Fix production #25

t0mdavid-m · 2025-05-25T19:06:19Z

Summary by CodeRabbit

Chores
- Updated application version to 0.8.3 in relevant configuration and workflow files.
Data Updates
- Added new mass spectrometry data and configuration files for recent analyses.
- Removed outdated or superseded data and parameter files.
- Updated configuration files with revised parameters, including expanded ion types and adjusted tolerance values.

coderabbitai · 2025-05-25T19:06:28Z

Caution

Review failed

The pull request is closed.

Walkthrough

This update increments the application version from 0.8.2 to 0.8.3 in both the build workflow and settings. It replaces and refreshes example data and configuration files across multiple workspaces, reflecting updated parameters, feature data, and spectrum files for mass spectrometry workflows, while removing outdated cached files.

Changes

Files/Paths	Change Summary
.github/workflows/build-windows-executable-app.yaml, settings.json	Updated version from 0.8.2 to 0.8.3 in workflow and settings.
example-data/workspaces/default/flashdeconv/cache/files/example_fd/toppic_ms1.feature, example-data/workspaces/default/flashdeconv/cache/files/example_fd/toppic_ms2.feature	Deleted old feature data files.
example-data/workspaces/default/flashdeconv/cache/files/example_fd_20250525-204033/toppic_ms1.feature, example-data/workspaces/default/flashdeconv/cache/files/example_fd_20250525-204033/toppic_ms2.feature, example-data/workspaces/default/flashdeconv/cache/files/example_fd_20250525-204033/FD_parameters.json	Added new feature and parameter files for updated cache.
example-data/workspaces/default/flashdeconv/params.json	Updated input file paths, lowered tolerance, added FDR reporting.
example-data/workspaces/default/flashtnt/params.json	Updated input files, tolerance, max charge, ion types, and tag minimum length in configuration.
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody/FD_parameters.json, example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody/FTnT_parameters.json, example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody/out_deconv.mzML, example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody/toppic_ms2.msalign	Deleted old parameter, msalign, and spectrum files from cache.
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/FTnT_parameters.json, example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/toppic_ms2.msalign	Added new FTnT parameters and msalign files to cache.
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_aqpz_20250525-203956/FTnT_parameters.json	Added new FTnT parameters file for spectrum aqpz.
example-data/workspaces/demo_antibody/flashtnt/cache/files/example_spectrum_antibody_20250525-100107/FTnT_parameters.json	Deleted old FTnT parameters file.
example-data/workspaces/demo_antibody/flashtnt/cache/files/example_spectrum_antibody_20250525-204250/FD_parameters.json, example-data/workspaces/demo_antibody/flashtnt/cache/files/example_spectrum_antibody_20250525-204250/FTnT_parameters.json, example-data/workspaces/demo_antibody/flashtnt/cache/files/example_spectrum_antibody_20250525-204250/out_deconv.mzML	Added new FD/FTnT parameter and spectrum files for updated cache.
example-data/workspaces/demo_antibody/flashtnt/params.json	Expanded ion types in FLASHTnT configuration.
example-data/workspaces/demo_aqpz/flashdeconv/cache/files/example_spectrum_aqpz_20250525-092833/FD_parameters.json, example-data/workspaces/demo_aqpz/flashtnt/cache/files/example_spectrum_aqpz_20250525-092909/FTnT_parameters.json	Deleted old FD and FTnT parameter files from demo_aqpz.

Possibly related PRs

OpenMS/FLASHApp#18: Updates the APP_NAME environment variable in the Windows build workflow, directly modifying the same workflow setting as this PR.
OpenMS/FLASHApp#24: Previously updated the version string in the Windows build workflow and settings file, indicating a direct continuation of version bump changes.
OpenMS/FLASHApp#21: Also updates the Windows build workflow's version, showing a related pattern of version management in the workflow files.

Poem

🐇
A hop from two to three, the version’s grown anew,
With data files refreshed and settings shining through.
Old caches swept away, new spectra in their place,
The rabbit leaps ahead—another version race!
🎉

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 5b1aafd and 0986925.

⛔ Files ignored due to path filters (98)

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📒 Files selected for processing (23)

.github/workflows/build-windows-executable-app.yaml (1 hunks)
example-data/workspaces/default/flashdeconv/cache/files/example_fd/toppic_ms1.feature (0 hunks)
example-data/workspaces/default/flashdeconv/cache/files/example_fd/toppic_ms2.feature (0 hunks)
example-data/workspaces/default/flashdeconv/cache/files/example_fd_20250525-204033/FD_parameters.json (1 hunks)
example-data/workspaces/default/flashdeconv/cache/files/example_fd_20250525-204033/toppic_ms1.feature (1 hunks)
example-data/workspaces/default/flashdeconv/cache/files/example_fd_20250525-204033/toppic_ms2.feature (1 hunks)
example-data/workspaces/default/flashdeconv/params.json (1 hunks)
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody/FD_parameters.json (0 hunks)
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody/FTnT_parameters.json (0 hunks)
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody/out_deconv.mzML (0 hunks)
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody/toppic_ms2.msalign (0 hunks)
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/FTnT_parameters.json (1 hunks)
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/toppic_ms2.msalign (1 hunks)
example-data/workspaces/default/flashtnt/cache/files/example_spectrum_aqpz_20250525-203956/FTnT_parameters.json (1 hunks)
example-data/workspaces/default/flashtnt/params.json (1 hunks)
example-data/workspaces/demo_antibody/flashtnt/cache/files/example_spectrum_antibody_20250525-100107/FTnT_parameters.json (0 hunks)
example-data/workspaces/demo_antibody/flashtnt/cache/files/example_spectrum_antibody_20250525-204250/FD_parameters.json (1 hunks)
example-data/workspaces/demo_antibody/flashtnt/cache/files/example_spectrum_antibody_20250525-204250/FTnT_parameters.json (1 hunks)
example-data/workspaces/demo_antibody/flashtnt/cache/files/example_spectrum_antibody_20250525-204250/out_deconv.mzML (1 hunks)
example-data/workspaces/demo_antibody/flashtnt/params.json (1 hunks)
example-data/workspaces/demo_aqpz/flashdeconv/cache/files/example_spectrum_aqpz_20250525-092833/FD_parameters.json (0 hunks)
example-data/workspaces/demo_aqpz/flashtnt/cache/files/example_spectrum_aqpz_20250525-092909/FTnT_parameters.json (0 hunks)
settings.json (1 hunks)

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t0mdavid-m added 12 commits May 25, 2025 12:32

update vue

904ed09

Merge branch 'develop' of github.com:OpenMS/FLASHApp into develop

c26950b

only store relevant file path

5b1ba3b

update example database entries

c0846db

bump version

7f6a05d

fix file references

808a4ce

log errors

ed5f9a5

fix workflow running on platforms other than linux

58c648f

Merge remote-tracking branch 'openms/develop' into fix_production

7771eb5

update example data

b9826b5

bump version

419e99f

Merge remote-tracking branch 'openms/develop' into fix_production

0986925

t0mdavid-m merged commit 70c8eba into develop May 25, 2025
3 of 4 checks passed

coderabbitai bot mentioned this pull request Jun 1, 2025

Make zip cross-os compatible #27

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Fix production #25

Fix production #25

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t0mdavid-m commented May 25, 2025 •

edited by coderabbitai bot

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Fix production #25

Fix production #25

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t0mdavid-m commented May 25, 2025 • edited by coderabbitai bot Loading Uh oh! There was an error while loading. Please reload this page.

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coderabbitai bot commented May 25, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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t0mdavid-m commented May 25, 2025 •

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coderabbitai bot commented May 25, 2025 •

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