From 70db1863028226f603dc08f33d2e3e96c915c27c Mon Sep 17 00:00:00 2001
From: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com>
Date: Fri, 23 Aug 2024 14:46:28 +0100
Subject: [PATCH 1/2] =?UTF-8?q?=F0=9F=90=9B=20Fix=20Immutable=20Output=20f?=
 =?UTF-8?q?rom=20`WSIReader`=20(#850)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Resolve issue #837

The output of WSI readers (read_rect, read_region, etc) are immutable, i.e. Read-only. We assume that created Numpy arrays created from PIL images in the `background_composite` are mutable by default.
After Numpy v1.16.0, doing np.asarray(pil_image) will return an immutable Numpy array. Gladly, there is an easy fix for this, we should use `np.array()` instead of `np.asarray`.
---
 tiatoolbox/utils/transforms.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tiatoolbox/utils/transforms.py b/tiatoolbox/utils/transforms.py
index adb769df9..8fd096b32 100644
--- a/tiatoolbox/utils/transforms.py
+++ b/tiatoolbox/utils/transforms.py
@@ -53,9 +53,9 @@ def background_composite(
     )
     composite.alpha_composite(image)
     if not alpha:
-        return np.asarray(composite.convert("RGB"))
+        return np.array(composite.convert("RGB"))
 
-    return np.asarray(composite)
+    return np.array(composite)
 
 
 def _convert_scalar_to_width_height(array: np.ndarray) -> np.ndarray:

From 015652cc5c2357070592c8d46f5f2ff9a905a5c6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 27 Aug 2024 13:36:31 +0100
Subject: [PATCH 2/2] [pre-commit.ci] pre-commit autoupdate (#851)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.1 → v0.6.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.1...v0.6.2)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* :pushpin: Update `ruff` version.


---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
---
 .github/workflows/python-package.yml       | 2 +-
 .pre-commit-config.yaml                    | 2 +-
 requirements/requirements_dev.txt          | 2 +-
 tiatoolbox/visualization/bokeh_app/main.py | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 688840262..559779617 100644
--- a/.github/workflows/python-package.yml
+++ b/.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==0.6.1 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.6.2 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 67256a495..5c608239e 100644
--- a/.pre-commit-config.yaml
+++ b/.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: v0.6.1
+    rev: v0.6.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
diff --git a/requirements/requirements_dev.txt b/requirements/requirements_dev.txt
index 111fe7e84..a8392667e 100644
--- a/requirements/requirements_dev.txt
+++ b/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==0.6.1  # This will be updated by pre-commit bot to latest version
+ruff==0.6.2  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1
diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index e86168506..6f9aff33d 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -689,7 +689,7 @@ def slide_toggle_cb(attr: str) -> None:  # noqa: ARG001
         UI["p"].renderers[0].alpha = 0.0
 
 
-def node_select_cb(attr: str, old: int, new: int) -> None:  # noqa: ARG001
+def node_select_cb(attr: str, old: int, new: int) -> None:
     """Placeholder callback to do something on node selection."""
     # Do something on node select if desired