refactor: restructure to Cargo workspace layout

- Library crate moved to crates/opentimstdf/
- Python bindings crate moved to crates/opentimstdf-py/
- pyproject.toml moved to repository root
- Root Cargo.toml rewritten as workspace manifest with shared metadata
- CI updated to use --workspace flag for clippy and test
- Publish workflow updated to reference new crate path
- Version bumped to 1.0.4

Author: Nathan-D-R

.github/workflows/ci.yml

@@ -35,7 +35,7 @@ jobs:
         run: cargo fmt --all -- --check
 
       - name: cargo clippy
-        run: cargo clippy --all-targets -- -D warnings
+        run: cargo clippy --workspace --all-targets -- -D warnings
 
       - name: cargo test
-        run: cargo test --all-targets
+        run: cargo test --workspace --all-targets

.github/workflows/publish.yml

@@ -47,7 +47,7 @@ jobs:
       - uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter --manifest-path python/Cargo.toml
+          args: --release --out dist --find-interpreter --manifest-path crates/opentimstdf-py/Cargo.toml
           manylinux: auto
       - uses: actions/upload-artifact@v4
         with:
@@ -62,7 +62,7 @@ jobs:
       - uses: PyO3/maturin-action@v1
         with:
           command: sdist
-          args: --out dist --manifest-path python/Cargo.toml
+          args: --out dist --manifest-path crates/opentimstdf-py/Cargo.toml
       - uses: actions/upload-artifact@v4
         with:
           name: sdist

.gitignore

@@ -14,7 +14,12 @@ nohup.out
 **/__pycache__/
 **/*.pyc
 **/*.pyo
-*.egg-info/
+**/*.egg-info/
+**/.pytest_cache/
+**/dist/
+**/*.so
+**/*.pyd
+**/*.dylib
 .venv/
 
 # Editor / OS

CHANGELOG.md

@@ -4,6 +4,15 @@ All notable changes to this project will be documented in this file.
 The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.0.4] - 2026-05-17
+
+### Changed
+
+- Restructured to a Cargo workspace layout. The library crate is now at
+  `crates/opentimstdf/` and the Python bindings crate at
+  `crates/opentimstdf-py/`. The `pyproject.toml` is now at the repository
+  root. No public API changes.
+
 ## [1.0.3] - 2026-05-17
 
 ### Fixed

Cargo.toml

@@ -1,25 +1,21 @@
-[package]
-name = "opentimstdf"
-version = "1.0.3"
+[workspace]
+resolver = "2"
+members = ["crates/opentimstdf", "crates/opentimstdf-py"]
+
+[workspace.package]
+version = "1.0.4"
 edition = "2021"
 rust-version = "1.75"
-description = "Rust reader for timsTOF .d/ (TDF) mass spectrometry bundles."
 authors = ["Nathan Riley <git@nathanriley.com>"]
 license = "Apache-2.0"
 repository = "https://github.com/Sigilweaver/OpenTimsTDF"
 homepage = "https://github.com/Sigilweaver/OpenTimsTDF"
-readme = "README.md"
 keywords = ["mass-spectrometry", "bruker", "timstof", "tdf", "proteomics"]
 categories = ["parser-implementations", "science"]
 
-[lints.rust]
-unsafe_code = "forbid"
-
-[dependencies]
-thiserror = "2"
-rusqlite = { version = "0.31", features = ["bundled"] }
-zstd = "0.13"
+[workspace.dependencies]
+opentimstdf = { path = "crates/opentimstdf" }
+pyo3 = { version = "0.22", features = ["extension-module", "abi3-py38"] }
 
-[[example]]
-name = "dump"
-path = "examples/dump.rs"
+[workspace.lints.rust]
+unsafe_code = "forbid"

crates/opentimstdf-py/Cargo.toml

@@ -0,0 +1,28 @@
+[package]
+name = "opentimstdf-py"
+description = "Python bindings for the OpenTimsTDF library."
+readme = "../../README.md"
+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
+publish = false
+
+[lib]
+name = "opentimstdf"
+crate-type = ["cdylib"]
+
+[lints.rust]
+unsafe_code = "allow"
+
+[lints.clippy]
+useless_conversion = "allow"
+
+[dependencies]
+opentimstdf.workspace = true
+pyo3 = { workspace = true }

python/src/lib.rs crates/opentimstdf-py/src/lib.rspython/src/lib.rs renamed to crates/opentimstdf-py/src/lib.rs

@@ -0,0 +1,21 @@
+[package]
+name = "opentimstdf"
+description = "Rust reader for timsTOF .d/ (TDF) mass spectrometry bundles."
+readme = "../../README.md"
+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
+
+[lints.rust]
+unsafe_code = "forbid"
+
+[dependencies]
+thiserror = "2"
+rusqlite = { version = "0.31", features = ["bundled"] }
+zstd = "0.13"