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validate_alignments removes sequences that are left with no residues after trimming, and logged each removal by looking the hash up in dict_hash_id. That dictionary is initialized empty and never populated, so the lookup always raised KeyError and killed the run at the very end of alignment validation. The branch only became reachable in 6d151a8, which fixed the membership test that had silently guarded it (a hash string was compared against a list of Funinfo objects, so it was never true). Take the id from the Funinfo being removed instead of any dictionary, and add regression tests covering the removal, the warning text, the rewritten trimmed alignment, and the untouched-alignment case. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EZTJs2CAFcHw9Ye4k7p9Mx
hasher.decode opened both the hashed input and the decoded output with the platform default encoding. On a cp949 (Korean) Windows console, any non-ASCII character in a sequence name, such as an accented author name, raised UnicodeEncodeError while writing, so decoding trees, SVGs and alignments crashed the run. CI never saw it because Linux and macOS default to UTF-8. Pin both ends to UTF-8, and read and write the test fixtures the same way so the round-trip test exercises the real contract on any locale. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EZTJs2CAFcHw9Ye4k7p9Mx
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EZTJs2CAFcHw9Ye4k7p9Mx
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