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Text/workflows dec19#26

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text/workflows-Dec19

Dec 26, 2025

Commits on Nov 27, 2025

Commits on Nov 28, 2025

initial section on desiderata
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Commits on Nov 29, 2025

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Commits on Dec 4, 2025

initial workflow development
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Commits on Dec 17, 2025

Commits on Dec 19, 2025

Commits on Dec 20, 2025

Commits on Dec 22, 2025

Optimize checkpoint storage and add selective checkpointing

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Fix: Restore layers['counts'] for HVG selection, delete after step 4

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Add steps 9-11 to default checkpoint steps

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Add step 8 (differential expression) to default checkpoint steps

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finished checkpointed workflow section
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Add Prefect-based workflow with parallel per-cell-type analysis

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Remove parallelization from Prefect workflow to reduce memory usage

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Pin numba<0.63 to fix pynndescent compatibility issue

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Update uv.lock for numba version constraint

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Add execution logging to Prefect workflow

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Disable numba JIT to fix Prefect/pynndescent compatibility

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Pre-warm numba before Prefect import to fix JIT compatibility

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Set NUMBA_CAPTURED_ERRORS=old_style to fix pynndescent print issue

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set log_prints=False to fix numba issue
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Commits on Dec 23, 2025

Commits on Dec 24, 2025