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Fix 'buffer source array is read-only' error#256

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jni merged 1 commit intomainfrom
map-array-workaround
Feb 6, 2026
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Fix 'buffer source array is read-only' error#256
jni merged 1 commit intomainfrom
map-array-workaround

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@jni jni commented Feb 6, 2026

Workaround for scikit-image/scikit-image#6378
Can be removed after scikit-image/scikit-image#7535
is released.

@jni jni merged commit 4eacfa6 into main Feb 6, 2026
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@jni jni deleted the map-array-workaround branch February 6, 2026 04:59
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jni commented Feb 6, 2026

For posterity, this was the failure log:

2026-02-05T13:52:48.1644315Z =================================== FAILURES ===================================
2026-02-05T13:52:48.1644859Z __________________________ test_fast_graph_center_idx __________________________
2026-02-05T13:52:48.1645130Z 
2026-02-05T13:52:48.1645236Z     def test_fast_graph_center_idx():
2026-02-05T13:52:48.1645510Z         s = csr.Skeleton(skeleton0)
2026-02-05T13:52:48.1645770Z >       i = csr._fast_graph_center_idx(s)
2026-02-05T13:52:48.1646037Z             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-02-05T13:52:48.1646203Z 
2026-02-05T13:52:48.1646484Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skan/test/test_csr.py:268: 
2026-02-05T13:52:48.1646996Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
2026-02-05T13:52:48.1647543Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skan/csr.py:1267: in _fast_graph_center_idx
2026-02-05T13:52:48.1648106Z     simp_csgraph, reduced_nodes = _simplify_graph(skel)
2026-02-05T13:52:48.1648421Z                                   ^^^^^^^^^^^^^^^^^^^^^
2026-02-05T13:52:48.1648881Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skan/csr.py:1242: in _simplify_graph
2026-02-05T13:52:48.1649369Z     src_relab, dst_relab = fw_map[src], fw_map[dst]
2026-02-05T13:52:48.1649646Z                            ^^^^^^^^^^^
2026-02-05T13:52:48.1650116Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skimage/util/_map_array.py:184: in __getitem__
2026-02-05T13:52:48.1650595Z     out = map_array(
2026-02-05T13:52:48.1651001Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skimage/util/_map_array.py:72: in map_array
2026-02-05T13:52:48.1651522Z     _map_array(input_arr, out_view, input_vals, output_vals)
2026-02-05T13:52:48.1652810Z skimage/util/_remap.pyx:10: in skimage.util._remap._map_array
2026-02-05T13:52:48.1653117Z     ???
2026-02-05T13:52:48.1653359Z <stringsource>:664: in View.MemoryView.memoryview_cwrapper
2026-02-05T13:52:48.1653652Z     ???
2026-02-05T13:52:48.1654044Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
2026-02-05T13:52:48.1654263Z 
2026-02-05T13:52:48.1654334Z >   ???
2026-02-05T13:52:48.1654542Z E   ValueError: buffer source array is read-only
2026-02-05T13:52:48.1654729Z 
2026-02-05T13:52:48.1654817Z <stringsource>:352: ValueError
2026-02-05T13:52:48.1655109Z __________________________________ test_sholl __________________________________
2026-02-05T13:52:48.1655339Z 
2026-02-05T13:52:48.1655421Z     def test_sholl():
2026-02-05T13:52:48.1655628Z         s = csr.Skeleton(skeleton0)
2026-02-05T13:52:48.1655948Z >       c, r, counts = csr.sholl_analysis(s, shells=np.arange(0, 5, 1.5))
2026-02-05T13:52:48.1656283Z                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-02-05T13:52:48.1656485Z 
2026-02-05T13:52:48.1656739Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skan/test/test_csr.py:278: 
2026-02-05T13:52:48.1657200Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
2026-02-05T13:52:48.1657687Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skan/csr.py:1352: in sholl_analysis
2026-02-05T13:52:48.1658165Z     center_idx = _fast_graph_center_idx(skeleton)
2026-02-05T13:52:48.1658436Z                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-02-05T13:52:48.1658884Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skan/csr.py:1267: in _fast_graph_center_idx
2026-02-05T13:52:48.1659381Z     simp_csgraph, reduced_nodes = _simplify_graph(skel)
2026-02-05T13:52:48.1659679Z                                   ^^^^^^^^^^^^^^^^^^^^^
2026-02-05T13:52:48.1660115Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skan/csr.py:1242: in _simplify_graph
2026-02-05T13:52:48.1660585Z     src_relab, dst_relab = fw_map[src], fw_map[dst]
2026-02-05T13:52:48.1660859Z                            ^^^^^^^^^^^
2026-02-05T13:52:48.1661320Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skimage/util/_map_array.py:184: in __getitem__
2026-02-05T13:52:48.1661788Z     out = map_array(
2026-02-05T13:52:48.1662352Z /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/skimage/util/_map_array.py:72: in map_array
2026-02-05T13:52:48.1662865Z     _map_array(input_arr, out_view, input_vals, output_vals)
2026-02-05T13:52:48.1663233Z skimage/util/_remap.pyx:10: in skimage.util._remap._map_array
2026-02-05T13:52:48.1663528Z     ???
2026-02-05T13:52:48.1663767Z <stringsource>:664: in View.MemoryView.memoryview_cwrapper
2026-02-05T13:52:48.1664052Z     ???
2026-02-05T13:52:48.1664267Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
2026-02-05T13:52:48.1664476Z 
2026-02-05T13:52:48.1664543Z >   ???
2026-02-05T13:52:48.1664756Z E   ValueError: buffer source array is read-only
2026-02-05T13:52:48.1664943Z 
2026-02-05T13:52:48.1665044Z <stringsource>:352: ValueError
2026-02-05T13:52:48.1665328Z =========================== short test summary info ============================
2026-02-05T13:52:48.1665833Z FAILED test/test_csr.py::test_fast_graph_center_idx - ValueError: buffer source array is read-only
2026-02-05T13:52:48.1666377Z FAILED test/test_csr.py::test_sholl - ValueError: buffer source array is read-only
2026-02-05T13:52:48.1666799Z ======================== 2 failed, 160 passed in 24.78s ========================

@jni jni mentioned this pull request Feb 6, 2026
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