Merge pull request #5 from theGreatHerrLebert/david@rustdf

David@rustdf

mscore/src/lib.rs

@@ -1,2 +1,2 @@
 pub mod mz_spectrum;
-pub use {mz_spectrum::MzSpectrum, mz_spectrum::TOFMzSpectrum, mz_spectrum::ImsSpectrum, mz_spectrum::TimsSpectrum, mz_spectrum::ImsFrame, mz_spectrum::TimsFrame};
+pub use {mz_spectrum::MzSpectrum, mz_spectrum::TOFMzSpectrum, mz_spectrum::ImsSpectrum, mz_spectrum::TimsSpectrum, mz_spectrum::ImsFrame, mz_spectrum::TimsFrame, mz_spectrum::MsType};

mscore/src/mz_spectrum.rs

@@ -1,6 +1,6 @@
 use std::fmt;
 use std::collections::BTreeMap;
-use std::fmt::Formatter;
+use std::fmt::{Display, Formatter};
 use itertools;
 
 /// Represents a mass spectrum with associated m/z values and intensities.
@@ -10,6 +10,58 @@ pub struct MzSpectrum {
     pub intensity: Vec<f64>,
 }
 
+/// Represents the type of spectrum.
+///
+/// # Description
+///
+/// The `SpecType` enum is used to distinguish between precursor and fragment spectra.
+///
+#[derive(Clone)]
+pub enum MsType {
+    Precursor,
+    FragmentDda,
+    FragmentDia,
+    Unknown,
+}
+
+impl MsType {
+    /// Returns the `MsType` enum corresponding to the given integer value.
+    ///
+    /// # Arguments
+    ///
+    /// * `ms_type` - An integer value corresponding to the `MsType` enum.
+    ///
+    pub fn new(ms_type: i32) -> MsType {
+        match ms_type {
+            0 => MsType::Precursor,
+            8 => MsType::FragmentDda,
+            9 => MsType::FragmentDia,
+            _ => MsType::Unknown,
+        }
+    }
+
+    /// Returns the integer value corresponding to the `MsType` enum.
+    pub fn to_i32(&self) -> i32 {
+        match self {
+            MsType::Precursor => 0,
+            MsType::FragmentDda => 8,
+            MsType::FragmentDia => 9,
+            MsType::Unknown => -1,
+        }
+    }
+}
+
+impl Display for MsType {
+    fn fmt(&self, f: &mut Formatter<'_>) -> fmt::Result {
+        match self {
+            MsType::Precursor => write!(f, "Precursor"),
+            MsType::FragmentDda => write!(f, "FragmentDda"),
+            MsType::FragmentDia => write!(f, "FragmentDia"),
+            MsType::Unknown => write!(f, "Unknown"),
+        }
+    }
+}
+
 impl MzSpectrum {
     /// Constructs a new `MzSpectrum`.
     ///
@@ -331,6 +383,7 @@ impl fmt::Display for ImsFrame {
 #[derive(Clone)]
 pub struct TimsFrame {
     pub frame_id: i32,
+    pub ms_type: MsType,
     pub retention_time: f64,
     pub scan: Vec<i32>,
     pub inv_mobility: Vec<f64>,
@@ -345,6 +398,7 @@ impl TimsFrame {
     /// # Arguments
     /// 
     /// * `frame_id` - index of frame in TDF raw file.
+    /// * `ms_type` - The type of frame.
     /// * `retention_time` - The retention time in seconds.
     /// * `scan` - A vector of scan IDs.
     /// * `inv_mobility` - A vector of inverse ion mobilities.
@@ -355,12 +409,13 @@ impl TimsFrame {
     /// # Examples
     /// 
     /// ```
+    /// use mscore::MsType;
     /// use mscore::TimsFrame;
-    /// 
-    /// let frame = TimsFrame::new(1, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
+    ///
+    /// let frame = TimsFrame::new(1, MsType::PRECURSOR, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
     /// ```
-    pub fn new(frame_id: i32, retention_time: f64, scan: Vec<i32>, inv_mobility: Vec<f64>, tof: Vec<i32>, mz: Vec<f64>, intensity: Vec<f64>) -> Self {
-        TimsFrame { frame_id, retention_time, scan, inv_mobility, tof, mz, intensity }
+    pub fn new(frame_id: i32, ms_type: MsType, retention_time: f64, scan: Vec<i32>, inv_mobility: Vec<f64>, tof: Vec<i32>, mz: Vec<f64>, intensity: Vec<f64>) -> Self {
+        TimsFrame { frame_id, ms_type, retention_time, scan, inv_mobility, tof, mz, intensity }
     }
 
     ///
@@ -447,7 +502,7 @@ impl fmt::Display for TimsFrame {
             .max_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(std::cmp::Ordering::Equal))
             .unwrap();
 
-        write!(f, "TimsFrame(id: {}, rt: {}, data points: {}, max by intensity: (mz: {}, intensity: {}))", self.frame_id, self.retention_time, self.scan.len(), format!("{:.3}", mz), i)
+        write!(f, "TimsFrame(id: {}, type: {}, rt: {}, data points: {}, max by intensity: (mz: {}, intensity: {}))", self.frame_id, self.ms_type, self.retention_time, self.scan.len(), format!("{:.3}", mz), i)
     }
 }
 

pyims/.github/workflows/CI.yml

@@ -0,0 +1,120 @@
+# This file is autogenerated by maturin v1.2.3
+# To update, run
+#
+#    maturin generate-ci github
+#
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - '*'
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target: [x86_64, x86, aarch64, armv7, s390x, ppc64le]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+  windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        target: [x64, x86]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          architecture: ${{ matrix.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+  macos:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    if: "startsWith(github.ref, 'refs/tags/')"
+    needs: [linux, windows, macos, sdist]
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: wheels
+      - name: Publish to PyPI
+        uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        with:
+          command: upload
+          args: --non-interactive --skip-existing *

pyims/.gitignore

@@ -0,0 +1,72 @@
+/target
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+.pytest_cache/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+.venv/
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+include/
+man/
+venv/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+pip-selfcheck.json
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+.DS_Store
+
+# Sphinx documentation
+docs/_build/
+
+# PyCharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Pyenv
+.python-version

pyims/Cargo.toml

@@ -0,0 +1,15 @@
+[package]
+name = "pyims"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "pyims"
+crate-type = ["cdylib"]
+
+[dependencies]
+pyo3 = { version = "0.19.2", features = ["extension-module"] }
+numpy = "0.19.0"
+mscore = {path = "../mscore"}
+rustdf = {path = "../rustdf"}

pyims/pyproject.toml

@@ -0,0 +1,16 @@
+[build-system]
+requires = ["maturin>=1.2,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "pyims"
+requires-python = ">=3.7"
+classifiers = [
+    "Programming Language :: Rust",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+]
+
+
+[tool.maturin]
+features = ["pyo3/extension-module"]

pyims/src/lib.rs

@@ -0,0 +1,14 @@
+mod pyhandle;
+mod py_mz_spectrum;
+
+use pyo3::prelude::*;
+use crate::pyhandle::PyTimsDataset;
+use crate::py_mz_spectrum::PyMzSpectrum;
+
+/// A Python module implemented in Rust.
+#[pymodule]
+fn pyims(_py: Python, m: &PyModule) -> PyResult<()> {
+    m.add_class::<PyTimsDataset>()?;
+    m.add_class::<PyMzSpectrum>()?;
+    Ok(())
+}