Merge branch 'main' into adapt-CI-mac

.github/workflows/test_and_deploy.yml

@@ -2,19 +2,27 @@ name: tests
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - "main"
     tags:
-      - '*'
+      - 'v*'
   pull_request:
-    branches: [ '*' ]
+  workflow_dispatch:
 
 jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: neuroinformatics-unit/actions/lint@v1
+      - uses: neuroinformatics-unit/actions/lint@v2
+
+  manifest:
+    name: Check Manifest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/check_manifest@v2
 
   test:
+    needs: [linting, manifest]
     name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
@@ -42,10 +50,13 @@ jobs:
         run: brew install hdf5
       # Setup pyqt libraries
       - uses: tlambert03/setup-qt-libs@v1
+      # Helps set up VTK with a headless display
+      - uses: pyvista/setup-headless-display-action@v2
       # Run tests
-      - uses: neuroinformatics-unit/actions/test@v1
+      - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           use-xvfb: true
 
   build_sdist_wheels:
@@ -54,19 +65,14 @@ jobs:
     if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:
-    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v1
+    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
 
 
   upload_all:
     name: Publish build distributions
     needs: [build_sdist_wheels]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
-      with:
-        name: artifact
-        path: dist
-    - uses: pypa/[email protected]
+    - uses: neuroinformatics-unit/actions/upload_pypi@v2
       with:
-        user: __token__
-        password: ${{ secrets.TWINE_API_KEY }}
+        secret-pypi-key: ${{ secrets.TWINE_API_KEY }}

.gitignore

@@ -1,20 +1,14 @@
-# Custom config files
-*.conf.custom
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
 
-# Cython
-*.c
-*.cpp
-
 # C extensions
 *.so
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -26,11 +20,9 @@ lib64/
 parts/
 sdist/
 var/
-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -50,9 +42,8 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
-*.cover
+*,cover
 .hypothesis/
-.pytest_cache/
 
 # Translations
 *.mo
@@ -61,63 +52,32 @@ coverage.xml
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
 
-# Flask stuff:
+# Flask instance folder
 instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
 
 # Sphinx documentation
-doc/build/
+docs/_build/
 
-# pydocmd
-_build/
-mkdocs.yml
+# MkDocs documentation
+/site/
 
 # PyBuilder
 target/
 
-# Jupyter Notebook
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
 .ipynb_checkpoints
 
 # pyenv
 .python-version
 
-# vscode
-.vscode
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-
-.idea/
+# OS
+.DS_Store
 
-*.~lock.*
-*.zip
+# written by setuptools_scm
+**/_version.py

.pre-commit-config.yaml

@@ -16,15 +16,15 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.4
+      rev: v0.3.5
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.10.1
+      rev: 24.3.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.6.1
+      rev: v1.9.0
       hooks:
           - id: mypy
             additional_dependencies:

CITATION.cff

@@ -0,0 +1,60 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: brainglobe-segmentation
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Adam
+    family-names: Tyson
+    email: [email protected]
+    affiliation: 'Sainsbury Wellcome Centre, University College London'
+  - given-names: Horst
+    family-names: Obenhaus
+  - given-names: BrainGlobe
+    family-names: Developers
+    email: [email protected]
+repository-code: 'https://github.com/brainglobe/brainglobe-segmentation'
+url: 'https://brainglobe.info'
+abstract: >-
+  Segmentation of anatomical structures in a common
+  coordinate space.
+license: BSD-3-Clause
+date-released: '2024-01-16'
+year: 2024
+preferred-citation:
+  type: article
+  authors:
+  - given-names: Adam
+    family-names: Tyson
+    affiliation: 'Sainsbury Wellcome Centre, University College London'
+  - given-names: Mateo
+    family-names: Velez-Fort
+  - given-names: Charly V.
+    family-names: Rousseau
+  - given-names: Lee
+    family-names: Cossell
+  - given-names: Chryssanthi
+    family-names: Tsitoura
+  - given-names: Stephen C.
+    family-names: Lenzi
+  - given-names: Horst A.
+    family-names: Obenhaus
+  - given-names: Federico
+    family-names: Claudi
+  - given-names: Tiago
+    family-names: Branco
+  - given-names: Troy W.
+    family-names: Margrie
+  doi: "10.1038/s41598-021-04676-9"
+  url: "https://doi.org/10.1038/s41598-021-04676-9"
+  journal: "Scientific Reports"
+  month: 1
+  year: 2022
+  title: "Accurate determination of marker location within whole-brain microscopy images"
+  issue: 1
+  volume: 12
+citation-sentence: "This project makes use of the brainglobe-segmentation plugin for segmentation of objects and regions of the brain."

MANIFEST.in

@@ -0,0 +1,12 @@
+include CITATION.cff
+include LICENSE
+include README.md
+
+exclude .pre-commit-config.yaml
+exclude codecov.yml
+
+include .napari/config.yml
+
+graft brainglobe_segmentation
+
+prune tests

README.md

@@ -2,26 +2,27 @@
 [![PyPI](https://img.shields.io/pypi/v/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation)
 [![Wheel](https://img.shields.io/pypi/wheel/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation)
 [![Development Status](https://img.shields.io/pypi/status/brainglobe-segmentation.svg)](https://github.com/brainglobe/brainglobe-segmentation)
-[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainglobe-segmentation/tests)](
-    https://github.com/brainglobe/brainglobe-segmentation/actions)
-[![codecov](https://codecov.io/gh/brainglobe/brainglobe-segmentation/branch/master/graph/badge.svg?token=WP9KTPZE5R)](https://codecov.io/gh/brainglobe/brainglobe-segmentation)[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
+[![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/brainglobe-segmentation/test_and_deploy.yml?branch=main)](https://github.com/brainglobe/brainglobe-segmentation/actions)
+[![codecov](https://codecov.io/gh/brainglobe/brainglobe-segmentation/graph/badge.svg?token=WP9KTPZE5R)](https://codecov.io/gh/brainglobe/brainglobe-segmentation)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
 
 # brainglobe-segmentation
 
-Segmentation of 1/2/3D brain structures in a common anatomical space
-
-`brainglobe-segmentation` is a companion to [`brainreg`](https://github.com/brainglobe/brainreg) allowing manual segmentation of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain region distribution, and visualisation (e.g. in [brainrender](https://github.com/brainglobe/brainrender)).
-`brainglobe-segmentation` is the successor to [`brainreg-segment`](https://github.com/brainglobe/brainreg-segmentation).
-
-`brainglobe-segmentation` and `brainreg` were developed by [Adam Tyson](https://github.com/adamltyson) and [Charly Rousseau](https://github.com/crousseau) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), based on [aMAP](https://doi.org/10.1038/ncomms11879) by [Christian Niedworok](https://github.com/cniedwor). The work was generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/).
+Segmentation of anatomical structures in a common coordinate space
 
 ## Installation
+**PyPI**
+```
+pip install brainglobe-segmentation
+```
 
-brainglobe-segmentation comes bundled with [`brainreg`](https://github.com/brainglobe/brainreg), so see the [brainreg installation instructions](https://brainglobe.info/documentation/brainreg/index.html).
-
-brainglobe-segmentation can be installed on it's own (`pip install brainglobe-segmentation`), but you will need to register your data with brainreg first.
+**conda**
+```
+conda install -c conda-forge brainglobe-segmentation
+```
 
+N.B. Your data will need to be registered to an anatomical atlas first.
 ## Usage
 
 See [user guide](https://brainglobe.info/documentation/brainglobe-segmentation/index.html).
@@ -30,7 +31,7 @@ If you have any questions, head over to the [image.sc forum](https://forum.image
 
 ## Contributing
 
-Contributions are very welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html).
+Contributions are very welcome. Please see the [developers guide](https://brainglobe.info/community/developers/index.html).
 
 ### Citing brainglobe-segmentation
 

brainglobe_segmentation/atlas/utils.py

@@ -1,6 +1,3 @@
-from bg_atlasapi.list_atlases import descriptors, utils
-
-
 def lateralise_atlas_image(
     masked_atlas_annotations,
     hemispheres,
@@ -24,18 +21,6 @@ def lateralise_atlas_image(
     return annotation_left, annotation_right
 
 
-def get_available_atlases():
-    """
-    Get the available brainglobe atlases
-    :return: Dict of available atlases (["name":version])
-    """
-    available_atlases = utils.conf_from_url(
-        descriptors.remote_url_base.format("last_versions.conf")
-    )
-    available_atlases = dict(available_atlases["atlases"])
-    return available_atlases
-
-
 def structure_from_viewer(coordinates, atlas_layer, atlas):
     """
     Get brain region info from mouse position in napari viewer.
@@ -51,7 +36,8 @@ def structure_from_viewer(coordinates, atlas_layer, atlas):
                     Layer, which contains the annotation / region
                     information for every structure in the (registered)
                     atlas
-    atlas         : Brainglobe atlas (bg_atlasapi.bg_atlas.BrainGlobeAtlas)
+    atlas         : Brainglobe atlas
+                    (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas)
 
     Returns
     -------

brainglobe_segmentation/image/utils.py

@@ -4,7 +4,7 @@
 
 def create_KDTree_from_image(image, value=0):
     """
-    Create a KDTree of points equalling a given value
+    Create a KDTree of points equaling a given value
     :param image: Image to be converted to points
     :param value: Value of image to be used
     :return: scipy.spatial.cKDTree object

brainglobe_segmentation/layout/gui_constants.py

@@ -32,9 +32,3 @@
 IMAGE_FILE_EXT = ".tiff"
 BOUNDARIES_STRING = "Boundaries"
 HEMISPHERES_STRING = "Hemispheres"
-
-# ORIENTATIONS = [
-#     "asl",
-#     "lsa",
-#     "sla",
-# ]  # When rolling through orientations of the brain, adhere to this order