Allow free rotation of the atlas

.github/workflows/test_and_deploy.yml

@@ -47,10 +47,28 @@ jobs:
         with:
           qt: true
 
+      # cache atlases needed by the tests
+      - name: Cache Atlases
+        id: atlas-cache
+        uses: actions/cache@v3
+        with:
+          path: | # ensure we don't cache any interrupted atlas download and extraction!
+            ~/.brainglobe/*
+            !~/.brainglobe/atlas.tar.gz
+          key: ${{ runner.os }}-cached-atlases
+          enableCrossOsArchive: false # ~ and $HOME evaluate to different places across OSs!
+
+      - if: ${{ steps.atlas-cache.outputs.cache-hit == 'true' }}
+        name: List files in brainglobe data folder # good to be able to sanity check that user data is as expected
+        run: |
+          ls -af ~/.brainglobe/
+
+
       # Run tests
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
 
   build_sdist_wheels:
     name: Build source distribution
@@ -66,11 +84,6 @@ jobs:
     needs: [build_sdist_wheels]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
-      with:
-        name: artifact
-        path: dist
-    - uses: pypa/gh-action-pypi-publish@v1.5.0
+    - uses: neuroinformatics-unit/actions/upload_pypi@v2
       with:
-        user: __token__
-        password: ${{ secrets.TWINE_API_KEY }}
+        secret-pypi-key: ${{ secrets.TWINE_API_KEY }}

.gitignore

@@ -82,3 +82,6 @@ venv/
 
 # written by setuptools_scm
 **/_version.py
+
+# Elastix related files
+/Logs/

.pre-commit-config.yaml

@@ -17,15 +17,15 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.9
+      rev: v0.3.5
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.12.1
+      rev: 24.3.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.8.0
+      rev: v1.9.0
       hooks:
           - id: mypy
             additional_dependencies:

MANIFEST.in

@@ -3,7 +3,6 @@ include README.md
 include .napari-hub/DESCRIPTION.md
 include .napari-hub/config.yml
 include brainglobe_registration/napari.yaml
-include brainglobe_registration/resources/brainglobe.png
 exclude .pre-commit-config.yaml
 
 recursive-include brainglobe_registration/parameters *.txt

brainglobe_registration/elastix/register.py

@@ -2,7 +2,7 @@
 
 import itk
 import numpy as np
-from bg_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi import BrainGlobeAtlas
 
 
 def get_atlas_by_name(atlas_name: str) -> BrainGlobeAtlas: