Add the C# implementation of MARS, and read Thermo, Bruker and Sciex directly - #9

Merged

maccoss merged 51 commits into

mainfrom

feature/dotnet-port

Aug 24, 2026

Commits on Aug 20, 2026

fix: report the installed package version from mars.__version__

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62904b6
feat: add a C# implementation of MARS targeting .NET 8 and .NET 10

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0599105
fix: keep vendored Osprey.ML sources untranslated so the drift guard works on Linux

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ce4bae2
ci: build, test, package and release the .NET implementation

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c2f8054
docs: make the README .NET-first and add a docs folder

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4c31850
docs: add a release-notes process with separate Python and .NET tracks

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207a231
feat: add --dump-matches and the scripts to difference it against the Python matcher

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4250f81
test: verify the C# matcher against the Python one row by row, and fix two CI breaks

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279b4e7
docs: record --dump-matches and the parity result in the .NET release notes

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b02bb7e

Commits on Aug 21, 2026

release: adopt CalVer v26.1.0 as the single release track and retire the Python release

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deae72e
feat: write the QC figures as a single self-contained HTML report

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c683d1d
docs: document the algorithms, the CLI, the model and how the code fits together

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7fd6c3b
feat: give mars qc the same figures, minus the ones that need a model

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389a14e
docs: note mars qc figures in the release notes

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e43b3f1
feat: cross-validate by peptide, and make the reported accuracy the honest one

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4a3b04b
feat: show cross-validation variance in the reports, and verify determinism on real data

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517de26
feat: merge cross-validation folds into one model, exactly

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04cbcd7
feat: merge the folds into one model and remove refit

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23283f8
docs: correct the --cv-folds help text for the merged model

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310e04f
feat: fit the correction model to all the data, and report both numbers

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91f4f8e
feat: refit without the rows the first pass could not explain

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3ffe594
feat: robust second pass, with trim as the default because Huber measured worse

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d46588c
test: verify the port on Orbitrap Astral data, and soften the Huber conclusion

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3d49694
feat: report ppm alongside Th, and rebuild the heatmap as a shared-scale pair

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896d130
feat: viridis density panels, readable labels, larger type

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cfee65a
feat: detect the mass analyzer and configure MARS for it

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35514d3
fix: stop mars verify destroying its input, and collect only what qc reads

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5c51a9b
docs: measure pwiz-sharp's Thermo reader against a real Astral raw

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bcf3f4f
docs: pwiz writer reproduces the byte-splice output exactly

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fed13cb
feat: write mzXML, mzMLb and mgf through pwiz

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a2e9b56
feat: read Thermo .raw directly, and write mzML or mzMLb from it

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92510a7

Commits on Aug 22, 2026

perf: parallelize the pwiz write, and pin the invariant culture

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d6220cc
build: publish a self-contained executable that reads vendor RAW

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8810149
feat: read Bruker and Sciex, and honour the scan-time unit

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46b42c7
feat: use injection time as a feature only when it varies

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e2d8ed3
docs: MARS sees timsTOF data as ~900 spectra per retention time

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4b0562f
feat: collapse the TIMS mobility dimension rather than modelling it

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b90d0bc
docs: bring the README, architecture and release notes up to date

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b8bbe8f
test: pin the scan-time unit and the pwiz batching

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0bcb605
ci: pin pwiz-sharp, build vendor support in CI and in releases

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8e13c2c
fix: register vendor readers from a static constructor, not a module initializer

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ce2c83b
docs: record that MARS ships the vendor SDKs, and when that changes

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1483211
docs: record how to find Skyline's install, verified against the one here

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16fedea
docs: prefer Skyline-daily, but check whichever SDK is found

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1ab25e2

Commits on Aug 23, 2026

docs: correct the Skyline discovery recipe against a real install

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3d89a4c
fix: --resolution was rejected as a typo, and warn on an over-wide tolerance

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d781f9c
feat: centroid profile spectra with the vendor's own algorithm

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73fc2e5
fix: keep the ion-population features when the injection time looks flat

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de1e286
fix: act on the Copilot review, and a dead temperature warning it pointed at

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0a1d327
docs: consolidate the release notes into one v26.1.0 file

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763eb2d
fix: path case, ppm array lengths, PNG dimensions, and a build command that cannot work

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0e8b241