mascope-opentfraw 1.2.0__tar.gz

mascope_opentfraw-1.2.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [1.2.0] - 2026-06-17
+
+Karsa fork release, published to PyPI as `mascope-opentfraw` (imported as
+`opentfraw`). Bundles the additions and fixes below; each is also opened upstream
+as a pull request (see `NOTICE`). This release exists to make the features
+available ahead of an upstream release and will be retired once they land
+upstream.
+
+### Added
+
+- Per-peak FT label data decoding for PacketHeader scans. The previously
+  skipped descriptor / unknown / triplet streams are now decoded:
+  `ScanDataPacket` gains `resolutions` (per-peak resolution) and
+  `noise_nodes` (the noise-vs-m/z function), plus `noise_at(mz)` to
+  interpolate per-peak noise/baseline. New `RawFileReader::read_scan_labels`
+  reads peaks + labels while skipping the profile signal, and the Python
+  binding exposes `RawFile.centroid_labels(scan_number)` returning
+  `mz`/`intensity`/`resolution`/`noise`/`baseline`/`signal_to_noise` arrays.
+- `RawFile.profile(scan_number)` (Python): returns the raw profile spectrum as
+  `(mz, intensity)` NumPy arrays, converting the frequency-domain bins via the
+  scan event's calibration coefficients. The Rust core already decoded profile
+  data (`ScanDataPacket.profile`, `Profile::to_mz_intensity`); this exposes it to
+  Python, which previously surfaced centroids only.
+- `RawFile.scan_parameters(scan_number)` (Python): returns the per-scan generic
+  ("trailer") parameters as a `{label: value}` dict (or `None`), mirroring the
+  vendor reader's trailer-extra information. Keys are the instrument's own
+  labels (e.g. `"HCD Energy V:"`, `"MS2 Isolation Width:"`); values keep their
+  stored type. The Rust core already decoded these (`scan_parameters` /
+  `GenericRecord`); this surfaces them to Python.
+
+### Fixed
+
+- Orbitrap Exploris scan events: the frequency->m/z calibration coefficients
+  and the MS2 precursor m/z are now decoded. The nparam/coefficients block is
+  read immediately after the scan-window FractionCollector (offset 80 for the
+  offset-64 FC family) instead of a fixed `body_size - 64`, which missed it on
+  Exploris (body_size 136) and left the profile m/z mis-converted. Dependent
+  MS2 scans whose reaction record starts at body offset 4 (Exploris) now have
+  their precursor m/z and activation energy recovered. Q Exactive / Fusion
+  decoding is unchanged.
+
+## [1.1.0] - 2026-05-31
+
+### Added
+
+- `CITATION.cff`: author identity (Nathan Riley + ORCID) and a
+  scaffolded `identifiers:` block ready for the Zenodo concept DOI.
+- `CONTRIBUTING.md`.
+- Docusaurus build job in CI.
+
+### Changed
+
+- **Panic surface eliminated (WP17).** Parsers no longer call
+  `unwrap()` in production code: a new `bytes` helper module
+  (`read_u32/f64_le`) returns `Error::UnexpectedEof { offset,
+  needed }`, and a `find_map` closure now uses `.ok()?` to preserve
+  `Option`. Library crate carries
+  `#![cfg_attr(not(test), warn(clippy::unwrap_used,
+  clippy::expect_used))]`.
+- Manifest hygiene (WP13): `homepage` set to <https://sigilweaver.app>
+  and `documentation` link added.
+- README badge block unified across the Sigilweaver portfolio.
+
+## [1.0.6] - 2026-05-21
+
+### Changed
+
+- Depend on `openproteo-core = "1.0.0"` (was `0.1.0`, yanked).
+- MSRV bumped from 1.75 to 1.85 (tracks `openproteo-core 1.0.0`).
+
+## [1.0.5] - 2026-05-18
+
+### Changed
+
+- Depend on `openproteo-core = "0.1.0"` from crates.io (no source change;
+  workspace dependency now carries an explicit registry version so the
+  crate can be published).
+- `SECURITY.md` added; coordinated-disclosure contact documented.
+
+## [1.0.4] - 2026-05-17
+
+### Changed
+
+- Restructured to a Cargo workspace layout. The library crate is now at
+  `crates/opentfraw/` and the Python bindings crate at
+  `crates/opentfraw-py/`. The `pyproject.toml` is now at the repository
+  root. No public API changes.
+
+## [1.0.3] - 2026-05-17
+
+### Fixed
+
+- `python/pyproject.toml`: revert `readme` to `"README.md"` and restore
+  `python/README.md` stub. Maturin sdist packaging prohibits `..` in
+  archive paths, causing the 1.0.2 sdist build to fail on CI.
+
+## [1.0.2] - 2026-05-17
+
+### Changed
+
+- Docs and source comments: replace em-dashes, en-dashes, smart quotes,
+  and ellipsis characters with ASCII equivalents.
+
+## [1.0.1] - 2026-05-17
+
+### Changed
+
+- README: standardize structure and docs link format (consistent with
+  OpenTimsTDF and OpenWRaw).
+
+## [1.0.0] - 2026-05-17
+
+First stable release. The public API of `opentfraw` is now considered
+stable and will follow semantic versioning. Format coverage is unchanged
+from 0.1.0 (LTQ FT, Q Exactive HF, Orbitrap Fusion Lumos, Orbitrap
+Exploris 480, TSQ Vantage, TSQ Quantiva, TSQ Altis).
+
+### Added
+
+- `ATTRIBUTION.md` (replaces `CREDITS.md`): tracks third-party notices for
+  bundled data and vendored code.
+- `publish.yml` GitHub Actions workflow: publishes the `opentfraw` crate
+  to crates.io and the Python wheel to PyPI via OIDC Trusted Publishing
+  on every `v*` tag push.
+
+### Changed
+
+- CI migrated from WarpBuild runners to standard GitHub-hosted
+  (`ubuntu-latest`, `macos-latest`, `windows-latest`).
+- Removed the `tools/` vendor SDK tree and `corpus/mzml/` binary corpus
+  from repository history (git history rewritten; total size reduced from
+  ~1.5 GB to ~660 KB).
+- Removed "Pure-Rust" marketing language from `README.md` and related
+  documentation (Python bindings use PyO3/maturin which pulls in a C
+  compiler at build time).
+- Renamed `CREDITS.md` to `ATTRIBUTION.md`.
+
+## [0.1.0] - 2026-05-16
+
+### Added
+
+- Rust parser for the Thermo Fisher RAW mass spectrometry file
+  format, no native or system dependencies.
+- Reader API for top-level structures: `FileHeader`, `AuditTag`,
+  `SeqRow`, `InjectionData`, `ASInfo`, `RawFileInfo`, `InstID`,
+  `RunHeader`, `SampleInfo`.
+- Per-scan API: scan-index entries, packet headers, profile chunks,
+  centroid peaks, scan events, scan parameters (generic records).
+- Error log and instrument log decoders.
+- Robust instrument-model detection via byte scan.
+- Frequency-to-m/z conversion using the per-segment calibration table.
+- `examples/dump.rs`: dump the contents of a RAW file as plain text.
+- `examples/to_mzml.rs`: convert a RAW file to mzML (centroid or
+  profile; optionally indexed).
+- Validated against ProteoWizard `msconvert` mzML output for a
+  multi-instrument PRIDE corpus (LTQ FT, Q Exactive HF, Orbitrap
+  Fusion Lumos, Orbitrap Exploris 480, TSQ Vantage, TSQ Quantiva,
+  TSQ Altis).
+- Optional Python bindings (`opentfraw-py`, not published to crates.io).
+- Format specification under `docs/docs/format/`.
+
+### Out of scope
+
+- Methods file (`MethodFile`) deep parse beyond byte-level layout.
+
+[1.0.1]: https://github.com/Sigilweaver/OpenTFRaw/releases/tag/v1.0.1
+[1.0.0]: https://github.com/Sigilweaver/OpenTFRaw/releases/tag/v1.0.0
+[0.1.0]: https://github.com/Sigilweaver/OpenTFRaw/releases/tag/v0.1.0

mascope_opentfraw-1.2.0/Cargo.lock

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mascope_opentfraw-1.2.0/Cargo.toml

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+[workspace]
+resolver = "2"
+members = ["crates/opentfraw", "crates/opentfraw-py"]
+
+[workspace.package]
+version = "1.2.0"
+edition = "2021"
+rust-version = "1.85"
+authors = ["Nathan Riley <git@nathanriley.com>"]
+license = "Apache-2.0"
+repository = "https://github.com/Sigilweaver/OpenTFRaw"
+homepage = "https://sigilweaver.app/opentfraw/"
+documentation = "https://sigilweaver.app/opentfraw/docs/"
+keywords = ["mass-spectrometry", "thermo", "raw", "proteomics", "orbitrap"]
+categories = ["parser-implementations", "science"]
+
+[workspace.dependencies]
+opentfraw = { path = "crates/opentfraw" }
+openproteo-core = "1.0.0"
+pyo3 = { version = "0.22", features = ["extension-module", "abi3-py38"] }
+numpy = "0.22"
+
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+unsafe_code = "forbid"

mascope_opentfraw-1.2.0/LICENSE

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+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+Copyright 2026 Sigilweaver Holdings LLC
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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