25194613229
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Ran 30 Apr 2026 11:35PM UTC

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Files 27

Run time 1min

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Committed 30 Apr 2026 11:34PM UTC coverage: 70.924% (+0.02%) from 70.9%

Build # 25194613229

Build Type

push

github

Committed by

web-flow

Commit Message

v1.30.21: Replace generate_observations_table merges with MultiIndex.reindex (#30) (#208)

The two ``obs.merge(...)`` calls (allele-level + single-sample fallback)
were dominated by pandas' block-manager consolidation pass on the
4.3M-row x ~50-col obs DataFrame. cProfile breakdown:

- _merge_blocks         ~6s
- numpy ndarray.copy    ~4s (driven by merge concat)
- _consolidate_inplace  ~7s

Both joins are simple lookups -- one against (pmid, allele), one
against pmid alone. Replacing them with ``set_index(...)[meta_cols]``
+ ``MultiIndex.reindex(obs_keys)`` skips the consolidation pass
entirely (the in-place column assignment doesn't trigger block
re-layout) and is functionally identical.

Wall-clock on the local 4.3M-row index:
- before: 29.4s warm
- after:  19.7s warm  (~1.5x faster, ~10s saved)

Match-type distribution unchanged (allele 1.46M, pool 1.36M,
fallback 484K, unmatched 996K -- byte-identical to v1.30.20).

Drive-by: keep the batched str-meta-cols fillna from earlier draft
of #30. Tiny win on its own but the block-wise variant is cleaner
than the per-column loop.

Closes #30 (well past the 3-4x estimate -- the v1.29.4 merges-to-map
optimizations had already absorbed most of that).

Coverage Stats

3676 of 5183 relevant lines covered (70.92%)

0.71 hits per line

Coverage Regressions

Lines	Coverage	∆	File
90	81.42	-0.11%	export.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	25194613229.1	30 Apr 2026 11:35PM UTC	27	70.92	GitHub Action Run

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