Migrate cellfinder into this package

.github/workflows/test_and_deploy.yml

@@ -3,19 +3,30 @@ name: tests
 on:
   push:
     branches:
-      - '*'
+      - "main"
     tags:
-      - '*'
+      - "*"
   pull_request:
+  workflow_dispatch:
+    inputs:
+      coredev:
+        description: 'Tests with development version of cellfinder-core?'
+        required: true
+        default: 'false'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
 
 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
@@ -24,20 +35,21 @@ jobs:
     needs: [linting, manifest]
     name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
+    env:
+      INPUT_COREDEV: ${{ github.event.inputs.coredev }}
     strategy:
+      fail-fast: false
       matrix:
-        # Run all supported Python versions on linux
-        python-version: ["3.8", "3.9", "3.10"]
+        # Run tests on ubuntu across all supported versions
+        python-version: ["3.9", "3.10"]
         os: [ubuntu-latest]
-        # Include one windows and macos run
+        # Include at least one MacOS and Windows test
         include:
         - os: macos-latest
           python-version: "3.10"
         - os: windows-latest
           python-version: "3.10"
-
     steps:
-      # Run tests
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
@@ -48,19 +60,19 @@ jobs:
     if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:
-    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
-
+      - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
 
   upload_all:
     name: Publish build distributions
     needs: [build_sdist_wheels]
     runs-on: ubuntu-latest
+    if: github.event_name == 'push' && github.ref_type == 'tag'
     steps:
-    - uses: actions/download-artifact@v3
-      with:
-        name: artifact
-        path: dist
-    - uses: pypa/[email protected]
-      with:
-        user: __token__
-        password: ${{ secrets.TWINE_API_KEY }}
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.TWINE_API_KEY }}

.gitignore

@@ -1,14 +1,20 @@
+# Custom config files
+*.conf.custom
+
 # Byte-compiled / optimized / DLL files
-__pycache__/
+**/__pycache__/**
 *.py[cod]
 *$py.class
 
+# Cython
+*.c
+*.cpp
+
 # C extensions
 *.so
 
 # Distribution / packaging
 .Python
-env/
 build/
 develop-eggs/
 dist/
@@ -20,9 +26,11 @@ lib64/
 parts/
 sdist/
 var/
+wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -42,8 +50,9 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
-*,cover
+*.cover
 .hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
@@ -52,22 +61,30 @@ coverage.xml
 # Django stuff:
 *.log
 local_settings.py
+db.sqlite3
 
-# Flask instance folder
+# Flask stuff:
 instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
 
 # Sphinx documentation
-docs/_build/
+doc/build/
+
+# pydocmd
+_build/
+mkdocs.yml
 
 # MkDocs documentation
-/site/
+site/
 
 # PyBuilder
 target/
 
 # Pycharm and VSCode
 .idea/
-venv/
 .vscode/
 
 # IPython Notebook
@@ -76,9 +93,42 @@ venv/
 # 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
+
+# mypy
+.mypy_cache/
+
+*.~lock.*
+
+pip-wheel-metadata/
+
 # OS
 .DS_Store
 
 # written by setuptools_scm
 **/_version.py
 benchmarks/results/*
+
+# Benchmarking with ASV
+.asv/

.pre-commit-config.yaml

@@ -1,7 +1,10 @@
+# Configuring https://pre-commit.ci/
+ci:
+    autoupdate_schedule: monthly
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.5.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -12,20 +15,21 @@ repos:
             args: [--fix=lf]
           - id: requirements-txt-fixer
           - id: trailing-whitespace
-    - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.272
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.1.4
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.3.0
+      rev: 23.10.1
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.3.0
+      rev: v1.6.1
       hooks:
           - id: mypy
             additional_dependencies:
                 - types-setuptools
+                - types-requests
     - repo: https://github.com/mgedmin/check-manifest
       rev: "0.49"
       hooks:

LICENSE

@@ -1,5 +1,6 @@
+BSD 3-Clause License
 
-Copyright (c) 2023, BrainGlobe developers
+Copyright (c) 2023, BrainGlobe developers.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -12,7 +13,7 @@ modification, are permitted provided that the following conditions are met:
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 
-* Neither the name of brainglobe-scripts nor the names of its
+* Neither the name of the copyright holder nor the names of its
   contributors may be used to endorse or promote products derived from
   this software without specific prior written permission.
 

MANIFEST.in

@@ -1,16 +1,25 @@
-include LICENSE
 include README.md
+include LICENSE
+include brainglobe_workflows/cellfinder/default_config.json
+
 exclude .pre-commit-config.yaml
+exclude *.yaml
+exclude *.yml
+exclude Dockerfile
+exclude *.ini
+exclude asv.conf.json
 
 recursive-include brainglobe_workflows *.py
-include brainglobe_workflows/cellfinder/default_config.json
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
-recursive-exclude docs *
-recursive-exclude tests *
 
-include *.json
-recursive-include benchmarks *.json
-recursive-include benchmarks *.py
-recursive-exclude benchmarks/results *
+global-include *.pxd
+
+prune benchmarks
+prune docs
+prune tests
+prune resources
+
+prune .github
+prune .tox

README.md

@@ -1 +1,74 @@
-# brainglobe-workflows
+[![Python Version](https://img.shields.io/pypi/pyversions/brainglobe-workflows.svg)](https://pypi.org/project/brainglobe-workflows)
+[![PyPI](https://img.shields.io/pypi/v/brainglobe-workflows.svg)](https://pypi.org/project/brainglobe-workflows)
+[![Downloads](https://pepy.tech/badge/brainglobe-workflows)](https://pepy.tech/project/brainglobe-workflows)
+[![Wheel](https://img.shields.io/pypi/wheel/brainglobe-workflows.svg)](https://pypi.org/project/brainglobe-workflows)
+[![Development Status](https://img.shields.io/pypi/status/brainglobe-workflows.svg)](https://github.com/brainglobe/brainglobe-workflows)
+[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainglobe-workflows/tests)](
+    https://github.com/brainglobe/brainglobe-workflows/actions)
+[![codecov](https://codecov.io/gh/brainglobe/brainglobe-workflows/branch/master/graph/badge.svg?token=s3MweEFPhl)](https://codecov.io/gh/brainglobe/brainglobe-workflows)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
+[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://brainglobe.info/developers/index.html)
+[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info/documentation/brainglobe-workflows/index.html)
+[![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
+
+# BrainGlobe Workflows
+
+`brainglobe-workflows` is a package that provides users with a number of out-of-the-box data analysis workflows employed in neuroscience, implemented using BrainGlobe tools.
+You can find the [full documentation](https://brainglobe.info/documentation/brainglobe-workflows/index.html), including that for the workflow tools provided, [on our website](https://brainglobe.info/documentation/brainglobe-workflows/index.html).
+
+At present, the package currently offers the following workflows:
+
+- [cellfinder](#cellfinder): Whole-brain detection, registration, and analysis.
+
+## Installation
+
+If you want to install BrainGlobe workflows as a standalone tool, you can run `pip install` in your desired environment:
+
+```bash
+pip install brainglobe-workflows
+```
+
+`brainglobe-workflows` is built using BrainGlobe tools, and it will automatically fetch the tools that it needs and install them into your environment.
+Once BrainGlobe version 1 is available, this package will fetch all BrainGlobe tools and handle their install into your environment, to prevent potential conflicts from partial-installs.
+
+## Contributing
+
+Contributions to BrainGlobe are more than welcome.
+Please see the [developers guide](https://brainglobe.info/developers/index.html).
+
+## Citing `brainglobe-workflows`
+
+**If you use any tools in the [brainglobe suite](https://brainglobe.info/documentation/index.html), please [let us know](mailto:[email protected]?subject=cellfinder), and we'd be happy to promote your paper/talk etc.**
+
+If you find [`cellfinder`](#cellfinder) useful, and use it in your research, please cite the paper outlining the cell detection algorithm:
+> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074
+[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
+>
+If you use any of the image registration functions in `cellfinder`, please also cite [`brainreg`](https://github.com/brainglobe/brainreg#citing-brainreg).
+
+---
+
+## Cellfinder
+
+Whole-brain cell detection, registration and analysis.
+
+If you want to just use the cell detection part of `cellfinder`, please see the standalone [cellfinder-core](https://github.com/brainglobe/cellfinder-core) package, or the [cellfinder plugin](https://github.com/brainglobe/cellfinder-napari) for [napari](https://napari.org/).
+
+`cellfinder` is a collection of tools developed by [Adam Tyson](https://github.com/adamltyson), [Charly Rousseau](https://github.com/crousseau) and [Christian Niedworok](https://github.com/cniedwor) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/).
+
+`cellfinder` is a designed for the analysis of whole-brain imaging data such as [serial-section imaging](https://sainsburywellcomecentre.github.io/OpenSerialSection/) and lightsheet imaging in cleared tissue.
+The aim is to provide a single solution for:
+
+- Cell detection (initial cell candidate detection and refinement using  deep learning) (using [cellfinder-core](https://github.com/brainglobe/cellfinder-core)),
+- Atlas registration (using [brainreg](https://github.com/brainglobe/brainreg)),
+- Analysis of cell positions in a common space.
+
+Basic usage:
+
+```bash
+cellfinder -s signal_images -b background_images -o output_dir --metadata metadata
+```
+
+Full documentation can be found [here](https://brainglobe.info/documentation/cellfinder/index.html).

brainglobe_workflows/__init__.py

@@ -1,7 +1,11 @@
-from importlib.metadata import PackageNotFoundError, version
+from importlib.metadata import PackageNotFoundError, metadata
 
 try:
-    __version__ = version("brainglobe-workflows")
+    __version__ = metadata("brainglobe_workflows")["version"]
+    __author__ = metadata("brainglobe_workflows")["author-email"]
+    __license__ = metadata("brainglobe_workflows")["license"]
 except PackageNotFoundError:
-    # package is not installed
+    # Package not installed
     pass
+
+del metadata