Fixed merge conflicts

brainglobe · Apr 23, 2024 · b172fd6 · b172fd6
2 parents 503f57e + 6436db4
commit b172fd6
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Showing 9 changed files with 24 additions and 67 deletions.
diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -51,6 +51,7 @@ jobs:
       - 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 +67,6 @@ jobs:
     needs: [build_sdist_wheels]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: neuroinformatics-unit/actions/upload_pypi@v2
       with:
-        name: artifact
-        path: dist
-    - uses: pypa/gh-action-pypi-publish@v1.5.0
-      with:
-        user: __token__
-        password: ${{ secrets.TWINE_API_KEY }}
+        secret-pypi-key: ${{ secrets.TWINE_API_KEY }}
diff --git a/.pre-commit-config.yaml b/.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:

diff --git a/MANIFEST.in b/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

diff --git a/brainglobe_registration/elastix/register.py b/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:

diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
@@ -15,9 +15,10 @@
 import napari.layers
 import numpy as np
 import numpy.typing as npt
-from bg_atlasapi import BrainGlobeAtlas
-from bg_atlasapi.list_atlases import get_downloaded_atlases
+from brainglobe_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi.list_atlases import get_downloaded_atlases
 from brainglobe_utils.qtpy.collapsible_widget import CollapsibleWidgetContainer
+from brainglobe_utils.qtpy.logo import header_widget
 from dask_image.ndinterp import affine_transform as dask_affine_transform
 from napari.qt.threading import thread_worker
 from napari.utils.notifications import show_error
@@ -30,7 +31,7 @@
 from skimage.segmentation import find_boundaries
 from skimage.transform import rescale
 
-from brainglobe_registration.utils.brainglobe_logo import header_widget
+from brainglobe_registration.elastix.register import run_registration
 from brainglobe_registration.utils.utils import (
     adjust_napari_image_layer,
     calculate_rotated_bounding_box,
@@ -141,7 +142,14 @@ def __init__(self, napari_viewer: Viewer):
         self.run_button.clicked.connect(self._on_run_button_click)
         self.run_button.setEnabled(False)
 
-        self.add_widget(header_widget(), collapsible=False)
+        self.add_widget(
+            header_widget(
+                "brainglobe-<br>registration",  # line break at <br>
+                "Registration with Elastix",
+                github_repo_name="brainglobe-registration",
+            ),
+            collapsible=False,
+        )
         self.add_widget(self.get_atlas_widget, widget_title="Select Images")
         self.add_widget(
             self.adjust_moving_image_widget, widget_title="Prepare Images"
@@ -255,7 +263,6 @@ def _on_adjust_moving_image_reset_button_click(self):
         adjust_napari_image_layer(self._moving_image, 0, 0, 0)
 
     def _on_run_button_click(self):
-        from brainglobe_registration.elastix.register import run_registration
 
         current_atlas_slice = self._viewer.dims.current_step[0]
 

diff --git a/brainglobe_registration/resources/brainglobe.png b/brainglobe_registration/resources/brainglobe.png
diff --git a/brainglobe_registration/utils/brainglobe_logo.py b/brainglobe_registration/utils/brainglobe_logo.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -24,11 +24,12 @@ classifiers = [
 
 dependencies = [
     "napari>=0.4.18",
-    "bg-atlasapi",
-    "brainglobe-utils>=0.3.4",
+    "brainglobe-atlasapi",
+    "brainglobe-utils>=0.4.3",
     "dask",
     "dask-image",
     "itk-elastix",
+    "lxml_html_clean",
     "numpy",
     "pytransform3d",
     "qtpy",

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -3,8 +3,8 @@
 
 import numpy as np
 import pytest
-from bg_atlasapi import BrainGlobeAtlas
-from bg_atlasapi import config as bg_config
+from brainglobe_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi import config as bg_config
 from PIL import Image