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sander-willems-bruker merged 110 commits intomainMannLabs/timsrust:mainfrom developMannLabs/timsrust:developCopy head branch name to clipboardJul 8, 2024

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Commits

Commits on Apr 5, 2024

• CHORE: version update to 0.2.5

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  c9e31f9

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• Merge branch 'main' into develop

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Commits on Apr 8, 2024

• CHORE: refactored converters to be more explicit

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• CHORE: grouped ms data together

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  8c39a9e

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• CHORE: renamed modules

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• CHORE: renamed vec_utils

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• FEAT: crude mgf writer implementation

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Commits on Apr 9, 2024

• CHORE: unified converter setup

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• CHORE: version update bigger than patch

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Commits on Apr 11, 2024

• CHORE: cleaned up precursor and frame structs in favor of simplicity

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Commits on Apr 12, 2024

• FEAT: Updated frames with ms info and quad settings

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Commits on Apr 23, 2024

• CHORE: partial move of writers to io

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• CHORE: move of tdf_blobs

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• DOCS: updated package to work in modules rather than forwrding structs

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Commits on Apr 26, 2024

• CHORE: rustfmt now has width 100

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• CHORE: undo rustfmt

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  cbbb37a

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• FEAT: new sql reader module

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• FIX: simplfy rt reading of precursors

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  48d18f8

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• FEAT: use new sql reader format to read frames

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  34f5ae6

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• FEAT: update TdfBlob with error handling and option to use non indexed reader

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• FEAT: included sql readers in io::common

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  4ed4557

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• FEAT: removed unused frame table

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  544cf6d

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• CHORE fully deprecated ms_data_blobs module in favor of TdfBlobs

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• FEAT: created new frame_reader module

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• CHORE: remove unused sql frame table

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• FEAT: exposed frame reader to crate

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  c2aada8

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• FEAT: updated TdfReader to use frameReader instead

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Commits on Apr 30, 2024

• CHORE: updated benchmarks

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Commits on Jun 14, 2024

• DOCS: typo

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  3032d6d

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• FIX: reading of acquisition software

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  abf3744

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• FEAT: cleaner reading of frames

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  e2a145f

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• FEAT: using iterator to read frames

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  d4de769

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• FEAT: updated frame reader

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  ded22c1

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• FEAT: github workflow update

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  9e4f050

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• FEAT: added intensity factors to frames

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  01555f9

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• FEAT: added rt converter to tdf reader and metada

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  1f221c3

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• CHORE: added type annotations to tdfblobs

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  22448c0

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• FEAT: cleaned up code

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  80c47fb

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• FEAT: removed old tdf and frame reader

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  0ae839d

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• CHORE: renamed io:common to io:file_readers

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  72217a9

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• FEAT: reformatted sql precursors

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  87a0b98

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• CHORE: refactored pasefmsmsframes

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  1b817de

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• CHORE: cargo fmt

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  17d2cf8

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• CHORE: simplificaiton of precursor reader

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  3b8a4ed

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• FIX: diaPASEF type typo

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Commits on Jun 24, 2024

• FIX: unified MsLevel parsing

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• FEAT: added metadata

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  ac6a23d

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• CHORE: updated sqlreadable trait name to ReadableSqlTable

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• FEAT: added hashmap reader for sql

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• FEAT: reamoved option to get connection from sqlreader

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• FEAT: make sqlhashmap propagate error

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  6f4f2a8

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• FEAT: implemented metadata reader

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  4e0e387

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• FEAT: fully refactored sql reader to use metadata struct

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• FIX: remove lingering module that was refactored

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  1eb57f9

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• FEAT: renamed tdf blobs to refelect reader

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  cee2b42

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• FEAT: refactored precursor reader in the new io structure

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• CHORE: cleaned tdf blob reader

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  d81d93f

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• FEAT: simplifying spectrum readers

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  4d0d7ca

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• FEAT: simplied old file reader for easier refactoring

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Commits on Jun 25, 2024

• DOCS: cleaned up io

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• CHORE: implemented MGFEntry as struct rather than impl for spectrum

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  e43da82

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• FIX: typos

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  7ec524b

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• FEAT: cleaner mgf writing

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  3faadc8

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• FIX: typo

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  7465040

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• FEAT: updated parquet reader

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  73dfbdc

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• FEAT: updated metadata path and precursor reader

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  4a25da9

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• FEAT: updated minitdf reader to muse precursor reader properly

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  0389075

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• CHORE: cleaned up minitdf spectrum reader

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  b98b5ab

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• CHORE: formatting of code

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  45e37d1

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• FEAT: added dummy code to start refactoring spectrum readers

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  5717c6d

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• CHORE: changed visibility of sub readers

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  5db16b3

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• CHORE: formatting

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  dd768d3

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• CHORE: simplify parquet table reading

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Commits on Jun 26, 2024

• FEATL simplifying frame reader

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  76f6f9b

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• FEAT: fully refactored minitdf spectrum reader

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  e806627

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• FEAT: made extension finder more generic

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  308b891

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• FEAT: started on refactoring of TDFSpectrumReader

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  1558d0c

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• CHORE: unify path reading functions

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Commits on Jul 1, 2024

• FIX: properly process empty frames

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Commits on Jul 3, 2024

• CHORE: simplification of vec utils filter with mask

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  da15c25

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• FEAT: added reading of frame groups and quad settings to sql reader

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• CHORE: udated quad settings types

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  cd47e8a

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• FEAT: added frame_group to frames

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• PERF: removed inline from tdf blobs to let compiler decide

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• DOCS: Updated file readerd docs and removed always calibrate option

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  7d7e40d

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• FEAT: Added quad setting (dia) data to frame reader

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  a0e6427

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• FEAT: reformatted spectrum reader (still not done)

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  9371c8e

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• FIX: read im values from file rather than hardcoded

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  668d74e

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• FIX: remove print from metadata

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  0ddd915

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• FEAT: added CE to spectrum rather than precursor

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  bdb7eed

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• FEAT: explicit intensity reader in frame for ICC data

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  bff0a73

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• CHORE: technical fix of tdf blob reader without effect

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  6d8ab0e

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• CHORE: simplified spectral ordering

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  2207459

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• FEAT: added timscompressiontype to metadata

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  149cfab

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• CHORE: made todos for refactoring

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  40a39f4

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• CHORE: made todo for refactoring

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  5405b67

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• CHORE: refactored tdf spectrum reader

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  a27e455

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• FEAT: added isolation width and mz to spectra

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  ccd8e3a

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• FEAT: renamed raw spextrum reader

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  c22682a

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• CHORE set reminders to update error handling ands docs

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  14783d9

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• DEBUG: updated main to move out of timsrust

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Commits on Jul 4, 2024

• CHORE: added todo to refactor frame reader

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  f1b31b7

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Commits on Jul 5, 2024

• FEAT: implemented a dia spectrum reader

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  d49ba77

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• FEAT: made proper quad_settings_reader that can be recycled

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  cd29750

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• FEAT: implemente None option for precursor charge and intensity

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  0eb51dd

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• FEAT: removed manual testing main in favor of showing timsrust is a library rather than executable

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  3b0636e

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• FEAT: option to filter spectra by top n peaks

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  2a6ff12

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• FIX: top_n for small values

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Commits on Jul 8, 2024

• FIX: implementation to take isoalation width and mz into account for minitdf. This is quite generix and could/should update in the future

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• FIX: failing tests

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