cellfinder 1.4.0a0__tar.gz → 1.5.0__tar.gz

{cellfinder-1.4.0a0 → cellfinder-1.5.0}/.github/workflows/test_and_deploy.yml

@@ -78,7 +78,7 @@ jobs:
       - name: Setup qtpy libraries
         uses: tlambert03/setup-qt-libs@v1
       # Setup VTK with headless display
-      - uses: pyvista/setup-headless-display-action@v2
+      - uses: pyvista/setup-headless-display-action@v3
       # Run all tests
       - uses: neuroinformatics-unit/actions/test@v2
         with:
@@ -86,6 +86,15 @@ jobs:
           secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           use-xvfb: true
 
+      - name: Notify slack on scheduled failure
+        if: failure() && github.event_name == 'schedule'
+        uses: ravsamhq/notify-slack-action@v2
+        with:
+          status: ${{ job.status }} # required
+          notify_when: 'failure'
+        env:
+          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_NOTIFYBOT_WEBHOOK_URL }} # required
+
   test_numba_disabled:
     needs: [linting, manifest]
     name: Run tests with numba disabled
@@ -117,7 +126,7 @@ jobs:
       - name: Setup qtpy libraries
         uses: tlambert03/setup-qt-libs@v1
       # Setup VTK with headless display
-      - uses: pyvista/setup-headless-display-action@v2
+      - uses: pyvista/setup-headless-display-action@v3
       # Run test suite with numba disabled
       - uses: neuroinformatics-unit/actions/test@v2
         with:
@@ -125,6 +134,15 @@ jobs:
           secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           codecov-flags: "numba"
 
+      - name: Notify slack on scheduled failure
+        if: failure() && github.event_name == 'schedule'
+        uses: ravsamhq/notify-slack-action@v2
+        with:
+          status: ${{ job.status }} # required
+          notify_when: 'failure'
+        env:
+          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_NOTIFYBOT_WEBHOOK_URL }} # required
+
   # Run brainglobe-workflows brainmapper-CLI tests to check for
   # breakages
   test_brainmapper_cli:
@@ -166,8 +184,9 @@ jobs:
         run: |
           python -m pytest --color=yes -v tests/brainmapper
 
+
   build_sdist_wheel:
-    name: Build source distribution and wheel
+    name: Build source distribution
     needs: [test, test_numba_disabled]
     if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
@@ -180,6 +199,11 @@ jobs:
     if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:
-    - uses: neuroinformatics-unit/actions/upload_pypi@v2
+    - uses: actions/download-artifact@v4
+      with:
+        name: artifact
+        path: dist
+    - uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        secret-pypi-key: ${{ secrets.TWINE_API_KEY }}
+        user: __token__
+        password: ${{ secrets.TWINE_API_KEY }}

{cellfinder-1.4.0a0 → cellfinder-1.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: cellfinder
-Version: 1.4.0a0
+Version: 1.5.0
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -32,7 +32,7 @@ Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
-Requires-Dist: keras==3.5.0
+Requires-Dist: keras>=3.7.0
 Requires-Dist: torch!=2.4,>=2.1.0
 Requires-Dist: tifffile
 Requires-Dist: tqdm
@@ -47,6 +47,7 @@ Requires-Dist: pytest-timeout; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pooch>=1; extra == "dev"
+Requires-Dist: qt-niu; extra == "dev"
 Provides-Extra: napari
 Requires-Dist: brainglobe-napari-io; extra == "napari"
 Requires-Dist: magicgui; extra == "napari"

{cellfinder-1.4.0a0 → cellfinder-1.5.0}/cellfinder/core/classify/classify.py

@@ -1,5 +1,6 @@
 import os
 from datetime import datetime
+from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import keras
@@ -68,7 +69,7 @@ def main(
         workers=workers,
     )
 
-    if trained_model and trained_model.suffix == ".h5":
+    if trained_model and Path(trained_model).suffix == ".h5":
         print(
             "Weights provided in place of the model, "
             "loading weights into default model."

{cellfinder-1.4.0a0 → cellfinder-1.5.0}/cellfinder/core/detect/filters/volume/ball_filter.py

@@ -266,22 +266,21 @@ class BallFilter:
         """
         if self.volume.shape[0]:
             if self.volume.shape[0] < self.kernel_z_size:
-                num_remaining_with_padding = 0
+                num_remaining_with_padding = self.volume.shape[0]
             else:
                 num_remaining = self.kernel_z_size - (self.middle_z_idx + 1)
                 num_remaining_with_padding = num_remaining + self.middle_z_idx
+            remaining_start = self.volume.shape[0] - num_remaining_with_padding
 
             self.volume = torch.cat(
-                [self.volume[-num_remaining_with_padding:, :, :], planes],
+                [self.volume[remaining_start:, :, :], planes],
                 dim=0,
             )
 
             if self.inside_brain_tiles is not None:
                 self.inside_brain_tiles = torch.cat(
                     [
-                        self.inside_brain_tiles[
-                            -num_remaining_with_padding:, :, :
-                        ],
+                        self.inside_brain_tiles[remaining_start:, :, :],
                         masks,
                     ],
                     dim=0,

{cellfinder-1.4.0a0 → cellfinder-1.5.0}/cellfinder/napari/curation.py

@@ -8,11 +8,11 @@ from brainglobe_napari_io.cellfinder.utils import convert_layer_to_cells
 from brainglobe_utils.cells.cells import Cell
 from brainglobe_utils.general.system import delete_directory_contents
 from brainglobe_utils.IO.yaml import save_yaml
-from brainglobe_utils.qtpy.dialog import display_warning
-from brainglobe_utils.qtpy.interaction import add_button, add_combobox
 from magicgui.widgets import ProgressBar
 from napari.qt.threading import thread_worker
 from napari.utils.notifications import show_info
+from qt_niu.dialog import display_warning
+from qt_niu.interaction import add_button, add_combobox
 from qtpy import QtCore
 from qtpy.QtWidgets import (
     QComboBox,

{cellfinder-1.4.0a0 → cellfinder-1.5.0}/cellfinder/napari/detect/detect.py

@@ -38,7 +38,7 @@ MIN_PLANES_ANALYSE = 0
 
 
 def get_heavy_widgets(
-    options: Dict[str, Any]
+    options: Dict[str, Any],
 ) -> Tuple[Callable, Callable, Callable]:
     # signal and other input are separated out from the main magicgui
     # parameter selections and are inserted as widget children in their own

{cellfinder-1.4.0a0 → cellfinder-1.5.0}/cellfinder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: cellfinder
-Version: 1.4.0a0
+Version: 1.5.0
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -32,7 +32,7 @@ Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
-Requires-Dist: keras==3.5.0
+Requires-Dist: keras>=3.7.0
 Requires-Dist: torch!=2.4,>=2.1.0
 Requires-Dist: tifffile
 Requires-Dist: tqdm
@@ -47,6 +47,7 @@ Requires-Dist: pytest-timeout; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pooch>=1; extra == "dev"
+Requires-Dist: qt-niu; extra == "dev"
 Provides-Extra: napari
 Requires-Dist: brainglobe-napari-io; extra == "napari"
 Requires-Dist: magicgui; extra == "napari"

{cellfinder-1.4.0a0 → cellfinder-1.5.0}/cellfinder.egg-info/requires.txt

@@ -7,7 +7,7 @@ numba
 numpy
 scikit-image
 scikit-learn
-keras==3.5.0
+keras>=3.7.0
 torch!=2.4,>=2.1.0
 tifffile
 tqdm
@@ -23,6 +23,7 @@ pytest-timeout
 pytest
 tox
 pooch>=1
+qt-niu
 
 [napari]
 brainglobe-napari-io

{cellfinder-1.4.0a0 → cellfinder-1.5.0}/pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
     "numpy",
     "scikit-image",
     "scikit-learn",
-    "keras==3.5.0",
+    "keras>=3.7.0",
     "torch>=2.1.0,!=2.4",
     "tifffile",
     "tqdm",
@@ -52,6 +52,7 @@ dev = [
     "pytest",
     "tox",
     "pooch >= 1",
+    "qt-niu"
 ]
 napari = [
     "brainglobe-napari-io",