_sample("ome-brightfield-pyramid-1-small")
+    return remote_sample("ome-brightfield-small-pyramid")
+
+
+@pytest.fixture(scope="session")
+def sample_ome_tiff_level_0(remote_sample: Callable) -> Path:
+    """Sample pytest fixture for ome-tiff image with one level.
+
+    Download ome-tiff image for pytest.
+
+    """
+    return remote_sample("ome-brightfield-small-level-0")
 
 
 @pytest.fixture(scope="session")

tests/models/test_arch_utils.py

@@ -28,7 +28,6 @@ def test_all() -> None:
     )
     assert np.sum(_output - output) == 0
 
-    #
     with pytest.raises(ValueError, match=r".*Unknown.*format.*"):
         centre_crop(_output[None, :, :, None], [2, 2], "NHWCT")
 

tests/models/test_hovernet.py

@@ -123,7 +123,6 @@ def test_unit_blocks() -> None:
     output = block(sample)
     assert np.sum(output.shape - np.array([1, 32, 15, 15])) == 0, f"{output.shape}"
 
-    #
     block = DenseBlock(16, [1, 3], [16, 16], 3)
     output = block(sample)
     assert output.shape[1] == 16 * 4, f"{output.shape}"

tests/test_init.py

@@ -72,8 +72,8 @@ def helper_logger_test(level: str) -> None:
         f'logger.{level.lower()}("Test if {level.lower()} is written to std{output}.")'
     )
 
-    proc = subprocess.Popen(
-        [  # noqa: S603, S607
+    proc = subprocess.Popen(  # noqa: S603
+        [  # noqa: S607
             "python",
             "-c",
             run_statement,

tests/test_tiffreader.py

@@ -13,7 +13,7 @@ def test_ome_missing_instrument_ref(
     remote_sample: Callable,
 ) -> None:
     """Test that an OME-TIFF can be read without instrument reference."""
-    sample = remote_sample("ome-brightfield-pyramid-1-small")
+    sample = remote_sample("ome-brightfield-small-level-0")
     wsi = wsireader.TIFFWSIReader(sample)
     page = wsi.tiff.pages[0]
     description = page.description
@@ -37,7 +37,7 @@ def test_ome_missing_physicalsize(
     remote_sample: Callable,
 ) -> None:
     """Test that an OME-TIFF can be read without physical size."""
-    sample = remote_sample("ome-brightfield-pyramid-1-small")
+    sample = remote_sample("ome-brightfield-small-level-0")
     wsi = wsireader.TIFFWSIReader(sample)
     page = wsi.tiff.pages[0]
     description = page.description
@@ -62,7 +62,7 @@ def test_ome_missing_physicalsizey(
     remote_sample: Callable,
 ) -> None:
     """Test that an OME-TIFF can be read without physical size."""
-    sample = remote_sample("ome-brightfield-pyramid-1-small")
+    sample = remote_sample("ome-brightfield-small-level-0")
     wsi = wsireader.TIFFWSIReader(sample)
     page = wsi.tiff.pages[0]
     description = page.description
@@ -86,7 +86,7 @@ def test_tiffreader_non_tiled_metadata(
     remote_sample: Callable,
 ) -> None:
     """Test that fetching metadata for non-tiled TIFF works."""
-    sample = remote_sample("ome-brightfield-pyramid-1-small")
+    sample = remote_sample("ome-brightfield-small-level-0")
     wsi = wsireader.TIFFWSIReader(sample)
     monkeypatch.setattr(wsi.tiff, "is_ome", False)
     monkeypatch.setattr(

tests/test_wsireader.py

@@ -959,15 +959,23 @@ def test_read_bounds_interpolated(sample_svs: Path) -> None:
 
 
 def test_read_bounds_level_consistency_openslide(sample_ndpi: Path) -> None:
-    """Test read_bounds produces the same visual field across resolution levels."""
+    """Test read_bounds produces the same visual field across resolution levels.
+
+    with OpenSlideWSIReader.
+
+    """
     wsi = wsireader.OpenSlideWSIReader(sample_ndpi)
     bounds = NDPI_TEST_TISSUE_BOUNDS
 
     read_bounds_level_consistency(wsi, bounds)
 
 
 def test_read_bounds_level_consistency_jp2(sample_jp2: Path) -> None:
-    """Test read_bounds produces the same visual field across resolution levels."""
+    """Test read_bounds produces the same visual field across resolution levels.
+
+    Using JP2WSIReader.
+
+    """
     bounds = JP2_TEST_TISSUE_BOUNDS
     wsi = wsireader.JP2WSIReader(sample_jp2)
 
@@ -1883,11 +1891,11 @@ def test_tiffwsireader_invalid_svs_metadata(
 
 
 def test_tiffwsireader_invalid_ome_metadata(
-    sample_ome_tiff: Path,
+    sample_ome_tiff_level_0: Path,
     monkeypatch: pytest.MonkeyPatch,
 ) -> None:
     """Test exception raised for invalid OME-XML metadata instrument."""
-    wsi = wsireader.TIFFWSIReader(sample_ome_tiff)
+    wsi = wsireader.TIFFWSIReader(sample_ome_tiff_level_0)
     monkeypatch.setattr(
         wsi.tiff.pages[0],
         "description",
@@ -2545,7 +2553,7 @@ def test_jp2_no_header(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
         },
         {
             "reader_class": TIFFWSIReader,
-            "sample_key": "ome-brightfield-pyramid-1-small",
+            "sample_key": "ome-brightfield-small-pyramid",
             "kwargs": {},
         },
         {

tiatoolbox/data/__init__.py

@@ -81,8 +81,8 @@ def _local_sample_path(path: str | Path) -> Path:
 
     """
     file_path = importlib_resources.files("tiatoolbox") / str(Path("data") / path)
-    with importlib_resources.as_file(file_path) as path:
-        return path
+    with importlib_resources.as_file(file_path) as file_path_:
+        return file_path_
 
 
 def stain_norm_target() -> np.ndarray:

tiatoolbox/data/remote_samples.yaml

@@ -25,8 +25,10 @@ files:
     url: [*wsis, "CMU-1-Small-Region.jpeg.tiff"]
   tiled-tiff-1-small-jp2k:
     url: [*wsis, "CMU-1-Small-Region.jp2k.tiff"]
-  ome-brightfield-pyramid-1-small:
-    url: [*wsis, "CMU-1-Small-Region.ome.tiff"]
+  ome-brightfield-small-level-0:
+    url: [*wsis, "CMU-1-Small-Region-Level-0.ome.tiff"]
+  ome-brightfield-small-pyramid:
+    url: [*wsis, "CMU-1-Small-Region-Pyramid.ome.tif"]
   two-tiled-pages:
     url: [*wsis, "two-tiled-pages.tiff"]
   ventana-tif:

tiatoolbox/utils/env_detection.py

@@ -250,12 +250,12 @@ def check_pixman_using_anaconda(versions: list) -> tuple[list, str]:
     """Using anaconda to check for pixman."""
     using = "conda"
     try:
-        conda_list = subprocess.Popen(
-            ("conda", "list"),  # noqa: S603
+        conda_list = subprocess.Popen(  # noqa: S603
+            ("conda", "list"),
             stdout=subprocess.PIPE,
         )
-        conda_pixman = subprocess.check_output(
-            ("grep", "pixman"),  # noqa: S603
+        conda_pixman = subprocess.check_output(  # noqa: S603
+            ("grep", "pixman"),
             stdin=conda_list.stdout,
         )
         conda_list.wait()
@@ -276,8 +276,8 @@ def check_pixman_using_dpkg(versions: list) -> tuple[list, str]:
     """Using dpkg to check for pixman."""
     using = "dpkg"
     try:
-        dkpg_output = subprocess.check_output(
-            ["/usr/bin/dpkg", "-s", "libpixman-1-0"],  # noqa: S603
+        dkpg_output = subprocess.check_output(  # noqa: S603
+            ["/usr/bin/dpkg", "-s", "libpixman-1-0"],
         )
     except subprocess.SubprocessError:
         dkpg_output = b""
@@ -296,12 +296,12 @@ def check_pixman_using_brew(versions: list) -> tuple[list, str]:
     """Using homebrew to check for pixman."""
     using = "brew"
     try:
-        brew_list = subprocess.Popen(
-            ("brew", "list", "--versions"),  # noqa: S603
+        brew_list = subprocess.Popen(  # noqa: S603
+            ("brew", "list", "--versions"),
             stdout=subprocess.PIPE,
         )
-        brew_pixman = subprocess.check_output(
-            ("grep", "pixman"),  # noqa: S603
+        brew_pixman = subprocess.check_output(  # noqa: S603
+            ("grep", "pixman"),
             stdin=brew_list.stdout,
         )
         brew_list.wait()
@@ -326,12 +326,12 @@ def check_pixman_using_macports(versions: list) -> tuple[list, str]:
 
     """
     using = "port"
-    port_list = subprocess.Popen(
-        ("port", "installed"),  # noqa: S603
+    port_list = subprocess.Popen(  # noqa: S603
+        ("port", "installed"),
         stdout=subprocess.PIPE,
     )
-    port_pixman = subprocess.check_output(
-        ("grep", "pixman"),  # noqa: S603
+    port_pixman = subprocess.check_output(  # noqa: S603
+        ("grep", "pixman"),
         stdin=port_list.stdout,
     )
     port_list.wait()

tiatoolbox/visualization/bokeh_app/main.py

@@ -28,10 +28,10 @@
     Column,
     ColumnDataSource,
     CustomJS,
+    CustomJSTickFormatter,
     DataTable,
     Div,
     Dropdown,
-    FuncTickFormatter,
     Glyph,
     HoverTool,
     HTMLTemplateFormatter,
@@ -630,7 +630,7 @@ def __init__(self: ViewerState, slide_path: str | Path) -> None:
         self.thickness = -1
         self.model_mpp = 0
         self.init = True
-        self.micron_formatter = FuncTickFormatter(
+        self.micron_formatter = CustomJSTickFormatter(
             args={"mpp": 0.1},
             code="""
                 return Math.round(tick*mpp)
@@ -2086,7 +2086,7 @@ def setup_doc(self: DocConfig, base_doc: Document) -> tuple[Row, Tabs]:
 
         # Set initial slide to first one in base folder
         slide_list = []
-        for ext in ["*.svs", "*ndpi", "*.tiff", "*.mrxs", "*.png", "*.jpg"]:
+        for ext in ["*.svs", "*ndpi", "*.tiff", "*.tif", "*.mrxs", "*.png", "*.jpg"]:
             slide_list.extend(list(doc_config["slide_folder"].glob(ext)))
             slide_list.extend(
                 list(doc_config["slide_folder"].glob(str(Path("*") / ext))),