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[FEATURE] PHIBF - #596

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smehringer wants to merge 8 commits into
seqan:mainfrom
smehringer:phibf_rebased
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smehringer wants to merge 8 commits into
seqan:mainfrom
smehringer:phibf_rebased

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@smehringer

@smehringer smehringer commented Oct 16, 2026 •

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@smehringer smehringer mentioned this pull request Oct 16, 2026
@seqan-actions seqan-actions added lint [INTERNAL] used for linting and removed lint [INTERNAL] used for linting labels Oct 16, 2026
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Documentation preview available at https://docs.seqan.de/preview/seqan/raptor/596

@seqan-actions seqan-actions added the lint [INTERNAL] used for linting label Oct 20, 2026
@seqan-actions seqan-actions removed the lint [INTERNAL] used for linting label Oct 20, 2026
@eseiler
eseiler self-requested a review October 26, 2026 12:33
@seqan-actions seqan-actions added lint [INTERNAL] used for linting and removed lint [INTERNAL] used for linting labels Oct 26, 2026
@seqan-actions seqan-actions added lint [INTERNAL] used for linting and removed lint [INTERNAL] used for linting labels Oct 26, 2026
eseiler and others added 2 commits October 26, 2026 19:16
…_test

icpx 2025.0 (and Clang 19) crash in SemaOpenMP::isOpenMPCapturedDecl when a function references a
namespace-scope structured binding while OpenMP is enabled, which hibf always does. Make the user
bins and the queries static members of the fixture; the queries become a small struct.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
search_partitioned_hibf wrote the timings after every part, even without --timing-output. The wall
clock timer is still running at that point, so its in_seconds() is 0 and cpu_usage_in_percent fails
`assert(elapsed_time_in_seconds > 0.0)` in Debug builds. Timings are now written only at the end, by
search_parsing.cpp when --timing-output is set; the timers are no longer reset between parts and
report totals over all parts.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@seqan-actions seqan-actions added lint [INTERNAL] used for linting and removed lint [INTERNAL] used for linting labels Oct 26, 2026
@eseiler

eseiler commented Oct 26, 2026

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I changed CPM to use your chopper branch and the hibf lib with the wyhash merge.
There is also a fix commit for an ICE on Intel. Another fix is for writing timing-files multiple times, which asserted in Debug. timing-files are handled "globally" in the caller (search_parsing).

@seqan-actions seqan-actions added lint [INTERNAL] used for linting and removed lint [INTERNAL] used for linting labels Oct 26, 2026
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codecov Bot commented Oct 26, 2026 •

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Codecov Report

❌ Patch coverage is 97.58065% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.18%. Comparing base (7367782) to head (db146bf).

Files with missing lines Patch % Lines
src/build/build_hibf.cpp 89.65% 3 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #596      +/-   ##
==========================================
+ Coverage   96.16%   96.18%   +0.02%     
==========================================
  Files          68       69       +1     
  Lines        2657     2750      +93     
  Branches       53       56       +3     
==========================================
+ Hits         2555     2645      +90     
- Misses        102      105       +3     
Flag Coverage Δ
experimental 80.11% <ø> (ø)
stable 99.77% <97.58%> (-0.13%) ⬇️

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3 participants