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

Author: shaneahmed

.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==0.5.0 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: v0.5.0
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

benchmarks/annotation_store.ipynb

@@ -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",

benchmarks/annotation_store_alloc.py

@@ -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/full-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",

examples/inference-pipelines/slide-graph.ipynb

@@ -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/notebook_urls.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

pre-commit/requirements_consistency.py

@@ -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==0.5.0  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

requirements/requirements_dev.txt

@@ -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")