diff --git a/README.md b/README.md index 6a52214..ca7a5f4 100644 --- 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., 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 new file mode 100644 index 0000000..407b6cf --- /dev/null +++ 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 b/brainglobe_segmentation/atlas/__init__.py similarity index 100% rename from brainreg_segment/atlas/__init__.py rename to brainglobe_segmentation/atlas/__init__.py diff --git a/brainreg_segment/atlas/utils.py b/brainglobe_segmentation/atlas/utils.py similarity index 100% rename from brainreg_segment/atlas/utils.py rename to brainglobe_segmentation/atlas/utils.py diff --git a/brainreg_segment/image/__init__.py b/brainglobe_segmentation/image/__init__.py similarity index 100% rename from brainreg_segment/image/__init__.py rename to brainglobe_segmentation/image/__init__.py diff --git a/brainreg_segment/image/utils.py b/brainglobe_segmentation/image/utils.py similarity index 100% rename from brainreg_segment/image/utils.py rename to brainglobe_segmentation/image/utils.py diff --git a/brainreg_segment/layout/__init__.py b/brainglobe_segmentation/layout/__init__.py similarity index 100% rename from brainreg_segment/layout/__init__.py rename to brainglobe_segmentation/layout/__init__.py diff --git a/brainreg_segment/layout/gui_constants.py b/brainglobe_segmentation/layout/gui_constants.py similarity index 100% rename from brainreg_segment/layout/gui_constants.py rename to brainglobe_segmentation/layout/gui_constants.py diff --git a/brainreg_segment/layout/gui_elements.py b/brainglobe_segmentation/layout/gui_elements.py similarity index 100% rename from brainreg_segment/layout/gui_elements.py rename to brainglobe_segmentation/layout/gui_elements.py diff --git a/brainreg_segment/layout/utils.py b/brainglobe_segmentation/layout/utils.py similarity index 100% rename from brainreg_segment/layout/utils.py rename to brainglobe_segmentation/layout/utils.py diff --git a/brainglobe_segmentation/napari.yaml b/brainglobe_segmentation/napari.yaml new file mode 100644 index 0000000..9f8021e --- /dev/null +++ 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 b/brainglobe_segmentation/paths.py similarity index 100% rename from brainreg_segment/paths.py rename to brainglobe_segmentation/paths.py diff --git a/brainreg_segment/regions/IO.py b/brainglobe_segmentation/regions/IO.py similarity index 100% rename from brainreg_segment/regions/IO.py rename to brainglobe_segmentation/regions/IO.py diff --git a/brainreg_segment/regions/__init__.py b/brainglobe_segmentation/regions/__init__.py similarity index 100% rename from brainreg_segment/regions/__init__.py rename to brainglobe_segmentation/regions/__init__.py diff --git a/brainreg_segment/regions/analysis.py b/brainglobe_segmentation/regions/analysis.py similarity index 99% rename from brainreg_segment/regions/analysis.py rename to brainglobe_segmentation/regions/analysis.py index 35a098d..f3f07c3 100644 --- a/brainreg_segment/regions/analysis.py +++ b/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 b/brainglobe_segmentation/regions/layers.py similarity index 100% rename from brainreg_segment/regions/layers.py rename to brainglobe_segmentation/regions/layers.py diff --git a/brainreg_segment/segment.py b/brainglobe_segmentation/segment.py similarity index 97% rename from brainreg_segment/segment.py rename to brainglobe_segmentation/segment.py index a7ca00c..18c04df 100644 --- a/brainreg_segment/segment.py +++ b/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/brainreg_segment/segmentation_panels/__init__.py b/brainglobe_segmentation/segmentation_panels/__init__.py similarity index 100% rename from brainreg_segment/segmentation_panels/__init__.py rename to brainglobe_segmentation/segmentation_panels/__init__.py diff --git a/brainreg_segment/segmentation_panels/regions.py b/brainglobe_segmentation/segmentation_panels/regions.py similarity index 96% rename from brainreg_segment/segmentation_panels/regions.py rename to brainglobe_segmentation/segmentation_panels/regions.py index d92af15..4b856b0 100644 --- a/brainreg_segment/segmentation_panels/regions.py +++ b/brainglobe_segmentation/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/brainreg_segment/segmentation_panels/tracks.py b/brainglobe_segmentation/segmentation_panels/tracks.py similarity index 96% rename from brainreg_segment/segmentation_panels/tracks.py rename to brainglobe_segmentation/segmentation_panels/tracks.py index ba1b9ae..78af874 100644 --- a/brainreg_segment/segmentation_panels/tracks.py +++ b/brainglobe_segmentation/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 b/brainglobe_segmentation/tracks/IO.py similarity index 100% rename from brainreg_segment/tracks/IO.py rename to brainglobe_segmentation/tracks/IO.py diff --git a/brainreg_segment/tracks/__init__.py b/brainglobe_segmentation/tracks/__init__.py similarity index 100% rename from brainreg_segment/tracks/__init__.py rename to brainglobe_segmentation/tracks/__init__.py diff --git a/brainreg_segment/tracks/analysis.py b/brainglobe_segmentation/tracks/analysis.py similarity index 98% rename from brainreg_segment/tracks/analysis.py rename to brainglobe_segmentation/tracks/analysis.py index e0435a9..de43fee 100644 --- a/brainreg_segment/tracks/analysis.py +++ b/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 b/brainglobe_segmentation/tracks/fit.py similarity index 100% rename from brainreg_segment/tracks/fit.py rename to brainglobe_segmentation/tracks/fit.py diff --git a/brainreg_segment/tracks/layers.py b/brainglobe_segmentation/tracks/layers.py similarity index 100% rename from brainreg_segment/tracks/layers.py rename to brainglobe_segmentation/tracks/layers.py diff --git a/brainreg_segment/__init__.py b/brainreg_segment/__init__.py deleted file mode 100644 index b7f0eb4..0000000 --- a/brainreg_segment/__init__.py +++ /dev/null @@ -1,17 +0,0 @@ -import warnings - -warnings.warn( - "brainreg-segment is deprecated. Please use brainglobe-segmentation instead: https://github.com/brainglobe/brainglobe-segmentation", - DeprecationWarning, -) - -from importlib.metadata import PackageNotFoundError, version -from . import * - -__author__ = "Adam Tyson" - -try: - __version__ = version("brainreg-segment") -except PackageNotFoundError: - # package is not installed - pass diff --git a/brainreg_segment/napari.yaml b/brainreg_segment/napari.yaml deleted file mode 100644 index 82d20ff..0000000 --- a/brainreg_segment/napari.yaml +++ /dev/null @@ -1,11 +0,0 @@ -name: brainreg-segment -schema_version: 0.1.0 -contributions: - commands: - - id: brainreg-segment.SegmentationWidget - title: Open segmentation widget - python_name: brainreg_segment.segment:SegmentationWidget - - widgets: - - command: brainreg-segment.SegmentationWidget - display_name: Region/track segmentation 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/conftest.py b/tests/conftest.py index b2c870a..35dd22d 100644 --- 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 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/tests/tests/test_integration/test_tracks/test_track_analysis.py b/tests/tests/test_integration/test_tracks/test_track_analysis.py index 82caa2b..3f4dea9 100644 --- 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 index 7202be0..37dc31d 100644 --- 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 index 05356a3..f6506d5 100644 --- 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 index 70ca81d..b2edda5 100644 --- 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 index ed5a249..d46efff 100644 --- 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 index 0e66fdc..7bd38af 100644 --- 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 index 201b7cc..691d8c7 100644 --- 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 index 6cf4fb4..1e5ef3b 100644 --- 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 index 20f363d..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 -W ignore::DeprecationWarning +commands = pytest -v --color=yes --cov=brainglobe_segmentation --cov-report=xml