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@@ -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 }} | ||
|
|
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| jobs: | ||
| linting: | ||
| name: Linting | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: neuroinformatics-unit/actions/lint@v2 | ||
|
|
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| 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" | ||
|
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||
| steps: | ||
| # Run tests | ||
| - uses: neuroinformatics-unit/actions/test@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
|
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@@ -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 | ||
|
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||
| - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2 | ||
|
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| 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 }} | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,26 @@ | ||
| include LICENSE | ||
| include README.md | ||
| include LICENSE | ||
|
|
||
| exclude .pre-commit-config.yaml | ||
| exclude *.yaml | ||
| exclude *.yml | ||
| exclude Dockerfile | ||
| exclude *.ini | ||
|
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||
| recursive-include brainglobe_workflows *.py | ||
| recursive-include brainglobe_workflows *.json | ||
| recursive-include brainglobe_workflows/configs *.json | ||
| recursive-include brainglobe_benchmarks *.py | ||
| recursive-exclude brainglobe_benchmarks/results * | ||
| include asv.conf.json | ||
|
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| recursive-exclude * __pycache__ | ||
| recursive-exclude * *.py[co] | ||
| recursive-exclude docs * | ||
| recursive-exclude tests * | ||
|
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||
| include asv.conf.json | ||
| recursive-include brainglobe_benchmarks *.py | ||
| recursive-include brainglobe_benchmarks *.json | ||
| recursive-exclude brainglobe_benchmarks/results * | ||
| global-include *.pxd | ||
|
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| prune docs | ||
| prune tests | ||
| prune resources | ||
|
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||
| prune .github | ||
| prune .tox |
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| @@ -1 +1,75 @@ | ||
| # brainglobe-workflows | ||
| [](https://pypi.org/project/brainglobe-workflows) | ||
| [](https://pypi.org/project/brainglobe-workflows) | ||
| [](https://pepy.tech/project/brainglobe-workflows) | ||
| [](https://pypi.org/project/brainglobe-workflows) | ||
| [](https://github.com/brainglobe/brainglobe-workflows) | ||
| []( | ||
| https://github.com/brainglobe/brainglobe-workflows/actions) | ||
| [](https://codecov.io/gh/brainglobe/brainglobe-workflows) | ||
| [](https://github.com/python/black) | ||
| [](https://pycqa.github.io/isort/) | ||
| [](https://github.com/pre-commit/pre-commit) | ||
| [](https://brainglobe.info/developers/index.html) | ||
| [](https://brainglobe.info/documentation/brainglobe-workflows/index.html) | ||
| [](https://twitter.com/brain_globe) | ||
|
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| # BrainGlobe Workflows | ||
|
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| `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 view the [full documentation for each workflow](https://brainglobe.info/documentation/brainglobe-workflows/index.html) online. | ||
| You can also find the documentation for the backend BrainGlobe tools these workflows use [on our website](https://brainglobe.info/). | ||
|
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| At present, the package offers the following workflows: | ||
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| - [cellfinder](#cellfinder): Whole-brain detection, registration, and analysis. | ||
|
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| ## Installation | ||
|
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| If you want to install BrainGlobe workflows as a standalone tool, you can run `pip install` in your desired environment: | ||
|
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| ```bash | ||
| pip install brainglobe-workflows | ||
| ``` | ||
|
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| `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. | ||
|
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| ## Contributing | ||
|
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| Contributions to BrainGlobe are more than welcome. | ||
| Please see the [developers guide](https://brainglobe.info/developers/index.html). | ||
|
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| ## Citing `brainglobe-workflows` | ||
|
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| **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.** | ||
|
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| 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). | ||
|
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||
| --- | ||
|
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| ## Cellfinder | ||
|
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| Whole-brain cell detection, registration and analysis. | ||
|
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| 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/). | ||
|
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| `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/). | ||
|
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| `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: | ||
|
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| - 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. | ||
|
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| Basic usage: | ||
|
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| ```bash | ||
| cellfinder -s signal_images -b background_images -o output_dir --metadata metadata | ||
| ``` | ||
|
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| Full documentation can be found [here](https://brainglobe.info/documentation/cellfinder/index.html). |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,11 @@ | ||
| from importlib.metadata import PackageNotFoundError, version | ||
| from importlib.metadata import PackageNotFoundError, metadata | ||
|
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| 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 | ||
|
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| del metadata |
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