openwraw 1.0.1__tar.gz

openwraw-1.0.1/CHANGELOG.md

@@ -0,0 +1,75 @@
+# 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).
+
+## [1.0.1] - 2026-05-17
+
+### Fixed
+
+- `pyproject.toml`: add `[tool.maturin] include` directive so the sdist
+  contains `LICENSE`, `README.md`, and `CHANGELOG.md`; PyPI was rejecting
+  the 1.0.0 sdist because `PKG-INFO` declared `License-File: LICENSE` but
+  the file was absent from the tarball.
+
+### Changed
+
+- README: standardize docs link format and section structure.
+- Docs: replace prose `--` with `-` in three pages (`guide/reader.md`,
+  `format/03-func-idx.md`, `format/04-func-dat.md`).
+
+## [1.0.0] - 2026-05-17
+
+First stable release. The public API of `openwraw` is now considered
+stable and will follow semantic versioning. Format coverage is unchanged
+from 0.1.0 (QTOF Ultima, SYNAPT G2-Si, Xevo G2-XS QTof).
+
+### Added
+
+- `ATTRIBUTION.md`: tracks third-party notices for bundled data.
+- `publish.yml` GitHub Actions workflow: publishes the `openwraw` crate
+  to crates.io and the Python wheel to PyPI via OIDC Trusted Publishing
+  on every `v*` tag push.
+- `Cargo.lock` is now committed to the repository for reproducible builds.
+- `[project.urls]` added to `pyproject.toml` (Homepage, Documentation,
+  Repository, Changelog).
+
+### Changed
+
+- Removed `openwraw-cli` crate: the CLI added unnecessary complexity for
+  a library-focused project; the Python bindings (`openwraw-py`) cover
+  interactive exploration needs adequately.
+- CI migrated from WarpBuild runners to standard GitHub-hosted
+  (`ubuntu-latest`, `macos-latest`, `windows-latest`).
+
+## [0.1.0] - 2026-05-16
+
+### Added
+
+- Rust reader for the Waters MassLynx RAW directory format with
+  zero external dependencies in the core crate.
+- Three spectrum encodings decoded and validated against PRIDE corpora:
+  - **Encoding A**: 6-byte records (QTOF Ultima class).
+  - **Encoding B**: 8-byte IMS cells (SYNAPT G2-Si with drift time).
+  - **Encoding C**: 8-byte sub-bin (Xevo G2-XS QTof).
+- Two scan-index variants decoded:
+  - **Variant A**: 22-byte records.
+  - **Variant B**: 30-byte records (modern instruments).
+- Parsers for ancillary files: `_HEADER.TXT`, `_extern.inf`,
+  `_FUNCTNS.INF`, `_FUNCnnn.IDX`, `_FUNCnnn.DAT`, `_CHROMS.INF`,
+  `_CHROnnnn.DAT`.
+- `openwraw-py` PyO3 Python bindings (`RawReader`, `read_spectrum`,
+  `read_ims_spectrum`, `read_chrom`).
+- 69 unit and integration tests covering the core crate.
+- Format specification under `docs/format/` (11 numbered documents
+  covering each on-disk file).
+
+### Out of scope
+
+- Function types beyond MS / MS/MS / chromatographic channels.
+
+[1.0.1]: https://github.com/Sigilweaver/OpenWRaw/releases/tag/v1.0.1
+[1.0.0]: https://github.com/Sigilweaver/OpenWRaw/releases/tag/v1.0.0
+[0.1.0]: https://github.com/Sigilweaver/OpenWRaw/releases/tag/v0.1.0

openwraw-1.0.1/Cargo.lock

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+# It is not intended for manual editing.
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openwraw-1.0.1/Cargo.toml

@@ -0,0 +1,21 @@
+[workspace]
+resolver = "2"
+members = ["crates/openwraw", "crates/openwraw-py"]
+
+[workspace.package]
+version = "1.0.1"
+edition = "2021"
+rust-version = "1.75"
+authors = ["Nathan Riley <git@nathanriley.com>"]
+license = "Apache-2.0"
+repository = "https://github.com/Sigilweaver/OpenWRaw"
+homepage = "https://github.com/Sigilweaver/OpenWRaw"
+keywords = ["mass-spectrometry", "waters", "masslynx", "raw", "proteomics"]
+categories = ["parser-implementations", "science"]
+
+[workspace.dependencies]
+openwraw = { path = "crates/openwraw" }
+pyo3 = { version = "0.28.3", features = ["extension-module"] }
+
+[workspace.lints.rust]
+unsafe_code = "forbid"

openwraw-1.0.1/LICENSE

@@ -0,0 +1,192 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+          informational purposes only and do not modify the License.
+          You may add Your own attribution notices within Derivative
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+          the NOTICE text from the Work, provided that such additional
+          attribution notices cannot be construed as modifying the License.
+
+      You may add Your own license statement for Your modifications and
+      may provide additional grant of rights to use, copy, modify, merge,
+      publish, distribute, sublicense, and/or sell copies of the
+      Contribution.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or exemplary damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or all other
+      commercial damages or losses), even if such Contributor has been
+      advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may offer only
+      conditions that are completely consistent with the terms of this License
+      and that require the appropriate indemnification and explanation to
+      any recipient of the Work or Derivative Works, so that it would be
+      possible for any such recipient to understand what obligations they are
+      assuming.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!) The text should be enclosed in the appropriate
+      comment syntax for the syntax format used in the source file.
+      You may also attach a machine-readable copy of the License
+      to your work if your desired:
+
+   Copyright 2026 Sigilweaver Holdings LLC
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

openwraw-1.0.1/PKG-INFO

@@ -0,0 +1,18 @@
+Metadata-Version: 2.4
+Name: openwraw
+Version: 1.0.1
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+License-File: LICENSE
+Summary: Python bindings for the OpenWRaw Waters MassLynx RAW file parser
+Home-Page: https://github.com/Sigilweaver/OpenWRaw
+Author-email: Nathan Riley <git@nathanriley.com>
+License: Apache-2.0
+Requires-Python: >=3.8
+Project-URL: Changelog, https://github.com/Sigilweaver/OpenWRaw/blob/main/CHANGELOG.md
+Project-URL: Documentation, https://sigilweaver.app/openwraw/docs/
+Project-URL: Homepage, https://sigilweaver.app/openwraw/
+Project-URL: Issues, https://github.com/Sigilweaver/OpenWRaw/issues
+Project-URL: Source, https://github.com/Sigilweaver/OpenWRaw

openwraw-1.0.1/README.md

@@ -0,0 +1,71 @@
+# OpenWRaw
+
+[![CI](https://github.com/Sigilweaver/OpenWRaw/actions/workflows/ci.yml/badge.svg)](https://github.com/Sigilweaver/OpenWRaw/actions/workflows/ci.yml)
+[![crates.io](https://img.shields.io/crates/v/openwraw.svg)](https://crates.io/crates/openwraw)
+[![PyPI](https://img.shields.io/pypi/v/openwraw.svg)](https://pypi.org/project/openwraw/)
+[![docs.rs](https://docs.rs/openwraw/badge.svg)](https://docs.rs/openwraw)
+[![License: Apache-2.0](https://img.shields.io/badge/License-Apache--2.0-blue.svg)](LICENSE)
+
+Rust and Python reader for the Waters MassLynx RAW mass spectrometry
+data format. Cross-platform (Linux, macOS, Windows), with no native or
+system dependencies.
+
+Full documentation: [sigilweaver.app/openwraw/docs](https://sigilweaver.app/openwraw/docs)
+
+## Install
+
+Rust:
+
+```sh
+cargo add openwraw
+```
+
+Python:
+
+```sh
+pip install openwraw
+```
+
+## Quickstart
+
+Rust:
+
+```rust
+use openwraw::RawReader;
+
+let r = RawReader::open("sample.raw")?;
+for f in r.functions() {
+    println!("function {}: {} scans", f.index, f.scan_count);
+}
+```
+
+Python:
+
+```python
+import openwraw
+
+r = openwraw.RawReader("sample.raw")
+spec = r.read_spectrum(1, 0)
+print(spec.mz[:5], spec.intensity[:5])
+```
+
+See the [docs site](https://sigilweaver.app/openwraw/docs) for the full
+quickstart, guide, and format specification.
+
+## Repository layout
+
+```
+crates/
+  openwraw/      Core Rust library (69 tests)
+  openwraw-py/   PyO3 / maturin Python bindings
+docs/            Docusaurus site (format spec + guides)
+```
+
+## License
+
+Apache-2.0 - see [LICENSE](LICENSE).
+
+Copyright 2026 Sigilweaver Holdings LLC.
+
+The format specification was developed by binary analysis of public
+mass-spectrometry datasets (PRIDE accessions).

openwraw-1.0.1/crates/openwraw/.gitignore

@@ -0,0 +1 @@
+/target

openwraw-1.0.1/crates/openwraw/Cargo.toml

@@ -0,0 +1,20 @@
+[package]
+name = "openwraw"
+description = "Rust reader for Waters MassLynx RAW mass spectrometry directories."
+version.workspace = true
+edition.workspace = true
+rust-version.workspace = true
+authors.workspace = true
+license.workspace = true
+repository.workspace = true
+homepage.workspace = true
+keywords.workspace = true
+categories.workspace = true
+readme = "README.md"
+
+[lints]
+workspace = true
+
+[dependencies]
+
+[dev-dependencies]

openwraw-1.0.1/crates/openwraw/README.md

@@ -0,0 +1,71 @@
+# OpenWRaw
+
+[![CI](https://github.com/Sigilweaver/OpenWRaw/actions/workflows/ci.yml/badge.svg)](https://github.com/Sigilweaver/OpenWRaw/actions/workflows/ci.yml)
+[![crates.io](https://img.shields.io/crates/v/openwraw.svg)](https://crates.io/crates/openwraw)
+[![PyPI](https://img.shields.io/pypi/v/openwraw.svg)](https://pypi.org/project/openwraw/)
+[![docs.rs](https://docs.rs/openwraw/badge.svg)](https://docs.rs/openwraw)
+[![License: Apache-2.0](https://img.shields.io/badge/License-Apache--2.0-blue.svg)](LICENSE)
+
+Rust and Python reader for the Waters MassLynx RAW mass spectrometry
+data format. Cross-platform (Linux, macOS, Windows), with no native or
+system dependencies.
+
+Full documentation: [sigilweaver.app/openwraw/docs](https://sigilweaver.app/openwraw/docs)
+
+## Install
+
+Rust:
+
+```sh
+cargo add openwraw
+```
+
+Python:
+
+```sh
+pip install openwraw
+```
+
+## Quickstart
+
+Rust:
+
+```rust
+use openwraw::RawReader;
+
+let r = RawReader::open("sample.raw")?;
+for f in r.functions() {
+    println!("function {}: {} scans", f.index, f.scan_count);
+}
+```
+
+Python:
+
+```python
+import openwraw
+
+r = openwraw.RawReader("sample.raw")
+spec = r.read_spectrum(1, 0)
+print(spec.mz[:5], spec.intensity[:5])
+```
+
+See the [docs site](https://sigilweaver.app/openwraw/docs) for the full
+quickstart, guide, and format specification.
+
+## Repository layout
+
+```
+crates/
+  openwraw/      Core Rust library (69 tests)
+  openwraw-py/   PyO3 / maturin Python bindings
+docs/            Docusaurus site (format spec + guides)
+```
+
+## License
+
+Apache-2.0 - see [LICENSE](LICENSE).
+
+Copyright 2026 Sigilweaver Holdings LLC.
+
+The format specification was developed by binary analysis of public
+mass-spectrometry datasets (PRIDE accessions).

openwraw-1.0.1/crates/openwraw/src/lib.rs

@@ -0,0 +1,33 @@
+pub mod raw;
+
+#[derive(Debug)]
+pub enum Error {
+    Io(std::io::Error),
+    Parse(String),
+}
+
+impl std::fmt::Display for Error {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Error::Io(e) => write!(f, "I/O error: {e}"),
+            Error::Parse(msg) => write!(f, "parse error: {msg}"),
+        }
+    }
+}
+
+impl std::error::Error for Error {
+    fn source(&self) -> Option<&(dyn std::error::Error + 'static)> {
+        match self {
+            Error::Io(e) => Some(e),
+            Error::Parse(_) => None,
+        }
+    }
+}
+
+impl From<std::io::Error> for Error {
+    fn from(e: std::io::Error) -> Self {
+        Error::Io(e)
+    }
+}
+
+pub type Result<T> = std::result::Result<T, Error>;