Prepare Workshop #45

t0mdavid-m · 2025-08-23T13:41:37Z

This PR adds the example data for the TDP Symposium 2025 Workshop.

Summary by CodeRabbit

New Features
- Added ready-to-run workshop sample data and presets for FLASHDeconv and FLASHTnT, including example parameters, feature tables, and deconvolved spectra to help users explore workflows without setup.
- Included configuration templates (.ini and JSON) to simplify tuning tolerances, charges, ion types, and FDR options.
Chores
- Bumped app version to 0.9.6.
- Updated Windows installer naming to reflect the new version.

coderabbitai · 2025-08-23T13:41:47Z

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Review failed

The pull request is closed.

Walkthrough

Bumps app/version identifiers to 0.9.6 and adds workshop example datasets and configurations for FLASHDeconv and FLASHTnT. New INI and JSON parameter files plus multiple cached feature and mzML artifacts are introduced under example-data/workspaces/workshop/*, without code or control-flow changes.

Changes

Cohort / File(s)	Change summary
CI/version bump `.github/workflows/build-windows-executable-app.yaml`, `settings.json`	Updated APP_NAME from FLASHApp-0.9.5 to FLASHApp-0.9.6 and settings.json version from 0.9.5 to 0.9.6.
Workshop configs (FLASHDeconv + FLASHTnT) `example-data/workspaces/workshop/flashdeconv/ini/FLASHDeconv.ini`, `example-data/workspaces/workshop/flashtnt/ini/FLASHDeconv.ini`, `example-data/workspaces/workshop/flashtnt/ini/FLASHTnT.ini`	Added OpenMS Param XML INI files defining full configuration schemas for FLASHDeconv and FLASHTnT.
Workshop params `example-data/workspaces/workshop/params.json`	Added workspace-level UI/config defaults (selected files, image format, intensity cutoff, dimensions, flag).
FLASHDeconv params `example-data/workspaces/workshop/flashdeconv/params.json`	Added JSON params for FLASHDeconv: mzML path, threads, SD:tol, FD:report_FDR.
FLASHTnT params `example-data/workspaces/workshop/flashtnt/params.json`	Added JSON params for FLASHTnT workflow: mzML/FASTA paths, threads, few_proteins, FLASHDeconv SD settings, FLASHTnT ion/tag/FDR settings.
FLASHDeconv cache (2025-05-25) `example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250525-204033/FD_parameters.json`, `.../toppic_ms1.feature`, `.../toppic_ms2.feature`	Added cached parameter JSON and TOPPIC MS1/MS2 feature tables for example_fd.mzML (205 MS1 features, 186 MS2 rows).
FLASHDeconv cache (2025-08-23) `example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250823-152120/FD_parameters.json`, `.../toppic_ms1.feature`, `.../toppic_ms2.feature`	Added cached parameter JSON and TOPPIC MS1/MS2 feature tables for example_fd.mzML (401 MS1 features, 191 MS2 data rows plus header).
FLASHTnT cache: example_fd (2025-08-23) `example-data/workspaces/workshop/flashtnt/cache/files/example_fd_20250823-151911/FD_parameters.json`, `.../FTnT_parameters.json`, `.../toppic_ms1.feature`, `.../toppic_ms2.feature`	Added SD and FTnT parameter JSONs; added TOPPIC MS1 (397 rows) and MS2 (188 rows) feature files for example_fd.mzML.
FLASHTnT cache: antibody (2025-05-25) `example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/FD_parameters.json`, `.../FTnT_parameters.json`, `.../out_deconv.mzML`, `.../toppic_ms2.feature`, `.../toppic_ms2.msalign`	Added SD/FTnT parameter JSONs; added deconvolved mzML, MS2 feature header, and msalign with one spectrum.
FLASHTnT cache: aqpz (2025-05-25) `example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_aqpz_20250525-203956/FD_parameters.json`, `.../FTnT_parameters.json`, `.../out_deconv.mzML`, `.../toppic_ms2.feature`, `.../toppic_ms2.msalign`	Added SD/FTnT parameter JSONs; added deconvolved mzML, MS2 feature header, and msalign with one spectrum.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

Fix openmp windows #41 — Similar version bump affecting APP_NAME in workflow and version in settings.json.
Fix production #24 — Updates the same CI workflow APP_NAME and release metadata alongside settings.json.
Fix sequence view #18 — Changes APP_NAME in the workflow and synchronizes settings.json version.

Poem

A whisk of versions—0.9.6 anew,
I thump my paws on data’s dew.
INIs bloom, JSONs align,
Features march in tidy line.
mzML moons glow byte-bright night—
Hippity-hop, we cache it right! 🐇✨

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📥 Commits

Reviewing files that changed from the base of the PR and between 5f3afa0 and 6bfb55b.

⛔ Files ignored due to path filters (55)

example-data/workspaces/workshop/flashdeconv/cache/cache.db is excluded by !**/*.db
example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250525-204033/FD_parameters.pkl.gz is excluded by !**/*.gz
example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250525-204033/out.tsv is excluded by !**/*.tsv
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example-data/workspaces/workshop/flashtnt/logs/commands-and-run-times.log is excluded by !**/*.log
example-data/workspaces/workshop/flashtnt/logs/minimal.log is excluded by !**/*.log

📒 Files selected for processing (28)

.github/workflows/build-windows-executable-app.yaml (1 hunks)
example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250525-204033/FD_parameters.json (1 hunks)
example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250525-204033/toppic_ms1.feature (1 hunks)
example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250525-204033/toppic_ms2.feature (1 hunks)
example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250823-152120/FD_parameters.json (1 hunks)
example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250823-152120/toppic_ms1.feature (1 hunks)
example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250823-152120/toppic_ms2.feature (1 hunks)
example-data/workspaces/workshop/flashdeconv/ini/FLASHDeconv.ini (1 hunks)
example-data/workspaces/workshop/flashdeconv/params.json (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_fd_20250823-151911/FD_parameters.json (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_fd_20250823-151911/FTnT_parameters.json (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_fd_20250823-151911/toppic_ms1.feature (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_fd_20250823-151911/toppic_ms2.feature (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/FD_parameters.json (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/FTnT_parameters.json (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/out_deconv.mzML (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/toppic_ms2.feature (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/toppic_ms2.msalign (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_aqpz_20250525-203956/FD_parameters.json (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_aqpz_20250525-203956/FTnT_parameters.json (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_aqpz_20250525-203956/out_deconv.mzML (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_aqpz_20250525-203956/toppic_ms2.feature (1 hunks)
example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_aqpz_20250525-203956/toppic_ms2.msalign (1 hunks)
example-data/workspaces/workshop/flashtnt/ini/FLASHDeconv.ini (1 hunks)
example-data/workspaces/workshop/flashtnt/ini/FLASHTnT.ini (1 hunks)
example-data/workspaces/workshop/flashtnt/params.json (1 hunks)
example-data/workspaces/workshop/params.json (1 hunks)
settings.json (1 hunks)

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t0mdavid-m added 2 commits August 23, 2025 15:36

add workshop workspace

d4abe86

bump version number

6bfb55b

t0mdavid-m merged commit 2e66cc8 into develop Aug 23, 2025
3 of 4 checks passed

coderabbitai bot mentioned this pull request Dec 19, 2025

Native Parquet Output Support for OpenSwathWorkflow OpenMS/OpenMS#8533

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