(wip) updates timsrust to v0.4.1 (#9)

* chore(timsrust)!: (wip) updated timsrust versioncargo
* chore: cargo update and fmt
* (chore) removed unused imports

Author: jspaezp

Cargo.lock

@@ -7,32 +7,37 @@ license = "Apache-2.0"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-timsrust = "= 0.2.2"
+timsrust = "= 0.4.1"
 
 # Serialization
-serde = { version = "1.0.193", features = ["derive"] }
-serde_json = "1.0.108"
-rayon = "1.8.0"
-indicatif = {version = "*", features = ["rayon"]}
-log = "0.4"
-pretty_env_logger = "0.4"
-num = "0.4.1"
-num-traits = "0.2.18"
-clap = {version = "4.4.17", features = ["derive"]}
+serde = { version = "1.0.210", features = ["derive"] }
+serde_json = "1.0.128"
+clap = { version = "4.4.17", features = ["derive"] }
 csv = "1.3.0"
+
+# Random ...
 rand = "0.8.5"
 
-sqlx = { version = "0.7.2", features = ["runtime-tokio-native-tls", "sqlite"]}
-libsqlite3-sys = "^0.26.0"
-tokio = {version="1.38.0", features = ["rt", "rt-multi-thread"]}
+# Paralellization
+rayon = "1.10.0"
+
+# Logging/ Messaging
+indicatif = { version = "*", features = ["rayon"] }
+log = "0.4.22"
+pretty_env_logger = "0.5"
+
+# Q: Not sure if I still use this
+num = "0.4.1"
+num-traits = "0.2.19"
 
 # Sage
 sage-core = { git = "https://github.com/lazear/sage.git", rev = "9e870429889b341c4773df32b65e553283301a93" }
-toml = "0.8.8"
+toml = "0.8.19"
 
 [features]
 par_dataprep = []
-less_parallel = [] # Mostly for profiling reasons ... looking at flamegraphs is hard with rayon...
+less_parallel = [
+] # Mostly for profiling reasons ... looking at flamegraphs is hard with rayon...
 
 [profile.release]
 lto = "thin"

Cargo.toml

@@ -20,17 +20,17 @@
 # dependencies not shared by any other crates, would be ignored, as the target
 # list here is effectively saying which targets you are building for.
 targets = [
-    { triple = "aarch64-apple-darwin" },
-    { triple = "x86_64-apple-darwin" },
-    { triple = "i686-pc-windows-gnu" },
-    { triple = "i686-pc-windows-msvc" },
-    { triple = "x86_64-pc-windows-gnu" },
-    { triple = "x86_64-pc-windows-msvc" },
-    { triple = "i686-unknown-linux-gnu" },
-    { triple = "x86_64-unknown-linux-gnu" },
-    { triple = "x86_64-unknown-linux-musl" },
-    # { triple = "wasm32-unknown-unknown" },
-    # { triple = "x86_64-unknown-redox" },
+  { triple = "aarch64-apple-darwin" },
+  { triple = "x86_64-apple-darwin" },
+  { triple = "i686-pc-windows-gnu" },
+  { triple = "i686-pc-windows-msvc" },
+  { triple = "x86_64-pc-windows-gnu" },
+  { triple = "x86_64-pc-windows-msvc" },
+  { triple = "i686-unknown-linux-gnu" },
+  { triple = "x86_64-unknown-linux-gnu" },
+  { triple = "x86_64-unknown-linux-musl" },
+  # { triple = "wasm32-unknown-unknown" },
+  # { triple = "x86_64-unknown-redox" },
 ]
 # When creating the dependency graph used as the source of truth when checks are
 # executed, this field can be used to prune crates from the graph, removing them
@@ -73,8 +73,8 @@ yanked = "warn"
 # A list of advisory IDs to ignore. Note that ignored advisories will still
 # output a note when they are encountered.
 ignore = [
-    #"RUSTSEC-0000-0000",
-    "RUSTSEC-2021-0145",  # atty... potential unaligner when using custom allocators.
+  #"RUSTSEC-0000-0000",
+  "RUSTSEC-2023-0086", # Lexical-core -> arrow issue, updated in main in Sept-2024, unreleased.
 ]
 # Threshold for security vulnerabilities, any vulnerability with a CVSS score
 # lower than the range specified will be ignored. Note that ignored advisories
@@ -101,13 +101,13 @@ version = 2
 # See https://spdx.org/licenses/ for list of possible licenses
 # [possible values: any SPDX 3.11 short identifier (+ optional exception)].
 allow = [
-    "MIT",
-    "Apache-2.0",
-    "Apache-2.0 WITH LLVM-exception",
-    "BSD-3-Clause",
-    "Unicode-DFS-2016",
-    "Zlib",
-    # Thank Jesus for rerun that compiled the following for me...
+  "MIT",
+  "Apache-2.0",
+  "Apache-2.0 WITH LLVM-exception",
+  "BSD-3-Clause",
+  "Unicode-DFS-2016",
+  "Zlib",
+  # Thank Jesus for rerun that compiled the following for me...
 ]
 
 # The confidence threshold for detecting a license from license text.
@@ -146,8 +146,8 @@ license-files = [{ path = "LICENSE", hash = 0xbd0eed23 }]
 # and the crate will be checked normally, which may produce warnings or errors
 # depending on the rest of your configuration
 #license-files = [
-    # Each entry is a crate relative path, and the (opaque) hash of its contents
-    #{ path = "LICENSE", hash = 0xbd0eed23 }
+# Each entry is a crate relative path, and the (opaque) hash of its contents
+#{ path = "LICENSE", hash = 0xbd0eed23 }
 #]
 
 [licenses.private]
@@ -160,7 +160,7 @@ ignore = false
 # is only published to private registries, and ignore is true, the crate will
 # not have its license(s) checked
 registries = [
-    #"https://sekretz.com/registry
+  #"https://sekretz.com/registry
 ]
 
 # This section is considered when running `cargo deny check bans`.
@@ -187,17 +187,17 @@ workspace-default-features = "allow"
 external-default-features = "allow"
 # List of crates that are allowed. Use with care!
 allow = [
-    #{ name = "ansi_term", version = "=0.11.0" },
+  #{ name = "ansi_term", version = "=0.11.0" },
 ]
 # List of crates to deny
 deny = [
-    # Each entry the name of a crate and a version range. If version is
-    # not specified, all versions will be matched.
-    #{ name = "ansi_term", version = "=0.11.0" },
-    #
-    # Wrapper crates can optionally be specified to allow the crate when it
-    # is a direct dependency of the otherwise banned crate
-    #{ name = "ansi_term", version = "=0.11.0", wrappers = [] },
+  # Each entry the name of a crate and a version range. If version is
+  # not specified, all versions will be matched.
+  #{ name = "ansi_term", version = "=0.11.0" },
+  #
+  # Wrapper crates can optionally be specified to allow the crate when it
+  # is a direct dependency of the otherwise banned crate
+  #{ name = "ansi_term", version = "=0.11.0", wrappers = [] },
 ]
 
 # List of features to allow/deny

deny.toml

@@ -1,3 +1,5 @@
+use timsrust::MSLevel;
+
 use crate::aggregation::aggregators::TimsPeakAggregator;
 use crate::aggregation::converters::{
     BypassDenseFrameBackConverter,
@@ -25,9 +27,12 @@ pub fn dbscan_denseframe(
     min_n: usize,
     min_intensity: u64,
 ) -> DenseFrame {
-    let out_frame_type: timsrust::FrameType = denseframe.frame_type;
+    let out_acq_type: timsrust::AcquisitionType = denseframe.acquisition_type;
     let out_rt: f64 = denseframe.rt;
     let out_index: usize = denseframe.index;
+    let out_ms_level: MSLevel = denseframe.ms_level;
+    let out_window_group_id = denseframe.window_group_id;
+    let out_correction_factor = denseframe.intensity_correction_factor;
 
     let prefiltered_peaks = {
         denseframe.sort_by_mz();
@@ -72,8 +77,11 @@ pub fn dbscan_denseframe(
         raw_peaks: peak_vec,
         index: out_index,
         rt: out_rt,
-        frame_type: out_frame_type,
+        acquisition_type: out_acq_type,
         sorted: None,
+        ms_level: out_ms_level,
+        window_group_id: out_window_group_id,
+        intensity_correction_factor: out_correction_factor,
     }
 }