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

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

@@ -39,4 +39,9 @@ jobs:
           tiatoolbox/__main__.py \
           tiatoolbox/typing.py \
           tiatoolbox/tiatoolbox.py \
-          tiatoolbox/utils/*.py
+          tiatoolbox/utils/*.py \
+          tiatoolbox/tools/__init__.py \
+          tiatoolbox/tools/stainextract.py \
+          tiatoolbox/tools/pyramid.py \
+          tiatoolbox/tools/tissuemask.py \
+          tiatoolbox/tools/graph.py

.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==0.1.13 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.2.1 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -68,7 +68,7 @@ repos:
         language: python
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.14
+    rev: v0.2.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

benchmarks/annotation_nquery.ipynb

@@ -71,7 +71,7 @@
     "from shapely.geometry import Polygon\n",
     "\n",
     "sys.path.append(\"..\")  # If running locally without pypi installed tiatoolbox\n",
-    "from tiatoolbox.annotation.storage import (  # noqa: E402\n",
+    "from tiatoolbox.annotation.storage import (\n",
     "    Annotation,\n",
     "    AnnotationStore,\n",
     "    DictionaryStore,\n",

benchmarks/annotation_store.ipynb

@@ -207,8 +207,8 @@
     "\n",
     "sys.path.append(\"..\")  # If running locally without pypi installed tiatoolbox\n",
     "\n",
-    "from tiatoolbox import logger  # noqa: E402\n",
-    "from tiatoolbox.annotation.storage import (  # noqa: E402\n",
+    "from tiatoolbox import logger\n",
+    "from tiatoolbox.annotation.storage import (\n",
     "    Annotation,\n",
     "    DictionaryStore,\n",
     "    SQLiteStore,\n",

benchmarks/annotation_store_alloc.py

@@ -139,12 +139,12 @@ def __exit__(self: memray, *args: object) -> None:
                 # Intentionally blank.
 
 
-import numpy as np  # noqa: E402
-import psutil  # noqa: E402
-from shapely.geometry import Polygon  # noqa: E402
-from tqdm import tqdm  # noqa: E402
+import numpy as np
+import psutil
+from shapely.geometry import Polygon
+from tqdm import tqdm
 
-from tiatoolbox.annotation.storage import (  # noqa: E402
+from tiatoolbox.annotation.storage import (
     Annotation,
     DictionaryStore,
     SQLiteStore,

examples/full-pipelines/slide-graph.ipynb

@@ -397,7 +397,7 @@
     "# https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/\n",
     "wsi_patient_codes = np.array([\"-\".join(v.split(\"-\")[:3]) for v in wsi_names])\n",
     "wsi_labels = np.array(\n",
-    "    [clinical_info[v] if v in clinical_info else np.nan for v in wsi_patient_codes],\n",
+    "    [clinical_info.get(v, np.nan) for v in wsi_patient_codes],\n",
     ")\n",
     "\n",
     "# * Filter the WSIs and paths that do not have labels\n",

pyproject.toml

@@ -72,7 +72,7 @@ search = 'TOOLBOX_VER: {current_version}'
 replace = 'TOOLBOX_VER: {new_version}'
 
 [tool.ruff]
-select = [
+lint.select = [
   "A",     # flake8-builtins
   "B",     # flake8-bugbear
   "D",     # pydocstyle, need to enable for docstrings check.
@@ -126,13 +126,13 @@ select = [
   "SLOT",  # flake8-slots
   "ASYNC", # flake8-async
 ]
-ignore = []
+lint.ignore = []
 # Allow Ruff to discover `*.ipynb` files.
 include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]
 
 # Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
-unfixable = []
+lint.fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
+lint.unfixable = []
 
 # Exclude a variety of commonly ignored directories.
 exclude = [
@@ -149,27 +149,27 @@ exclude = [
 ]
 
 # Ignore `F401` (import violations) in all `__init__.py` files.
-per-file-ignores = {"__init__.py" = ["F401"], "tests/*" = ["T201", "PGH001", "SLF001", "S101", "PLR2004"], "benchmarks/*" = ["T201", "INP001"], "pre-commit/*" = ["T201", "INP001"], "tiatoolbox/cli/*" = ["PLR0913"]}
+lint.per-file-ignores = {"__init__.py" = ["F401"], "tests/*" = ["T201", "PGH001", "SLF001", "S101", "PLR2004"], "benchmarks/*" = ["T201", "INP001"], "pre-commit/*" = ["T201", "INP001"], "tiatoolbox/cli/*" = ["PLR0913"]}
 
 # Same as Black.
 line-length = 88
 
 # Allow unused variables when underscore-prefixed.
-dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+lint.dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 
 # Minimum Python version 3.8.
 target-version = "py38"
 
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
 # Unlike Flake8, default to a complexity level of 10.
 max-complexity = 14
 
 # need to enable for docstrings check.
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
  # Use Google-style docstrings.
 convention = "google"
 
-[tool.ruff.pylint]
+[tool.ruff.lint.pylint]
 max-args = 10
 
 [tool.mypy]

requirements/requirements_dev.txt

@@ -12,7 +12,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.1.13  # This will be updated by pre-commit bot to latest version
+ruff==0.2.1  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1