sys.setrecursionlimit(10_000) in hapclust/dipclust Permanently Alters Global Python State

[kunal-10-cloud]

Description

Both hapclust.py:89 and dipclust.py:92 call sys.setrecursionlimit(10_000) as a side effect of plotting dendrograms, but never restore the original limit. This permanently modifies the global Python recursion limit for the entire process, affecting all subsequent code — not just malariagen_data.

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How to Reproduce

import sys
print(sys.getrecursionlimit())  # 1000 (default)
 
import malariagen_data
ag3 = malariagen_data.Ag3()
 
# Call any function that triggers hapclust or dipclust:
ag3.plot_haplotype_clustering(region="2L:28,545,000-28,550,000", analysis="gamb_colu")
 
print(sys.getrecursionlimit())  # 10000 — permanently changed!
 
# Now ALL code in this notebook/session uses the elevated limit,
# potentially masking stack overflow bugs in unrelated code.

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Why It Is Important

• Side-effect pollution: A plotting function should not permanently modify global interpreter state. Users working in long-running Jupyter sessions have no idea their recursion limit changed.
• Masks bugs: Legitimate RecursionError bugs in user code or other libraries will be silently suppressed because the limit is now 10x higher.
• Memory risk: A deeper call stack consumes more memory per thread. In environments with many threads (e.g., dask distributed workers), this compounds.

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Proposed Fix

The fix is trivial — wrap the recursion limit change in a try/finally block to restore the original limit:

# Before (current behaviour)
sys.setrecursionlimit(10_000)
# ... dendrogram computation ...
 
# After (proposed fix)
_original_limit = sys.getrecursionlimit()
try:
    sys.setrecursionlimit(10_000)
    # ... dendrogram computation ...
finally:
    sys.setrecursionlimit(_original_limit)

This pattern should be applied in both:

• hapclust.py line 89
• dipclust.py line 92

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Expected Impact After Resolution

The recursion limit is temporarily elevated only for the duration of the dendrogram computation and immediately restored afterward, eliminating global state pollution.

[kunal-10-cloud]

Hi @jonbrenas, i have raised a PR(#1306 ) against this issue, please look at it once whenever you are available
Please let me know if any changes are required