Rename to brainglobe-segmentation (#139)

* Revert "Mark as deprecated and add import warning" This reverts commit e6bf8e2. * Rename source folder * Fix test imports * Update package metadata * Another source code pass
brainglobe · Nov 6, 2023 · a3d0d0c · a3d0d0c
1 parent 04bc1a2
commit a3d0d0c
Show file tree

Hide file tree

Showing 39 changed files with 89 additions and 92 deletions.
diff --git a/README.md b/README.md
@@ -1,44 +1,39 @@
-# This package is deprecated!
-
-Please use [`brainglobe-segmentation` instead](https://github.com/brainglobe/brainglobe-segmentation).
-
-The old README can be found below.
-
----
-
-[![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., V&eacute;lez-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
@@ -0,0 +1,10 @@
+from importlib.metadata import PackageNotFoundError, version
+from . import *
+
+__author__ = "Adam Tyson"
+
+try:
+    __version__ = version("brainglobe-segmentation")
+except PackageNotFoundError:
+    # package is not installed
+    pass
diff --git a/brainreg_segment/atlas/__init__.py → brainglobe_segmentation/atlas/__init__.py b/brainreg_segment/atlas/__init__.py → brainglobe_segmentation/atlas/__init__.py
diff --git a/brainreg_segment/atlas/utils.py → brainglobe_segmentation/atlas/utils.py b/brainreg_segment/atlas/utils.py → brainglobe_segmentation/atlas/utils.py
diff --git a/brainreg_segment/image/__init__.py → brainglobe_segmentation/image/__init__.py b/brainreg_segment/image/__init__.py → brainglobe_segmentation/image/__init__.py
diff --git a/brainreg_segment/image/utils.py → brainglobe_segmentation/image/utils.py b/brainreg_segment/image/utils.py → brainglobe_segmentation/image/utils.py
diff --git a/brainreg_segment/layout/__init__.py → brainglobe_segmentation/layout/__init__.py b/brainreg_segment/layout/__init__.py → brainglobe_segmentation/layout/__init__.py
diff --git a/brainreg_segment/layout/gui_constants.py → ...lobe_segmentation/layout/gui_constants.py b/brainreg_segment/layout/gui_constants.py → ...lobe_segmentation/layout/gui_constants.py
diff --git a/brainreg_segment/layout/gui_elements.py → ...globe_segmentation/layout/gui_elements.py b/brainreg_segment/layout/gui_elements.py → ...globe_segmentation/layout/gui_elements.py
diff --git a/brainreg_segment/layout/utils.py → brainglobe_segmentation/layout/utils.py b/brainreg_segment/layout/utils.py → brainglobe_segmentation/layout/utils.py
diff --git a/brainglobe_segmentation/napari.yaml b/brainglobe_segmentation/napari.yaml
@@ -0,0 +1,11 @@
+name: brainglobe-segmentation
+schema_version: 0.1.0
+contributions:
+  commands:
+  - id: brainglobe-segmentation.SegmentationWidget
+    title: Open segmentation widget
+    python_name: brainglobe_segmentation.segment:SegmentationWidget
+
+  widgets:
+  - command: brainglobe-segmentation.SegmentationWidget
+    display_name: Region/track segmentation
diff --git a/brainreg_segment/paths.py → brainglobe_segmentation/paths.py b/brainreg_segment/paths.py → brainglobe_segmentation/paths.py
diff --git a/brainreg_segment/regions/IO.py → brainglobe_segmentation/regions/IO.py b/brainreg_segment/regions/IO.py → brainglobe_segmentation/regions/IO.py
diff --git a/brainreg_segment/regions/__init__.py → brainglobe_segmentation/regions/__init__.py b/brainreg_segment/regions/__init__.py → brainglobe_segmentation/regions/__init__.py
diff --git a/brainreg_segment/regions/analysis.py → brainglobe_segmentation/regions/analysis.py b/brainreg_segment/regions/analysis.py → brainglobe_segmentation/regions/analysis.py
@@ -5,7 +5,7 @@
 from napari.qt.threading import thread_worker
 from skimage.measure import regionprops_table
 
-from brainreg_segment.atlas.utils import lateralise_atlas_image
+from brainglobe_segmentation.atlas.utils import lateralise_atlas_image
 
 
 @thread_worker

diff --git a/brainreg_segment/regions/layers.py → brainglobe_segmentation/regions/layers.py b/brainreg_segment/regions/layers.py → brainglobe_segmentation/regions/layers.py
diff --git a/brainreg_segment/segment.py → brainglobe_segmentation/segment.py b/brainreg_segment/segment.py → brainglobe_segmentation/segment.py
@@ -8,11 +8,11 @@
 from qtpy import QtCore
 from qtpy.QtWidgets import QFileDialog, QGridLayout, QGroupBox, QLabel, QWidget
 
-from brainreg_segment.atlas.utils import (
+from brainglobe_segmentation.atlas.utils import (
     get_available_atlases,
     structure_from_viewer,
 )
-from brainreg_segment.layout.gui_constants import (
+from brainglobe_segmentation.layout.gui_constants import (
     BOUNDARIES_STRING,
     COLUMN_WIDTH,
     DISPLAY_REGION_INFO,
@@ -23,15 +23,21 @@
     WINDOW_HEIGHT,
     WINDOW_WIDTH,
 )
-from brainreg_segment.layout.gui_elements import add_button, add_combobox
-from brainreg_segment.layout.utils import display_warning
-from brainreg_segment.paths import Paths
-from brainreg_segment.regions.IO import export_label_layers, save_label_layers
+from brainglobe_segmentation.layout.gui_elements import (
+    add_button,
+    add_combobox,
+)
+from brainglobe_segmentation.layout.utils import display_warning
+from brainglobe_segmentation.paths import Paths
+from brainglobe_segmentation.regions.IO import (
+    export_label_layers,
+    save_label_layers,
+)
 
 ### SEGMENTATION
-from brainreg_segment.segmentation_panels.regions import RegionSeg
-from brainreg_segment.segmentation_panels.tracks import TrackSeg
-from brainreg_segment.tracks.IO import export_splines, save_track_layers
+from brainglobe_segmentation.segmentation_panels.regions import RegionSeg
+from brainglobe_segmentation.segmentation_panels.tracks import TrackSeg
+from brainglobe_segmentation.tracks.IO import export_splines, save_track_layers
 
 ### LAYOUT HELPERS
 

diff --git a/...g_segment/segmentation_panels/__init__.py → ...mentation/segmentation_panels/__init__.py b/...g_segment/segmentation_panels/__init__.py → ...mentation/segmentation_panels/__init__.py
diff --git a/...eg_segment/segmentation_panels/regions.py → ...gmentation/segmentation_panels/regions.py b/...eg_segment/segmentation_panels/regions.py → ...gmentation/segmentation_panels/regions.py
@@ -1,7 +1,7 @@
 # RegionSeg
 from qtpy.QtWidgets import QGridLayout, QGroupBox
 
-from brainreg_segment.layout.gui_constants import (
+from brainglobe_segmentation.layout.gui_constants import (
     BRUSH_SIZE,
     CALCULATE_VOLUMES_DEFAULT,
     COLUMN_WIDTH,
@@ -11,13 +11,13 @@
     SEGM_METHODS_PANEL_ALIGN,
     SUMMARIZE_VOLUMES_DEFAULT,
 )
-from brainreg_segment.layout.gui_elements import (
+from brainglobe_segmentation.layout.gui_elements import (
     add_button,
     add_checkbox,
 )
-from brainreg_segment.layout.utils import display_info, display_warning
-from brainreg_segment.regions.analysis import region_analysis
-from brainreg_segment.regions.layers import (
+from brainglobe_segmentation.layout.utils import display_info, display_warning
+from brainglobe_segmentation.regions.analysis import region_analysis
+from brainglobe_segmentation.regions.layers import (
     add_existing_region_segmentation,
     add_new_region_layer,
     add_region_from_existing_layer,

diff --git a/...reg_segment/segmentation_panels/tracks.py → ...egmentation/segmentation_panels/tracks.py b/...reg_segment/segmentation_panels/tracks.py → ...egmentation/segmentation_panels/tracks.py
@@ -4,8 +4,8 @@
 import numpy as np
 from qtpy.QtWidgets import QGridLayout, QGroupBox
 
-from brainreg_segment.image.utils import create_KDTree_from_image
-from brainreg_segment.layout.gui_constants import (
+from brainglobe_segmentation.image.utils import create_KDTree_from_image
+from brainglobe_segmentation.layout.gui_constants import (
     COLUMN_WIDTH,
     FIT_DEGREE_DEFAULT,
     POINT_SIZE,
@@ -17,15 +17,15 @@
     SUMMARISE_TRACK_DEFAULT,
     TRACK_FILE_EXT,
 )
-from brainreg_segment.layout.gui_elements import (
+from brainglobe_segmentation.layout.gui_elements import (
     add_button,
     add_checkbox,
     add_float_box,
     add_int_box,
 )
-from brainreg_segment.layout.utils import display_info, display_warning
-from brainreg_segment.tracks.analysis import track_analysis
-from brainreg_segment.tracks.layers import (
+from brainglobe_segmentation.layout.utils import display_info, display_warning
+from brainglobe_segmentation.tracks.analysis import track_analysis
+from brainglobe_segmentation.tracks.layers import (
     add_existing_track_layers,
     add_new_track_layer,
     add_track_from_existing_layer,

diff --git a/brainreg_segment/tracks/IO.py → brainglobe_segmentation/tracks/IO.py b/brainreg_segment/tracks/IO.py → brainglobe_segmentation/tracks/IO.py
diff --git a/brainreg_segment/tracks/__init__.py → brainglobe_segmentation/tracks/__init__.py b/brainreg_segment/tracks/__init__.py → brainglobe_segmentation/tracks/__init__.py
diff --git a/brainreg_segment/tracks/analysis.py → brainglobe_segmentation/tracks/analysis.py b/brainreg_segment/tracks/analysis.py → brainglobe_segmentation/tracks/analysis.py
@@ -1,7 +1,7 @@
 import numpy as np
 import pandas as pd
 
-from brainreg_segment.tracks.fit import spline_fit
+from brainglobe_segmentation.tracks.fit import spline_fit
 
 
 def track_analysis(

diff --git a/brainreg_segment/tracks/fit.py → brainglobe_segmentation/tracks/fit.py b/brainreg_segment/tracks/fit.py → brainglobe_segmentation/tracks/fit.py
diff --git a/brainreg_segment/tracks/layers.py → brainglobe_segmentation/tracks/layers.py b/brainreg_segment/tracks/layers.py → brainglobe_segmentation/tracks/layers.py
diff --git a/brainreg_segment/__init__.py b/brainreg_segment/__init__.py
diff --git a/brainreg_segment/napari.yaml b/brainreg_segment/napari.yaml
diff --git 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/conftest.py b/tests/conftest.py
@@ -4,7 +4,7 @@
 import pytest
 from bg_atlasapi import BrainGlobeAtlas
 
-from brainreg_segment.segment import SegmentationWidget
+from brainglobe_segmentation.segment import SegmentationWidget
 
 atlas_name = "allen_mouse_50um"
 brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output"

diff --git 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/tests/tests/test_integration/test_tracks/test_track_analysis.py b/tests/tests/test_integration/test_tracks/test_track_analysis.py
@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 
-from brainreg_segment.tracks.analysis import run_track_analysis
+from brainglobe_segmentation.tracks.analysis import run_track_analysis
 
 tracks_dir = Path.cwd() / "tests" / "data" / "tracks"
 

diff --git a/tests/tests/test_unit/test_atlas/test_atlas_utils.py b/tests/tests/test_unit/test_atlas/test_atlas_utils.py
@@ -1,6 +1,6 @@
 import numpy as np
 
-from brainreg_segment.atlas import utils as atlas_utils
+from brainglobe_segmentation.atlas import utils as atlas_utils
 
 atlas_name = "allen_mouse_50um"
 

diff --git a/tests/tests/test_unit/test_image/test_image_utils.py b/tests/tests/test_unit/test_image/test_image_utils.py
@@ -1,6 +1,6 @@
 import numpy as np
 
-from brainreg_segment.image.utils import create_KDTree_from_image
+from brainglobe_segmentation.image.utils import create_KDTree_from_image
 
 image = np.array(
     (

diff --git a/tests/tests/test_unit/test_regions/test_region_IO.py b/tests/tests/test_unit/test_regions/test_region_IO.py
@@ -3,7 +3,7 @@
 
 import tifffile
 
-from brainreg_segment.regions import IO as region_IO
+from brainglobe_segmentation.regions import IO as region_IO
 
 regions_dir = Path.cwd() / "tests" / "data" / "regions"
 VOXEL_SIZE = 100

diff --git a/tests/tests/test_unit/test_regions/test_region_analysis.py b/tests/tests/test_unit/test_regions/test_region_analysis.py
@@ -6,7 +6,7 @@
 import tifffile
 from napari.layers import Labels
 
-from brainreg_segment.regions.analysis import (
+from brainglobe_segmentation.regions.analysis import (
     check_list_only_nones,
     summarise_brain_regions,
     summarise_single_brain_region,

diff --git a/tests/tests/test_unit/test_segmentation_panels/test_regions.py b/tests/tests/test_unit/test_segmentation_panels/test_regions.py
@@ -1,7 +1,7 @@
 import numpy as np
 from napari.layers import Labels
 
-from brainreg_segment.segmentation_panels.regions import (
+from brainglobe_segmentation.segmentation_panels.regions import (
     check_segmentation_in_correct_space,
 )
 

diff --git a/tests/tests/test_unit/test_tracks/test_track_IO.py b/tests/tests/test_unit/test_tracks/test_track_IO.py
@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 
-from brainreg_segment.tracks import IO
+from brainglobe_segmentation.tracks import IO
 
 tracks_dir = Path.cwd() / "tests" / "data" / "tracks"
 

diff --git a/tests/tests/test_unit/test_tracks/test_track_analysis_tools.py b/tests/tests/test_unit/test_tracks/test_track_analysis_tools.py
@@ -2,7 +2,10 @@
 import pytest
 from pandas import read_csv
 
-from brainreg_segment.tracks.analysis import analyse_track_anatomy, spline_fit
+from brainglobe_segmentation.tracks.analysis import (
+    analyse_track_anatomy,
+    spline_fit,
+)
 
 
 @pytest.fixture

diff --git a/tox.ini b/tox.ini
@@ -25,4 +25,4 @@ deps =
     pyqt5
     magicgui
 
-commands = pytest -v --color=yes --cov=brainreg_segment --cov-report=xml -W ignore::DeprecationWarning
+commands = pytest -v --color=yes --cov=brainglobe_segmentation --cov-report=xml