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

@@ -0,0 +1,122 @@
+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:
+
+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:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
+
+  manifest:
+    name: Check Manifest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/check_manifest@v2
+
+  test:
+    needs: [linting, manifest]
+    name: Run package tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # Run all supported Python versions on linux
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+        # Include one windows, one macos run
+        include:
+        - os: macos-latest
+          python-version: "3.10"
+        - os: windows-latest
+          python-version: "3.10"
+
+    steps:
+      # Cache the tensorflow model so we don't have to remake it every time
+      - name: Cache tensorflow model
+        uses: actions/cache@v3
+        with:
+          path: "~/.cellfinder"
+          key: models-${{ 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: ${{ matrix.python-version }}
+          use-xvfb: true
+
+  # Run cellfinder tests to make sure cellfinder is still compatible
+  # with cellfinder-core
+  test_cellfinder:
+    needs: [linting, manifest]
+    name: Run cellfinder tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cache tensorflow model
+        uses: actions/cache@v3
+        with:
+          path: "~/.cellfinder"
+          key: models-${{ hashFiles('~/.cellfinder/**') }}
+
+      - name: Checkout cellfinder
+        uses: actions/checkout@v3
+        with:
+          repository: 'brainglobe/cellfinder'
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+          # Install latest SHA on this cellfinder-core branch
+          python -m pip install git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA
+          # Install checked out copy of cellfinder
+          python -m pip install .[dev]
+
+      - name: Run cellfinder tests
+        run: |
+          python -m pytest --color=yes -v
+
+  build_sdist_wheel:
+    name: Build source distribution and wheel
+    needs: [test, test_cellfinder]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    steps:
+    - uses:  neuroinformatics-unit/actions/build_sdist_wheels@v2
+
+  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

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+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

@@ -0,0 +1,145 @@
+# Custom config files
+*.conf.custom
+
+# Byte-compiled / optimized / DLL files
+**/__pycache__/
+*.py[cod]
+*$py.class
+
+# Cython
+*.c
+*.cpp
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+.napari_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+doc/build/
+
+# pydocmd
+_build/
+mkdocs.yml
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.envrc
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+.idea/
+
+*.~lock.*
+
+pip-wheel-metadata/
+
+mprofile*.dat
+
+*.DS_Store
+
+# asv
+.asv
+benchmarks/results
+benchmarks/html
+benchmarks/env
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+*/_version.py
+
+.idea/

.napari/config.yml

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+# 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