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

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

@@ -44,4 +44,7 @@ jobs:
           tiatoolbox/tools/stainextract.py \
           tiatoolbox/tools/pyramid.py \
           tiatoolbox/tools/tissuemask.py \
-          tiatoolbox/tools/graph.py
+          tiatoolbox/tools/graph.py \
+          tiatoolbox/tools/stainnorm.py \
+          tiatoolbox/tools/stainaugment.py \
+          tiatoolbox/tools/patchextraction.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==0.3.2 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.3.3 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -58,18 +58,13 @@ repos:
       - id: rst-backticks           # Detect common mistake of using single backticks when writing rst.
       - 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: 24.2.0 # Replace with any tag/version: https://github.com/psf/black/tags
-    hooks:
-      - id: black
-        language_version: python3 # Should be a command that runs python3.+
-        additional_dependencies: ['click==8.0.4']  # Currently >8.0.4 breaks black
-      - id: black-jupyter
-        language: python
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.3.2
+    rev: v0.3.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
         types_or: [python, pyi, jupyter]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]

README.md

@@ -36,11 +36,6 @@
   <a href="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox">
       <img src="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox/branch/master/graph/badge.svg?token=7UZEMacQHm" alt="Code Coverage"/>
   </a>
-<br>
-<br>
- <a href="https://github.com/psf/black">
-      <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code Style black"/>
-    </a>
 <a href="https://github.com/astral-sh/ruff">
       <img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Code Style black"/>
     </a>

benchmarks/annotation_store_alloc.py

@@ -267,10 +267,13 @@ def main(
     if tracker_filepath.is_file():
         tracker_filepath.unlink()
 
-    with NamedTemporaryFile(mode="w+") as temp_file, memray.Tracker(
-        tracker_filepath,
-        native_traces=True,
-        follow_fork=True,
+    with (
+        NamedTemporaryFile(mode="w+") as temp_file,
+        memray.Tracker(
+            tracker_filepath,
+            native_traces=True,
+            follow_fork=True,
+        ),
     ):
         io = ":memory:" if in_memory else temp_file  # Backing (memory/disk)
         print(f"Storing {size[0] * size[1]} cells")

pyproject.toml

@@ -1,28 +1,6 @@
 [tool.pytest.ini_options]
   collect_ignore = ["setup.py", "benchmark/"]
 
-[tool.black]
-  exclude = '''
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-    | docs
-    | data
-    | setup.py
-  )/
-  '''
-  include = '\.pyi?$'
-  line-length = 88
-  target-version = ['py37', 'py38', 'py39', 'py310']
-
-
 [tool.coverage.run]
   branch = true
   source = ['tiatoolbox']
@@ -126,7 +104,8 @@ lint.select = [
   "SLOT",  # flake8-slots
   "ASYNC", # flake8-async
 ]
-lint.ignore = []
+# Ignore rules which conflict with ruff formatter.
+lint.ignore = ["COM812", "ISC001",]
 # Allow Ruff to discover `*.ipynb` files.
 include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]
 
@@ -172,6 +151,27 @@ convention = "google"
 [tool.ruff.lint.pylint]
 max-args = 10
 
+[tool.ruff.format]
+exclude = [
+    ".eggs",
+    ".git",
+    ".ruff_cache",
+    ".svn",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "build",
+    "dist",
+    "venv",
+    ".hg",
+    ".mypy_cache",
+    "buck-out",
+    "docs",
+    "data",
+    "setup.py",
+]
+skip-magic-trailing-comma = false
+
 [tool.mypy]
 ignore_missing_imports = true
 python_version = 3.9

requirements/requirements_dev.txt

@@ -1,6 +1,5 @@
 -r requirements.txt
 -r ../docs/requirements.txt
-black>=23.3.0
 coverage>=7.0.0
 docutils>=0.18.1
 jinja2>=3.0.3, <3.1.0
@@ -12,7 +11,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.3.2  # This will be updated by pre-commit bot to latest version
+ruff==0.3.3  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tests/test_annotation_stores.py

@@ -1550,8 +1550,7 @@ def test_query_predicate_callable(
         store.patch(keys[0], properties={"class": 123})
         results = store.query(
             # (0, 0, 1024, 1024),  # noqa: ERA001
-            where=lambda props: props.get("class")
-            == 123,
+            where=lambda props: props.get("class") == 123,
         )
         assert len(results) == 1
 

tests/test_tiatoolbox.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 """Pytests for `tiatoolbox` package."""
+
 from __future__ import annotations
 
 from click.testing import CliRunner

tiatoolbox/annotation/storage.py

@@ -2177,8 +2177,7 @@ def __init__(
         # Check if the path is a non-empty file
         exists = (
             # Use 'and' to short-circuit
-            self.path.is_file()
-            and self.path.stat().st_size > 0
+            self.path.is_file() and self.path.stat().st_size > 0
         )
         self.cons = {}
         self.con.execute("BEGIN")
@@ -2478,7 +2477,7 @@ def compile_options() -> list[str]:
         with sqlite3.connect(":memory:") as conn:
             conn.enable_load_extension(True)  # noqa: FBT003
             options = conn.execute("pragma compile_options").fetchall()
-        return [opt for opt, in options]
+        return [opt for (opt,) in options]
 
     def close(self: SQLiteStore) -> None:
         """Closes :class:`SQLiteStore` from file pointer or path."""
@@ -2861,7 +2860,7 @@ def iquery(
                 for key, properties in cur.fetchall()
                 if where(json.loads(properties))
             ]
-        return [key for key, in cur.fetchall()]
+        return [key for (key,) in cur.fetchall()]
 
     def query(
         self: SQLiteStore,

tiatoolbox/data/__init__.py

@@ -1,5 +1,6 @@
 # skipcq: PTC-W6004  # noqa: ERA001
 """Package to define datasets available to download via TIAToolbox."""
+
 from __future__ import annotations
 
 import importlib.resources as importlib_resources

tiatoolbox/models/engine/multi_task_segmentor.py

@@ -19,6 +19,7 @@
 # ***** END GPL LICENSE BLOCK *****
 
 """This module enables multi-task segmentors."""
+
 from __future__ import annotations
 
 import shutil
@@ -156,7 +157,8 @@ def _process_tile_predictions(
     sem_maps = [out for out in out_dicts if isinstance(out, np.ndarray)]
     # Some output maps may not be aggregated into a single map - combine these
     sem_maps = [
-        np.argmax(s, axis=-1) if s.ndim == 3 else s for s in sem_maps  # noqa: PLR2004
+        np.argmax(s, axis=-1) if s.ndim == 3 else s  # noqa: PLR2004
+        for s in sem_maps
     ]
 
     new_inst_dicts, remove_insts_in_origs = [], []