From 7d17da109af1b527bf13d44ffa5a2625313f8975 Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Date: Fri, 2 Feb 2024 16:59:33 +0000
Subject: [PATCH 1/6] Use the update upload_pypi action (#29)

See https://github.com/neuroinformatics-unit/movement/pull/108
---
 .github/workflows/test_and_deploy.yml | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index c00e554..5501042 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -66,11 +66,6 @@ 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 }}

From 36403631c8646bc409476c791189e9a62def6c33 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 6 Feb 2024 15:12:04 +0000
Subject: [PATCH 2/6] [pre-commit.ci] pre-commit autoupdate (#30)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.2.0)
- [github.com/psf/black: 23.12.1 → 24.1.1](https://github.com/psf/black/compare/23.12.1...24.1.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6ffb785..7577ee0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,11 +17,11 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.9
+      rev: v0.2.0
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.12.1
+      rev: 24.1.1
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy

From 9d54161f3d737906fa1248570301ab3a9f3d2a7f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 4 Apr 2024 11:18:30 +0100
Subject: [PATCH 3/6] [pre-commit.ci] pre-commit autoupdate (#31)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.0...v0.3.5)
- [github.com/psf/black: 24.1.1 → 24.3.0](https://github.com/psf/black/compare/24.1.1...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7577ee0..f719a01 100644
--- 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: v0.2.0
+      rev: v0.3.5
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 24.1.1
+      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:

From ef2174d4ccdc8f695a8d50c83d5879f03ef4dc69 Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Date: Fri, 12 Apr 2024 18:05:54 +0100
Subject: [PATCH 4/6] Import header from brainglobe-utils (#33)

* import header from brainglobe-utils

* split package name over two lines

* remove brainglobe png from manifest

* add brainglobe-utils dependency
---
 MANIFEST.in                                   |   1 -
 .../registration_widget.py                    |  10 +++-
 .../resources/brainglobe.png                  | Bin 21216 -> 0 bytes
 .../utils/brainglobe_logo.py                  |  46 ------------------
 pyproject.toml                                |   1 +
 5 files changed, 9 insertions(+), 49 deletions(-)
 delete mode 100644 brainglobe_registration/resources/brainglobe.png
 delete mode 100644 brainglobe_registration/utils/brainglobe_logo.py

diff --git a/MANIFEST.in b/MANIFEST.in
index b0e8711..902dcc4 100644
--- 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/registration_widget.py b/brainglobe_registration/registration_widget.py
index ddecb4a..7db58d3 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -13,6 +13,7 @@
 import numpy as np
 from bg_atlasapi import BrainGlobeAtlas
 from bg_atlasapi.list_atlases import get_downloaded_atlases
+from brainglobe_utils.qtpy.logo import header_widget
 from napari.viewer import Viewer
 from qtpy.QtCore import Qt
 from qtpy.QtWidgets import (
@@ -25,7 +26,6 @@
 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,
@@ -85,7 +85,13 @@ def __init__(self, napari_viewer: Viewer):
             self._moving_image = None
 
         self.setLayout(QVBoxLayout())
-        self.layout().addWidget(header_widget())
+        self.layout().addWidget(
+            header_widget(
+                "brainglobe-<br>registration",  # line break at <br>
+                "Registration with Elastix",
+                github_repo_name="brainglobe-registration",
+            )
+        )
 
         self.main_tabs = QTabWidget(parent=self)
         self.main_tabs.setTabPosition(QTabWidget.West)
diff --git a/brainglobe_registration/resources/brainglobe.png b/brainglobe_registration/resources/brainglobe.png
deleted file mode 100644
index 427bdaba9b89f967c183f4a998e7e642df50600d..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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z6YPE^?}t2&UCCZC7lCSUheV;SgJQza=RfxBf|e3?2|-b2cOd9&@i_=0J1IkuqdE+_
zef<A+TZoi(gGY^oghcx_vBbZ(B|xtnYp^*z>6@MGy`s}ZCX)-$1!Ov%?gFa1n&Ob#
zj*Pl}(4b1O(~D<lFHcb%R<#UQAquC+-CurIjy7V{NkR2yz?D8$P)^EtciA-563vE(
zT9ppT=%M)T%COP84Os}vMRP`KZG4$0H8md2&h&u)rgUQzf<owHV@AQU-FxVIQ%nEy
z)W~5<ym>tcKC9VyBGlC)m294HNful|L^&MIiZYf?{a%%!3e})@7BrScn+TNcHiEw`
z`7u4!D+-s!`w~@T#U~X+h2<GNa*#U^+0X#8E4zh4yvWN8y(<1Ds)S1A3Vi-rMKb0g
z$USXkB~tg07->)s>nFN=jq%0@CwPt?kJFajjEjwJt=wQkw-+Dx&8C6v>;>#g9a46@
zBMo-Bp|zDi38d$)gip}9{Bz3B63vPO7dz-{r9Y<I3XUecE(dL>A2OB}71m?SAAr1$
z%8KXO)8jmOFu%a{)Jw9fxB=m=f`gzW((Hl%dcYth$*0^JsyU3sVp#-j4<;(YcdC5j
z>F#sqos_}U1Cs!z089j!#*Qt3Ndva=Ul+i)|6rWQn<VZMst;P)zhg{}lM~E9B{a&m
n?B8mPd3ivi{GYF`PJu`e*7E2-|9)n;bEA!ggE_@4;O>6_hRC_w

diff --git a/brainglobe_registration/utils/brainglobe_logo.py b/brainglobe_registration/utils/brainglobe_logo.py
deleted file mode 100644
index e387adb..0000000
--- a/brainglobe_registration/utils/brainglobe_logo.py
+++ /dev/null
@@ -1,46 +0,0 @@
-from importlib.resources import files
-
-from qtpy.QtWidgets import QGroupBox, QHBoxLayout, QLabel, QVBoxLayout, QWidget
-
-brainglobe_logo = files("brainglobe_registration").joinpath(
-    "resources/brainglobe.png"
-)
-
-_logo_html = f"""
-<h1>
-<img src="{brainglobe_logo}"width="100">
-<\h1>
-"""
-
-
-def _docs_links_widget(parent: QWidget = None):
-    _docs_links_html = """
-    <h3>
-    <p><a href="https://brainglobe.info" style="color:gray;">Website</a></p>
-    <p><a href="https://github.com/brainglobe/brainglobe-registration" style="color:gray;">Source</a></p>
-    </h3>
-    """  # noqa: E501
-    docs_links_widget = QLabel(_docs_links_html, parent=parent)
-    docs_links_widget.setOpenExternalLinks(True)
-    return docs_links_widget
-
-
-def _logo_widget(parent: QWidget = None):
-    return QLabel(_logo_html, parent=None)
-
-
-def header_widget(parent: QWidget = None):
-    box = QGroupBox(parent)
-    box.setFlat(True)
-    box.setLayout(QVBoxLayout())
-    box.layout().addWidget(QLabel("<h2>brainglobe-registration</h2>"))
-    subbox = QGroupBox(parent)
-    subbox.setFlat(True)
-    subbox.setLayout(QHBoxLayout())
-    subbox.layout().setSpacing(0)
-    subbox.layout().setContentsMargins(0, 0, 0, 0)
-    subbox.setStyleSheet("border: 0;")
-    subbox.layout().addWidget(_logo_widget(parent=box))
-    subbox.layout().addWidget(_docs_links_widget(parent=box))
-    box.layout().addWidget(subbox)
-    return box
diff --git a/pyproject.toml b/pyproject.toml
index aeb282b..4eacaf8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,6 +25,7 @@ classifiers = [
 dependencies = [
     "napari>=0.4.18",
     "bg-atlasapi",
+    "brainglobe-utils>=0.4.3",
     "numpy",
     "qtpy",
     "itk-elastix",

From b02d396ae5d8e99d3afe9b749807e023b04b5e3c Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Date: Mon, 22 Apr 2024 15:29:14 +0100
Subject: [PATCH 5/6] Update requirements (#34)

* import header from brainglobe-utils

* split package name over two lines

* remove brainglobe png from manifest

* add brainglobe-utils dependency

* Switched from bg-atlasapi to brainglobe-atlasapi

* Added lxml_html_clean explicitly to requirements

* Pinned itk to 5.4rc2 for now as 5.4rc3 cased a seg fault

* Undo itk pin

---------

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
---
 brainglobe_registration/elastix/register.py    | 2 +-
 brainglobe_registration/registration_widget.py | 4 ++--
 pyproject.toml                                 | 7 ++++---
 tests/conftest.py                              | 4 ++--
 4 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/brainglobe_registration/elastix/register.py b/brainglobe_registration/elastix/register.py
index 955ed44..d04d918 100644
--- 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
index 7db58d3..d389d0c 100644
--- a/brainglobe_registration/registration_widget.py
+++ b/brainglobe_registration/registration_widget.py
@@ -11,8 +11,8 @@
 from pathlib import Path
 
 import numpy as np
-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.logo import header_widget
 from napari.viewer import Viewer
 from qtpy.QtCore import Qt
diff --git a/pyproject.toml b/pyproject.toml
index 4eacaf8..5927e6f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,12 +24,13 @@ classifiers = [
 
 dependencies = [
     "napari>=0.4.18",
-    "bg-atlasapi",
+    "brainglobe-atlasapi",
     "brainglobe-utils>=0.4.3",
+    "itk-elastix",
+    "lxml_html_clean",
     "numpy",
+    "pytransform3d",
     "qtpy",
-    "itk-elastix",
-    "pytransform3d"
 ]
 
 [project.urls]
diff --git a/tests/conftest.py b/tests/conftest.py
index a7708ef..df32c05 100644
--- 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
 
 

From 6436db4d3e3ea234e21369bcc5a877c539a646ae Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Date: Mon, 22 Apr 2024 15:33:09 +0100
Subject: [PATCH 6/6] add codecov token (#35)

---
 .github/workflows/test_and_deploy.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 5501042..c26cbd4 100644
--- 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