Require zarr>=3 on Python >= 3.11 to fix numcodecs 0.16 clash#289
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JoOkuma merged 1 commit intoroyerlab:mainfrom May 1, 2026
Merged
Require zarr>=3 on Python >= 3.11 to fix numcodecs 0.16 clash#289JoOkuma merged 1 commit intoroyerlab:mainfrom
JoOkuma merged 1 commit intoroyerlab:mainfrom
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zarr 2.x's util.py imports cbuffer_sizes/cbuffer_metainfo from
numcodecs.blosc at module load. numcodecs >= 0.16 dropped those
symbols. On Python 3.11+ the resolver freely picks zarr 2.18.x with
numcodecs >= 0.16, so any 'import zarr' (e.g. via geff_spec) raises
ImportError and tests are cancelled.
On Python 3.10 the resolver is forced to numcodecs <= 0.13.1 anyway
(numcodecs >= 0.14 requires Python >= 3.11), so the broken pair is
unreachable and zarr 2.18 keeps working there.
tracksdata's code already uses zarr v3 APIs at runtime
('from zarr.storage import StoreLike') so the constraint just makes
explicit what we already require.
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Branches 858 858
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…rlab#289) zarr 2.x's util.py imports cbuffer_sizes/cbuffer_metainfo from numcodecs.blosc at module load. numcodecs >= 0.16 dropped those symbols. On Python 3.11+ the resolver freely picks zarr 2.18.x with numcodecs >= 0.16, so any 'import zarr' (e.g. via geff_spec) raises ImportError and tests are cancelled. On Python 3.10 the resolver is forced to numcodecs <= 0.13.1 anyway (numcodecs >= 0.14 requires Python >= 3.11), so the broken pair is unreachable and zarr 2.18 keeps working there. tracksdata's code already uses zarr v3 APIs at runtime ('from zarr.storage import StoreLike') so the constraint just makes explicit what we already require.
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* block _root signals while updating the view * save signal state in remove_node in case signal deconnects (would only happen in rare multithreading case) * precomit fixes * stop black and ruff from fighting * Require zarr>=3 on Python >= 3.11 to avoid numcodecs 0.16 clash (#289) zarr 2.x's util.py imports cbuffer_sizes/cbuffer_metainfo from numcodecs.blosc at module load. numcodecs >= 0.16 dropped those symbols. On Python 3.11+ the resolver freely picks zarr 2.18.x with numcodecs >= 0.16, so any 'import zarr' (e.g. via geff_spec) raises ImportError and tests are cancelled. On Python 3.10 the resolver is forced to numcodecs <= 0.13.1 anyway (numcodecs >= 0.14 requires Python >= 3.11), so the broken pair is unreachable and zarr 2.18 keeps working there. tracksdata's code already uses zarr v3 APIs at runtime ('from zarr.storage import StoreLike') so the constraint just makes explicit what we already require. * Update src/tracksdata/graph/_test/test_graph_view_signals.py Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com> * Update src/tracksdata/graph/_test/test_graph_view_signals.py Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com> * Update src/tracksdata/graph/_test/test_graph_view_signals.py Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com> --------- Co-authored-by: Jordão Bragantini <jordao.bragantini@czbiohub.org> Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com>
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* block _root signals while updating the view * save signal state in remove_node in case signal deconnects (would only happen in rare multithreading case) * precomit fixes * stop black and ruff from fighting * Require zarr>=3 on Python >= 3.11 to avoid numcodecs 0.16 clash (royerlab#289) zarr 2.x's util.py imports cbuffer_sizes/cbuffer_metainfo from numcodecs.blosc at module load. numcodecs >= 0.16 dropped those symbols. On Python 3.11+ the resolver freely picks zarr 2.18.x with numcodecs >= 0.16, so any 'import zarr' (e.g. via geff_spec) raises ImportError and tests are cancelled. On Python 3.10 the resolver is forced to numcodecs <= 0.13.1 anyway (numcodecs >= 0.14 requires Python >= 3.11), so the broken pair is unreachable and zarr 2.18 keeps working there. tracksdata's code already uses zarr v3 APIs at runtime ('from zarr.storage import StoreLike') so the constraint just makes explicit what we already require. * Update src/tracksdata/graph/_test/test_graph_view_signals.py Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com> * Update src/tracksdata/graph/_test/test_graph_view_signals.py Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com> * Update src/tracksdata/graph/_test/test_graph_view_signals.py Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com> --------- Co-authored-by: Jordão Bragantini <jordao.bragantini@czbiohub.org> Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com>
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On Python 3.11+ the resolver freely picks
zarr==2.18.xtogether withnumcodecs>=0.16. Newer numcodecs droppedcbuffer_sizes/cbuffer_metainfo, which zarr 2.x'sutil.pyimports at module load — soimport zarr(e.g. viageff_spec) ImportErrors and CI tests are cancelled. End users hit the same bug withpip installon Py3.11.On Py3.10 the resolver is forced to
numcodecs<=0.13(newer numcodecs requires Py>=3.11), so the broken pair is unreachable and zarr 2.18 keeps working there.Marker-gated lower bound on zarr that only constrains the affected Python versions. Our code already imports zarr v3 APIs (
from zarr.storage import StoreLike), so this just makes explicit what we already require.