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Make generated structure writes collision-safe - #260

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Daniel Zügner (danielzuegner) merged 2 commits into
mainfrom
fix/issue-255-safe-output-writes
Aug 27, 2026
Merged

Make generated structure writes collision-safe#260
Daniel Zügner (danielzuegner) merged 2 commits into
mainfrom
fix/issue-255-safe-output-writes

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Summary

  • write generated CIF payloads directly into the ZIP archive instead of shared /tmp/gen_*.cif files
  • eliminate cross-run collisions and leaked temporary files
  • propagate structure and trajectory write failures so generation exits unsuccessfully instead of silently losing outputs
  • add regression coverage for archive contents and write errors

Fixes #255

Write CIF payloads directly into the output archive and propagate structure and trajectory write failures instead of silently returning success.\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>\nCopilot-Session: 6d151412-121a-41f5-a0ab-bd6a3614c96e
Comment thread mattergen/tests/test_output_writes.py Outdated
Address review feedback.\n\nCo-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>\nCopilot-Session: 6d151412-121a-41f5-a0ab-bd6a3614c96e
@danielzuegner
Daniel Zügner (danielzuegner) merged commit e7f89a5 into main Aug 27, 2026
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mattergen-generate writes temp CIFs to hard-coded /tmp and swallows write errors (silent missing outputs, cross-run collisions)

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