From e35357de2981a61fd92110cf0e894eef8ca29919 Mon Sep 17 00:00:00 2001
From: Michael Lazear <michaellazear92@gmail.com>
Date: Wed, 25 Oct 2023 19:20:29 -0700
Subject: [PATCH] Release v0.14.4

---
 CHANGELOG.md                      |  8 ++++++++
 Cargo.lock                        |  6 +++---
 crates/sage-cli/Cargo.toml        |  2 +-
 crates/sage-cloudpath/Cargo.toml  |  2 +-
 crates/sage-cloudpath/src/lib.rs  |  2 +-
 crates/sage-cloudpath/src/tdf.rs  | 33 ++++++++-----------------------
 crates/sage-cloudpath/src/util.rs |  2 +-
 crates/sage/Cargo.toml            |  2 +-
 8 files changed, 24 insertions(+), 33 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5819a8b..f78d5c0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,14 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.14.4]
+### Added
+- **Unstable feature**: Preliminary support for reading Bruker .d folders (ddaPASEF; no MS1/LFQ support yet)
+### Changed
+- Retention times are converted to minutes
+### Fixed
+- Fixed bug where charge state 1 would never be searched
+
 ## [v0.14.3]
 ### Fixed
 - Hotfix for bug in parquet LFQ writer
diff --git a/Cargo.lock b/Cargo.lock
index 5ca4281..5859a1c 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2081,7 +2081,7 @@ checksum = "4501abdff3ae82a1c1b477a17252eb69cee9e66eb915c1abaa4f44d873df9f09"
 
 [[package]]
 name = "sage-cli"
-version = "0.14.3"
+version = "0.14.4"
 dependencies = [
  "anyhow",
  "clap",
@@ -2102,7 +2102,7 @@ dependencies = [
 
 [[package]]
 name = "sage-cloudpath"
-version = "0.14.3"
+version = "0.14.4"
 dependencies = [
  "async-compression",
  "aws-config",
@@ -2126,7 +2126,7 @@ dependencies = [
 
 [[package]]
 name = "sage-core"
-version = "0.14.3"
+version = "0.14.4"
 dependencies = [
  "dashmap",
  "fnv",
diff --git a/crates/sage-cli/Cargo.toml b/crates/sage-cli/Cargo.toml
index 01341fc..ec9ac45 100644
--- a/crates/sage-cli/Cargo.toml
+++ b/crates/sage-cli/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "sage-cli"
-version = "0.14.3"
+version = "0.14.4"
 authors = ["Michael Lazear <michaellazear92@gmail.com"]
 edition = "2021"
 rust-version = "1.62"
diff --git a/crates/sage-cloudpath/Cargo.toml b/crates/sage-cloudpath/Cargo.toml
index 636b159..b275e79 100644
--- a/crates/sage-cloudpath/Cargo.toml
+++ b/crates/sage-cloudpath/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "sage-cloudpath"
-version = "0.14.3"
+version = "0.14.4"
 authors = ["Michael Lazear <michaellazear92@gmail.com"]
 edition = "2021"
 rust-version = "1.62"
diff --git a/crates/sage-cloudpath/src/lib.rs b/crates/sage-cloudpath/src/lib.rs
index 01a411b..281164e 100644
--- a/crates/sage-cloudpath/src/lib.rs
+++ b/crates/sage-cloudpath/src/lib.rs
@@ -281,7 +281,7 @@ pub enum Error {
     #[error("MzML error: {0}")]
     MzML(#[from] mzml::MzMLError),
     #[error("TDF error: {0}")]
-    TDF(#[from] tdf::TdfError),
+    TDF(#[from] timsrust::Error),
 }
 
 #[cfg(test)]
diff --git a/crates/sage-cloudpath/src/tdf.rs b/crates/sage-cloudpath/src/tdf.rs
index 478de02..f9dda33 100644
--- a/crates/sage-cloudpath/src/tdf.rs
+++ b/crates/sage-cloudpath/src/tdf.rs
@@ -1,24 +1,20 @@
 use rayon::prelude::*;
 use sage_core::spectrum::{Precursor, RawSpectrum, Representation};
-use std::fmt::{Display, Formatter};
-use timsrust;
 
-#[derive(Default)]
-pub struct TdfReader {}
+pub struct TdfReader;
 
 impl TdfReader {
     pub fn parse(
         &self,
         path_name: impl AsRef<str>,
         file_id: usize,
-    ) -> Result<Vec<RawSpectrum>, TdfError> {
+    ) -> Result<Vec<RawSpectrum>, timsrust::Error> {
         let dda_spectra: Vec<timsrust::Spectrum> =
-            timsrust::FileReader::new(path_name.as_ref().to_string())
-                .unwrap()
-                .read_all_spectra();
-        let spectra: Vec<RawSpectrum> = dda_spectra
+            timsrust::FileReader::new(path_name.as_ref())?.read_all_spectra();
+        let spectra: Vec<RawSpectrum> = (0..dda_spectra.len())
             .into_par_iter()
-            .map(|dda_spectrum| {
+            .map(|index| {
+                let dda_spectrum = &dda_spectra[index];
                 let mut precursor: Precursor = Precursor::default();
                 let dda_precursor: timsrust::Precursor =
                     dda_spectrum.precursor.unwrap_as_precursor();
@@ -28,10 +24,10 @@ impl TdfReader {
                 precursor.intensity = Option::from(dda_precursor.intensity as f32);
                 precursor.spectrum_ref = Option::from(dda_precursor.frame_index.to_string());
                 let spectrum: RawSpectrum = RawSpectrum {
-                    file_id: file_id,
+                    file_id,
                     precursors: vec![precursor],
                     representation: Representation::Centroid,
-                    scan_start_time: dda_precursor.rt as f32,
+                    scan_start_time: dda_precursor.rt as f32 / 60.0,
                     ion_injection_time: dda_precursor.rt as f32,
                     total_ion_current: 0.0,
                     mz: dda_spectrum.mz_values.iter().map(|&x| x as f32).collect(),
@@ -47,16 +43,3 @@ impl TdfReader {
         Ok(spectra)
     }
 }
-
-#[derive(thiserror::Error, Debug)]
-pub enum TdfError {
-    Unreadable,
-}
-
-impl Display for TdfError {
-    fn fmt(&self, f: &mut Formatter<'_>) -> std::fmt::Result {
-        match self {
-            TdfError::Unreadable => f.write_str("Tdf Error : Malformed data."),
-        }
-    }
-}
diff --git a/crates/sage-cloudpath/src/util.rs b/crates/sage-cloudpath/src/util.rs
index b2ba4b3..1d6eb2f 100644
--- a/crates/sage-cloudpath/src/util.rs
+++ b/crates/sage-cloudpath/src/util.rs
@@ -16,7 +16,7 @@ pub fn read_mzml<S: AsRef<str>>(
 }
 
 pub fn read_tdf<S: AsRef<str>>(s: S, file_id: usize) -> Result<Vec<RawSpectrum>, Error> {
-    let res = crate::tdf::TdfReader::default().parse(s, file_id);
+    let res = crate::tdf::TdfReader.parse(s, file_id);
     match res {
         Ok(t) => Ok(t),
         Err(e) => Err(Error::TDF(e)),
diff --git a/crates/sage/Cargo.toml b/crates/sage/Cargo.toml
index 55d2955..8339757 100644
--- a/crates/sage/Cargo.toml
+++ b/crates/sage/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "sage-core"
-version = "0.14.3"
+version = "0.14.4"
 authors = ["Michael Lazear <michaellazear92@gmail.com"]
 edition = "2021"
 rust-version = "1.62"