fix+ci: check no fix branching works

.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

.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: |

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)
 
 
 

requirements-dev.txt

@@ -0,0 +1,2 @@
+pytest
+crackle-codec