Update package metadata

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)

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

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]
 

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]]))

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