From daa13e2f46f8832f5e52c8f7bc734896e03abb75 Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Date: Fri, 12 Apr 2024 16:34:55 +0100
Subject: [PATCH 1/4] Cellfinder test fix (#400)

---
 cellfinder/core/download/download.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/cellfinder/core/download/download.py b/cellfinder/core/download/download.py
index 00d6dee3..cd96616f 100644
--- a/cellfinder/core/download/download.py
+++ b/cellfinder/core/download/download.py
@@ -2,6 +2,7 @@
 import shutil
 import tarfile
 import urllib.request
+from pathlib import Path
 
 from brainglobe_utils.general.config import get_config_obj
 from brainglobe_utils.general.system import disk_free_gb
@@ -124,5 +125,8 @@ def write_model_to_config(new_model_path, orig_config, custom_config):
         data[i] = line.replace(
             f"model_path = '{orig_path}", f"model_path = '{new_model_path}"
         )
+
+    custom_config_path = Path(custom_config)
+    custom_config_path.parent.mkdir(parents=True, exist_ok=True)
     with open(custom_config, "w") as out_conf:
         out_conf.writelines(data)

From 152ece572a10dda7c96b270f2a1c213e87ae944c Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Date: Mon, 15 Apr 2024 12:00:06 +0100
Subject: [PATCH 2/4] Import header from brainglobe-utils (#399)

* import header from brainglobe-utils

* bump brainglobe-utils version and ensure new header is created every time
---
 cellfinder/napari/detect/detect.py      |   8 ++----
 cellfinder/napari/images/brainglobe.png | Bin 21216 -> 0 bytes
 cellfinder/napari/train/train.py        |  11 ++------
 cellfinder/napari/utils.py              |  35 +++++++++---------------
 pyproject.toml                          |   2 +-
 5 files changed, 18 insertions(+), 38 deletions(-)
 delete mode 100644 cellfinder/napari/images/brainglobe.png

diff --git a/cellfinder/napari/detect/detect.py b/cellfinder/napari/detect/detect.py
index 396f90b6..f0efe488 100644
--- a/cellfinder/napari/detect/detect.py
+++ b/cellfinder/napari/detect/detect.py
@@ -11,9 +11,8 @@
 from cellfinder.core.classify.cube_generator import get_cube_depth_min_max
 from cellfinder.napari.utils import (
     add_layers,
-    header_label_widget,
+    cellfinder_header,
     html_label_widget,
-    widget_header,
 )
 
 from .detect_containers import (
@@ -40,7 +39,6 @@ def detect_widget() -> FunctionGui:
     progress_bar = ProgressBar()
 
     @magicgui(
-        header=header_label_widget,
         detection_label=html_label_widget("Cell detection", tag="h3"),
         **DataInputs.widget_representation(),
         **DetectionInputs.widget_representation(),
@@ -52,7 +50,6 @@ def detect_widget() -> FunctionGui:
         scrollable=True,
     )
     def widget(
-        header,
         detection_label,
         data_options,
         viewer: napari.Viewer,
@@ -205,8 +202,7 @@ def update_progress_bar(label: str, max: int, value: int):
         worker.update_progress_bar.connect(update_progress_bar)
         worker.start()
 
-    widget.header.value = widget_header
-    widget.header.native.setOpenExternalLinks(True)
+    widget.native.layout().insertWidget(0, cellfinder_header())
 
     @widget.reset_button.changed.connect
     def restore_defaults():
diff --git a/cellfinder/napari/images/brainglobe.png b/cellfinder/napari/images/brainglobe.png
deleted file mode 100644
index 427bdaba9b89f967c183f4a998e7e642df50600d..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/cellfinder/napari/train/train.py b/cellfinder/napari/train/train.py
index 4d5e005b..d604bf4b 100644
--- a/cellfinder/napari/train/train.py
+++ b/cellfinder/napari/train/train.py
@@ -8,11 +8,7 @@
 from qtpy.QtWidgets import QScrollArea
 
 from cellfinder.core.train.train_yml import run as train_yml
-from cellfinder.napari.utils import (
-    header_label_widget,
-    html_label_widget,
-    widget_header,
-)
+from cellfinder.napari.utils import cellfinder_header, html_label_widget
 
 from .train_containers import (
     MiscTrainingInputs,
@@ -41,7 +37,6 @@ def run_training(
 
 def training_widget() -> FunctionGui:
     @magicgui(
-        header=header_label_widget,
         training_label=html_label_widget("Network training", tag="h3"),
         **TrainingDataInputs.widget_representation(),
         **OptionalNetworkInputs.widget_representation(),
@@ -52,7 +47,6 @@ def training_widget() -> FunctionGui:
         scrollable=True,
     )
     def widget(
-        header: dict,
         training_label: dict,
         data_options: dict,
         yaml_files: Path,
@@ -161,8 +155,7 @@ def widget(
             )
             worker.start()
 
-    widget.header.value = widget_header
-    widget.header.native.setOpenExternalLinks(True)
+    widget.native.layout().insertWidget(0, cellfinder_header())
 
     @widget.reset_button.changed.connect
     def restore_defaults():
diff --git a/cellfinder/napari/utils.py b/cellfinder/napari/utils.py
index 689b2842..d48b81fb 100644
--- a/cellfinder/napari/utils.py
+++ b/cellfinder/napari/utils.py
@@ -4,21 +4,7 @@
 import numpy as np
 import pandas as pd
 from brainglobe_utils.cells.cells import Cell
-from pkg_resources import resource_filename
-
-brainglobe_logo = resource_filename(
-    "cellfinder", "napari/images/brainglobe.png"
-)
-
-
-widget_header = """
-<p>Efficient cell detection in large images.</p>
-<p><a href="https://brainglobe.info" style="color:gray;">Website</a></p>
-<p><a href="https://brainglobe.info/documentation/cellfinder/user-guide/napari-plugin/index.html" style="color:gray;">Documentation</a></p>
-<p><a href="https://github.com/brainglobe/cellfinder" style="color:gray;">Source</a></p>
-<p><a href="https://doi.org/10.1371/journal.pcbi.1009074" style="color:gray;">Citation</a></p>
-<p><small>For help, hover the cursor over each parameter.</small>
-"""  # noqa: E501
+from brainglobe_utils.qtpy.logo import header_widget
 
 
 def html_label_widget(label: str, *, tag: str = "b") -> dict:
@@ -31,13 +17,18 @@ def html_label_widget(label: str, *, tag: str = "b") -> dict:
     )
 
 
-header_label_widget = html_label_widget(
-    f"""
-<img src="{brainglobe_logo}"width="100">
-<p>cellfinder</p>
-""",
-    tag="h1",
-)
+def cellfinder_header():
+    """
+    Create the header containing the brainglobe logo and documentation links
+    for all cellfinder widgets.
+    """
+    return header_widget(
+        "cellfinder",
+        "Efficient cell detection in large images.",
+        documentation_path="cellfinder/user-guide/napari-plugin/index.html",
+        citation_doi="https://doi.org/10.1371/journal.pcbi.1009074",
+        help_text="For help, hover the cursor over each parameter.",
+    )
 
 
 def add_layers(points: List[Cell], viewer: napari.Viewer) -> None:
diff --git a/pyproject.toml b/pyproject.toml
index efdb36f0..6e5ac59d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,7 +20,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "brainglobe-utils>=0.4.2",
+    "brainglobe-utils>=0.4.3",
     "brainglobe-napari-io>=0.3.4",
     "dask[array]",
     "fancylog>=0.0.7",

From 389e455c9aa5728853be5a3841c5a89610f16a3a Mon Sep 17 00:00:00 2001
From: Matt Einhorn <matt@einhorn.dev>
Date: Tue, 16 Apr 2024 09:29:41 -0400
Subject: [PATCH 3/4] Separate napari image parameter to prevent magicgui
 slowdown (#401)

* Separate image parameter to prevent magicgui slowdown.

* Fix parameters not initialized.

* Apply suggestions from code review

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

---------

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
---
 cellfinder/napari/detect/detect.py | 89 +++++++++++++++++++++++++++---
 1 file changed, 82 insertions(+), 7 deletions(-)

diff --git a/cellfinder/napari/detect/detect.py b/cellfinder/napari/detect/detect.py
index f0efe488..eaaab20f 100644
--- a/cellfinder/napari/detect/detect.py
+++ b/cellfinder/napari/detect/detect.py
@@ -38,6 +38,59 @@ def detect_widget() -> FunctionGui:
     """
     progress_bar = ProgressBar()
 
+    # options that is filled in from the gui
+    options = {"signal_image": None, "background_image": None, "viewer": None}
+
+    # signal and background images are separated out from the main magicgui
+    # parameter selections and are inserted as widget children in their own
+    # sub-containers of the root. Because if these image parameters are
+    # included in the root widget, every time *any* parameter updates, the gui
+    # freezes for a bit likely because magicgui is processing something for
+    # all the parameters when any parameter changes. And this processing takes
+    # particularly long for image parameters. Placing them as sub-containers
+    # alleviates this
+    @magicgui(
+        call_button=False,
+        persist=False,
+        scrollable=False,
+        labels=False,
+        auto_call=True,
+    )
+    def signal_image_opt(
+        viewer: napari.Viewer,
+        signal_image: napari.layers.Image,
+    ):
+        """
+        magicgui widget for setting the signal_image parameter.
+
+        Parameters
+        ----------
+        signal_image : napari.layers.Image
+             Image layer containing the labelled cells
+        """
+        options["signal_image"] = signal_image
+        options["viewer"] = viewer
+
+    @magicgui(
+        call_button=False,
+        persist=False,
+        scrollable=False,
+        labels=False,
+        auto_call=True,
+    )
+    def background_image_opt(
+        background_image: napari.layers.Image,
+    ):
+        """
+        magicgui widget for setting the background image parameter.
+
+        Parameters
+        ----------
+        background_image : napari.layers.Image
+             Image layer without labelled cells
+        """
+        options["background_image"] = background_image
+
     @magicgui(
         detection_label=html_label_widget("Cell detection", tag="h3"),
         **DataInputs.widget_representation(),
@@ -52,9 +105,6 @@ def detect_widget() -> FunctionGui:
     def widget(
         detection_label,
         data_options,
-        viewer: napari.Viewer,
-        signal_image: napari.layers.Image,
-        background_image: napari.layers.Image,
         voxel_size_z: float,
         voxel_size_y: float,
         voxel_size_x: float,
@@ -83,10 +133,6 @@ def widget(
 
         Parameters
         ----------
-        signal_image : napari.layers.Image
-             Image layer containing the labelled cells
-        background_image : napari.layers.Image
-             Image layer without labelled cells
         voxel_size_z : float
             Size of your voxels in the axial dimension
         voxel_size_y : float
@@ -129,9 +175,24 @@ def widget(
         reset_button :
             Reset parameters to default
         """
+        # we must manually call so that the parameters of these functions are
+        # initialized and updated. Because, if the images are open in napari
+        # before we open cellfinder, then these functions may never be called,
+        # even though the image filenames are shown properly in the parameters
+        # in the gui. Likely auto_call doesn't make magicgui call the functions
+        # in this circumstance, only if the parameters are updated once
+        # cellfinder plugin is fully open and initialized
+        signal_image_opt()
+        background_image_opt()
+
+        signal_image = options["signal_image"]
+        background_image = options["background_image"]
+        viewer = options["viewer"]
+
         if signal_image is None or background_image is None:
             show_info("Both signal and background images must be specified.")
             return
+
         data_inputs = DataInputs(
             signal_image.data,
             background_image.data,
@@ -222,6 +283,20 @@ def restore_defaults():
     # Insert progress bar before the run and reset buttons
     widget.insert(-3, progress_bar)
 
+    # add the signal and background image parameters
+    # make it look as if it's directly in the root container
+    signal_image_opt.margins = 0, 0, 0, 0
+    # the parameters are updated using `auto_call` only. If False, magicgui
+    # passes these as args to widget(), which doesn't list them as args
+    signal_image_opt.gui_only = True
+    widget.insert(3, signal_image_opt)
+    widget.signal_image_opt.label = "Signal image"
+
+    background_image_opt.margins = 0, 0, 0, 0
+    background_image_opt.gui_only = True
+    widget.insert(4, background_image_opt)
+    widget.background_image_opt.label = "Background image"
+
     scroll = QScrollArea()
     scroll.setWidget(widget._widget._qwidget)
     widget._widget._qwidget = scroll

From 560909ff6eb74072d970b4752665a29382be368a Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Date: Thu, 18 Apr 2024 10:49:17 +0100
Subject: [PATCH 4/4] Add codecov token (#403)

* add codecov token

* generate xml coverage report

* add timeout to testing jobs
---
 .github/workflows/test_and_deploy.yml | 4 ++++
 pyproject.toml                        | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 1ae8ae98..2bf9e976 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -65,11 +65,13 @@ jobs:
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           use-xvfb: true
 
   test_numba_disabled:
     needs: [linting, manifest]
     name: Run tests with numba disabled
+    timeout-minutes: 60
     runs-on: ubuntu-latest
     env:
        NUMBA_DISABLE_JIT: "1"
@@ -89,6 +91,7 @@ jobs:
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: "3.10"
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           codecov-flags: "numba"
 
   # Run brainglobe-workflows brainmapper-CLI tests to check for
@@ -96,6 +99,7 @@ jobs:
   test_brainmapper_cli:
     needs: [linting, manifest]
     name: Run brainmapper tests to check for breakages
+    timeout-minutes: 60
     runs-on: ubuntu-latest
     steps:
       - name: Cache tensorflow model
diff --git a/pyproject.toml b/pyproject.toml
index 6e5ac59d..2eeeb61e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -120,7 +120,7 @@ python =
     3.10: py310
 
 [testenv]
-commands = python -m pytest -v --color=yes
+commands = python -m pytest -v --color=yes --cov=cellfinder --cov-report=xml
 deps =
     pytest
     pytest-cov