Standardise package structure

.github/workflows/test_and_deploy.yml

@@ -1,90 +1,95 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: tests
 
 on:
   push:
     branches:
       - main
-      - npe2
     tags:
       - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
   pull_request:
     branches:
       - main
-      - npe2
   workflow_dispatch:
 
 jobs:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
+
+  manifest:
+    name: Check Manifest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/check_manifest@v2
+
   test:
-    name: ${{ matrix.platform }} py${{ matrix.python-version }}
-    runs-on: ${{ matrix.platform }}
+    needs: [linting, manifest]
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.8', '3.9', '3.10']
+        # Run all supported Python versions on linux
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest]
+        # Include one windows and macos run
+        include:
+        - os: macos-latest
+          python-version: "3.10"
+        - os: windows-latest
+          python-version: "3.10"
 
     steps:
-      - uses: actions/checkout@v3
-
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
       # these libraries enable testing on Qt on linux
-      - uses: tlambert03/setup-qt-libs@v1
+      - uses: pyvista/setup-headless-display-action@v2
+        with:
+          qt: true
 
-      # strategy borrowed from vispy for installing opengl libs on windows
-      - name: Install Windows OpenGL
-        if: runner.os == 'Windows'
-        run: |
-          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
-          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+      # 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!
 
-      # note: if you need dependencies from conda, considering using
-      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
-      # and
-      # tox-conda: https://github.com/tox-dev/tox-conda
-      - name: Install dependencies
+      - 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: |
-          python -m pip install --upgrade pip
-          python -m pip install setuptools tox tox-gh-actions
+          ls -af ~/.brainglobe/
 
-      # this runs the platform-specific tests declared in tox.ini
-      - name: Test with tox
-        uses: aganders3/headless-gui@v1
+      # Run tests
+      - uses: neuroinformatics-unit/actions/test@v2
         with:
-          run: python -m tox
-        env:
-          PLATFORM: ${{ matrix.platform }}
-
-      - name: Coverage
-        uses: codecov/codecov-action@v3
+          python-version: ${{ matrix.python-version }}
 
-  deploy:
-    # this will run when you have tagged a commit, starting with "v*"
-    # and requires that you have put your twine API key in your
-    # github secrets (see readme for details)
+  build_sdist_wheels:
+    name: Build source distribution
     needs: [test]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
-    if: contains(github.ref, 'tags')
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -U setuptools setuptools_scm wheel twine build
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
-        run: |
-          git tag
-          python -m build .
-          twine upload dist/*
+    - 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]
+      with:
+        user: __token__
+        password: ${{ secrets.TWINE_API_KEY }}

.gitignore

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

.pre-commit-config.yaml

@@ -1,10 +1,7 @@
-# Configuring https://pre-commit.ci/
-ci:
-    autoupdate_schedule: monthly
-
+exclude: 'conf.py'
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.5.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -16,17 +13,26 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.0.292
+      rev: v0.1.6
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.9.1
+      rev: 23.11.0
       hooks:
           - id: black
-    # - repo: https://github.com/pre-commit/mirrors-mypy
-    #   rev: v1.5.1
-    #   hooks:
-    #       - id: mypy
-    #         additional_dependencies:
-    #             - types-setuptools
-    #             - types-requests
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.7.0
+      hooks:
+          - id: mypy
+            additional_dependencies:
+                - types-setuptools
+    - repo: https://github.com/mgedmin/check-manifest
+      rev: "0.49"
+      hooks:
+          - id: check-manifest
+            args: [--no-build-isolation]
+            additional_dependencies: [setuptools-scm]
+    - repo: https://github.com/tlambert03/napari-plugin-checks
+      rev: v0.3.0
+      hooks:
+        - id: napari-plugin-checks

MANIFEST.in

@@ -1,5 +1,15 @@
 include LICENSE
 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
+recursive-include brainglobe_registration/resources *.tif
+recursive-exclude imgs *.png
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
+recursive-exclude docs *
+recursive-exclude tests *

src/brainglobe_registration/elastix/register.py → brainglobe_registration/elastix/register.py

@@ -1,7 +1,8 @@
+from typing import List
+
 import itk
 import numpy as np
 from bg_atlasapi import BrainGlobeAtlas
-from typing import List
 
 
 def get_atlas_by_name(atlas_name: str) -> BrainGlobeAtlas:
@@ -27,7 +28,7 @@ def run_registration(
     atlas_image,
     moving_image,
     annotation_image,
-    parameter_lists: List[tuple[str, dict]] = None,
+    parameter_lists: List[tuple[str, dict]],
 ) -> tuple[np.ndarray, itk.ParameterObject, np.ndarray]:
     """
     Run the registration process on the given images.
@@ -92,7 +93,7 @@ def run_registration(
     )
 
 
-def setup_parameter_object(parameter_lists: List[tuple[str, dict]] = None):
+def setup_parameter_object(parameter_lists: List[tuple[str, dict]]):
     """
     Set up the parameter object for the registration process.
 

src/brainglobe_registration/registration_widget.py → brainglobe_registration/registration_widget.py

@@ -11,39 +11,37 @@
 from pathlib import Path
 
 import numpy as np
-
-from brainglobe_registration.elastix.register import run_registration
-from brainglobe_registration.widgets.select_images_view import SelectImagesView
-from brainglobe_registration.widgets.adjust_moving_image_view import (
-    AdjustMovingImageView,
-)
-from brainglobe_registration.widgets.parameter_list_view import (
-    RegistrationParameterListView,
-)
-from brainglobe_registration.widgets.transform_select_view import (
-    TransformSelectView,
-)
-from brainglobe_registration.utils.utils import (
-    adjust_napari_image_layer,
-    open_parameter_file,
-    find_layer_index,
-    get_image_layer_names,
-)
-
 from bg_atlasapi import BrainGlobeAtlas
 from bg_atlasapi.list_atlases import get_downloaded_atlases
 from napari.viewer import Viewer
 from qtpy.QtCore import Qt
 from qtpy.QtWidgets import (
     QGroupBox,
+    QPushButton,
+    QTabWidget,
     QVBoxLayout,
     QWidget,
-    QTabWidget,
-    QPushButton,
 )
 from skimage.segmentation import find_boundaries
 
+from brainglobe_registration.elastix.register import run_registration
 from brainglobe_registration.utils.brainglobe_logo import header_widget
+from brainglobe_registration.utils.utils import (
+    adjust_napari_image_layer,
+    find_layer_index,
+    get_image_layer_names,
+    open_parameter_file,
+)
+from brainglobe_registration.widgets.adjust_moving_image_view import (
+    AdjustMovingImageView,
+)
+from brainglobe_registration.widgets.parameter_list_view import (
+    RegistrationParameterListView,
+)
+from brainglobe_registration.widgets.select_images_view import SelectImagesView
+from brainglobe_registration.widgets.transform_select_view import (
+    TransformSelectView,
+)
 
 
 class RegistrationWidget(QWidget):
@@ -54,7 +52,11 @@ def __init__(self, napari_viewer: Viewer):
         self._atlas: BrainGlobeAtlas = None
         self._moving_image = None
 
-        self.transform_params = {"rigid": {}, "affine": {}, "bspline": {}}
+        self.transform_params: dict[str, dict] = {
+            "rigid": {},
+            "affine": {},
+            "bspline": {},
+        }
         self.transform_selections = []
 
         for transform_type in self.transform_params:

src/brainglobe_registration/utils/brainglobe_logo.py → brainglobe_registration/utils/brainglobe_logo.py

@@ -1,11 +1,6 @@
-"""
-Can this be imorted from brainrender-napari? We can also move this to a bgutils maybe?
-"""
-
-
 from importlib.resources import files
 
-from qtpy.QtWidgets import QGroupBox, QHBoxLayout, QLabel, QWidget, QVBoxLayout
+from qtpy.QtWidgets import QGroupBox, QHBoxLayout, QLabel, QVBoxLayout, QWidget
 
 brainglobe_logo = files("brainglobe_registration").joinpath(
     "resources/brainglobe.png"

src/brainglobe_registration/utils/utils.py → brainglobe_registration/utils/utils.py

@@ -1,9 +1,10 @@
-import napari
-from pytransform3d.rotations import active_matrix_from_angle
-import numpy as np
 from pathlib import Path
 from typing import List
 
+import napari
+import numpy as np
+from pytransform3d.rotations import active_matrix_from_angle
+
 
 def adjust_napari_image_layer(
     image_layer: napari.layers.Image, x: int, y: int, rotate: float