diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 8bd634c..82f4bb4 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -13,7 +13,7 @@ jobs: linting: runs-on: ubuntu-latest steps: - - uses: neuroinformatics-unit/actions/lint@v1 + - uses: neuroinformatics-unit/actions/lint@v2 manifest: name: Check Manifest @@ -48,7 +48,7 @@ jobs: # Helps set up VTK with a headless display - uses: pyvista/setup-headless-display-action@v2 # Run tests - - uses: neuroinformatics-unit/actions/test@v1 + - uses: neuroinformatics-unit/actions/test@v2 with: python-version: ${{ matrix.python-version }} use-xvfb: true @@ -59,7 +59,7 @@ jobs: if: github.event_name == 'push' && github.ref_type == 'tag' runs-on: ubuntu-latest steps: - - uses: neuroinformatics-unit/actions/build_sdist_wheels@v1 + - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2 upload_all: diff --git a/brainglobe_segmentation/regions/IO.py b/brainglobe_segmentation/regions/IO.py index a8027da..994c7d1 100644 --- a/brainglobe_segmentation/regions/IO.py +++ b/brainglobe_segmentation/regions/IO.py @@ -1,8 +1,8 @@ from pathlib import Path -import imio import numpy as np from brainglobe_utils.general.pathlib import append_to_pathlib_stem +from brainglobe_utils.image_io import to_tiff from brainglobe_utils.IO.surfaces import marching_cubes_to_obj from skimage import measure @@ -97,7 +97,7 @@ def save_regions_to_file( name = label_layer.name filename = destination_directory / (name + image_extension) - imio.to_tiff(data.astype(np.int16), filename) + to_tiff(data.astype(np.int16), filename) def export_regions_to_file(image, filename, voxel_size, ignore_empty=True): diff --git a/pyproject.toml b/pyproject.toml index 8f0634c..0591e56 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,8 +20,7 @@ requires-python = ">=3.9" dependencies = [ "bg-atlasapi", "brainglobe-napari-io >=0.3.0", - "brainglobe-utils >=0.2.7", - "imio", + "brainglobe-utils >=0.4.0", "napari >=0.4.5", "numpy", "pandas[hdf5]", @@ -114,5 +113,4 @@ deps = magicgui commands = pytest -v --color=yes --cov=brainglobe_segmentation --cov-report=xml - """