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Sync with template (4aa6051) - #141
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# Conflicts: # settings.json
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* Local runs: a killed workflow no longer shows as running A run whose process was killed (the app force-closed) left its pid files behind, so the Run page showed it as running forever and Start did nothing. get_workflow_status now removes the pid files of processes that are gone (psutil, with a check for reused pids) and says in the log that the run was interrupted. Online the pid files belong to a queue worker and are left alone. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGemGMkNWksd4J4wfeiw * PR media Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGemGMkNWksd4J4wfeiw * Remove PR media Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGemGMkNWksd4J4wfeiw --------- Co-authored-by: Claude <noreply@anthropic.com>
…it with (#560) * CLAUDE.md: rules for agents on where a change goes and what to build it with Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGeoPCJhBPK4Moxhwjkg * CLAUDE.md: app dependencies, exact openms-insight pin Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGeoPCJhBPK4Moxhwjkg --------- Co-authored-by: Claude <noreply@anthropic.com>
Between a tool's exit and wait() the process is a zombie, and the Run page's status check (pid_files.reap) removes the pid file of a zombie. run_command() then raised FileNotFoundError on its own unlink and the workflow failed although the tool had succeeded. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGekq5UCb6U4f2bXigdC
On macOS and Linux the desktop app reads Thermo .raw files with OpenMS's built-in reader (share/OpenMS/openms_thermo_bridge) on a bundled .NET runtime instead of ThermoRawFileParser. The About dialog now shows the RawFileReader notice for that reader too, lists it under Programs, and lists the .NET runtime (DOTNET_ROOT) with its license and notices under Libraries. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGenTCt1fet8pkp5v8T2
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGenTCt1fet8pkp5v8T2
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGenTCt1fet8pkp5v8T2
…mo-reader About dialog: list OpenMS's built-in Thermo reader and the .NET runtime
Local runs: a tool's pid file removed by the status check no longer fails the workflow
The full images include RawFileReader in /thirdparty/ThermoRawFileParser. Put Thermo's notice and terms next to its THERMO_LICENSE as NOTICE.txt, so the About dialog lists it, and print it when the container starts. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGenTCt1fet8pkp5v8T2
…er-thermo Ship Thermo's RawFileReader notice in the full Docker images
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FkEGenTCt1fet8pkp5v8T2
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Requested by Tom · project thread
Merges streamlit-template main (4aa6051) into this app. Among the changes:
NOTICE.txtnext toTHERMO_LICENSE, listed in the About dialog and printed at container start (Ship Thermo's RawFileReader notice in the full Docker images streamlit-template#570).Conflicts were resolved by keeping files this app removed or owns. Merge with a merge commit, not squash.
https://claude.ai/code/session_01FkEGenTCt1fet8pkp5v8T2
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