From ef7bb80e5545137e7b708a930f5e439622ef689d Mon Sep 17 00:00:00 2001 From: willGraham01 <1willgraham@gmail.com> Date: Wed, 1 Nov 2023 10:50:03 +0000 Subject: [PATCH] Update package metadata --- README.md | 33 ++++++++++--------- brainglobe_segmentation/__init__.py | 2 +- pyproject.toml | 16 ++++----- .../test_integration/test_gui/test_gui.py | 2 +- tox.ini | 2 +- 5 files changed, 29 insertions(+), 26 deletions(-) diff --git a/README.md b/README.md index 22011dd..ca7a5f4 100644 --- a/README.md +++ b/README.md @@ -1,36 +1,39 @@ -[![Python Version](https://img.shields.io/pypi/pyversions/brainreg-segment.svg)](https://pypi.org/project/brainreg-segment) -[![PyPI](https://img.shields.io/pypi/v/brainreg-segment.svg)](https://pypi.org/project/brainreg-segment) -[![Wheel](https://img.shields.io/pypi/wheel/brainreg-segment.svg)](https://pypi.org/project/brainreg-segment) -[![Development Status](https://img.shields.io/pypi/status/brainreg-segment.svg)](https://github.com/brainglobe/brainreg-segment) -[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainreg-segment/tests)]( - https://github.com/brainglobe/brainreg-segment/actions) -[![codecov](https://codecov.io/gh/brainglobe/brainreg-segment/branch/master/graph/badge.svg?token=WP9KTPZE5R)](https://codecov.io/gh/brainglobe/brainreg-segment)[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black) +[![Python Version](https://img.shields.io/pypi/pyversions/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation) +[![PyPI](https://img.shields.io/pypi/v/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation) +[![Wheel](https://img.shields.io/pypi/wheel/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation) +[![Development Status](https://img.shields.io/pypi/status/brainglobe-segmentation.svg)](https://github.com/brainglobe/brainglobe-segmentation) +[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainglobe-segmentation/tests)]( + https://github.com/brainglobe/brainglobe-segmentation/actions) +[![codecov](https://codecov.io/gh/brainglobe/brainglobe-segmentation/branch/master/graph/badge.svg?token=WP9KTPZE5R)](https://codecov.io/gh/brainglobe/brainglobe-segmentation)[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black) [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe) -# brainreg-segment +# brainglobe-segmentation + Segmentation of 1/2/3D brain structures in a common anatomical space -`brainreg-segment` is a companion to [`brainreg`](https://github.com/brainglobe/brainreg) allowing manual segmentation of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain region distribution, and visualisation (e.g. in [brainrender](https://github.com/brainglobe/brainrender)). +`brainglobe-segmentation` is a companion to [`brainreg`](https://github.com/brainglobe/brainreg) allowing manual segmentation of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain region distribution, and visualisation (e.g. in [brainrender](https://github.com/brainglobe/brainrender)). +`brainglobe-segmentation` is the successor to [`brainreg-segment`](https://github.com/brainglobe/brainreg-segmentation). -`brainreg-segment` and `brainreg` were developed by [Adam Tyson](https://github.com/adamltyson) and [Charly Rousseau](https://github.com/crousseau) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), based on [aMAP](https://doi.org/10.1038/ncomms11879) by [Christian Niedworok](https://github.com/cniedwor). The work was generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/). +`brainglobe-segmentation` and `brainreg` were developed by [Adam Tyson](https://github.com/adamltyson) and [Charly Rousseau](https://github.com/crousseau) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), based on [aMAP](https://doi.org/10.1038/ncomms11879) by [Christian Niedworok](https://github.com/cniedwor). The work was generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/). ## Installation -brainreg-segment comes bundled with [`brainreg`](https://github.com/brainglobe/brainreg), so see the [brainreg installation instructions](https://brainglobe.info/documentation/brainreg/index.html). +brainglobe-segmentation comes bundled with [`brainreg`](https://github.com/brainglobe/brainreg), so see the [brainreg installation instructions](https://brainglobe.info/documentation/brainreg/index.html). -brainreg-segment can be installed on it's own (`pip install brainreg-segment`), but you will need to register your data with brainreg first. +brainglobe-segmentation can be installed on it's own (`pip install brainglobe-segmentation`), but you will need to register your data with brainreg first. ## Usage -See [user guide](https://brainglobe.info/documentation/brainreg-segment/index.html). +See [user guide](https://brainglobe.info/documentation/brainglobe-segmentation/index.html). If you have any questions, head over to the [image.sc forum](https://forum.image.sc/tag/brainglobe). ## Contributing + Contributions are very welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html). -### Citing brainreg-segment +### Citing brainglobe-segmentation -If you find brainreg-segment useful, and use it in your research, please let us know and also cite the paper: +If you find brainglobe-segmentation useful, and use it in your research, please let us know and also cite the paper: > Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12, 867 [doi.org/10.1038/s41598-021-04676-9](https://doi.org/10.1038/s41598-021-04676-9) diff --git a/brainglobe_segmentation/__init__.py b/brainglobe_segmentation/__init__.py index 653a478..407b6cf 100644 --- a/brainglobe_segmentation/__init__.py +++ b/brainglobe_segmentation/__init__.py @@ -4,7 +4,7 @@ __author__ = "Adam Tyson" try: - __version__ = version("brainreg-segment") + __version__ = version("brainglobe-segmentation") except PackageNotFoundError: # package is not installed pass diff --git a/pyproject.toml b/pyproject.toml index 2198290..eecf01e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [project] -name = "brainreg-segment" +name = "brainglobe-segmentation" description = "Manual segmentation of 3D brain structures in a common anatomical space" readme = "README.md" authors = [ @@ -35,9 +35,9 @@ dynamic = ["version"] [project.urls] Homepage = "https://brainglobe.info/" -"Source Code" = "https://github.com/brainglobe/brainreg-segment" -"Bug Tracker" = "https://github.com/brainglobe/brainreg-segment/issues" -Documentation = "https://docs.brainglobe.info/brainreg-segment" +"Source Code" = "https://github.com/brainglobe/brainglobe-segmentation" +"Bug Tracker" = "https://github.com/brainglobe/brainglobe-segmentation/issues" +Documentation = "https://docs.brainglobe.info/brainglobe-segmentation" "User Support" = "https://forum.image.sc/tag/brainglobe" [project.optional-dependencies] @@ -53,13 +53,13 @@ dev = [ ] [project.entry-points."napari.manifest"] -cellfinder-napari = "brainreg_segment:napari.yaml" +cellfinder-napari = "brainglobe_segmentation:napari.yaml" [project.scripts] -brainreg-segment = "brainreg_segment.segment:main" +brainglobe-segmentation = "brainglobe_segmentation.segment:main" [project.entry-points."napari.plugin"] -brainreg-segment = "brainreg_segment.plugins" +brainglobe-segmentation = "brainglobe_segmentation.plugins" [build-system] requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"] @@ -69,7 +69,7 @@ build-backend = "setuptools.build_meta" include-package-data = true [tool.setuptools.packages.find] -include = ["brainreg_segment*"] +include = ["brainglobe_segmentation*"] [tool.setuptools_scm] diff --git a/tests/tests/test_integration/test_gui/test_gui.py b/tests/tests/test_integration/test_gui/test_gui.py index e9f278a..0e7456c 100644 --- a/tests/tests/test_integration/test_gui/test_gui.py +++ b/tests/tests/test_integration/test_gui/test_gui.py @@ -30,7 +30,7 @@ def test_load_atlas_space(segmentation_widget): def test_layer_deletion(segmentation_widget): """ Check that remove_layers() doesn't remove any layers that were present - before brainreg-segment added layers + before brainglobe-segmentation added layers """ assert len(segmentation_widget.viewer.layers) == 0 segmentation_widget.viewer.add_points(np.array([[1, 1], [2, 2]])) diff --git a/tox.ini b/tox.ini index cab063d..031ceba 100644 --- a/tox.ini +++ b/tox.ini @@ -25,4 +25,4 @@ deps = pyqt5 magicgui -commands = pytest -v --color=yes --cov=brainreg_segment --cov-report=xml +commands = pytest -v --color=yes --cov=brainglobe_segmentation --cov-report=xml