diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 50192f3..9ab8799 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -93,7 +93,7 @@ jobs: uses: actions/checkout@v3 - name: Setup mamba environment - uses: mamba-org/setup-micromamba@v1 + uses: mamba-org/setup-micromamba@v2 with: init-shell: bash environment-name: niftyreg-env diff --git a/tests/test_brainreg_napari.py b/tests/test_brainreg_napari.py index 0bd38f7..e06ec7c 100644 --- a/tests/test_brainreg_napari.py +++ b/tests/test_brainreg_napari.py @@ -76,10 +76,6 @@ def test_workflow(make_napari_viewer, tmp_path): assert isinstance(boundaries, napari.layers.Image) -@pytest.mark.xfail( - reason="See https://github.com/brainglobe/cellfinder/issues/443", - raises=AssertionError, -) def test_orientation_check( make_napari_viewer, tmp_path, atlas_choice="allen_mouse_50um" ): @@ -130,9 +126,10 @@ def test_orientation_check( ar_projection = viewer.layers["Ref. proj. 1"].data import numpy as np - assert ar_projection.shape[1] // 2 == 114 - assert np.all(ar_projection[:, 114] == 0) - assert not np.all(ar_projection[:, 115] == 0) + midpoint = atlas.shape[2] // 2 + assert ar_projection.shape[1] // 2 == midpoint + assert np.all(ar_projection[:, midpoint - 1] == 0) + assert not np.all(ar_projection[:, midpoint] == 0) def run_and_check_orientation_check(widget, viewer, brain_layer, atlas):