diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml index 3d27610..25676b0 100644 --- a/.github/workflows/build_wheel.yml +++ b/.github/workflows/build_wheel.yml @@ -28,13 +28,13 @@ jobs: uses: docker/setup-qemu-action@v1 - name: Build wheels - uses: pypa/cibuildwheel@v2.19.1 + uses: pypa/cibuildwheel@v2.22.0 # to supply options, put them in 'env', like: env: CIBW_ARCHS_LINUX: ${{matrix.arch}} CIBW_BEFORE_BUILD: pip install numpy setuptools wheel cython CIBW_ARCHS_MACOS: "x86_64 arm64" - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v3 with: path: ./wheelhouse/*.whl \ No newline at end of file diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index bab383a..63e33c3 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -27,7 +27,7 @@ jobs: run: | python -m pip install --upgrade pip pip install cython numpy setuptools wheel - pip install -r requirements.txt pytest + pip install -r requirements.txt -r requirements-dev.txt pip install -e . - name: Test with pytest run: | diff --git a/automated_test.py b/automated_test.py index a0a653a..788acef 100644 --- a/automated_test.py +++ b/automated_test.py @@ -8,6 +8,11 @@ import kimimaro.skeletontricks from kimimaro.utility import moving_average +@pytest.fixture +def connectomics_data(): + import crackle + return crackle.load("benchmarks/connectomics.npy.ckl.gz") + def test_empty_image(): labels = np.zeros( (256, 256, 256), dtype=bool) skels = kimimaro.skeletonize(labels, fix_borders=True) @@ -502,7 +507,8 @@ def test_moving_average(): assert np.all(res == ans) assert len(ans) == len(data) - +def test_no_fix_branching(connectomics_data): + kimimaro.skeletonize(connectomics_data[:,:,100], fix_branching=False) diff --git a/requirements-dev.txt b/requirements-dev.txt new file mode 100644 index 0000000..4536535 --- /dev/null +++ b/requirements-dev.txt @@ -0,0 +1,2 @@ +pytest +crackle-codec \ No newline at end of file