Merge branch 'main' into dev

.github/workflows/test_and_deploy.yml

@@ -27,14 +27,16 @@ jobs:
     strategy:
       matrix:
         # Run all supported Python versions on linux
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest]
-        # Include one windows and macos run
+        # Include one windows two macos runs (intel and arm based)
         include:
-        - os: macos-latest
-          python-version: "3.10"
+        - os: macos-13 # Intel Mac
+          python-version: "3.12"
+        - os: macos-latest # ARM Mac
+          python-version: "3.12"
         - os: windows-latest
-          python-version: "3.10"
+          python-version: "3.12"
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ ci:
 exclude: 'conf.py'
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.5.0
+      rev: v4.6.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -17,15 +17,15 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.3.5
+      rev: v0.5.0
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 24.3.0
+      rev: 24.4.2
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.9.0
+      rev: v1.10.1
       hooks:
           - id: mypy
             additional_dependencies:

README.md

@@ -56,19 +56,13 @@ To install latest development version :
 
     pip install git+https://github.com/brainglobe/brainglobe-registration.git
 
-## Contributing
-
-Contributions are very welcome. Tests can be run with [tox], please ensure
-the coverage at least stays the same before you submit a pull request.
-
 ## License
 
 Distributed under the terms of the [BSD-3] license,
 "brainglobe-registration" is free and open source software
 
-## Issues
-
-If you encounter any problems, please [file an issue] along with a detailed description.
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
 
 
 ## Acknowledgements

brainglobe_registration/registration_widget.py

@@ -95,6 +95,11 @@ def __init__(self, napari_viewer: Viewer):
         else:
             self._moving_image = None
 
+        self.main_tabs = QTabWidget(parent=self)
+        self.main_tabs.setTabPosition(QTabWidget.West)
+
+        self.parameters_tab = QTabWidget()
+
         self.get_atlas_widget = SelectImagesView(
             available_atlases=self._available_atlases,
             sample_image_names=self._sample_images,

pyproject.toml

@@ -3,7 +3,7 @@ name = "brainglobe-registration"
 authors = [{name = "Brainglobe Developers", email= "[email protected]"}]
 description = "A napari plugin for registration to a  BrainGlobe atlas."
 readme = "README.md"
-requires-python = ">=3.9.0"
+requires-python = ">=3.10"
 dynamic = ["version"]
 
 license = {text = "BSD-3-Clause"}
@@ -14,9 +14,9 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Operating System :: OS Independent",
     "License :: OSI Approved :: BSD License",
     "Topic :: Scientific/Engineering :: Image Processing",
@@ -84,7 +84,7 @@ markers = [
 ]
 
 [tool.black]
-target-version = ['py39', 'py310', 'py311']
+target-version = ['py310','py311', 'py312']
 skip-string-normalization = false
 line-length = 79
 
@@ -110,14 +110,14 @@ fix = true
 [tool.tox]
 legacy_tox_ini = """
 [tox]
-envlist = py{39,310,311}
+envlist = py{310,311,312}
 isolated_build = True
 
 [gh-actions]
 python =
-    3.9: py39
     3.10: py310
     3.11: py311
+    3.12: py312
 
 [testenv]
 extras =