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# Python
__pycache__/
*.py[cod]
*.pyd
*.so
.pytest_cache/
.mypy_cache/
.ruff_cache/
*.egg-info/
build/
dist/
# Jupyter
.ipynb_checkpoints/
# IDE / Editor
.idea/
.vscode/
.serena/
# Logs / outputs
logs/
*.log
outputs/
# Model checkpoints
checkpoints/
*.pth
*.pt
*.ckpt
*.pkl
# Large scientific data (recommend external hosting)
*.h5
*.hdf5
*.mzML
*.mzml
# OpenMemory - IDE/Assistant specific rules
.windsurf/rules/openmemory.md
webserver/PLAN.md
webserver/README.md
webserver/start.sh
webserver/backend/app.py
webserver/backend/config.py
webserver/backend/ion_labels.py
webserver/backend/job_manager.py
webserver/backend/predictor.py
webserver/backend/requirements.txt
webserver/backend/schemas.py
webserver/backend/spectrum_render.py
webserver/backend/jobs/0ce364d8/input.csv
webserver/backend/jobs/239ff1df/input.csv
webserver/backend/jobs/26cad4dc/input.csv
webserver/backend/jobs/452195d0/input.csv
webserver/backend/jobs/64928c48/input.csv
webserver/backend/jobs/72d177f0/input.csv
webserver/backend/jobs/86e88f74/input.csv
webserver/backend/jobs/afae31d4/input.csv
webserver/backend/jobs/b5db3bc8/input.csv
webserver/backend/jobs/d8015faf/input.csv
webserver/backend/jobs/e6b4ebcd/input.csv
webserver/backend/jobs/edc293cc/input.csv
webserver/frontend/.gitignore
webserver/frontend/eslint.config.js
webserver/frontend/index.html
webserver/frontend/package-lock.json
webserver/frontend/package.json
webserver/frontend/playwright.config.ts
webserver/frontend/README.md
webserver/frontend/tsconfig.app.json
webserver/frontend/tsconfig.json
webserver/frontend/tsconfig.node.json
webserver/frontend/vite.config.ts
webserver/frontend/public/vite.svg
webserver/frontend/src/api.ts
webserver/frontend/src/App.tsx
webserver/frontend/src/index.css
webserver/frontend/src/main.tsx
webserver/frontend/src/ToastContext.tsx
webserver/frontend/src/assets/react.svg
webserver/frontend/src/components/BatchMode.tsx
webserver/frontend/src/components/CsvUpload.tsx
webserver/frontend/src/components/Header.tsx
webserver/frontend/src/components/IonTable.tsx
webserver/frontend/src/components/JobHistory.tsx
webserver/frontend/src/components/JobStatus.tsx
webserver/frontend/src/components/PeptideForm.tsx
webserver/frontend/src/components/PixelToast.tsx
webserver/frontend/src/components/SingleMode.tsx
webserver/frontend/src/components/SpectrumImage.tsx
webserver/frontend/src/lib/utils.ts
webserver/frontend/test-results/.last-run.json
webserver/frontend/tests/api-health.spec.ts
webserver/frontend/tests/batch-mode.spec.ts
webserver/frontend/tests/single-mode.spec.ts
webserver/frontend/tests/fixtures/invalid_columns.csv
webserver/frontend/tests/fixtures/valid_3rows.csv
webserver/frontend/tests/fixtures/valid_20rows.csv
webserver/frontend/tests/pages/BatchModePage.ts
webserver/frontend/tests/pages/SingleModePage.ts
openmemory.md
.serena/memories/github_push_dns_check_2026_02_15.md
.serena/memories/github_remote_compare_and_pushability_2026_02_15.md
.serena/memories/ms2int_skill_prod_refactor_2026_02_16.md
.serena/memories/py_prod_refactor_skill_2026_02_16.md
.serena/memories/readme_replace_flr_with_rescore_2026_02_17.md
.serena/memories/rename_train_data_arg_2026_02_17.md
.serena/memories/set_default_push_to_github_main_2026_02_15.md
.serena/memories/spectrum_processing_run_output_param_2026_02_17.md
.serena/memories/spectrum_processing_unmodified_merge_phospho_mode_2026_02_16.md
.serena/memories/unified_filter_U_and_final_h5_explicit_2026_02_17.md
.gitignore
.gitignore
data/rescore/1.msms_filtered_unmodified_lenle30.txt
data/rescore/msms_specid.tsv
data/rescore/mokapot/mokapot.peptides.txt
data/rescore/mokapot/mokapot.psms.txt
bkp/phosphorylation/0.filter_msms_30_phospho.py
bkp/phosphorylation/1.make_msms_specid.py
bkp/phosphorylation/run.py
bkp/phosphorylation/step1_create_msms_search_file.py
bkp/phosphorylation/step2_process_df_h5.py
bkp/phosphorylation/step3_generate_train_data.py
bkp/phosphorylation/step4_merge_final_data.py
.serena/project.yml