Cellfinder merge

.codecov.yml

@@ -9,7 +9,7 @@ comment: false
 flags:
   numba:
     paths:
-      - src/cellfinder_core/detect/filters/plane/tile_walker.py
-      - src/cellfinder_core/detect/filters/volume/ball_filter.py
-      - src/cellfinder_core/detect/filters/volume/structure_detection.py
+      - cellfinder/core/detect/filters/plane/tile_walker.py
+      - cellfinder/core/detect/filters/volume/ball_filter.py
+      - cellfinder/core/detect/filters/volume/structure_detection.py
     carryforward: true

.github/workflows/plugin_preview.yml

@@ -0,0 +1,19 @@
+name: napari hub Preview Page # we use this name to find your preview page artifact, so don't change it!
+# For more info on this action, see https://github.com/chanzuckerberg/napari-hub-preview-action/blob/main/action.yml
+
+on:
+  pull_request:
+
+jobs:
+  preview-page:
+    name: Preview Page Deploy
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: napari hub Preview Page Builder
+        uses: chanzuckerberg/[email protected]
+        with:
+          hub-ref: main

.github/workflows/test_and_deploy.yml

@@ -1,12 +1,23 @@
 name: tests
 
 on:
+  # Only run on pushes to main, or when version tags are pushed
   push:
-    branches: [ main ]
+    branches:
+      - "main"
     tags:
-      - '*'
+      - "v**"
+  # Run on all pull-requests
   pull_request:
-    branches: [ '*' ]
+  # Allow workflow dispatch from GitHub
+  workflow_dispatch:
+
+concurrency:
+  # Cancel this workflow if it is running,
+  # and then changes are applied on top of the HEAD of the branch,
+  # triggering another run of the workflow
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   linting:
@@ -22,6 +33,7 @@ jobs:
 
   test:
     needs: [linting, manifest]
+    name: Run package tests
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -31,20 +43,25 @@ jobs:
         # Include one windows, one macos run
         include:
         - os: macos-latest
-          python-version: "3.9"
+          python-version: "3.10"
         - os: windows-latest
-          python-version: "3.9"
+          python-version: "3.10"
 
     steps:
+      # Cache the tensorflow model so we don't have to remake it every time
       - name: Cache tensorflow model
         uses: actions/cache@v3
         with:
           path: "~/.cellfinder"
           key: models-${{ hashFiles('~/.cellfinder/**') }}
+      # Setup pyqt libraries
+      - name: Setup qtpy libraries
+        uses: tlambert03/setup-qt-libs@v1
+      # Run all tests
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
-
+          use-xvfb: true
 
   # Run cellfinder tests to make sure cellfinder is still compatible
   # with cellfinder-core
@@ -77,7 +94,6 @@ jobs:
           # Install checked out copy of cellfinder
           python -m pip install .[dev]
 
-
       - name: Run cellfinder tests
         run: |
           python -m pytest --color=yes -v

.github/workflows/test_include_guard.yaml

@@ -5,7 +5,8 @@ name: Test Tensorflow include guards
 on:
   pull_request:
   push:
-    branches: [main]
+    branches:
+      - main
 
 jobs:
   tensorflow_guards:
@@ -31,7 +32,8 @@ jobs:
         with:
           fail-on-error: true
           script: |
-            import cellfinder_core
+            import cellfinder.core
+            import cellfinder.napari
 
       - name: Uninstall tensorflow
         run: python -m pip uninstall -y tensorflow
@@ -42,7 +44,7 @@ jobs:
         with:
           fail-on-error: false
           script: |
-            import cellfinder_core
+            import cellfinder.core
 
       # exit 1 will force an actions exit with a failure reported
       - name: Flag error thrown by broken import

.gitignore

@@ -2,7 +2,7 @@
 *.conf.custom
 
 # Byte-compiled / optimized / DLL files
-__pycache__/
+**/__pycache__/
 *.py[cod]
 *$py.class
 
@@ -15,6 +15,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -53,6 +54,7 @@ coverage.xml
 *.cover
 .hypothesis/
 .pytest_cache/
+.napari_cache/
 
 # Translations
 *.mo
@@ -77,10 +79,13 @@ doc/build/
 _build/
 mkdocs.yml
 
+# MkDocs documentation
+/site/
+
 # PyBuilder
 target/
 
-# Jupyter Notebook
+# IPython Notebook
 .ipynb_checkpoints
 
 # pyenv
@@ -130,3 +135,11 @@ mprofile*.dat
 benchmarks/results
 benchmarks/html
 benchmarks/env
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+*/_version.py
+
+.idea/

.napari/config.yml

@@ -0,0 +1,14 @@
+# Add labels from the EDAM Bioimaging ontology
+labels:
+  ontology: EDAM-BIOIMAGING:alpha06
+  terms:
+  - Image feature detection
+  - 3D image
+  - Image registration
+  - Multi-photon microscopy
+  - Light-sheet microscopy
+  - Image segmentation
+  - Image thresholding
+  - Image annotation
+  - Object classification
+  - Object feature extraction

.pre-commit-config.yaml

@@ -23,15 +23,3 @@ repos:
       rev: 23.7.0
       hooks:
           - id: black
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.5.1
-      hooks:
-          - id: mypy
-            args: [--config-file, pyproject.toml]
-            exclude: benchmarks/benchmarks/tools/IO.py
-            additional_dependencies:
-                - types-setuptools
-                - types-requests
-                - types-tqdm
-                - dask
-                - numpy