Fix #1308: Scope dask.config.set() to specific operations instead of module import#1309
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khushthecoder wants to merge 3 commits intomalariagen:masterfrom
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Fix #1308: Scope dask.config.set() to specific operations instead of module import#1309khushthecoder wants to merge 3 commits intomalariagen:masterfrom
khushthecoder wants to merge 3 commits intomalariagen:masterfrom
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April 17, 2026 22:06
…nstead of module import Move the `split_native_chunks` config override from module-level in ag3.py to context managers within the specific methods that require it. This prevents importing malariagen_data from silently modifying global dask configuration, which could degrade performance for unrelated dask workloads in the same Python session. Affected operations: - util._da_compress(): wraps da.compress() call - snp_data.snp_genotypes(): wraps da.compress() and da.take() calls - snp_data._locate_site_class(): wraps da.take() call
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Summary
Fixes #1308
ag3.pyline 10 executesdask.config.set(**{"array.slicing.split_native_chunks": False})at module import time, which silently disables a dask performance optimization globally for the entire Python process — not justmalariagen_dataoperations.This PR scopes the config override to context managers (
with dask.config.set(...)) within the specific methods that require it, so the config is restored immediately after each operation completes.Changes
malariagen_data/ag3.py: Removed the module-leveldask.config.set()call and the now-unusedimport dask.malariagen_data/util.py: Added scopeddask.config.set()context manager aroundda.compress()in_da_compress().malariagen_data/anoph/snp_data.py: Added scopeddask.config.set()context managers around:da.compress()insnp_genotypes()(sample filtering)da.take()insnp_genotypes()(sample indexing)da.take()in_locate_site_class()(site annotation subsetting)Why This Matters
import malariagen_datano longer modifies global dask configuration.malariagen_datawith other dask tools won't see unexplained behavior changes.Related: #1305 (same class of issue — global state mutation that leaks beyond
malariagen_data's scope)Test Plan
ruff checkpasses on all changed filesruff formatpasses on all changed filesimport malariagen_datano longer modifiesdask.config