Merge cellfinder-core and cellfinder-napari into this package

.codecov.yml

@@ -0,0 +1,15 @@
+comment: false
+
+
+# Add a numba flag to any files that contain code jit compiled
+# with numba. Tests are run without Numba compilation on the main
+# branch to collect code coverage, and the carryforward flags are
+# used to make sure coverage of these files does not decrease on
+# pull requests.
+flags:
+  numba:
+    paths:
+      - 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/test_and_deploy.yml

@@ -1,107 +1,124 @@
 name: tests
 
 on:
+  # Only run on pushes to main, or when version tags are pushed
   push:
     branches:
       - "main"
     tags:
-      - "*"
+      - "v**"
+  # Run on all pull-requests
   pull_request:
+  # Allow workflow dispatch from GitHub
   workflow_dispatch:
-    inputs:
-      coredev:
-        description: 'Tests with development version of cellfinder-core?'
-        required: true
-        default: 'false'
 
-env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: ${{ github.repository }}
+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:
-    name: Linting
     runs-on: ubuntu-latest
     steps:
       - uses: neuroinformatics-unit/actions/lint@v2
 
   manifest:
-    name: Check manifest
+    name: Check Manifest
     runs-on: ubuntu-latest
     steps:
       - uses: neuroinformatics-unit/actions/check_manifest@v2
 
   test:
-    needs: [linting,manifest]
+    needs: [linting, manifest]
+    name: Run package tests
     runs-on: ${{ matrix.os }}
-    env:
-      INPUT_COREDEV: ${{ github.event.inputs.coredev }}
     strategy:
-      fail-fast: false
       matrix:
-        # Run across a mixture of Python versions and operating systems
+        # Run all supported Python versions on linux
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+        # Include one windows, one macos run
         include:
         - os: macos-latest
           python-version: "3.10"
         - os: windows-latest
-          python-version: "3.9"
-        - os: ubuntu-latest
           python-version: "3.10"
+
     steps:
+      # Cache the tensorflow model so we don't have to remake it every time
+      - name: Cache tensorflow model
+        uses: actions/cache@v3
+        with:
+          path: "~/.cellfinder"
+          key: models-${{ hashFiles('~/.cellfinder/**') }}
+      # Setup pyqt libraries
+      - name: Setup qtpy libraries
+        uses: tlambert03/setup-qt-libs@v1
+      # Setup VTK with headless display
+      - uses: pyvista/setup-headless-display-action@v2
+      # Run all tests
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          use-xvfb: true
 
-  build_sdist_wheels:
-    name: Build source distribution
-    needs: [test]
-    if: github.event_name == 'push' && github.ref_type == 'tag'
+  # Run brainglobe-workflows cellfinder-CLI tests to check for
+  # breakages
+  test_cellfinder_cli:
+    needs: [linting, manifest]
+    name: Run cellfinder CLI to check for breakages
     runs-on: ubuntu-latest
     steps:
-      - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
+      - name: Cache tensorflow model
+        uses: actions/cache@v3
+        with:
+          path: "~/.cellfinder"
+          key: models-${{ hashFiles('~/.cellfinder/**') }}
 
-  deploy:
-    needs: [build_sdist_wheels]
-    runs-on: ubuntu-latest
-    if: github.event_name == 'push' && github.ref_type == 'tag'
-    steps:
-      - uses: actions/download-artifact@v3
+      - name: Checkout brainglobe-workflows
+        uses: actions/checkout@v3
         with:
-          name: artifact
-          path: dist
-      - uses: pypa/[email protected]
+          repository: 'brainglobe/brainglobe-workflows'
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
         with:
-          user: __token__
-          password: ${{ secrets.TWINE_API_KEY }}
+          python-version: "3.10"
 
-  build-and-push-docker:
-    needs: deploy
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+          # Install latest SHA on this cellfinder branch
+          python -m pip install git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA
+          # Install checked out copy of brainglobe-workflows
+          python -m pip install .[dev]
 
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v2
+      - name: Run cellfinder CLI test from brainglobe-workflows
+        run: |
+          python -m pytest --color=yes -v tests/cellfinder
 
-      - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+  build_sdist_wheel:
+    name: Build source distribution and wheel
+    needs: [test, test_cellfinder_cli]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    steps:
+    - uses:  neuroinformatics-unit/actions/build_sdist_wheels@v2
 
-      - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
-        with:
-          context: .
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+  upload_all:
+    name: Publish build distributions
+    needs: [build_sdist_wheel]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v3
+      with:
+        name: artifact
+        path: dist
+    - uses: pypa/[email protected]
+      with:
+        user: __token__
+        password: ${{ secrets.TWINE_API_KEY }}

.github/workflows/test_include_guard.yaml

@@ -0,0 +1,60 @@
+name: Test Tensorflow include guards
+# These tests check that the include guards checking for tensorflow's availability
+# behave as expected on ubuntu and macOS.
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  tensorflow_guards:
+    name: Test include guards
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install via pip
+        run: python -m pip install -e .
+
+      - name: Test (working) import
+        uses: jannekem/run-python-script-action@v1
+        with:
+          fail-on-error: true
+          script: |
+            import cellfinder.core
+            import cellfinder.napari
+
+      - name: Uninstall tensorflow
+        run: python -m pip uninstall -y tensorflow
+
+      - name: Test (broken) import
+        id: broken_import
+        uses: jannekem/run-python-script-action@v1
+        with:
+          fail-on-error: false
+          script: |
+            import cellfinder.core
+
+      # exit 1 will force an actions exit with a failure reported
+      - name: Flag error thrown by broken import
+        if: steps.broken_import.outputs.error == 'false'
+        run: |
+          echo "Broken import test result was: ${{ steps.broken_import.outputs.error }}"
+          exit 1
+
+      # add an additional step to confirm an error occurred in the import
+      - name: Confirm error was thrown by broken import
+        if: steps.broken_import.outputs.error == 'true'
+        run: |
+          echo "Broken import test result was: ${{ steps.broken_import.outputs.error }}"

.github/workflows/test_numba_off.yml

@@ -0,0 +1,27 @@
+name: Test with numba turned off
+# These tests are relatively slow (~20 minutes), but are used
+# to collect code coverage on areas of code that are otherwise
+# optimised by numba.
+
+on:
+  push:
+    branches: [ main ]
+
+
+jobs:
+  test_numba_disabled:
+    name: Run tests
+    runs-on: ubuntu-latest
+    env:
+       NUMBA_DISABLE_JIT: "1"
+
+    steps:
+      - name: Cache tensorflow model
+        uses: actions/cache@v3
+        with:
+          path: "~/.cellfinder"
+          key: models-${{ hashFiles('~/.cellfinder/**') }}
+      - uses: neuroinformatics-unit/actions/test@v2
+        with:
+          python-version: "3.10"
+          codecov-flags: "numba"

.gitignore

@@ -2,7 +2,7 @@
 *.conf.custom
 
 # Byte-compiled / optimized / DLL files
-**/__pycache__/**
+**/__pycache__/
 *.py[cod]
 *$py.class
 
@@ -15,6 +15,7 @@
 
 # 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
@@ -121,6 +126,20 @@ venv.bak/
 
 pip-wheel-metadata/
 
+mprofile*.dat
+
 *.DS_Store
 
-*.vscode/
+# asv
+.asv
+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

@@ -4,7 +4,7 @@ ci:
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.5.0
+      rev: v4.4.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -16,17 +16,10 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.4
+      rev: v0.0.285
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.10.1
+      rev: 23.7.0
       hooks:
           - id: black
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.6.1
-      hooks:
-          - id: mypy
-            additional_dependencies:
-                - types-setuptools
-                - types-requests