From d5a3d9191685cffef3efc727fae3ecc04a0470bd Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Mon, 16 Sep 2024 18:36:32 -0700
Subject: [PATCH 1/3] chore(timsrust)!: (wip) updated timsrust versioncargo

---
 Cargo.lock                                  | 1277 +------------------
 Cargo.toml                                  |    6 +-
 src/aggregation/dbscan/denseframe_dbscan.rs |   17 +-
 src/aggregation/ms_denoise.rs               |  156 +--
 src/aggregation/tracing.rs                  |   35 +-
 src/main.rs                                 |   31 +-
 src/ms/frames/dense_frame_window.rs         |   86 +-
 src/ms/frames/frame_slice.rs                |  201 ++-
 src/ms/frames/frame_slice_rt_window.rs      |   10 +-
 src/ms/frames/frames.rs                     |   72 +-
 src/ms/frames/mod.rs                        |    3 +-
 src/ms/mod.rs                               |    1 -
 src/ms/tdf.rs                               |  567 --------
 src/scoring.rs                              |   16 +-
 14 files changed, 497 insertions(+), 1981 deletions(-)
 delete mode 100644 src/ms/tdf.rs

diff --git a/Cargo.lock b/Cargo.lock
index 10ad791..697d2a5 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2,15 +2,6 @@
 # It is not intended for manual editing.
 version = 3
 
-[[package]]
-name = "addr2line"
-version = "0.22.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6e4503c46a5c0c7844e948c9a4d6acd9f50cccb4de1c48eb9e291ea17470c678"
-dependencies = [
- "gimli",
-]
-
 [[package]]
 name = "adler"
 version = "1.0.2"
@@ -55,12 +46,6 @@ dependencies = [
  "alloc-no-stdlib",
 ]
 
-[[package]]
-name = "allocator-api2"
-version = "0.2.18"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5c6cb57a04249c6480766f7f7cef5467412af1490f8d1e243141daddada3264f"
-
 [[package]]
 name = "android-tzdata"
 version = "0.1.1"
@@ -112,7 +97,7 @@ version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391"
 dependencies = [
- "windows-sys 0.52.0",
+ "windows-sys",
 ]
 
 [[package]]
@@ -122,7 +107,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19"
 dependencies = [
  "anstyle",
- "windows-sys 0.52.0",
+ "windows-sys",
 ]
 
 [[package]]
@@ -213,22 +198,13 @@ dependencies = [
  "num",
 ]
 
-[[package]]
-name = "atoi"
-version = "2.0.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f28d99ec8bfea296261ca1af174f24225171fea9664ba9003cbebee704810528"
-dependencies = [
- "num-traits",
-]
-
 [[package]]
 name = "atty"
 version = "0.2.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
 dependencies = [
- "hermit-abi 0.1.19",
+ "hermit-abi",
  "libc",
  "winapi",
 ]
@@ -239,33 +215,12 @@ version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0"
 
-[[package]]
-name = "backtrace"
-version = "0.3.73"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5cc23269a4f8976d0a4d2e7109211a419fe30e8d88d677cd60b6bc79c5732e0a"
-dependencies = [
- "addr2line",
- "cc",
- "cfg-if",
- "libc",
- "miniz_oxide",
- "object",
- "rustc-demangle",
-]
-
 [[package]]
 name = "base64"
 version = "0.21.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9d297deb1925b89f2ccc13d7635fa0714f12c87adce1c75356b39ca9b7178567"
 
-[[package]]
-name = "base64ct"
-version = "1.6.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8c3c1a368f70d6cf7302d78f8f7093da241fb8e8807c05cc9e51a125895a6d5b"
-
 [[package]]
 name = "bitflags"
 version = "1.3.2"
@@ -277,18 +232,6 @@ name = "bitflags"
 version = "2.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "cf4b9d6a944f767f8e5e0db018570623c85f3d925ac718db4e06d0187adb21c1"
-dependencies = [
- "serde",
-]
-
-[[package]]
-name = "block-buffer"
-version = "0.10.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71"
-dependencies = [
- "generic-array",
-]
 
 [[package]]
 name = "brotli"
@@ -319,9 +262,9 @@ checksum = "79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c"
 
 [[package]]
 name = "bytemuck"
-version = "1.16.0"
+version = "1.18.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "78834c15cb5d5efe3452d58b1e8ba890dd62d21907f867f383358198e56ebca5"
+checksum = "94bbb0ad554ad961ddc5da507a12a29b14e4ae5bda06b19f575a3e6079d2e2ae"
 
 [[package]]
 name = "byteorder"
@@ -361,7 +304,7 @@ dependencies = [
  "android-tzdata",
  "iana-time-zone",
  "num-traits",
- "windows-targets 0.52.5",
+ "windows-targets",
 ]
 
 [[package]]
@@ -392,7 +335,7 @@ version = "4.5.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c780290ccf4fb26629baa7a1081e68ced113f1d3ec302fa5948f1c381ebf06c6"
 dependencies = [
- "heck 0.5.0",
+ "heck",
  "proc-macro2",
  "quote",
  "syn 2.0.66",
@@ -420,15 +363,9 @@ dependencies = [
  "lazy_static",
  "libc",
  "unicode-width",
- "windows-sys 0.52.0",
+ "windows-sys",
 ]
 
-[[package]]
-name = "const-oid"
-version = "0.9.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c2459377285ad874054d797f3ccebf984978aa39129f6eafde5cdc8315b612f8"
-
 [[package]]
 name = "const-random"
 version = "0.1.18"
@@ -449,46 +386,12 @@ dependencies = [
  "tiny-keccak",
 ]
 
-[[package]]
-name = "core-foundation"
-version = "0.9.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "91e195e091a93c46f7102ec7818a2aa394e1e1771c3ab4825963fa03e45afb8f"
-dependencies = [
- "core-foundation-sys",
- "libc",
-]
-
 [[package]]
 name = "core-foundation-sys"
 version = "0.8.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f"
 
-[[package]]
-name = "cpufeatures"
-version = "0.2.12"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "53fe5e26ff1b7aef8bca9c6080520cfb8d9333c7568e1829cef191a9723e5504"
-dependencies = [
- "libc",
-]
-
-[[package]]
-name = "crc"
-version = "3.2.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "69e6e4d7b33a94f0991c26729976b10ebde1d34c3ee82408fb536164fa10d636"
-dependencies = [
- "crc-catalog",
-]
-
-[[package]]
-name = "crc-catalog"
-version = "2.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "19d374276b40fb8bbdee95aef7c7fa6b5316ec764510eb64b8dd0e2ed0d7e7f5"
-
 [[package]]
 name = "crc32fast"
 version = "1.4.2"
@@ -517,15 +420,6 @@ dependencies = [
  "crossbeam-utils",
 ]
 
-[[package]]
-name = "crossbeam-queue"
-version = "0.3.11"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "df0346b5d5e76ac2fe4e327c5fd1118d6be7c51dfb18f9b7922923f287471e35"
-dependencies = [
- "crossbeam-utils",
-]
-
 [[package]]
 name = "crossbeam-utils"
 version = "0.8.20"
@@ -538,16 +432,6 @@ version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7a81dae078cea95a014a339291cec439d2f232ebe854a9d672b796c6afafa9b7"
 
-[[package]]
-name = "crypto-common"
-version = "0.1.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3"
-dependencies = [
- "generic-array",
- "typenum",
-]
-
 [[package]]
 name = "csv"
 version = "1.3.0"
@@ -583,29 +467,6 @@ dependencies = [
  "rayon",
 ]
 
-[[package]]
-name = "der"
-version = "0.7.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f55bf8e7b65898637379c1b74eb1551107c8294ed26d855ceb9fd1a09cfc9bc0"
-dependencies = [
- "const-oid",
- "pem-rfc7468",
- "zeroize",
-]
-
-[[package]]
-name = "digest"
-version = "0.10.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9ed9a281f7bc9b7576e61468ba615a66a5c8cfdff42420a70aa82701a3b1e292"
-dependencies = [
- "block-buffer",
- "const-oid",
- "crypto-common",
- "subtle",
-]
-
 [[package]]
 name = "displaydoc"
 version = "0.1.7"
@@ -617,20 +478,11 @@ dependencies = [
  "syn 1.0.109",
 ]
 
-[[package]]
-name = "dotenvy"
-version = "0.15.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1aaf95b3e5c8f23aa320147307562d361db0ae0d51242340f558153b4eb2439b"
-
 [[package]]
 name = "either"
 version = "1.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3dca9240753cf90908d7e4aac30f630662b02aebaa1b58a3cadabdb23385b58b"
-dependencies = [
- "serde",
-]
 
 [[package]]
 name = "encode_unicode"
@@ -657,38 +509,11 @@ version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5"
 
-[[package]]
-name = "errno"
-version = "0.3.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "534c5cf6194dfab3db3242765c03bbe257cf92f22b38f6bc0c58d59108a820ba"
-dependencies = [
- "libc",
- "windows-sys 0.52.0",
-]
-
-[[package]]
-name = "etcetera"
-version = "0.8.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "136d1b5283a1ab77bd9257427ffd09d8667ced0570b6f938942bc7568ed5b943"
-dependencies = [
- "cfg-if",
- "home",
- "windows-sys 0.48.0",
-]
-
-[[package]]
-name = "event-listener"
-version = "2.5.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0206175f82b8d6bf6652ff7d71a1e27fd2e4efde587fd368662814d6ec1d9ce0"
-
 [[package]]
 name = "fallible-iterator"
-version = "0.2.0"
+version = "0.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4443176a9f2c162692bd3d352d745ef9413eec5782a80d8fd6f8a1ac692a07f7"
+checksum = "2acce4a10f12dc2fb14a218589d4f1f62ef011b2d0cc4b3cb1bba8e94da14649"
 
 [[package]]
 name = "fallible-streaming-iterator"
@@ -696,12 +521,6 @@ version = "0.1.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7360491ce676a36bf9bb3c56c1aa791658183a54d2744120f27285738d90465a"
 
-[[package]]
-name = "fastrand"
-version = "2.1.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9fc0510504f03c51ada170672ac806f1f105a88aa97a5281117e1ddc3368e51a"
-
 [[package]]
 name = "flatbuffers"
 version = "23.5.26"
@@ -722,129 +541,12 @@ dependencies = [
  "miniz_oxide",
 ]
 
-[[package]]
-name = "flume"
-version = "0.11.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "55ac459de2512911e4b674ce33cf20befaba382d05b62b008afc1c8b57cbf181"
-dependencies = [
- "futures-core",
- "futures-sink",
- "spin 0.9.8",
-]
-
 [[package]]
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 version = "1.0.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
 
-[[package]]
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-version = "0.3.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f6f339eb8adc052cd2ca78910fda869aefa38d22d5cb648e6485e4d3fc06f3b1"
-dependencies = [
- "foreign-types-shared",
-]
-
-[[package]]
-name = "foreign-types-shared"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
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-
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-dependencies = [
- "percent-encoding",
-]
-
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-dependencies = [
- "futures-core",
- "futures-sink",
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-
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-version = "0.3.30"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dfc6580bb841c5a68e9ef15c77ccc837b40a7504914d52e47b8b0e9bbda25a1d"
-
-[[package]]
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-version = "0.3.30"
-source = "registry+https://github.com/rust-lang/crates.io-index"
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-dependencies = [
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- "futures-task",
- "futures-util",
-]
-
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
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-dependencies = [
- "futures-core",
- "lock_api",
- "parking_lot",
-]
-
-[[package]]
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-version = "0.3.30"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a44623e20b9681a318efdd71c299b6b222ed6f231972bfe2f224ebad6311f0c1"
-
-[[package]]
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-version = "0.3.30"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9fb8e00e87438d937621c1c6269e53f536c14d3fbd6a042bb24879e57d474fb5"
-
-[[package]]
-name = "futures-task"
-version = "0.3.30"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "38d84fa142264698cdce1a9f9172cf383a0c82de1bddcf3092901442c4097004"
-
-[[package]]
-name = "futures-util"
-version = "0.3.30"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3d6401deb83407ab3da39eba7e33987a73c3df0c82b4bb5813ee871c19c41d48"
-dependencies = [
- "futures-core",
- "futures-io",
- "futures-sink",
- "futures-task",
- "memchr",
- "pin-project-lite",
- "pin-utils",
- "slab",
-]
-
-[[package]]
-name = "generic-array"
-version = "0.14.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a"
-dependencies = [
- "typenum",
- "version_check",
-]
-
 [[package]]
 name = "getrandom"
 version = "0.2.15"
@@ -856,12 +558,6 @@ dependencies = [
  "wasi",
 ]
 
-[[package]]
-name = "gimli"
-version = "0.29.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "40ecd4077b5ae9fd2e9e169b102c6c330d0605168eb0e8bf79952b256dbefffd"
-
 [[package]]
 name = "half"
 version = "2.4.1"
@@ -880,27 +576,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1"
 dependencies = [
  "ahash",
- "allocator-api2",
 ]
 
 [[package]]
 name = "hashlink"
-version = "0.8.4"
+version = "0.9.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e8094feaf31ff591f651a2664fb9cfd92bba7a60ce3197265e9482ebe753c8f7"
+checksum = "6ba4ff7128dee98c7dc9794b6a411377e1404dba1c97deb8d1a55297bd25d8af"
 dependencies = [
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 ]
 
-[[package]]
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-version = "0.4.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
-dependencies = [
- "unicode-segmentation",
-]
-
 [[package]]
 name = "heck"
 version = "0.5.0"
@@ -916,45 +602,6 @@ dependencies = [
  "libc",
 ]
 
-[[package]]
-name = "hermit-abi"
-version = "0.3.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024"
-
-[[package]]
-name = "hex"
-version = "0.4.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f24254aa9a54b5c858eaee2f5bccdb46aaf0e486a595ed5fd8f86ba55232a70"
-
-[[package]]
-name = "hkdf"
-version = "0.12.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7b5f8eb2ad728638ea2c7d47a21db23b7b58a72ed6a38256b8a1849f15fbbdf7"
-dependencies = [
- "hmac",
-]
-
-[[package]]
-name = "hmac"
-version = "0.12.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6c49c37c09c17a53d937dfbb742eb3a961d65a994e6bcdcf37e7399d0cc8ab5e"
-dependencies = [
- "digest",
-]
-
-[[package]]
-name = "home"
-version = "0.5.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e3d1354bf6b7235cb4a0576c2619fd4ed18183f689b12b006a0ee7329eeff9a5"
-dependencies = [
- "windows-sys 0.52.0",
-]
-
 [[package]]
 name = "humantime"
 version = "1.3.0"
@@ -987,16 +634,6 @@ dependencies = [
  "cc",
 ]
 
-[[package]]
-name = "idna"
-version = "0.5.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "634d9b1461af396cad843f47fdba5597a4f9e6ddd4bfb6ff5d85028c25cb12f6"
-dependencies = [
- "unicode-bidi",
- "unicode-normalization",
-]
-
 [[package]]
 name = "indexmap"
 version = "2.2.6"
@@ -1043,7 +680,6 @@ dependencies = [
  "clap",
  "csv",
  "indicatif",
- "libsqlite3-sys",
  "log",
  "num",
  "num-traits",
@@ -1053,9 +689,7 @@ dependencies = [
  "sage-core",
  "serde",
  "serde_json",
- "sqlx",
  "timsrust",
- "tokio",
  "toml",
 ]
 
@@ -1103,9 +737,6 @@ name = "lazy_static"
 version = "1.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
-dependencies = [
- "spin 0.5.2",
-]
 
 [[package]]
 name = "lexical-core"
@@ -1185,9 +816,9 @@ checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
 
 [[package]]
 name = "libsqlite3-sys"
-version = "0.26.0"
+version = "0.28.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "afc22eff61b133b115c6e8c74e818c628d6d5e7a502afea6f64dee076dd94326"
+checksum = "0c10584274047cb335c23d3e61bcef8e323adae7c5c8c760540f73610177fc3f"
 dependencies = [
  "cc",
  "pkg-config",
@@ -1204,12 +835,6 @@ dependencies = [
  "num-traits",
 ]
 
-[[package]]
-name = "linux-raw-sys"
-version = "0.4.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89"
-
 [[package]]
 name = "lock_api"
 version = "0.4.12"
@@ -1246,16 +871,6 @@ dependencies = [
  "libc",
 ]
 
-[[package]]
-name = "md-5"
-version = "0.10.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d89e7ee0cfbedfc4da3340218492196241d89eefb6dab27de5df917a6d2e78cf"
-dependencies = [
- "cfg-if",
- "digest",
-]
-
 [[package]]
 name = "memchr"
 version = "2.7.2"
@@ -1263,10 +878,13 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d"
 
 [[package]]
-name = "minimal-lexical"
-version = "0.2.1"
+name = "memmap2"
+version = "0.9.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
+checksum = "fd3f7eed9d3848f8b98834af67102b720745c4ec028fcd0aa0239277e7de374f"
+dependencies = [
+ "libc",
+]
 
 [[package]]
 name = "miniz_oxide"
@@ -1277,44 +895,6 @@ dependencies = [
  "adler",
 ]
 
-[[package]]
-name = "mio"
-version = "0.8.11"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a4a650543ca06a924e8b371db273b2756685faae30f8487da1b56505a8f78b0c"
-dependencies = [
- "libc",
- "wasi",
- "windows-sys 0.48.0",
-]
-
-[[package]]
-name = "native-tls"
-version = "0.2.12"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a8614eb2c83d59d1c8cc974dd3f920198647674a0a035e1af1fa58707e317466"
-dependencies = [
- "libc",
- "log",
- "openssl",
- "openssl-probe",
- "openssl-sys",
- "schannel",
- "security-framework",
- "security-framework-sys",
- "tempfile",
-]
-
-[[package]]
-name = "nom"
-version = "7.1.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a"
-dependencies = [
- "memchr",
- "minimal-lexical",
-]
-
 [[package]]
 name = "num"
 version = "0.4.3"
@@ -1340,27 +920,10 @@ dependencies = [
 ]
 
 [[package]]
-name = "num-bigint-dig"
-version = "0.8.4"
+name = "num-complex"
+version = "0.4.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dc84195820f291c7697304f3cbdadd1cb7199c0efc917ff5eafd71225c136151"
-dependencies = [
- "byteorder",
- "lazy_static",
- "libm",
- "num-integer",
- "num-iter",
- "num-traits",
- "rand",
- "smallvec",
- "zeroize",
-]
-
-[[package]]
-name = "num-complex"
-version = "0.4.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495"
+checksum = "73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495"
 dependencies = [
  "num-traits",
 ]
@@ -1406,81 +969,18 @@ dependencies = [
  "libm",
 ]
 
-[[package]]
-name = "num_cpus"
-version = "1.16.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4161fcb6d602d4d2081af7c3a45852d875a03dd337a6bfdd6e06407b61342a43"
-dependencies = [
- "hermit-abi 0.3.9",
- "libc",
-]
-
 [[package]]
 name = "number_prefix"
 version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
 
-[[package]]
-name = "object"
-version = "0.36.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "576dfe1fc8f9df304abb159d767a29d0476f7750fbf8aa7ad07816004a207434"
-dependencies = [
- "memchr",
-]
-
 [[package]]
 name = "once_cell"
 version = "1.19.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
 
-[[package]]
-name = "openssl"
-version = "0.10.66"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9529f4786b70a3e8c61e11179af17ab6188ad8d0ded78c5529441ed39d4bd9c1"
-dependencies = [
- "bitflags 2.5.0",
- "cfg-if",
- "foreign-types",
- "libc",
- "once_cell",
- "openssl-macros",
- "openssl-sys",
-]
-
-[[package]]
-name = "openssl-macros"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.66",
-]
-
-[[package]]
-name = "openssl-probe"
-version = "0.1.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ff011a302c396a5197692431fc1948019154afc178baf7d8e37367442a4601cf"
-
-[[package]]
-name = "openssl-sys"
-version = "0.9.103"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f9e8deee91df40a943c71b917e5874b951d32a802526c85721ce3b776c929d6"
-dependencies = [
- "cc",
- "libc",
- "pkg-config",
- "vcpkg",
-]
-
 [[package]]
 name = "ordered-float"
 version = "2.10.1"
@@ -1490,16 +990,6 @@ dependencies = [
  "num-traits",
 ]
 
-[[package]]
-name = "parking_lot"
-version = "0.12.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f1bf18183cf54e8d6059647fc3063646a1801cf30896933ec2311622cc4b9a27"
-dependencies = [
- "lock_api",
- "parking_lot_core",
-]
-
 [[package]]
 name = "parking_lot_core"
 version = "0.9.10"
@@ -1508,9 +998,9 @@ checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8"
 dependencies = [
  "cfg-if",
  "libc",
- "redox_syscall 0.5.1",
+ "redox_syscall",
  "smallvec",
- "windows-targets 0.52.5",
+ "windows-targets",
 ]
 
 [[package]]
@@ -1541,7 +1031,7 @@ dependencies = [
  "snap",
  "thrift",
  "twox-hash",
- "zstd",
+ "zstd 0.12.4",
 ]
 
 [[package]]
@@ -1550,54 +1040,6 @@ version = "1.0.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a"
 
-[[package]]
-name = "pem-rfc7468"
-version = "0.7.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "88b39c9bfcfc231068454382784bb460aae594343fb030d46e9f50a645418412"
-dependencies = [
- "base64ct",
-]
-
-[[package]]
-name = "percent-encoding"
-version = "2.3.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e3148f5046208a5d56bcfc03053e3ca6334e51da8dfb19b6cdc8b306fae3283e"
-
-[[package]]
-name = "pin-project-lite"
-version = "0.2.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bda66fc9667c18cb2758a2ac84d1167245054bcf85d5d1aaa6923f45801bdd02"
-
-[[package]]
-name = "pin-utils"
-version = "0.1.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8b870d8c151b6f2fb93e84a13146138f05d02ed11c7e7c54f8826aaaf7c9f184"
-
-[[package]]
-name = "pkcs1"
-version = "0.7.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c8ffb9f10fa047879315e6625af03c164b16962a5368d724ed16323b68ace47f"
-dependencies = [
- "der",
- "pkcs8",
- "spki",
-]
-
-[[package]]
-name = "pkcs8"
-version = "0.10.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f950b2377845cebe5cf8b5165cb3cc1a5e0fa5cfa3e1f7f55707d8fd82e0a7b7"
-dependencies = [
- "der",
- "spki",
-]
-
 [[package]]
 name = "pkg-config"
 version = "0.3.30"
@@ -1700,15 +1142,6 @@ dependencies = [
  "crossbeam-utils",
 ]
 
-[[package]]
-name = "redox_syscall"
-version = "0.4.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
-dependencies = [
- "bitflags 1.3.2",
-]
-
 [[package]]
 name = "redox_syscall"
 version = "0.5.1"
@@ -1747,31 +1180,11 @@ version = "0.8.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56"
 
-[[package]]
-name = "rsa"
-version = "0.9.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5d0e5124fcb30e76a7e79bfee683a2746db83784b86289f6251b54b7950a0dfc"
-dependencies = [
- "const-oid",
- "digest",
- "num-bigint-dig",
- "num-integer",
- "num-traits",
- "pkcs1",
- "pkcs8",
- "rand_core",
- "signature",
- "spki",
- "subtle",
- "zeroize",
-]
-
 [[package]]
 name = "rusqlite"
-version = "0.29.0"
+version = "0.31.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "549b9d036d571d42e6e85d1c1425e2ac83491075078ca9a15be021c56b1641f2"
+checksum = "b838eba278d213a8beaf485bd313fd580ca4505a00d5871caeb1457c55322cae"
 dependencies = [
  "bitflags 2.5.0",
  "fallible-iterator",
@@ -1781,12 +1194,6 @@ dependencies = [
  "smallvec",
 ]
 
-[[package]]
-name = "rustc-demangle"
-version = "0.1.24"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "719b953e2095829ee67db738b3bfa9fa368c94900df327b3f07fe6e794d2fe1f"
-
 [[package]]
 name = "rustc_version"
 version = "0.4.0"
@@ -1796,19 +1203,6 @@ dependencies = [
  "semver",
 ]
 
-[[package]]
-name = "rustix"
-version = "0.38.34"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "70dc5ec042f7a43c4a73241207cecc9873a06d45debb38b329f8541d85c2730f"
-dependencies = [
- "bitflags 2.5.0",
- "errno",
- "libc",
- "linux-raw-sys",
- "windows-sys 0.52.0",
-]
-
 [[package]]
 name = "ryu"
 version = "1.0.18"
@@ -1829,44 +1223,12 @@ dependencies = [
  "serde",
 ]
 
-[[package]]
-name = "schannel"
-version = "0.1.23"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fbc91545643bcf3a0bbb6569265615222618bdf33ce4ffbbd13c4bbd4c093534"
-dependencies = [
- "windows-sys 0.52.0",
-]
-
 [[package]]
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 version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
 
-[[package]]
-name = "security-framework"
-version = "2.11.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c627723fd09706bacdb5cf41499e95098555af3c3c29d014dc3c458ef6be11c0"
-dependencies = [
- "bitflags 2.5.0",
- "core-foundation",
- "core-foundation-sys",
- "libc",
- "security-framework-sys",
-]
-
-[[package]]
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-version = "2.11.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "317936bbbd05227752583946b9e66d7ce3b489f84e11a94a510b4437fef407d7"
-dependencies = [
- "core-foundation-sys",
- "libc",
-]
-
 [[package]]
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 version = "1.0.23"
@@ -1881,18 +1243,18 @@ checksum = "a3f0bf26fd526d2a95683cd0f87bf103b8539e2ca1ef48ce002d67aad59aa0b4"
 
 [[package]]
 name = "serde"
-version = "1.0.202"
+version = "1.0.210"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "226b61a0d411b2ba5ff6d7f73a476ac4f8bb900373459cd00fab8512828ba395"
+checksum = "c8e3592472072e6e22e0a54d5904d9febf8508f65fb8552499a1abc7d1078c3a"
 dependencies = [
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 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.202"
+version = "1.0.210"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6048858004bcff69094cd972ed40a32500f153bd3be9f716b2eed2e8217c4838"
+checksum = "243902eda00fad750862fc144cea25caca5e20d615af0a81bee94ca738f1df1f"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1901,11 +1263,12 @@ dependencies = [
 
 [[package]]
 name = "serde_json"
-version = "1.0.117"
+version = "1.0.128"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "455182ea6142b14f93f4bc5320a2b31c1f266b66a4a5c858b013302a5d8cbfc3"
+checksum = "6ff5456707a1de34e7e37f2a6fd3d3f808c318259cbd01ab6377795054b483d8"
 dependencies = [
  "itoa",
+ "memchr",
  "ryu",
  "serde",
 ]
@@ -1919,47 +1282,6 @@ dependencies = [
  "serde",
 ]
 
-[[package]]
-name = "sha1"
-version = "0.10.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e3bf829a2d51ab4a5ddf1352d8470c140cadc8301b2ae1789db023f01cedd6ba"
-dependencies = [
- "cfg-if",
- "cpufeatures",
- "digest",
-]
-
-[[package]]
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-version = "0.10.8"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "793db75ad2bcafc3ffa7c68b215fee268f537982cd901d132f89c6343f3a3dc8"
-dependencies = [
- "cfg-if",
- "cpufeatures",
- "digest",
-]
-
-[[package]]
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-version = "2.2.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "77549399552de45a898a580c1b41d445bf730df867cc44e6c0233bbc4b8329de"
-dependencies = [
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- "rand_core",
-]
-
-[[package]]
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-dependencies = [
- "autocfg",
-]
-
 [[package]]
 name = "smallvec"
 version = "1.13.2"
@@ -1972,275 +1294,18 @@ version = "1.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1b6b67fb9a61334225b5b790716f609cd58395f895b3fe8b328786812a40bc3b"
 
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
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-dependencies = [
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- "windows-sys 0.52.0",
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-
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-
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-
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-
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-
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- "rand",
- "serde",
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- "sha1",
- "sha2",
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- "futures-util",
- "libsqlite3-sys",
- "log",
- "percent-encoding",
- "serde",
- "sqlx-core",
- "tracing",
- "url",
-]
-
 [[package]]
 name = "static_assertions"
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 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f"
 
-[[package]]
-name = "stringprep"
-version = "0.1.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7b4df3d392d81bd458a8a621b8bffbd2302a12ffe288a9d931670948749463b1"
-dependencies = [
- "unicode-bidi",
- "unicode-normalization",
- "unicode-properties",
-]
-
 [[package]]
 name = "strsim"
 version = "0.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 
-[[package]]
-name = "subtle"
-version = "2.6.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0d0208408ba0c3df17ed26eb06992cb1a1268d41b2c0e12e65203fbe3972cee5"
-
 [[package]]
 name = "syn"
 version = "1.0.109"
@@ -2263,18 +1328,6 @@ dependencies = [
  "unicode-ident",
 ]
 
-[[package]]
-name = "tempfile"
-version = "3.10.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "85b77fafb263dd9d05cbeac119526425676db3784113aa9295c88498cbf8bff1"
-dependencies = [
- "cfg-if",
- "fastrand",
- "rustix",
- "windows-sys 0.52.0",
-]
-
 [[package]]
 name = "termcolor"
 version = "1.4.1"
@@ -2317,18 +1370,20 @@ dependencies = [
 
 [[package]]
 name = "timsrust"
-version = "0.2.2"
+version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a0791ad8b3836b6a582b1bfb563c04d0e09acdaf85e45c16d3158a0bcb164b6"
+checksum = "4e6cc90c026b287bcea09d4a68231ee81dc3ec773447894134ad226fff006a20"
 dependencies = [
  "bytemuck",
- "byteorder",
  "linreg",
+ "memmap2",
  "parquet",
  "rayon",
  "rusqlite",
+ "serde",
+ "serde_json",
  "thiserror",
- "zstd",
+ "zstd 0.13.2",
 ]
 
 [[package]]
@@ -2340,48 +1395,6 @@ dependencies = [
  "crunchy",
 ]
 
-[[package]]
-name = "tinyvec"
-version = "1.6.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50"
-dependencies = [
- "tinyvec_macros",
-]
-
-[[package]]
-name = "tinyvec_macros"
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-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20"
-
-[[package]]
-name = "tokio"
-version = "1.38.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ba4f4a02a7a80d6f274636f0aa95c7e383b912d41fe721a31f29e29698585a4a"
-dependencies = [
- "backtrace",
- "bytes",
- "libc",
- "mio",
- "num_cpus",
- "pin-project-lite",
- "socket2",
- "windows-sys 0.48.0",
-]
-
-[[package]]
-name = "tokio-stream"
-version = "0.1.15"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "267ac89e0bec6e691e5813911606935d77c476ff49024f98abcea3e7b15e37af"
-dependencies = [
- "futures-core",
- "pin-project-lite",
- "tokio",
-]
-
 [[package]]
 name = "toml"
 version = "0.8.13"
@@ -2416,38 +1429,6 @@ dependencies = [
  "winnow",
 ]
 
-[[package]]
-name = "tracing"
-version = "0.1.40"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c3523ab5a71916ccf420eebdf5521fcef02141234bbc0b8a49f2fdc4544364ef"
-dependencies = [
- "log",
- "pin-project-lite",
- "tracing-attributes",
- "tracing-core",
-]
-
-[[package]]
-name = "tracing-attributes"
-version = "0.1.27"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "34704c8d6ebcbc939824180af020566b01a7c01f80641264eba0999f6c2b6be7"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.66",
-]
-
-[[package]]
-name = "tracing-core"
-version = "0.1.32"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c06d3da6113f116aaee68e4d601191614c9053067f9ab7f6edbcb161237daa54"
-dependencies = [
- "once_cell",
-]
-
 [[package]]
 name = "twox-hash"
 version = "1.6.3"
@@ -2458,68 +1439,18 @@ dependencies = [
  "static_assertions",
 ]
 
-[[package]]
-name = "typenum"
-version = "1.17.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825"
-
-[[package]]
-name = "unicode-bidi"
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-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "08f95100a766bf4f8f28f90d77e0a5461bbdb219042e7679bebe79004fed8d75"
-
 [[package]]
 name = "unicode-ident"
 version = "1.0.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
 
-[[package]]
-name = "unicode-normalization"
-version = "0.1.23"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a56d1686db2308d901306f92a263857ef59ea39678a5458e7cb17f01415101f5"
-dependencies = [
- "tinyvec",
-]
-
-[[package]]
-name = "unicode-properties"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e4259d9d4425d9f0661581b804cb85fe66a4c631cadd8f490d1c13a35d5d9291"
-
-[[package]]
-name = "unicode-segmentation"
-version = "1.11.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d4c87d22b6e3f4a18d4d40ef354e97c90fcb14dd91d7dc0aa9d8a1172ebf7202"
-
 [[package]]
 name = "unicode-width"
 version = "0.1.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "68f5e5f3158ecfd4b8ff6fe086db7c8467a2dfdac97fe420f2b7c4aa97af66d6"
 
-[[package]]
-name = "unicode_categories"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "39ec24b3121d976906ece63c9daad25b85969647682eee313cb5779fdd69e14e"
-
-[[package]]
-name = "url"
-version = "2.5.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "22784dbdf76fdde8af1aeda5622b546b422b6fc585325248a2bf9f5e41e94d6c"
-dependencies = [
- "form_urlencoded",
- "idna",
- "percent-encoding",
-]
-
 [[package]]
 name = "utf8parse"
 version = "0.2.2"
@@ -2544,12 +1475,6 @@ version = "0.11.0+wasi-snapshot-preview1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
-[[package]]
-name = "wasite"
-version = "0.1.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b8dad83b4f25e74f184f64c43b150b91efe7647395b42289f38e50566d82855b"
-
 [[package]]
 name = "wasm-bindgen"
 version = "0.2.92"
@@ -2604,16 +1529,6 @@ version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96"
 
-[[package]]
-name = "whoami"
-version = "1.5.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a44ab49fad634e88f55bf8f9bb3abd2f27d7204172a112c7c9987e01c1c94ea9"
-dependencies = [
- "redox_syscall 0.4.1",
- "wasite",
-]
-
 [[package]]
 name = "winapi"
 version = "0.3.9"
@@ -2636,7 +1551,7 @@ version = "0.1.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b"
 dependencies = [
- "windows-sys 0.52.0",
+ "windows-sys",
 ]
 
 [[package]]
@@ -2651,16 +1566,7 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9"
 dependencies = [
- "windows-targets 0.52.5",
-]
-
-[[package]]
-name = "windows-sys"
-version = "0.48.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9"
-dependencies = [
- "windows-targets 0.48.5",
+ "windows-targets",
 ]
 
 [[package]]
@@ -2669,22 +1575,7 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
 dependencies = [
- "windows-targets 0.52.5",
-]
-
-[[package]]
-name = "windows-targets"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c"
-dependencies = [
- "windows_aarch64_gnullvm 0.48.5",
- "windows_aarch64_msvc 0.48.5",
- "windows_i686_gnu 0.48.5",
- "windows_i686_msvc 0.48.5",
- "windows_x86_64_gnu 0.48.5",
- "windows_x86_64_gnullvm 0.48.5",
- "windows_x86_64_msvc 0.48.5",
+ "windows-targets",
 ]
 
 [[package]]
@@ -2693,46 +1584,28 @@ version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb"
 dependencies = [
- "windows_aarch64_gnullvm 0.52.5",
- "windows_aarch64_msvc 0.52.5",
- "windows_i686_gnu 0.52.5",
+ "windows_aarch64_gnullvm",
+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
  "windows_i686_gnullvm",
- "windows_i686_msvc 0.52.5",
- "windows_x86_64_gnu 0.52.5",
- "windows_x86_64_gnullvm 0.52.5",
- "windows_x86_64_msvc 0.52.5",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
 ]
 
-[[package]]
-name = "windows_aarch64_gnullvm"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
-
 [[package]]
 name = "windows_aarch64_gnullvm"
 version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263"
 
-[[package]]
-name = "windows_aarch64_msvc"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
-
 [[package]]
 name = "windows_aarch64_msvc"
 version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6"
 
-[[package]]
-name = "windows_i686_gnu"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
-
 [[package]]
 name = "windows_i686_gnu"
 version = "0.52.5"
@@ -2745,48 +1618,24 @@ version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9"
 
-[[package]]
-name = "windows_i686_msvc"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
-
 [[package]]
 name = "windows_i686_msvc"
 version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf"
 
-[[package]]
-name = "windows_x86_64_gnu"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
-
 [[package]]
 name = "windows_x86_64_gnu"
 version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9"
 
-[[package]]
-name = "windows_x86_64_gnullvm"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
-
 [[package]]
 name = "windows_x86_64_gnullvm"
 version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596"
 
-[[package]]
-name = "windows_x86_64_msvc"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
-
 [[package]]
 name = "windows_x86_64_msvc"
 version = "0.52.5"
@@ -2823,18 +1672,21 @@ dependencies = [
 ]
 
 [[package]]
-name = "zeroize"
-version = "1.8.1"
+name = "zstd"
+version = "0.12.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ced3678a2879b30306d323f4542626697a464a97c0a07c9aebf7ebca65cd4dde"
+checksum = "1a27595e173641171fc74a1232b7b1c7a7cb6e18222c11e9dfb9888fa424c53c"
+dependencies = [
+ "zstd-safe 6.0.6",
+]
 
 [[package]]
 name = "zstd"
-version = "0.12.4"
+version = "0.13.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1a27595e173641171fc74a1232b7b1c7a7cb6e18222c11e9dfb9888fa424c53c"
+checksum = "fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9"
 dependencies = [
- "zstd-safe",
+ "zstd-safe 7.2.1",
 ]
 
 [[package]]
@@ -2847,6 +1699,15 @@ dependencies = [
  "zstd-sys",
 ]
 
+[[package]]
+name = "zstd-safe"
+version = "7.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059"
+dependencies = [
+ "zstd-sys",
+]
+
 [[package]]
 name = "zstd-sys"
 version = "2.0.10+zstd.1.5.6"
diff --git a/Cargo.toml b/Cargo.toml
index 5717454..0806300 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -7,7 +7,7 @@ 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"] }
@@ -22,10 +22,6 @@ clap = {version = "4.4.17", features = ["derive"]}
 csv = "1.3.0"
 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"]}
-
 # Sage
 sage-core = { git = "https://github.com/lazear/sage.git", rev = "9e870429889b341c4773df32b65e553283301a93" }
 toml = "0.8.8"
diff --git a/src/aggregation/dbscan/denseframe_dbscan.rs b/src/aggregation/dbscan/denseframe_dbscan.rs
index 87feca7..03b4268 100644
--- a/src/aggregation/dbscan/denseframe_dbscan.rs
+++ b/src/aggregation/dbscan/denseframe_dbscan.rs
@@ -1,3 +1,9 @@
+use timsrust::{
+    AcquisitionType,
+    MSLevel,
+    QuadrupoleSettings,
+};
+
 use crate::aggregation::aggregators::TimsPeakAggregator;
 use crate::aggregation::converters::{
     BypassDenseFrameBackConverter,
@@ -6,6 +12,7 @@ use crate::aggregation::converters::{
 use crate::aggregation::dbscan::dbscan::dbscan_generic;
 use crate::ms::frames::{
     DenseFrame,
+    SingleQuadrupoleSettings,
     TimsPeak,
 };
 use crate::space::space_generics::{
@@ -25,9 +32,12 @@ 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 +82,11 @@ 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,
     }
 }
 
diff --git a/src/aggregation/ms_denoise.rs b/src/aggregation/ms_denoise.rs
index e41125f..31b3cb2 100644
--- a/src/aggregation/ms_denoise.rs
+++ b/src/aggregation/ms_denoise.rs
@@ -1,5 +1,6 @@
 use core::fmt::Debug;
 use core::panic;
+use std::path::Path;
 
 use indicatif::ParallelProgressIterator;
 use log::{
@@ -13,7 +14,17 @@ use serde::{
     Deserialize,
     Serialize,
 };
-use timsrust::Frame;
+use timsrust::converters::{
+    Scan2ImConverter,
+    Tof2MzConverter,
+};
+use timsrust::{
+    AcquisitionType,
+    Frame,
+    MSLevel,
+    QuadrupoleSettings,
+    TimsRustError,
+};
 
 use super::aggregators::aggregate_clusters;
 use super::dbscan::runner::dbscan_label_clusters;
@@ -28,11 +39,9 @@ use crate::ms::frames::{
     DenseFrameWindow,
     ExpandedFrameSlice,
     FrameSlice,
-    MsMsFrameSliceWindowInfo,
+    SingleQuadrupoleSettings,
     TimsPeak,
 };
-use crate::ms::tdf;
-use crate::ms::tdf::DIAFrameInfo;
 use crate::space::space_generics::{
     AsNDPointsAtIndex,
     IntenseAtIndex,
@@ -167,9 +176,8 @@ fn _denoise_denseframe(
 
 fn denoise_frame_slice_window(
     frameslice_window: &[ExpandedFrameSlice],
-    ims_converter: &timsrust::Scan2ImConverter,
-    mz_converter: &timsrust::Tof2MzConverter,
-    _dia_frame_info: &DIAFrameInfo,
+    ims_converter: &Scan2ImConverter,
+    mz_converter: &Tof2MzConverter,
     min_n: usize,
     min_intensity: u64,
     _mz_scaling: f64,
@@ -224,23 +232,7 @@ fn denoise_frame_slice_window(
     );
 
     let ref_frame = &frameslice_window[frameslice_window.len() / 2];
-    if ref_frame.slice_window_info.is_none() {
-        panic!("No slice window info found");
-    }
-
-    let slice_info = ref_frame.slice_window_info.as_ref().unwrap();
-    let quad_group_id = match slice_info {
-        MsMsFrameSliceWindowInfo::WindowGroup(x) => *x,
-        MsMsFrameSliceWindowInfo::SingleWindow(x) => x.global_quad_row_id,
-    };
-    let min_mz = match slice_info {
-        MsMsFrameSliceWindowInfo::WindowGroup(_x) => 0.0,
-        MsMsFrameSliceWindowInfo::SingleWindow(x) => x.mz_start,
-    };
-    let max_mz = match slice_info {
-        MsMsFrameSliceWindowInfo::WindowGroup(_x) => 0.0,
-        MsMsFrameSliceWindowInfo::SingleWindow(x) => x.mz_end,
-    };
+    let quad_settings = ref_frame.quadrupole_settings.clone();
 
     let mut raw_peaks: Vec<TimsPeak> = centroids
         .into_iter()
@@ -266,15 +258,16 @@ fn denoise_frame_slice_window(
             raw_peaks,
             index: ref_frame.parent_frame_index,
             rt: ref_frame.rt,
-            frame_type: timsrust::FrameType::MS2(timsrust::AcquisitionType::DIAPASEF),
+            acquisition_type: ref_frame.acquisition_type,
+            ms_level: ref_frame.ms_level,
             sorted: None,
+            window_group_id: ref_frame.window_group_id,
+            intensity_correction_factor: ref_frame.intensity_correction_factor,
         },
         ims_max: max_ims,
         ims_min: min_ims,
-        mz_start: min_mz as f64,
-        mz_end: max_mz as f64,
-        group_id: quad_group_id,
-        quad_group_id,
+        group_id: ref_frame.window_group_id.into(),
+        quadrupole_setting: quad_settings,
     };
     maybe_save_json_if_debugging(
         &out,
@@ -287,9 +280,8 @@ fn denoise_frame_slice_window(
 
 fn denoise_frame_slice(
     frame_window: &FrameSlice,
-    ims_converter: &timsrust::Scan2ImConverter,
-    mz_converter: &timsrust::Tof2MzConverter,
-    dia_frame_info: &DIAFrameInfo,
+    ims_converter: &Scan2ImConverter,
+    mz_converter: &Tof2MzConverter,
     min_n: usize,
     min_intensity: u64,
     mz_scaling: f64,
@@ -297,12 +289,8 @@ fn denoise_frame_slice(
     ims_scaling: f32,
     max_ims_extension: f32,
 ) -> DenseFrameWindow {
-    let denseframe_window = DenseFrameWindow::from_frame_window(
-        frame_window,
-        ims_converter,
-        mz_converter,
-        dia_frame_info,
-    );
+    let denseframe_window =
+        DenseFrameWindow::from_frame_window(frame_window, ims_converter, mz_converter);
     let denoised_frame = _denoise_denseframe(
         denseframe_window.frame,
         min_n,
@@ -317,10 +305,8 @@ fn denoise_frame_slice(
         frame: denoised_frame,
         ims_min: denseframe_window.ims_min,
         ims_max: denseframe_window.ims_max,
-        mz_start: denseframe_window.mz_start,
-        mz_end: denseframe_window.mz_end,
         group_id: denseframe_window.group_id,
-        quad_group_id: denseframe_window.quad_group_id,
+        quadrupole_setting: denseframe_window.quadrupole_setting,
     }
 }
 
@@ -365,8 +351,8 @@ struct FrameDenoiser {
     ims_scaling: f32,
     max_mz_extension: f64,
     max_ims_extension: f32,
-    ims_converter: timsrust::Scan2ImConverter,
-    mz_converter: timsrust::Tof2MzConverter,
+    ims_converter: Scan2ImConverter,
+    mz_converter: Tof2MzConverter,
 }
 
 impl<'a> Denoiser<'a, Frame, DenseFrame, Converters, Option<usize>> for FrameDenoiser {
@@ -394,9 +380,8 @@ struct DIAFrameDenoiser {
     max_mz_extension: f64,
     ims_scaling: f32,
     max_ims_extension: f32,
-    dia_frame_info: DIAFrameInfo,
-    ims_converter: timsrust::Scan2ImConverter,
-    mz_converter: timsrust::Tof2MzConverter,
+    ims_converter: Scan2ImConverter,
+    mz_converter: Tof2MzConverter,
 }
 
 // impl DIAFrameDenoiser {
@@ -433,7 +418,23 @@ impl<'a> Denoiser<'a, Frame, Vec<DenseFrameWindow>, Converters, Option<usize>>
     {
         info!("Denoising (centroiding) {} frames", elems.len());
 
-        let mut frame_window_slices = self.dia_frame_info.split_frame_windows(&elems);
+        let mut flat_windows: Vec<FrameSlice<'_>> = elems
+            .par_iter()
+            .flat_map(|x: &Frame| FrameSlice::from_frame(x))
+            .collect();
+
+        flat_windows.par_sort_unstable_by(|a, b| {
+            a.quadrupole_settings
+                .partial_cmp(&b.quadrupole_settings)
+                .unwrap()
+        });
+
+        let mut break_points = vec![0];
+        for i in 1..flat_windows.len() {
+            if flat_windows[i].quadrupole_settings != flat_windows[i - 1].quadrupole_settings {
+                break_points.push(i);
+            }
+        }
 
         // If profiling and having the "IONMESH_PROFILE_NUM_WINDOWS" env variable set
         // then only process the first N slices of windows.
@@ -441,7 +442,8 @@ impl<'a> Denoiser<'a, Frame, Vec<DenseFrameWindow>, Converters, Option<usize>>
         if let Ok(num_windows) = std::env::var("IONMESH_PROFILE_NUM_WINDOWS") {
             let num_windows: usize = num_windows.parse().unwrap();
             log::warn!("Profiling: Only processing {} windows", num_windows);
-            frame_window_slices.truncate(num_windows);
+            flat_windows.truncate(break_points[num_windows]);
+            break_points.truncate(num_windows);
         }
 
         // This warning reders to denoise_frame_slice_window.
@@ -450,9 +452,12 @@ impl<'a> Denoiser<'a, Frame, Vec<DenseFrameWindow>, Converters, Option<usize>>
         // by timsrust ...
         warn!("Using prototype function for denoising, scalings are hard-coded");
 
-        let mut out = Vec::with_capacity(frame_window_slices.len());
-        let num_windows = frame_window_slices.len();
-        for (i, sv) in frame_window_slices.iter().enumerate() {
+        let num_windows = break_points.len() - 1;
+        let mut out = Vec::with_capacity(num_windows);
+        let frame_window_slices: Vec<(usize, &[FrameSlice])> = (0..num_windows)
+            .map(|i| (i, &flat_windows[break_points[i]..break_points[i + 1]]))
+            .collect();
+        for (i, sv) in frame_window_slices.iter() {
             info!("Denoising window {}/{}", i + 1, num_windows);
             let start_tot_peaks = sv.iter().map(|x| x.num_ndpoints() as u64).sum::<u64>();
             let progbar = indicatif::ProgressBar::new(sv.len() as u64);
@@ -462,7 +467,6 @@ impl<'a> Denoiser<'a, Frame, Vec<DenseFrameWindow>, Converters, Option<usize>>
                     x,
                     &self.ims_converter,
                     &self.mz_converter,
-                    &self.dia_frame_info,
                     self.min_n,
                     self.min_intensity,
                     self.mz_scaling,
@@ -481,7 +485,7 @@ impl<'a> Denoiser<'a, Frame, Vec<DenseFrameWindow>, Converters, Option<usize>>
                     .map(lambda_denoise)
                     .collect::<Vec<_>>()
             } else {
-                sv.into_par_iter()
+                sv.par_iter()
                     .map(|x| ExpandedFrameSlice::from_frame_slice(x))
                     .collect::<Vec<ExpandedFrameSlice>>()
                     .par_windows(3)
@@ -518,18 +522,22 @@ pub fn read_all_ms1_denoising(
     max_mz_extension: f64,
     ims_scaling: f32,
     max_ims_extension: f32,
-) -> Vec<DenseFrame> {
-    let reader = timsrust::FileReader::new(path).unwrap();
+) -> Result<Vec<DenseFrame>, TimsRustError> {
+    let metadata_path = Path::new(&path.clone()).join("analysis.tdf");
+    let reader = timsrust::readers::FrameReader::new(path).unwrap();
+    let metadata = timsrust::readers::MetadataReader::new(metadata_path).unwrap();
 
     let mut timer = utils::ContextTimer::new("Reading all MS1 frames", true, utils::LogLevel::INFO);
 
-    let mut frames = reader.read_all_ms1_frames();
+    let frames: Result<Vec<Frame>, _> = reader.get_all_ms1().into_iter().collect();
     timer.stop(true);
 
-    let ims_converter = reader.get_scan_converter().unwrap();
-    let mz_converter = reader.get_tof_converter().unwrap();
+    let mut frames = frames?;
+
+    let ims_converter = metadata.im_converter;
+    let mz_converter = metadata.mz_converter;
 
-    frames.retain(|frame| matches!(frame.frame_type, timsrust::FrameType::MS1));
+    frames.retain(|frame| matches!(frame.ms_level, MSLevel::MS1));
 
     // let min_intensity = 100u64;
     // let min_n: usize = 3;
@@ -548,29 +556,32 @@ pub fn read_all_ms1_denoising(
         utils::ContextTimer::new("Denoising all MS1 frames", true, utils::LogLevel::INFO);
     let out = ms1_denoiser.par_denoise_slice(frames);
     timer.stop(true);
-    out
+    Ok(out)
 }
 
 // This could probably be a macro ...
 pub fn read_all_dia_denoising(
     path: String,
     config: DenoiseConfig,
-) -> (Vec<Vec<DenseFrameWindow>>, DIAFrameInfo) {
+) -> Result<(Vec<Vec<DenseFrameWindow>>, Vec<QuadrupoleSettings>), TimsRustError> {
     let mut timer = utils::ContextTimer::new("Reading all DIA frames", true, utils::LogLevel::INFO);
-    let reader = timsrust::FileReader::new(path.clone()).unwrap();
+    let metadata_path = Path::new(&path.clone()).join("analysis.tdf");
+    let reader = timsrust::readers::FrameReader::new(path)?;
+    let metadata = timsrust::readers::MetadataReader::new(metadata_path.clone())?;
+    let quad_settings = timsrust::readers::QuadrupoleSettingsReader::new(metadata_path)?;
 
-    let dia_info = tdf::read_dia_frame_info(path.clone()).unwrap();
-    let mut frames = reader.read_all_ms2_frames();
+    let frames: Result<Vec<Frame>, _> = reader.get_all_ms2().into_iter().collect();
 
-    let ims_converter = reader.get_scan_converter().unwrap();
-    let mz_converter = reader.get_tof_converter().unwrap();
+    let ims_converter = metadata.im_converter;
+    let mz_converter = metadata.mz_converter;
     timer.stop(true);
 
-    frames.retain(|frame| {
-        matches!(
-            frame.frame_type,
-            timsrust::FrameType::MS2(timsrust::AcquisitionType::DIAPASEF)
-        )
+    let mut frames = frames?;
+
+    frames.retain(|frame| match (frame.ms_level, frame.acquisition_type) {
+        (MSLevel::MS2, AcquisitionType::DIAPASEF) => true,
+        (MSLevel::MS2, AcquisitionType::DiagonalDIAPASEF) => true,
+        _ => false,
     });
 
     let denoiser = DIAFrameDenoiser {
@@ -580,7 +591,6 @@ pub fn read_all_dia_denoising(
         max_mz_extension: config.max_mz_expansion_ratio.into(),
         ims_scaling: config.ims_scaling,
         max_ims_extension: config.max_ims_expansion_ratio,
-        dia_frame_info: dia_info.clone(),
         ims_converter,
         mz_converter,
     };
@@ -589,5 +599,5 @@ pub fn read_all_dia_denoising(
     let split_frames = denoiser.par_denoise_slice(frames);
     timer.stop(true);
 
-    (split_frames, dia_info)
+    Ok((split_frames, quad_settings))
 }
diff --git a/src/aggregation/tracing.rs b/src/aggregation/tracing.rs
index d0fd27f..199a149 100644
--- a/src/aggregation/tracing.rs
+++ b/src/aggregation/tracing.rs
@@ -227,10 +227,16 @@ impl TraceLike<f32> for BaseTrace {
     }
 }
 
+pub fn calculate_cycle_time(frames: &[DenseFrameWindow]) -> f64 {
+    let rts = frames.iter().map(|x| x.frame.rt).collect::<Vec<f64>>();
+    let rt_diffs = rts.windows(2).map(|x| x[1] - x[0]).collect::<Vec<f64>>();
+    let cycle_time = rt_diffs.iter().sum::<f64>() / rt_diffs.len() as f64;
+    cycle_time
+}
+
 pub fn combine_traces(
     grouped_denseframe_windows: Vec<Vec<DenseFrameWindow>>,
     config: TracingConfig,
-    rt_binsize: f32,
 ) -> Vec<Vec<BaseTrace>> {
     // mz_scaling: f64,
     // rt_scaling: f64,
@@ -241,12 +247,18 @@ pub fn combine_traces(
 
     let mut timer = utils::ContextTimer::new("Tracing peaks in time", true, utils::LogLevel::INFO);
 
-    let grouped_windows: Vec<Vec<TimeTimsPeak>> = grouped_denseframe_windows
+    // rt_binsize: f32,
+
+    let grouped_windows: Vec<(f64, Vec<TimeTimsPeak>)> = grouped_denseframe_windows
         .into_iter()
-        .map(_flatten_denseframe_vec)
+        .map(|x| {
+            let cycle_time = calculate_cycle_time(&x);
+            let o = _flatten_denseframe_vec(x);
+            (cycle_time, o)
+        })
         .collect();
 
-    let combine_lambda = |x: Vec<TimeTimsPeak>| {
+    let combine_lambda = |cycle_time: f64, x: Vec<TimeTimsPeak>| {
         combine_single_window_traces2(
             x,
             config.mz_scaling.into(),
@@ -257,18 +269,21 @@ pub fn combine_traces(
             config.max_ims_expansion_ratio,
             config.min_n.into(),
             config.min_neighbor_intensity,
-            rt_binsize,
+            cycle_time as f32,
         )
     };
 
     // Combine the traces
     let out: Vec<Vec<BaseTrace>> = if cfg!(feature = "less_parallel") {
         warn!("Running in single-threaded mode");
-        grouped_windows.into_iter().map(combine_lambda).collect()
+        grouped_windows
+            .into_iter()
+            .map(|x| combine_lambda(x.0, x.1))
+            .collect()
     } else {
         grouped_windows
             .into_par_iter()
-            .map(combine_lambda)
+            .map(|x| combine_lambda(x.0, x.1))
             .collect()
     };
 
@@ -381,12 +396,16 @@ fn _flatten_denseframe_vec(denseframe_windows: Vec<DenseFrameWindow>) -> Vec<Tim
         .flat_map(|dfw| {
             let mut out = Vec::new();
             for peak in dfw.frame.raw_peaks {
+                let mz_start = dfw.quadrupole_setting.isolation_mz
+                    - (dfw.quadrupole_setting.isolation_width / 2.);
+                let mz_end = dfw.quadrupole_setting.isolation_mz
+                    + (dfw.quadrupole_setting.isolation_width / 2.);
                 out.push(TimeTimsPeak {
                     mz: peak.mz,
                     intensity: peak.intensity as u64,
                     rt: dfw.frame.rt as f32,
                     ims: peak.mobility,
-                    quad_low_high: (dfw.mz_start, dfw.mz_end),
+                    quad_low_high: (mz_start, mz_end),
                     n_peaks: 1,
                 });
             }
diff --git a/src/main.rs b/src/main.rs
index fe0557c..2a39caf 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -18,6 +18,7 @@ extern crate log;
 extern crate pretty_env_logger;
 
 use std::fs;
+use std::io::Error;
 use std::path::Path;
 
 use clap::Parser;
@@ -77,7 +78,7 @@ impl Config {
     }
 }
 
-fn main() {
+fn main() -> Result<(), std::io::Error> {
     let args = Args::parse();
 
     if args.write_template {
@@ -90,7 +91,7 @@ fn main() {
         } else {
             std::fs::write(out_path.clone(), config_str).unwrap();
             println!("Wrote default config to {}", out_path);
-            return;
+            return Ok(());
         }
     }
 
@@ -130,14 +131,22 @@ fn main() {
         .map(|path| out_path_dir.join(path).to_path_buf());
 
     log::info!("Reading DIA data from: {}", path_use);
-    let (dia_frames, dia_info) =
+    let tmp =
         aggregation::ms_denoise::read_all_dia_denoising(path_use.clone(), config.denoise_config);
 
-    let cycle_time = dia_info.calculate_cycle_time();
+    let (dia_frames, dia_info) = match tmp {
+        Ok(x) => x,
+        Err(e) => {
+            log::error!("Error reading DIA data: {:?}", e);
+            return Err(std::io::Error::new(
+                std::io::ErrorKind::Other,
+                e.to_string(),
+            ));
+        },
+    };
 
     // TODO add here expansion limits
-    let mut traces =
-        aggregation::tracing::combine_traces(dia_frames, config.tracing_config, cycle_time);
+    let mut traces = aggregation::tracing::combine_traces(dia_frames, config.tracing_config);
 
     // let out = match out_traces_path {
     //     Some(out_path) => aggregation::tracing::write_trace_csv(&traces, out_path),
@@ -225,11 +234,7 @@ fn main() {
         config.sage_search_config,
         out_path_features.clone(),
         1,
-    );
-    match score_out {
-        Ok(_) => {},
-        Err(e) => {
-            log::error!("Error scoring pseudospectra: {:?}", e);
-        },
-    }
+    )?;
+
+    Ok(())
 }
diff --git a/src/ms/frames/dense_frame_window.rs b/src/ms/frames/dense_frame_window.rs
index 9e38787..2cfe89e 100644
--- a/src/ms/frames/dense_frame_window.rs
+++ b/src/ms/frames/dense_frame_window.rs
@@ -1,25 +1,26 @@
+use std::sync::Arc;
+
 use log::info;
 use serde::Serialize;
-use timsrust::{
-    ConvertableIndex,
-    Frame,
+use timsrust::converters::{
+    ConvertableDomain,
     Scan2ImConverter,
     Tof2MzConverter,
 };
+use timsrust::{
+    AcquisitionType,
+    Frame,
+};
 
 use super::frames::SortingOrder;
 use super::{
     DenseFrame,
     FrameSlice,
+    SingleQuadrupoleSettings,
     TimsPeak,
 };
-use crate::ms::frames::MsMsFrameSliceWindowInfo;
-use crate::ms::tdf::{
-    DIAFrameInfo,
-    ScanRange,
-};
 
-pub type Converters = (timsrust::Scan2ImConverter, timsrust::Tof2MzConverter);
+pub type Converters = (Scan2ImConverter, Tof2MzConverter);
 fn check_peak_sanity(peak: &TimsPeak) {
     debug_assert!(peak.intensity > 0);
     debug_assert!(peak.mz > 0.);
@@ -32,68 +33,51 @@ pub struct DenseFrameWindow {
     pub frame: DenseFrame,
     pub ims_min: f32,
     pub ims_max: f32,
-    pub mz_start: f64,
-    pub mz_end: f64,
     pub group_id: usize,
-    pub quad_group_id: usize,
+    pub quadrupole_setting: SingleQuadrupoleSettings,
 }
 
+
 impl DenseFrameWindow {
     pub fn from_frame_window(
         frame_window: &FrameSlice,
         ims_converter: &Scan2ImConverter,
         mz_converter: &Tof2MzConverter,
-        dia_info: &DIAFrameInfo,
     ) -> DenseFrameWindow {
-        let (window_group_id, ww_quad_group_id, scan_start) = match frame_window.slice_window_info {
-            None => {
-                panic!("No window info")
-                // This branch points to an error in logic ...
-                // The window info should always be present in this context.
-            },
-            Some(MsMsFrameSliceWindowInfo::WindowGroup(_)) => {
+        let window_group_id = frame_window.window_group_id;
+        let foo = match frame_window.acquisition_type {
+            AcquisitionType::DiagonalDIAPASEF => {
                 // This branch should be easy to implement for things like synchro pasef...
                 // Some details to iron out though ...
                 panic!("Not implemented")
             },
-            Some(MsMsFrameSliceWindowInfo::SingleWindow(ref x)) => {
-                let window_group_id = x.window_group_id;
-                let ww_quad_group_id = x.within_window_quad_group_id;
-                let scan_start = frame_window.scan_start;
-                (window_group_id, ww_quad_group_id, scan_start)
+            AcquisitionType::DIAPASEF => {
+                frame_window.quadrupole_settings.clone()
+
+                // let window_group_id = frame_window.window_group_id;
+                // let ww_quad_group_id = x.within_window_quad_group_id;
+                // let scan_start = frame_window.scan_start;
+                // (window_group_id, ww_quad_group_id, scan_start)
             },
+            _ => panic!("Not implemented"),
         };
 
         // NOTE: I am swapping here the 'scan start' to be the `ims_end` because
         // the first scans have lower 1/k0 values.
-        let ims_max = ims_converter.convert(scan_start as u32) as f32;
+        let ims_max = ims_converter.convert(foo.scan_start as u32) as f32;
         let ims_min =
-            ims_converter.convert((frame_window.scan_offsets.len() + scan_start) as u32) as f32;
+            ims_converter.convert((frame_window.scan_offsets.len() + foo.scan_start) as u32) as f32;
 
         debug_assert!(ims_max <= ims_min);
 
-        let scan_range: Option<&ScanRange> =
-            dia_info.get_quad_windows(window_group_id, ww_quad_group_id);
-        let scan_range = match scan_range {
-            Some(x) => x,
-            None => {
-                panic!(
-                    "No scan range for window_group_id: {}, within_window_quad_group_id: {}",
-                    window_group_id, ww_quad_group_id
-                );
-            },
-        };
-
         let frame = DenseFrame::from_frame_window(frame_window, ims_converter, mz_converter);
 
         DenseFrameWindow {
             frame,
             ims_min,
             ims_max,
-            mz_start: scan_range.iso_low as f64,
-            mz_end: scan_range.iso_high as f64,
-            group_id: window_group_id,
-            quad_group_id: ww_quad_group_id,
+            group_id: window_group_id.into(),
+            quadrupole_setting: foo,
         }
     }
 }
@@ -134,14 +118,18 @@ impl DenseFrame {
 
         let index = frame.index;
         let rt = frame.rt;
-        let frame_type = frame.frame_type;
+        let acquisition_type = frame.acquisition_type;
+        let ms_level = frame.ms_level;
 
         DenseFrame {
             raw_peaks: peaks,
             index,
             rt,
-            frame_type,
+            acquisition_type,
+            ms_level,
             sorted: None,
+            intensity_correction_factor: frame.intensity_correction_factor,
+            window_group_id: frame.window_group,
         }
     }
 
@@ -189,14 +177,18 @@ impl DenseFrame {
 
         let index = frame_window.parent_frame_index;
         let rt = frame_window.rt;
-        let frame_type = frame_window.frame_type;
+        let acquisition_type = frame_window.acquisition_type;
+        let ms_level = frame_window.ms_level;
 
         DenseFrame {
             raw_peaks: peaks,
             index,
             rt,
-            frame_type,
+            acquisition_type,
+            ms_level,
             sorted: None,
+            intensity_correction_factor: frame_window.intensity_correction_factor,
+            window_group_id: frame_window.window_group_id,
         }
     }
 
diff --git a/src/ms/frames/frame_slice.rs b/src/ms/frames/frame_slice.rs
index 48ba993..c034708 100644
--- a/src/ms/frames/frame_slice.rs
+++ b/src/ms/frames/frame_slice.rs
@@ -1,12 +1,17 @@
 use std::fmt;
+use std::sync::Arc;
 
 use serde::Serialize;
 use timsrust::{
+    AcquisitionType,
     Frame,
-    FrameType,
+    MSLevel,
+    QuadrupoleSettings,
 };
 
-use super::FrameMsMsWindowInfo;
+use super::SingleQuadrupoleSettings;
+use crate::aggregation::ms_denoise;
+use crate::space::quad;
 use crate::space::space_generics::{
     AsNDPointsAtIndex,
     IntenseAtIndex,
@@ -94,26 +99,32 @@ impl fmt::Display for ScanOutOfBoundsError {
 ///
 /// Renamed from the frame:
 ///    - parent_frame_index   34 // renamed from Frame.index for clarity.
+///    - window_group_id   4 // renamed from Frame.window_group for clarity.
 ///
 /// Additions for FrameSlice:
 ///    - scan_start       123  // The scan number of the first scan offset in the current window.
-///    - slice_window_info Some(MsMsFrameSliceWindowInfo::SingleWindow(FrameMsMsWindow))
 #[derive(Debug, Clone, Serialize)]
 pub struct FrameSlice<'a> {
-    // pub scan_offsets: &'a [usize], // Timsrust changed this later ...
-    pub scan_offsets: &'a [u64],
+    pub scan_offsets: &'a [usize],
     pub tof_indices: &'a [u32],
     pub intensities: &'a [u32],
     pub parent_frame_index: usize,
     pub rt: f64,
+    pub window_group_id: u8,
+    pub intensity_correction_factor: f64,
 
     #[serde(skip)]
-    pub frame_type: FrameType,
+    pub ms_level: MSLevel,
+
+    #[serde(skip)]
+    pub acquisition_type: AcquisitionType,
+
+    #[serde(skip)]
+    pub quadrupole_settings: SingleQuadrupoleSettings,
 
     // From this point on they are local implementations
     // Before they are used from the timsrust crate.
     pub scan_start: usize,
-    pub slice_window_info: Option<MsMsFrameSliceWindowInfo>,
 }
 
 #[derive(Debug, Clone, Serialize)]
@@ -123,19 +134,43 @@ pub struct ExpandedFrameSlice {
     pub intensities: Vec<u32>,
     pub parent_frame_index: usize,
     pub rt: f64,
-    pub slice_window_info: Option<MsMsFrameSliceWindowInfo>,
+    pub window_group_id: u8,
+    pub intensity_correction_factor: f64,
+
+    #[serde(skip)]
+    pub quadrupole_settings: SingleQuadrupoleSettings,
+
+    #[serde(skip)]
+    pub acquisition_type: AcquisitionType,
 
     #[serde(skip)]
-    pub frame_type: FrameType,
+    pub ms_level: MSLevel,
 }
 
 impl<'a> FrameSlice<'a> {
-    pub fn slice_frame(
+    pub fn from_frame(frame: &'a Frame) -> Vec<FrameSlice<'a>> {
+        let quad_settings = frame.quadrupole_settings.clone();
+        if quad_settings.len() == 0 {
+            panic!("Runtime error, at this stage at least one quadrupole setting is required");
+        }
+
+        let out = (0..quad_settings.len())
+            .map(|i| {
+                let quad_info =
+                    SingleQuadrupoleSettings::from_quad_settings(quad_settings.clone(), i);
+                FrameSlice::slice_frame(frame, quad_info)
+            })
+            .collect::<Vec<_>>();
+
+        out
+    }
+
+    fn slice_frame(
         frame: &'a Frame,
-        scan_start: usize,
-        scan_end: usize,
-        slice_window_info: Option<MsMsFrameSliceWindowInfo>,
+        quad_info: SingleQuadrupoleSettings,
     ) -> FrameSlice<'a> {
+        let scan_start = quad_info.scan_start;
+        let scan_end = quad_info.scan_end;
         let scan_offsets = &frame.scan_offsets[scan_start..=scan_end];
 
         let indprt_start = scan_offsets[0] as usize;
@@ -151,7 +186,7 @@ impl<'a> FrameSlice<'a> {
             for i in 1..(scan_offsets.len() - 1) {
                 debug_assert!(scan_offsets[i] <= scan_offsets[i + 1]);
                 debug_assert!(
-                    (scan_offsets[i + 1] - init_offset) <= tof_indices.len() as u64,
+                    (scan_offsets[i + 1] - init_offset) <= tof_indices.len(),
                     "scan_offsets[i+1]: {}, init_offset: {}, tof_indices.len(): {}",
                     scan_offsets[i + 1],
                     init_offset,
@@ -166,9 +201,12 @@ impl<'a> FrameSlice<'a> {
             intensities,
             parent_frame_index: frame.index,
             rt: frame.rt,
-            frame_type: frame.frame_type,
+            ms_level: frame.ms_level,
+            acquisition_type: frame.acquisition_type,
             scan_start,
-            slice_window_info,
+            quadrupole_settings: quad_info,
+            window_group_id: frame.window_group,
+            intensity_correction_factor: frame.intensity_correction_factor,
         }
     }
 
@@ -183,7 +221,7 @@ impl<'a> FrameSlice<'a> {
         local_index: usize,
     ) -> usize {
         debug_assert!(local_index < self.tof_indices.len());
-        let search_val = self.scan_offsets[0] + local_index as u64;
+        let search_val = self.scan_offsets[0] + local_index;
         let loc = self
             .scan_offsets
             .binary_search_by(|x| x.partial_cmp(&search_val).unwrap());
@@ -399,8 +437,9 @@ impl ExpandedFrameSlice {
     pub fn from_frame_slice(frame_slice: &FrameSlice) -> ExpandedFrameSlice {
         let parent_frame_index = frame_slice.parent_frame_index;
         let rt = frame_slice.rt;
-        let slice_window_info = frame_slice.slice_window_info.clone();
-        let frame_type = frame_slice.frame_type;
+        let quadrupole_settings = frame_slice.quadrupole_settings.clone();
+        let acquisition_type = frame_slice.acquisition_type;
+        let ms_level = frame_slice.ms_level;
         let scan_numbers = frame_slice.explode_scan_numbers();
 
         // Sort all arrays on the tof indices.
@@ -430,8 +469,11 @@ impl ExpandedFrameSlice {
             intensities,
             parent_frame_index,
             rt,
-            slice_window_info,
-            frame_type,
+            quadrupole_settings,
+            acquisition_type,
+            ms_level,
+            window_group_id: frame_slice.window_group_id.clone(),
+            intensity_correction_factor: frame_slice.intensity_correction_factor.clone(),
         }
     }
 }
@@ -439,37 +481,77 @@ impl ExpandedFrameSlice {
 // Tests for the FrameSlice
 #[cfg(test)]
 mod tests {
+    use std::sync::Arc;
+
+    use timsrust::{
+        MSLevel,
+        QuadrupoleSettings,
+    };
+
     use super::*;
 
     fn sample_frame() -> Frame {
+        let ms1_quad_settings = QuadrupoleSettings {
+            index: 0,
+            scan_starts: vec![],
+            scan_ends: vec![],
+            isolation_mz: vec![],
+            isolation_width: vec![],
+            collision_energy: vec![],
+        };
+        let arc_ms1_quad_settings = Arc::new(ms1_quad_settings);
         Frame {
             index: 0,
             scan_offsets: vec![0, 0, 0, 0, 0, 3, 5, 6],
             tof_indices: vec![100, 101, 102, 10, 20, 30],
             intensities: vec![123, 111, 12, 3, 4, 1],
             rt: 65.34,
-            frame_type: FrameType::MS1,
+            ms_level: MSLevel::MS1,
+            acquisition_type: AcquisitionType::DIAPASEF,
+            quadrupole_settings: arc_ms1_quad_settings,
+            window_group: 0,
+            intensity_correction_factor: 1.,
         }
     }
 
     #[test]
     fn test_frame_slice() {
         let frame = sample_frame();
-        let frame_slice = FrameSlice::slice_frame(&frame, 3, 5, None);
+        let quad_setting = SingleQuadrupoleSettings {
+            parent_index: 0,
+            scan_start: 3,
+            scan_end: 5,
+            isolation_mz: 100.,
+            isolation_max: 100.,
+            isolation_min: 100.,
+            isolation_width: 25.,
+            collision_energy: 10.,
+        };
+        let frame_slice = FrameSlice::slice_frame(&frame, quad_setting);
 
         assert_eq!(frame_slice.scan_offsets, &[0, 0, 3]);
         assert_eq!(frame_slice.tof_indices, &[100, 101, 102]);
         assert_eq!(frame_slice.intensities, &[123, 111, 12]);
         assert_eq!(frame_slice.parent_frame_index, 0);
         assert_eq!(frame_slice.rt, 65.34);
-        assert_eq!(frame_slice.frame_type, FrameType::MS1);
+        assert_eq!(frame_slice.ms_level, MSLevel::MS1);
         assert_eq!(frame_slice.scan_start, 3);
     }
 
     #[test]
     fn test_global_scan_at_index() {
         let frame = sample_frame();
-        let frame_slice = FrameSlice::slice_frame(&frame, 3, 5, None);
+        let quad_setting = SingleQuadrupoleSettings {
+            parent_index: 0,
+            scan_start: 3,
+            scan_end: 5,
+            isolation_mz: 100.,
+            isolation_max: 100.,
+            isolation_min: 100.,
+            isolation_width: 25.,
+            collision_energy: 10.,
+        };
+        let frame_slice = FrameSlice::slice_frame(&frame, quad_setting);
 
         assert_eq!(frame_slice.tof_indices, &[100, 101, 102]);
         assert_eq!(frame_slice.global_scan_at_index(0), 4);
@@ -482,7 +564,17 @@ mod tests {
     fn test_global_scan_at_index_oob_fails() {
         // these should fail ... test that it fails.
         let frame = sample_frame();
-        let frame_slice = FrameSlice::slice_frame(&frame, 3, 5, None);
+        let quad_setting = SingleQuadrupoleSettings {
+            parent_index: 0,
+            scan_start: 3,
+            scan_end: 5,
+            isolation_mz: 100.,
+            isolation_max: 100.,
+            isolation_min: 100.,
+            isolation_width: 25.,
+            collision_energy: 10.,
+        };
+        let frame_slice = FrameSlice::slice_frame(&frame, quad_setting);
         assert_eq!(frame_slice.tof_indices, &[100, 101, 102]);
         frame_slice.global_scan_at_index(3);
     }
@@ -490,7 +582,17 @@ mod tests {
     #[test]
     fn test_explode_scan_numbers() {
         let frame = sample_frame();
-        let frame_slice = FrameSlice::slice_frame(&frame, 3, 5, None);
+        let quad_setting = SingleQuadrupoleSettings {
+            parent_index: 0,
+            scan_start: 3,
+            scan_end: 5,
+            isolation_mz: 100.,
+            isolation_max: 100.,
+            isolation_min: 100.,
+            isolation_width: 25.,
+            collision_energy: 10.,
+        };
+        let frame_slice = FrameSlice::slice_frame(&frame, quad_setting);
         assert_eq!(frame_slice.tof_indices, &[100, 101, 102]);
         assert_eq!(frame_slice.scan_offsets, &[0, 0, 3]);
         assert_eq!(frame_slice.explode_scan_numbers(), vec![4, 4, 4]);
@@ -499,7 +601,17 @@ mod tests {
     #[test]
     fn test_tof_intensities_at_scan() {
         let frame = sample_frame();
-        let frame_slice = FrameSlice::slice_frame(&frame, 3, 5, None);
+        let quad_setting = SingleQuadrupoleSettings {
+            parent_index: 0,
+            scan_start: 3,
+            scan_end: 5,
+            isolation_mz: 100.,
+            isolation_max: 100.,
+            isolation_min: 100.,
+            isolation_width: 25.,
+            collision_energy: 10.,
+        };
+        let frame_slice = FrameSlice::slice_frame(&frame, quad_setting);
 
         assert_eq!(frame_slice.tof_indices, &[100, 101, 102]);
         assert_eq!(frame_slice.scan_offsets, &[0, 0, 3]);
@@ -547,7 +659,17 @@ mod tests {
     #[test]
     fn test_tof_range_in_tolerance_at_scan() {
         let frame = sample_frame();
-        let frame_slice = FrameSlice::slice_frame(&frame, 3, 7, None);
+        let quad_setting = SingleQuadrupoleSettings {
+            parent_index: 0,
+            scan_start: 3,
+            scan_end: 7,
+            isolation_mz: 100.,
+            isolation_max: 100.,
+            isolation_min: 100.,
+            isolation_width: 25.,
+            collision_energy: 10.,
+        };
+        let frame_slice = FrameSlice::slice_frame(&frame, quad_setting);
 
         assert_eq!(frame_slice.tof_indices, &[100, 101, 102, 10, 20, 30]);
         assert_eq!(frame_slice.scan_offsets, &[0, 0, 3, 5, 6]);
@@ -617,13 +739,26 @@ mod tests {
     }
 
     fn sample_ms2_frame() -> Frame {
+        let ms2_quad_settings = QuadrupoleSettings {
+            index: 0,
+            scan_starts: vec![2, 6],
+            scan_ends: vec![5, 9],
+            isolation_mz: vec![100., 101.],
+            isolation_width: vec![25., 25.],
+            collision_energy: vec![10., 10.],
+        };
+        let arc_ms2_quad_settings = Arc::new(ms2_quad_settings);
         Frame {
             index: 0,
             scan_offsets: vec![0, 0, 3, 5, 6],
             tof_indices: vec![100, 101, 102, 10, 20, 30],
             intensities: vec![123, 111, 12, 3, 4, 1],
             rt: 65.34,
-            frame_type: FrameType::MS2(timsrust::AcquisitionType::DIAPASEF),
+            ms_level: MSLevel::MS2,
+            acquisition_type: AcquisitionType::DIAPASEF,
+            quadrupole_settings: arc_ms2_quad_settings,
+            window_group: 1,
+            intensity_correction_factor: 1.,
         }
     }
 }
@@ -912,9 +1047,3 @@ impl RangeSet {
         false
     }
 }
-
-#[derive(Debug, Clone, Serialize)]
-pub enum MsMsFrameSliceWindowInfo {
-    WindowGroup(usize),
-    SingleWindow(FrameMsMsWindowInfo),
-}
diff --git a/src/ms/frames/frame_slice_rt_window.rs b/src/ms/frames/frame_slice_rt_window.rs
index 825a81e..d123558 100644
--- a/src/ms/frames/frame_slice_rt_window.rs
+++ b/src/ms/frames/frame_slice_rt_window.rs
@@ -1,6 +1,10 @@
 use log::trace;
 use serde::Serialize;
-use timsrust::ConvertableIndex;
+use timsrust::converters::{
+    ConvertableDomain,
+    Scan2ImConverter,
+    Tof2MzConverter,
+};
 
 use super::{
     ExpandedFrameSlice,
@@ -225,8 +229,8 @@ pub struct RawScaleTimsPeak {
 impl RawScaleTimsPeak {
     pub fn to_timspeak(
         &self,
-        mz_converter: &timsrust::Tof2MzConverter,
-        ims_converter: &timsrust::Scan2ImConverter,
+        mz_converter: &Tof2MzConverter,
+        ims_converter: &Scan2ImConverter,
     ) -> TimsPeak {
         TimsPeak {
             intensity: self.intensity as u32,
diff --git a/src/ms/frames/frames.rs b/src/ms/frames/frames.rs
index 13d7851..fa6351a 100644
--- a/src/ms/frames/frames.rs
+++ b/src/ms/frames/frames.rs
@@ -1,5 +1,11 @@
+use std::sync::Arc;
+
 use serde::Serialize;
-pub use timsrust::FrameType;
+pub use timsrust::{
+    AcquisitionType,
+    MSLevel,
+    QuadrupoleSettings,
+};
 
 use crate::space::space_generics::HasIntensity;
 
@@ -56,23 +62,63 @@ pub struct DenseFrame {
     pub raw_peaks: Vec<TimsPeak>,
     pub index: usize,
     pub rt: f64,
+    pub window_group_id: u8,
+    pub intensity_correction_factor: f64,
+
+    #[serde(skip_serializing)]
+    pub acquisition_type: AcquisitionType,
 
     #[serde(skip_serializing)]
-    pub frame_type: FrameType,
+    pub ms_level: MSLevel,
 
     #[serde(skip_serializing)]
     pub sorted: Option<SortingOrder>,
 }
 
-/// Information on the context of a window in a frame.
-///
-/// This adds to a frame slice the context of the what isolation was used
-/// to generate the frame slice.
-#[derive(Debug, Clone, Serialize)]
-pub struct FrameMsMsWindowInfo {
-    pub mz_start: f32,
-    pub mz_end: f32,
-    pub window_group_id: usize,
-    pub within_window_quad_group_id: usize,
-    pub global_quad_row_id: usize,
+#[derive(Debug, Clone, Serialize, PartialEq)]
+pub struct SingleQuadrupoleSettings {
+    pub parent_index: usize,
+    pub scan_start: usize,
+    pub scan_end: usize,
+    pub isolation_mz: f64,
+    pub isolation_max: f64,
+    pub isolation_min: f64,
+    pub isolation_width: f64,
+    pub collision_energy: f64,
+}
+
+impl SingleQuadrupoleSettings {
+    pub fn from_quad_settings(
+        quad_settings: Arc<QuadrupoleSettings>,
+        index: usize,
+    ) -> Self {
+        let isolation_mz = quad_settings.isolation_mz[index];
+        let isolation_width = quad_settings.isolation_width[index];
+        let isolation_max = isolation_mz + (isolation_width / 2.);
+        let isolation_min = isolation_mz - (isolation_width / 2.);
+        let collision_energy = quad_settings.collision_energy[index];
+
+        Self {
+            parent_index: quad_settings.index,
+            scan_start: quad_settings.scan_starts[index],
+            scan_end: quad_settings.scan_ends[index],
+            isolation_mz,
+            isolation_max,
+            isolation_min,
+            isolation_width,
+            collision_energy,
+        }
+    }
+}
+
+impl PartialOrd for SingleQuadrupoleSettings {
+    fn partial_cmp(
+        &self,
+        other: &Self,
+    ) -> Option<std::cmp::Ordering> {
+        match self.parent_index.partial_cmp(&other.parent_index) {
+            Some(std::cmp::Ordering::Equal) => self.scan_start.partial_cmp(&other.scan_start),
+            x => x,
+        }
+    }
 }
diff --git a/src/ms/frames/mod.rs b/src/ms/frames/mod.rs
index 64a8db0..0f36625 100644
--- a/src/ms/frames/mod.rs
+++ b/src/ms/frames/mod.rs
@@ -9,10 +9,9 @@ pub use dense_frame_window::{
 pub use frame_slice::{
     ExpandedFrameSlice,
     FrameSlice,
-    MsMsFrameSliceWindowInfo,
 };
 pub use frames::{
     DenseFrame,
-    FrameMsMsWindowInfo,
+    SingleQuadrupoleSettings,
     TimsPeak,
 };
diff --git a/src/ms/mod.rs b/src/ms/mod.rs
index 1e9820a..5f89a78 100644
--- a/src/ms/mod.rs
+++ b/src/ms/mod.rs
@@ -1,3 +1,2 @@
 pub mod frames;
 pub mod sorting;
-pub mod tdf;
diff --git a/src/ms/tdf.rs b/src/ms/tdf.rs
deleted file mode 100644
index 6fbfea2..0000000
--- a/src/ms/tdf.rs
+++ /dev/null
@@ -1,567 +0,0 @@
-use std::path::Path;
-
-use log::{
-    debug,
-    info,
-};
-use sqlx::{
-    FromRow,
-    Pool,
-    Sqlite,
-    SqlitePool,
-};
-use timsrust::{
-    ConvertableIndex,
-    Frame,
-};
-use tokio;
-use tokio::runtime::Runtime;
-
-use crate::ms::frames::{
-    FrameMsMsWindowInfo,
-    FrameSlice,
-    MsMsFrameSliceWindowInfo,
-};
-
-// Diaframemsmsinfo = vec of frame_id -> windowgroup_id
-// diaframemsmswindows = vec[(windowgroup_id, scanstart, scanend, iso_mz, iso_with, nce)]
-
-#[derive(Debug, Clone)]
-pub struct ScanRange {
-    pub row_id: usize,
-    pub scan_start: usize,
-    pub scan_end: usize,
-    pub iso_mz: f32,
-    pub iso_width: f32,
-    pub nce: f32,
-    pub ims_start: f32,
-    pub ims_end: f32,
-    pub iso_low: f32,
-    pub iso_high: f32,
-    pub window_group_id: usize,
-    pub within_window_quad_group_id: usize,
-}
-
-impl ScanRange {
-    pub fn new(
-        row_id: usize,
-        window_group_id: usize,
-        within_window_quad_group_id: usize,
-        scan_start: usize,
-        scan_end: usize,
-        iso_mz: f32,
-        iso_width: f32,
-        nce: f32,
-        scan_converter: &timsrust::Scan2ImConverter,
-    ) -> Self {
-        // Note that here I swap the start and end,
-        // because lower scan numbers are actually
-        // higher 1/k0 values. ... i think...
-        let ims_end = scan_converter.convert(scan_start as u32);
-        let ims_start = scan_converter.convert(scan_end as u32);
-
-        debug_assert!(ims_start < ims_end);
-        let iso_low = iso_mz - iso_width / 2.0;
-        let iso_high = iso_mz + iso_width / 2.0;
-
-        Self {
-            row_id,
-            scan_start,
-            scan_end,
-            iso_mz,
-            iso_width,
-            nce,
-            ims_start: ims_start as f32,
-            ims_end: ims_end as f32,
-            iso_low,
-            iso_high,
-            window_group_id,
-            within_window_quad_group_id,
-        }
-    }
-}
-
-impl From<ScanRange> for FrameMsMsWindowInfo {
-    fn from(val: ScanRange) -> Self {
-        FrameMsMsWindowInfo {
-            mz_start: val.iso_low,
-            mz_end: val.iso_high,
-            window_group_id: val.window_group_id,
-            within_window_quad_group_id: val.within_window_quad_group_id,
-            global_quad_row_id: val.row_id,
-        }
-    }
-}
-
-#[derive(Debug, Clone)]
-pub struct DIAWindowGroup {
-    pub window_group_id: usize,
-    pub scan_ranges: Vec<ScanRange>,
-}
-
-#[derive(Debug, Clone)]
-pub enum GroupingLevel {
-    WindowGroup, // Technically this is the same as the frame level ...
-    QuadWindowGroup,
-}
-
-#[derive(Debug, Clone)]
-pub struct DIAFrameInfo {
-    pub groups: Vec<Option<DIAWindowGroup>>,
-    /// Frame Groups is a vec of length equal to the number of frames.
-    /// Each element is an Option<usize> that is the index of the group
-    /// that the frame belongs to.
-    pub frame_groups: Vec<Option<usize>>,
-    pub retention_times: Vec<Option<f32>>,
-    pub grouping_level: GroupingLevel,
-    pub number_of_groups: usize,
-
-    /// The row to group is meant to map the `Isolation window row id`
-    /// to the grouping level it will have... for diaPASEF, since every
-    /// scan range has a different quand window, the number of distinct
-    /// groups is the number of scan ranges (window groups+scan range
-    /// combinations). For the case of diagonal PASEF, the number of
-    /// groups is the number of window groups, since the scan ranges
-    /// are not independent from each other.
-    pub row_to_group: Vec<usize>,
-}
-
-// TODO rename or split this ... since it is becoming more
-// of a splitter than a frame info reader.
-// Maybe a builder -> splitter pattern?
-impl DIAFrameInfo {
-    pub fn get_dia_frame_window_group(
-        &self,
-        frame_id: usize,
-    ) -> Option<&DIAWindowGroup> {
-        let group_id = self.frame_groups[frame_id];
-        match group_id {
-            None => None,
-            Some(group_id) => self.groups[group_id].as_ref(),
-        }
-    }
-
-    async fn rts_from_tdf_connection(conn: &Pool<Sqlite>) -> Result<Vec<Option<f32>>, sqlx::Error> {
-        // To calculate cycle time ->
-        // DiaFrameMsMsInfo -> Get the frames that match a specific id (one for each ...)
-        // Frames -> SELECT id, time FROM Frames -> make a Vec<Option<f32>>, map the former
-        // framer id list (no value should be None).
-        // Scan diff the new vec!
-        let results: Vec<(i32, f32)> = sqlx::query_as("SELECT Id, Time FROM Frames")
-            .fetch_all(conn)
-            .await?;
-        let mut retention_times = Vec::new();
-        for row in results.iter() {
-            let id: usize = row.0 as usize;
-            let time: f32 = row.1;
-            retention_times.resize(id + 1, None);
-            retention_times[id] = Some(time);
-        }
-        Ok(retention_times)
-    }
-
-    pub fn calculate_cycle_time(&self) -> f32 {
-        let mut group_cycle_times = Vec::new();
-
-        for (i, group) in self.groups.iter().enumerate() {
-            if group.is_none() {
-                continue;
-            }
-
-            let mapping_frames: Vec<usize> = self
-                .frame_groups
-                .iter()
-                .enumerate()
-                .filter(|(_, group_id)| {
-                    if group_id.is_none() {
-                        return false;
-                    }
-                    let group_id = group_id.unwrap();
-                    group_id == i
-                })
-                .map(|(frame_id, _group_id)| frame_id)
-                .collect();
-
-            let local_times = mapping_frames
-                .iter()
-                .map(|frame_id| self.retention_times[*frame_id].unwrap())
-                .scan(0.0, |acc, x| {
-                    let out = x - *acc;
-                    *acc = x;
-                    Some(out)
-                })
-                .collect::<Vec<_>>();
-
-            let cycle_time = local_times.iter().sum::<f32>() / local_times.len() as f32;
-            group_cycle_times.push(cycle_time);
-        }
-
-        debug!("Group cycle times: {:?}", group_cycle_times);
-        let avg_cycle_time = group_cycle_times.iter().sum::<f32>() / group_cycle_times.len() as f32;
-        avg_cycle_time
-    }
-
-    pub fn split_frame<'a, 'b>(
-        &'b self,
-        frame: &'a Frame,
-        window_group: &DIAWindowGroup,
-    ) -> Result<Vec<FrameSlice>, &'static str>
-    where
-        'a: 'b,
-    {
-        let mut out_frames = Vec::new();
-        for scan_range in window_group.scan_ranges.iter() {
-            let slice_w_info: MsMsFrameSliceWindowInfo =
-                MsMsFrameSliceWindowInfo::SingleWindow(scan_range.clone().into());
-            let frame_slice = FrameSlice::slice_frame(
-                frame,
-                scan_range.scan_start,
-                scan_range.scan_end,
-                Some(slice_w_info),
-            );
-            out_frames.push(frame_slice);
-        }
-
-        Ok(out_frames)
-    }
-
-    pub fn split_frame_windows<'a>(
-        &'a self,
-        frames: &'a [Frame],
-    ) -> Vec<Vec<FrameSlice>> {
-        let mut out = Vec::new();
-
-        match self.grouping_level {
-            GroupingLevel::WindowGroup => {
-                for _ in 0..(self.groups.len() + 1) {
-                    out.push(Vec::new());
-                }
-            },
-            GroupingLevel::QuadWindowGroup => {
-                for _ in 0..(self.row_to_group.len() + 1) {
-                    out.push(Vec::new());
-                }
-            },
-        }
-
-        for frame in frames {
-            let group = self
-                .get_dia_frame_window_group(frame.index)
-                .expect("Frame is not in MS2 frames");
-
-            match self.grouping_level {
-                GroupingLevel::WindowGroup => {
-                    panic!("WindowGroup grouping level not implemented for splitting frames")
-                    //out[group.id].push(frame_window);
-                },
-                GroupingLevel::QuadWindowGroup => {
-                    let frame_windows = self
-                        .split_frame(frame, group)
-                        .expect("Error splitting frame");
-                    for frame_window in frame_windows {
-                        match &frame_window.slice_window_info {
-                            None => {
-                                panic!("Frame window has no slice window info")
-                            },
-                            Some(MsMsFrameSliceWindowInfo::SingleWindow(scan_range)) => {
-                                out[scan_range.global_quad_row_id].push(frame_window);
-                            },
-                            Some(MsMsFrameSliceWindowInfo::WindowGroup(group)) => {
-                                out[*group].push(frame_window);
-                            },
-                        }
-                    }
-                },
-            }
-        }
-
-        // Sort by ascending rt
-        for group in out.iter_mut() {
-            group.sort_by(|a, b| a.rt.partial_cmp(&b.rt).unwrap());
-        }
-        out.retain(|x| !x.is_empty());
-
-        // Debug assert that the frames are sorted by rt
-        if cfg!(debug_assertions) {
-            for group in out.iter() {
-                for i in 0..(group.len() - 1) {
-                    debug_assert!(group[i].rt <= group[i + 1].rt);
-                }
-            }
-        }
-
-        out
-    }
-
-    pub fn get_quad_windows(
-        &self,
-        scan_group_id: usize,
-        quad_group_id: usize,
-    ) -> Option<&ScanRange> {
-        let group = self.groups[scan_group_id].as_ref();
-        let group = match group {
-            None => {
-                panic!(
-                    "Group not found for scan group id: {}, in groups n={}",
-                    scan_group_id,
-                    self.groups.len()
-                )
-            },
-            Some(group) => group,
-        };
-
-        let quad_group = group.scan_ranges.get(quad_group_id);
-        let quad_group = match quad_group {
-            None => {
-                panic!(
-                    "Quad group not found for quad group id: {}, in scan_ranges {:?}",
-                    quad_group_id, group.scan_ranges
-                )
-            },
-            Some(quad_group) => quad_group,
-        };
-
-        Some(quad_group)
-    }
-}
-
-// Reference for the tables:
-
-// CREATE TABLE DiaFrameMsMsInfo (
-//     Frame INTEGER PRIMARY KEY,
-//     WindowGroup INTEGER NOT NULL,
-//     FOREIGN KEY (Frame) REFERENCES Frames (Id),
-//     FOREIGN KEY (WindowGroup) REFERENCES DiaFrameMsMsWindowGroups (Id)
-//  )
-
-// CREATE TABLE DiaFrameMsMsWindows (
-//     WindowGroup INTEGER NOT NULL,
-//     ScanNumBegin INTEGER NOT NULL,
-//     ScanNumEnd INTEGER NOT NULL,
-//     IsolationMz REAL NOT NULL,
-//     IsolationWidth REAL NOT NULL,
-//     CollisionEnergy REAL NOT NULL,
-//     PRIMARY KEY(WindowGroup, ScanNumBegin),
-//     FOREIGN KEY (WindowGroup) REFERENCES DiaFrameMsMsWindowGroups (Id)
-//  ) WITHOUT ROWID
-
-#[derive(Clone, FromRow, Debug)]
-pub struct DiaFrameMsMsWindowInfo {
-    #[sqlx(rename = "WindowGroup")]
-    pub window_group: i32,
-    #[sqlx(rename = "ScanNumBegin")]
-    pub scan_num_begin: i32,
-    #[sqlx(rename = "ScanNumEnd")]
-    pub scan_num_end: i32,
-    #[sqlx(rename = "IsolationMz")]
-    pub isolation_mz: f32,
-    #[sqlx(rename = "IsolationWidth")]
-    pub isolation_width: f32,
-    #[sqlx(rename = "CollisionEnergy")]
-    pub collision_energy: f32,
-}
-
-impl DiaFrameMsMsWindowInfo {
-    fn into_scan_range(
-        &self,
-        id: usize,
-        quad_id: usize,
-        scan_converter: &timsrust::Scan2ImConverter,
-    ) -> ScanRange {
-        ScanRange::new(
-            id,
-            self.window_group as usize,
-            quad_id,
-            self.scan_num_begin as usize,
-            self.scan_num_end as usize,
-            self.isolation_mz,
-            self.isolation_width,
-            self.collision_energy,
-            scan_converter,
-        )
-    }
-}
-
-#[derive(Debug)]
-pub struct FrameInfoBuilder {
-    pub tdf_path: String,
-    pub scan_converter: timsrust::Scan2ImConverter,
-}
-
-impl FrameInfoBuilder {
-    pub fn from_dotd_path(dotd_path: String) -> Self {
-        let reader = timsrust::FileReader::new(dotd_path.clone()).unwrap();
-        let scan_converter = reader.get_scan_converter().unwrap();
-
-        // Find an 'analysis.tdf' file inside the dotd file (directory).
-        let tdf_path = Path::new(dotd_path.as_str())
-            .join("analysis.tdf")
-            .into_os_string()
-            .into_string()
-            .unwrap();
-        info!("tdf_path: {:?}", tdf_path);
-        Self {
-            tdf_path,
-            scan_converter,
-        }
-    }
-
-    pub fn build(&self) -> Result<DIAFrameInfo, sqlx::Error> {
-        let rt = Runtime::new().unwrap();
-
-        rt.block_on(async { self.build_async().await })
-    }
-
-    async fn build_async(&self) -> Result<DIAFrameInfo, sqlx::Error> {
-        let db = SqlitePool::connect(&self.tdf_path).await?;
-
-        // This vec maps frame_id -> window_group_id
-        let frame_info = self.get_frame_mapping(&db).await?;
-
-        // This vec maps window_group_id -> Vec<ScanRange>
-        // And also returns the grouping level.
-        let (group_mapping, grouping_level, row_to_group) = self.get_frame_windows(&db).await?;
-        let number_of_groups = row_to_group.iter().max().unwrap() + 1;
-
-        debug!("Number of groups: {}", number_of_groups);
-
-        let max_window_id = group_mapping.len() - 1;
-
-        let mut groups_vec_o = (0..(max_window_id + 1)).map(|_| None).collect::<Vec<_>>();
-        for (i, scan_ranges) in group_mapping.into_iter().enumerate() {
-            let scan_ranges = match scan_ranges {
-                None => continue,
-                Some(scan_ranges) => scan_ranges,
-            };
-            debug!("Scan ranges i={}: {:?}", i, scan_ranges);
-            if cfg!(debug_assertions) {
-                for scan_range in scan_ranges.iter() {
-                    debug_assert!(scan_range.window_group_id == i)
-                }
-            };
-            if scan_ranges.is_empty() {
-                continue;
-            } else {
-                groups_vec_o[i] = Some(DIAWindowGroup {
-                    window_group_id: i,
-                    scan_ranges,
-                });
-            }
-        }
-
-        let frame_info = DIAFrameInfo {
-            groups: groups_vec_o,
-            frame_groups: frame_info,
-            retention_times: DIAFrameInfo::rts_from_tdf_connection(&db).await?,
-            grouping_level,
-            number_of_groups,
-            row_to_group,
-        };
-
-        Ok(frame_info)
-    }
-
-    async fn get_frame_mapping(
-        &self,
-        db: &Pool<Sqlite>,
-    ) -> Result<Vec<Option<usize>>, sqlx::Error> {
-        let result: Vec<(i32, i32)> =
-            sqlx::query_as("SELECT Frame, WindowGroup FROM DiaFrameMsMsInfo;")
-                .fetch_all(db)
-                .await?;
-
-        let frame_info = result
-            .iter()
-            .map(|(id, group)| (*id as usize, *group as usize))
-            .collect::<Vec<(usize, usize)>>();
-
-        let max_id = frame_info.iter().map(|(id, _)| id).max().unwrap();
-        let mut ids_map_vec = vec![None; max_id + 1];
-        for (id, group) in frame_info {
-            ids_map_vec[id] = Some(group);
-        }
-
-        Ok(ids_map_vec)
-    }
-
-    async fn get_frame_windows(
-        &self,
-        db: &Pool<Sqlite>,
-    ) -> Result<(Vec<Option<Vec<ScanRange>>>, GroupingLevel, Vec<usize>), sqlx::Error> {
-        let result: Vec<DiaFrameMsMsWindowInfo> = sqlx::query_as::<_, DiaFrameMsMsWindowInfo>(
-            "SELECT
-                WindowGroup,
-                ScanNumBegin,
-                ScanNumEnd,
-                IsolationMz,
-                IsolationWidth,
-                CollisionEnergy
-            FROM DiaFrameMsMsWindows",
-        )
-        .fetch_all(db)
-        .await
-        .unwrap();
-
-        let grouping_level = if result.len() > 200 {
-            log::info!(
-                "More than 200 scan ranges, using WindowGroup grouping level. (diagonal PASEF?)"
-            );
-            GroupingLevel::WindowGroup
-        } else {
-            log::info!(
-                "Less than 200 scan ranges detected, using QuadWindowGroup grouping level. \
-                 (diaPASEF?)"
-            );
-            GroupingLevel::QuadWindowGroup
-        };
-
-        let max_window_id: usize = result
-            .iter()
-            .map(|window| window.window_group)
-            .max()
-            .unwrap() as usize;
-
-        let mut group_map_vec: Vec<Option<Vec<ScanRange>>> = vec![None; max_window_id + 1];
-
-        let mut scangroup_id = 0;
-        let mut row_to_group = Vec::new();
-        for window in result {
-            // TODO this is maybe a good place to make the trouping ...
-            // If its diapasef, the groups are quad+window groups.
-            // If its diagonal, the groups are only window groups.
-            let usize_wg = window.window_group as usize;
-            if group_map_vec[usize_wg].is_none() {
-                group_map_vec[usize_wg] = Some(Vec::new());
-            }
-
-            match &mut group_map_vec[usize_wg] {
-                None => continue,
-                Some(scan_ranges) => {
-                    let quad_id = scan_ranges.len();
-                    scan_ranges.push(window.into_scan_range(
-                        scangroup_id,
-                        quad_id,
-                        &self.scan_converter,
-                    ));
-                    scangroup_id += 1;
-                },
-            }
-
-            match grouping_level {
-                GroupingLevel::WindowGroup => {
-                    row_to_group.push(usize_wg);
-                },
-                GroupingLevel::QuadWindowGroup => {
-                    row_to_group.push(scangroup_id);
-                },
-            }
-        }
-        Ok((group_map_vec, grouping_level, row_to_group))
-    }
-}
-
-// TODO refactor this to make it a constructor method ...
-pub fn read_dia_frame_info(dotd_file: String) -> Result<DIAFrameInfo, sqlx::Error> {
-    let builder = FrameInfoBuilder::from_dotd_path(dotd_file);
-    builder.build()
-}
diff --git a/src/scoring.rs b/src/scoring.rs
index 5d053f4..ebbc807 100644
--- a/src/scoring.rs
+++ b/src/scoring.rs
@@ -194,7 +194,7 @@ pub fn score_pseudospectra(
     config: SageSearchConfig,
     out_path_features: Option<PathBuf>,
     num_report_psms: usize,
-) -> Result<Vec<Feature>, Box<dyn Error>> {
+) -> Result<Vec<Feature>, std::io::Error> {
     // 1. Buid raw spectra from the pseudospectra
 
     let take_top_n = 250;
@@ -256,8 +256,18 @@ pub fn score_pseudospectra(
         config.fasta_path.clone(),
         parameters.decoy_tag.clone(),
         parameters.generate_decoys,
-    )
-    .expect("Error reading fasta");
+    );
+
+    let sage_fasta = match sage_fasta {
+        Ok(x) => x,
+        Err(e) => {
+            log::error!("Error reading fasta: {:?}", e);
+            return Err(std::io::Error::new(
+                std::io::ErrorKind::Other,
+                e.to_string(),
+            ));
+        },
+    };
 
     let db = parameters.clone().build(sage_fasta);
 

From 63c343cd6fa052e04924daee7c360c9998cf9405 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Thu, 26 Sep 2024 10:02:12 -0700
Subject: [PATCH 2/3] chore: cargo update and fmt

---
 Cargo.lock                          | 401 +++++++++++++---------------
 Cargo.toml                          |  31 ++-
 deny.toml                           |  62 ++---
 src/aggregation/tracing.rs          |   6 +-
 src/ms/frames/dense_frame_window.rs |   1 -
 tests/test_window_parsing.rs        |  69 -----
 6 files changed, 249 insertions(+), 321 deletions(-)
 delete mode 100644 tests/test_window_parsing.rs

diff --git a/Cargo.lock b/Cargo.lock
index 697d2a5..542b15f 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -3,10 +3,10 @@
 version = 3
 
 [[package]]
-name = "adler"
-version = "1.0.2"
+name = "adler2"
+version = "2.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
+checksum = "512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627"
 
 [[package]]
 name = "ahash"
@@ -63,9 +63,9 @@ dependencies = [
 
 [[package]]
 name = "anstream"
-version = "0.6.14"
+version = "0.6.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b"
+checksum = "64e15c1ab1f89faffbf04a634d5e1962e9074f2741eef6d97f3c4e322426d526"
 dependencies = [
  "anstyle",
  "anstyle-parse",
@@ -78,36 +78,36 @@ dependencies = [
 
 [[package]]
 name = "anstyle"
-version = "1.0.7"
+version = "1.0.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b"
+checksum = "1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1"
 
 [[package]]
 name = "anstyle-parse"
-version = "0.2.4"
+version = "0.2.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4"
+checksum = "eb47de1e80c2b463c735db5b217a0ddc39d612e7ac9e2e96a5aed1f57616c1cb"
 dependencies = [
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle-query"
-version = "1.1.0"
+version = "1.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391"
+checksum = "6d36fc52c7f6c869915e99412912f22093507da8d9e942ceaf66fe4b7c14422a"
 dependencies = [
- "windows-sys",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "anstyle-wincon"
-version = "3.0.3"
+version = "3.0.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19"
+checksum = "5bf74e1b6e971609db8ca7a9ce79fd5768ab6ae46441c572e46cf596f59e57f8"
 dependencies = [
  "anstyle",
- "windows-sys",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -198,17 +198,6 @@ dependencies = [
  "num",
 ]
 
-[[package]]
-name = "atty"
-version = "0.2.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
-dependencies = [
- "hermit-abi",
- "libc",
- "winapi",
-]
-
 [[package]]
 name = "autocfg"
 version = "1.3.0"
@@ -229,9 +218,9 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
 
 [[package]]
 name = "bitflags"
-version = "2.5.0"
+version = "2.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cf4b9d6a944f767f8e5e0db018570623c85f3d925ac718db4e06d0187adb21c1"
+checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de"
 
 [[package]]
 name = "brotli"
@@ -274,19 +263,19 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
 [[package]]
 name = "bytes"
-version = "1.6.1"
+version = "1.7.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a12916984aab3fa6e39d655a33e09c0071eb36d6ab3aea5c2d78551f1df6d952"
+checksum = "428d9aa8fbc0670b7b8d6030a7fadd0f86151cae55e4dbbece15f3780a3dfaf3"
 
 [[package]]
 name = "cc"
-version = "1.0.98"
+version = "1.1.21"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "41c270e7540d725e65ac7f1b212ac8ce349719624d7bcff99f8e2e488e8cf03f"
+checksum = "07b1695e2c7e8fc85310cde85aeaab7e3097f593c91d209d3f9df76c928100f0"
 dependencies = [
  "jobserver",
  "libc",
- "once_cell",
+ "shlex",
 ]
 
 [[package]]
@@ -309,9 +298,9 @@ dependencies = [
 
 [[package]]
 name = "clap"
-version = "4.5.7"
+version = "4.5.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5db83dced34638ad474f39f250d7fea9598bdd239eaced1bdf45d597da0f433f"
+checksum = "b0956a43b323ac1afaffc053ed5c4b7c1f1800bacd1683c353aabbb752515dd3"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -319,9 +308,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.5.7"
+version = "4.5.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f7e204572485eb3fbf28f871612191521df159bc3e15a9f5064c66dba3a8c05f"
+checksum = "4d72166dd41634086d5803a47eb71ae740e61d84709c36f3c34110173db3961b"
 dependencies = [
  "anstream",
  "anstyle",
@@ -331,27 +320,27 @@ dependencies = [
 
 [[package]]
 name = "clap_derive"
-version = "4.5.5"
+version = "4.5.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c780290ccf4fb26629baa7a1081e68ced113f1d3ec302fa5948f1c381ebf06c6"
+checksum = "4ac6a0c7b1a9e9a5186361f67dfa1b88213572f427fb9ab038efb2bd8c582dab"
 dependencies = [
  "heck",
  "proc-macro2",
  "quote",
- "syn 2.0.66",
+ "syn 2.0.77",
 ]
 
 [[package]]
 name = "clap_lex"
-version = "0.7.1"
+version = "0.7.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4b82cf0babdbd58558212896d1a4272303a57bdb245c2bf1147185fb45640e70"
+checksum = "1462739cb27611015575c0c11df5df7601141071f07518d56fcc1be504cbec97"
 
 [[package]]
 name = "colorchoice"
-version = "1.0.1"
+version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422"
+checksum = "d3fd119d74b830634cea2a0f58bbd0d54540518a14397557951e79340abc28c0"
 
 [[package]]
 name = "console"
@@ -363,7 +352,7 @@ dependencies = [
  "lazy_static",
  "libc",
  "unicode-width",
- "windows-sys",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -388,9 +377,9 @@ dependencies = [
 
 [[package]]
 name = "core-foundation-sys"
-version = "0.8.6"
+version = "0.8.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f"
+checksum = "773648b94d0e5d620f64f280777445740e61fe701025087ec8b57f45c791888b"
 
 [[package]]
 name = "crc32fast"
@@ -480,9 +469,9 @@ dependencies = [
 
 [[package]]
 name = "either"
-version = "1.12.0"
+version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3dca9240753cf90908d7e4aac30f630662b02aebaa1b58a3cadabdb23385b58b"
+checksum = "60b1af1c220855b6ceac025d3f6ecdd2b7c4894bfe9cd9bda4fbb4bc7c0d4cf0"
 
 [[package]]
 name = "encode_unicode"
@@ -492,12 +481,12 @@ checksum = "a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f"
 
 [[package]]
 name = "env_logger"
-version = "0.7.1"
+version = "0.10.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "44533bbbb3bb3c1fa17d9f2e4e38bbbaf8396ba82193c4cb1b6445d711445d36"
+checksum = "4cd405aab171cb85d6735e5c8d9db038c17d3ca007a4d2c25f337935c3d90580"
 dependencies = [
- "atty",
  "humantime",
+ "is-terminal",
  "log",
  "regex",
  "termcolor",
@@ -533,9 +522,9 @@ dependencies = [
 
 [[package]]
 name = "flate2"
-version = "1.0.30"
+version = "1.0.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5f54427cfd1c7829e2a139fcefea601bf088ebca651d2bf53ebc600eac295dae"
+checksum = "324a1be68054ef05ad64b861cc9eaf1d623d2d8cb25b4bf2cb9cdd902b4bf253"
 dependencies = [
  "crc32fast",
  "miniz_oxide",
@@ -595,27 +584,21 @@ checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
 [[package]]
 name = "hermit-abi"
-version = "0.1.19"
+version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33"
-dependencies = [
- "libc",
-]
+checksum = "fbf6a919d6cf397374f7dfeeea91d974c7c0a7221d0d0f4f20d859d329e53fcc"
 
 [[package]]
 name = "humantime"
-version = "1.3.0"
+version = "2.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "df004cfca50ef23c36850aaaa59ad52cc70d0e90243c3c7737a4dd32dc7a3c4f"
-dependencies = [
- "quick-error",
-]
+checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4"
 
 [[package]]
 name = "iana-time-zone"
-version = "0.1.60"
+version = "0.1.61"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e7ffbb5a1b541ea2561f8c41c087286cc091e21e556a4f09a8f6cbf17b69b141"
+checksum = "235e081f3925a06703c2d0117ea8b91f042756fd6e7a6e5d901e8ca1a996b220"
 dependencies = [
  "android_system_properties",
  "core-foundation-sys",
@@ -636,9 +619,9 @@ dependencies = [
 
 [[package]]
 name = "indexmap"
-version = "2.2.6"
+version = "2.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "168fb715dda47215e360912c096649d23d58bf392ac62f73919e831745e40f26"
+checksum = "68b900aa2f7301e21c36462b170ee99994de34dff39a4a6a528e80e7376d07e5"
 dependencies = [
  "equivalent",
  "hashbrown",
@@ -693,11 +676,22 @@ dependencies = [
  "toml",
 ]
 
+[[package]]
+name = "is-terminal"
+version = "0.4.13"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "261f68e344040fbd0edea105bef17c66edf46f984ddb1115b775ce31be948f4b"
+dependencies = [
+ "hermit-abi",
+ "libc",
+ "windows-sys 0.52.0",
+]
+
 [[package]]
 name = "is_terminal_polyfill"
-version = "1.70.0"
+version = "1.70.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f8478577c03552c21db0e2724ffb8986a5ce7af88107e6be5d2ee6e158c12800"
+checksum = "7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf"
 
 [[package]]
 name = "itertools"
@@ -716,27 +710,27 @@ checksum = "49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b"
 
 [[package]]
 name = "jobserver"
-version = "0.1.31"
+version = "0.1.32"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d2b099aaa34a9751c5bf0878add70444e1ed2dd73f347be99003d4577277de6e"
+checksum = "48d1dbcbbeb6a7fec7e059840aa538bd62aaccf972c7346c4d9d2059312853d0"
 dependencies = [
  "libc",
 ]
 
 [[package]]
 name = "js-sys"
-version = "0.3.69"
+version = "0.3.70"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "29c15563dc2726973df627357ce0c9ddddbea194836909d655df6a75d2cf296d"
+checksum = "1868808506b929d7b0cfa8f75951347aa71bb21144b7791bae35d9bccfcfe37a"
 dependencies = [
  "wasm-bindgen",
 ]
 
 [[package]]
 name = "lazy_static"
-version = "1.4.0"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
+checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
 [[package]]
 name = "lexical-core"
@@ -804,9 +798,9 @@ dependencies = [
 
 [[package]]
 name = "libc"
-version = "0.2.155"
+version = "0.2.159"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c"
+checksum = "561d97a539a36e26a9a5fad1ea11a3039a67714694aaa379433e580854bc3dc5"
 
 [[package]]
 name = "libm"
@@ -847,25 +841,24 @@ dependencies = [
 
 [[package]]
 name = "log"
-version = "0.4.21"
+version = "0.4.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c"
+checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24"
 
 [[package]]
 name = "lz4"
-version = "1.24.0"
+version = "1.28.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7e9e2dd86df36ce760a60f6ff6ad526f7ba1f14ba0356f8254fb6905e6494df1"
+checksum = "4d1febb2b4a79ddd1980eede06a8f7902197960aa0383ffcfdd62fe723036725"
 dependencies = [
- "libc",
  "lz4-sys",
 ]
 
 [[package]]
 name = "lz4-sys"
-version = "1.9.4"
+version = "1.11.1+lz4-1.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "57d27b317e207b10f69f5e75494119e391a96f48861ae870d1da6edac98ca900"
+checksum = "6bd8c0d6c6ed0cd30b3652886bb8711dc4bb01d637a68105a3d5158039b418e6"
 dependencies = [
  "cc",
  "libc",
@@ -873,9 +866,9 @@ dependencies = [
 
 [[package]]
 name = "memchr"
-version = "2.7.2"
+version = "2.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d"
+checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
 [[package]]
 name = "memmap2"
@@ -888,11 +881,11 @@ dependencies = [
 
 [[package]]
 name = "miniz_oxide"
-version = "0.7.3"
+version = "0.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "87dfd01fe195c66b572b37921ad8803d010623c0aca821bea2302239d155cdae"
+checksum = "e2d80299ef12ff69b16a84bb182e3b9df68b5a91574d3d4fa6e41b65deec4df1"
 dependencies = [
- "adler",
+ "adler2",
 ]
 
 [[package]]
@@ -911,9 +904,9 @@ dependencies = [
 
 [[package]]
 name = "num-bigint"
-version = "0.4.5"
+version = "0.4.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c165a9ab64cf766f73521c0dd2cfdff64f488b8f0b3e621face3462d3db536d7"
+checksum = "a5e44f723f1133c9deac646763579fdb3ac745e418f2a7af9cd0c431da1f20b9"
 dependencies = [
  "num-integer",
  "num-traits",
@@ -1042,27 +1035,30 @@ checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a"
 
 [[package]]
 name = "pkg-config"
-version = "0.3.30"
+version = "0.3.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec"
+checksum = "953ec861398dccce10c670dfeaf3ec4911ca479e9c02154b3a215178c5f566f2"
 
 [[package]]
 name = "portable-atomic"
-version = "1.6.0"
+version = "1.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0"
+checksum = "d30538d42559de6b034bc76fd6dd4c38961b1ee5c6c56e3808c50128fdbc22ce"
 
 [[package]]
 name = "ppv-lite86"
-version = "0.2.17"
+version = "0.2.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
+checksum = "77957b295656769bb8ad2b6a6b09d897d94f05c41b069aede1fcdaa675eaea04"
+dependencies = [
+ "zerocopy",
+]
 
 [[package]]
 name = "pretty_env_logger"
-version = "0.4.0"
+version = "0.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "926d36b9553851b8b0005f1275891b392ee4d2d833852c417ed025477350fb9d"
+checksum = "865724d4dbe39d9f3dd3b52b88d859d66bcb2d6a0acfd5ea68a65fb66d4bdc1c"
 dependencies = [
  "env_logger",
  "log",
@@ -1070,24 +1066,18 @@ dependencies = [
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.83"
+version = "1.0.86"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b33eb56c327dec362a9e55b3ad14f9d2f0904fb5a5b03b513ab5465399e9f43"
+checksum = "5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77"
 dependencies = [
  "unicode-ident",
 ]
 
-[[package]]
-name = "quick-error"
-version = "1.2.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
-
 [[package]]
 name = "quote"
-version = "1.0.36"
+version = "1.0.37"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7"
+checksum = "b5b9d34b8991d19d98081b46eacdd8eb58c6f2b201139f7c5f643cc155a633af"
 dependencies = [
  "proc-macro2",
 ]
@@ -1144,18 +1134,18 @@ dependencies = [
 
 [[package]]
 name = "redox_syscall"
-version = "0.5.1"
+version = "0.5.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "469052894dcb553421e483e4209ee581a45100d31b4018de03e5a7ad86374a7e"
+checksum = "355ae415ccd3a04315d3f8246e86d67689ea74d88d915576e1589a351062a13b"
 dependencies = [
- "bitflags 2.5.0",
+ "bitflags 2.6.0",
 ]
 
 [[package]]
 name = "regex"
-version = "1.10.4"
+version = "1.10.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c"
+checksum = "4219d74c6b67a3654a9fbebc4b419e22126d13d2f3c4a07ee0cb61ff79a79619"
 dependencies = [
  "aho-corasick",
  "memchr",
@@ -1165,9 +1155,9 @@ dependencies = [
 
 [[package]]
 name = "regex-automata"
-version = "0.4.6"
+version = "0.4.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea"
+checksum = "38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df"
 dependencies = [
  "aho-corasick",
  "memchr",
@@ -1176,9 +1166,9 @@ dependencies = [
 
 [[package]]
 name = "regex-syntax"
-version = "0.8.3"
+version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56"
+checksum = "7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b"
 
 [[package]]
 name = "rusqlite"
@@ -1186,7 +1176,7 @@ version = "0.31.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b838eba278d213a8beaf485bd313fd580ca4505a00d5871caeb1457c55322cae"
 dependencies = [
- "bitflags 2.5.0",
+ "bitflags 2.6.0",
  "fallible-iterator",
  "fallible-streaming-iterator",
  "hashlink",
@@ -1196,9 +1186,9 @@ dependencies = [
 
 [[package]]
 name = "rustc_version"
-version = "0.4.0"
+version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366"
+checksum = "cfcb3a22ef46e85b45de6ee7e79d063319ebb6594faafcf1c225ea92ab6e9b92"
 dependencies = [
  "semver",
 ]
@@ -1258,7 +1248,7 @@ checksum = "243902eda00fad750862fc144cea25caca5e20d615af0a81bee94ca738f1df1f"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.66",
+ "syn 2.0.77",
 ]
 
 [[package]]
@@ -1275,13 +1265,19 @@ dependencies = [
 
 [[package]]
 name = "serde_spanned"
-version = "0.6.6"
+version = "0.6.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "79e674e01f999af37c49f70a6ede167a8a60b2503e56c5599532a65baa5969a0"
+checksum = "87607cb1398ed59d48732e575a4c28a7a8ebf2454b964fe3f224f2afc07909e1"
 dependencies = [
  "serde",
 ]
 
+[[package]]
+name = "shlex"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
+
 [[package]]
 name = "smallvec"
 version = "1.13.2"
@@ -1319,9 +1315,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.66"
+version = "2.0.77"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c42f3f41a2de00b01c0aaad383c5a45241efc8b2d1eda5661812fda5f3cdcff5"
+checksum = "9f35bcdf61fd8e7be6caf75f429fdca8beb3ed76584befb503b1569faee373ed"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1339,22 +1335,22 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "1.0.61"
+version = "1.0.64"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c546c80d6be4bc6a00c0f01730c08df82eaa7a7a61f11d656526506112cc1709"
+checksum = "d50af8abc119fb8bb6dbabcfa89656f46f84aa0ac7688088608076ad2b459a84"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.61"
+version = "1.0.64"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46c3384250002a6d5af4d114f2845d37b57521033f30d5c3f46c4d70e1197533"
+checksum = "08904e7672f5eb876eaaf87e0ce17857500934f4981c4a0ab2b4aa98baac7fc3"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.66",
+ "syn 2.0.77",
 ]
 
 [[package]]
@@ -1397,9 +1393,9 @@ dependencies = [
 
 [[package]]
 name = "toml"
-version = "0.8.13"
+version = "0.8.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a4e43f8cc456c9704c851ae29c67e17ef65d2c30017c17a9765b89c382dc8bba"
+checksum = "a1ed1f98e3fdc28d6d910e6737ae6ab1a93bf1985935a1193e68f93eeb68d24e"
 dependencies = [
  "serde",
  "serde_spanned",
@@ -1409,18 +1405,18 @@ dependencies = [
 
 [[package]]
 name = "toml_datetime"
-version = "0.6.6"
+version = "0.6.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4badfd56924ae69bcc9039335b2e017639ce3f9b001c393c1b2d1ef846ce2cbf"
+checksum = "0dd7358ecb8fc2f8d014bf86f6f638ce72ba252a2c3a2572f2a795f1d23efb41"
 dependencies = [
  "serde",
 ]
 
 [[package]]
 name = "toml_edit"
-version = "0.22.13"
+version = "0.22.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c127785850e8c20836d49732ae6abfa47616e60bf9d9f57c43c250361a9db96c"
+checksum = "4ae48d6208a266e853d946088ed816055e556cc6028c5e8e2b84d9fa5dd7c7f5"
 dependencies = [
  "indexmap",
  "serde",
@@ -1441,15 +1437,15 @@ dependencies = [
 
 [[package]]
 name = "unicode-ident"
-version = "1.0.12"
+version = "1.0.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
+checksum = "e91b56cd4cadaeb79bbf1a5645f6b4f8dc5bde8834ad5894a8db35fda9efa1fe"
 
 [[package]]
 name = "unicode-width"
-version = "0.1.12"
+version = "0.1.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "68f5e5f3158ecfd4b8ff6fe086db7c8467a2dfdac97fe420f2b7c4aa97af66d6"
+checksum = "7dd6e30e90baa6f72411720665d41d89b9a3d039dc45b8faea1ddd07f617f6af"
 
 [[package]]
 name = "utf8parse"
@@ -1465,9 +1461,9 @@ checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
 
 [[package]]
 name = "version_check"
-version = "0.9.4"
+version = "0.9.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
+checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a"
 
 [[package]]
 name = "wasi"
@@ -1477,34 +1473,35 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wasm-bindgen"
-version = "0.2.92"
+version = "0.2.93"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4be2531df63900aeb2bca0daaaddec08491ee64ceecbee5076636a3b026795a8"
+checksum = "a82edfc16a6c469f5f44dc7b571814045d60404b55a0ee849f9bcfa2e63dd9b5"
 dependencies = [
  "cfg-if",
+ "once_cell",
  "wasm-bindgen-macro",
 ]
 
 [[package]]
 name = "wasm-bindgen-backend"
-version = "0.2.92"
+version = "0.2.93"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "614d787b966d3989fa7bb98a654e369c762374fd3213d212cfc0251257e747da"
+checksum = "9de396da306523044d3302746f1208fa71d7532227f15e347e2d93e4145dd77b"
 dependencies = [
  "bumpalo",
  "log",
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.66",
+ "syn 2.0.77",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-macro"
-version = "0.2.92"
+version = "0.2.93"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a1f8823de937b71b9460c0c34e25f3da88250760bec0ebac694b49997550d726"
+checksum = "585c4c91a46b072c92e908d99cb1dcdf95c5218eeb6f3bf1efa991ee7a68cccf"
 dependencies = [
  "quote",
  "wasm-bindgen-macro-support",
@@ -1512,54 +1509,32 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro-support"
-version = "0.2.92"
+version = "0.2.93"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7"
+checksum = "afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.66",
+ "syn 2.0.77",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-shared"
-version = "0.2.92"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96"
-
-[[package]]
-name = "winapi"
-version = "0.3.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419"
-dependencies = [
- "winapi-i686-pc-windows-gnu",
- "winapi-x86_64-pc-windows-gnu",
-]
-
-[[package]]
-name = "winapi-i686-pc-windows-gnu"
-version = "0.4.0"
+version = "0.2.93"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
+checksum = "c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484"
 
 [[package]]
 name = "winapi-util"
-version = "0.1.8"
+version = "0.1.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b"
+checksum = "cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb"
 dependencies = [
- "windows-sys",
+ "windows-sys 0.59.0",
 ]
 
-[[package]]
-name = "winapi-x86_64-pc-windows-gnu"
-version = "0.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
-
 [[package]]
 name = "windows-core"
 version = "0.52.0"
@@ -1578,11 +1553,20 @@ dependencies = [
  "windows-targets",
 ]
 
+[[package]]
+name = "windows-sys"
+version = "0.59.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b"
+dependencies = [
+ "windows-targets",
+]
+
 [[package]]
 name = "windows-targets"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb"
+checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973"
 dependencies = [
  "windows_aarch64_gnullvm",
  "windows_aarch64_msvc",
@@ -1596,79 +1580,80 @@ dependencies = [
 
 [[package]]
 name = "windows_aarch64_gnullvm"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263"
+checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
 
 [[package]]
 name = "windows_aarch64_msvc"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6"
+checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
 
 [[package]]
 name = "windows_i686_gnu"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670"
+checksum = "8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b"
 
 [[package]]
 name = "windows_i686_gnullvm"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9"
+checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
 
 [[package]]
 name = "windows_i686_msvc"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf"
+checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
 
 [[package]]
 name = "windows_x86_64_gnu"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9"
+checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
 
 [[package]]
 name = "windows_x86_64_gnullvm"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596"
+checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
 
 [[package]]
 name = "windows_x86_64_msvc"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0"
+checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
 
 [[package]]
 name = "winnow"
-version = "0.6.8"
+version = "0.6.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c3c52e9c97a68071b23e836c9380edae937f17b9c4667bd021973efc689f618d"
+checksum = "36c1fec1a2bb5866f07c25f68c26e565c4c200aebb96d7e55710c19d3e8ac49b"
 dependencies = [
  "memchr",
 ]
 
 [[package]]
 name = "zerocopy"
-version = "0.7.34"
+version = "0.7.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae87e3fcd617500e5d106f0380cf7b77f3c6092aae37191433159dda23cfb087"
+checksum = "1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0"
 dependencies = [
+ "byteorder",
  "zerocopy-derive",
 ]
 
 [[package]]
 name = "zerocopy-derive"
-version = "0.7.34"
+version = "0.7.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "15e934569e47891f7d9411f1a451d947a60e000ab3bd24fbb970f000387d1b3b"
+checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.66",
+ "syn 2.0.77",
 ]
 
 [[package]]
@@ -1710,9 +1695,9 @@ dependencies = [
 
 [[package]]
 name = "zstd-sys"
-version = "2.0.10+zstd.1.5.6"
+version = "2.0.13+zstd.1.5.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c253a4914af5bafc8fa8c86ee400827e83cf6ec01195ec1f1ed8441bf00d65aa"
+checksum = "38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa"
 dependencies = [
  "cc",
  "pkg-config",
diff --git a/Cargo.toml b/Cargo.toml
index 0806300..d3a6dee 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -10,25 +10,34 @@ license = "Apache-2.0"
 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"
 
+# 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"
diff --git a/deny.toml b/deny.toml
index 51e81af..ee0e475 100644
--- a/deny.toml
+++ b/deny.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
diff --git a/src/aggregation/tracing.rs b/src/aggregation/tracing.rs
index 199a149..5aa22d0 100644
--- a/src/aggregation/tracing.rs
+++ b/src/aggregation/tracing.rs
@@ -231,6 +231,9 @@ pub fn calculate_cycle_time(frames: &[DenseFrameWindow]) -> f64 {
     let rts = frames.iter().map(|x| x.frame.rt).collect::<Vec<f64>>();
     let rt_diffs = rts.windows(2).map(|x| x[1] - x[0]).collect::<Vec<f64>>();
     let cycle_time = rt_diffs.iter().sum::<f64>() / rt_diffs.len() as f64;
+
+    assert!(cycle_time > 0.);
+
     cycle_time
 }
 
@@ -251,7 +254,8 @@ pub fn combine_traces(
 
     let grouped_windows: Vec<(f64, Vec<TimeTimsPeak>)> = grouped_denseframe_windows
         .into_iter()
-        .map(|x| {
+        .map(|mut x| {
+            x.par_sort_unstable_by(|a, b| a.frame.rt.partial_cmp(&b.frame.rt).unwrap());
             let cycle_time = calculate_cycle_time(&x);
             let o = _flatten_denseframe_vec(x);
             (cycle_time, o)
diff --git a/src/ms/frames/dense_frame_window.rs b/src/ms/frames/dense_frame_window.rs
index 2cfe89e..9b25e53 100644
--- a/src/ms/frames/dense_frame_window.rs
+++ b/src/ms/frames/dense_frame_window.rs
@@ -37,7 +37,6 @@ pub struct DenseFrameWindow {
     pub quadrupole_setting: SingleQuadrupoleSettings,
 }
 
-
 impl DenseFrameWindow {
     pub fn from_frame_window(
         frame_window: &FrameSlice,
diff --git a/tests/test_window_parsing.rs b/tests/test_window_parsing.rs
deleted file mode 100644
index 9df5bda..0000000
--- a/tests/test_window_parsing.rs
+++ /dev/null
@@ -1,69 +0,0 @@
-use ionmesh::ms::tdf::{
-    FrameInfoBuilder,
-    GroupingLevel,
-};
-
-#[test]
-fn test_dia_pasef() {
-    let finfo_b = FrameInfoBuilder::from_dotd_path("tests/data/diapasef_tdf/data.d".into());
-    let finfo = finfo_b.build();
-
-    assert!(finfo.is_ok());
-
-    let finfo = finfo.unwrap();
-
-    // The number of ids in `DiaFrameMsMsWindowGroups` + 1 bc 0 is not used
-    assert_eq!(finfo.groups.len(), 9);
-
-    assert!(finfo.groups[0].is_none());
-    for group in finfo.groups.iter().skip(1) {
-        assert!(group.is_some());
-    }
-
-    // Make sure the grouping is correctly assigned... for diaPASEF it should
-    // be `QuadWindowGroup`
-    match finfo.grouping_level {
-        GroupingLevel::QuadWindowGroup => {},
-        GroupingLevel::WindowGroup => {
-            assert!(false);
-        },
-    }
-
-    // Make sure the grouping is correct.
-    // For this diapasef file  is 8 * 2 (8 window groups, 2 isolation windows per group)
-    assert_eq!(finfo.row_to_group.iter().max().unwrap(), &(8 * 2));
-
-    // println!("{:?}", finfo);
-    // assert!(false)
-}
-
-#[test]
-fn test_synchro_dia_pasef() {
-    let finfo_b = FrameInfoBuilder::from_dotd_path("tests/data/synchropasef_tdf/data.d".into());
-    let finfo = finfo_b.build();
-
-    assert!(finfo.is_ok());
-
-    let finfo = finfo.unwrap();
-
-    // The number of ids in `DiaFrameMsMsWindowGroups` + 1, bc 0 is not used
-    assert_eq!(finfo.groups.len(), 5);
-    assert!(finfo.groups[0].is_none());
-    for group in finfo.groups.iter().skip(1) {
-        assert!(group.is_some());
-    }
-
-    // Make sure the grouping is correctly assigned... for diaPASEF it should
-    // be `QuadWindowGroup`
-    match finfo.grouping_level {
-        GroupingLevel::QuadWindowGroup => {
-            assert!(false);
-        },
-        GroupingLevel::WindowGroup => {},
-    }
-
-    // Make sure the grouping is correct.
-    assert_eq!(finfo.row_to_group.iter().max().unwrap(), &4);
-
-    // println!("{:?}", finfo);
-}

From 541a335dcafebafadc42272ca32e8ba03b649be3 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Thu, 26 Sep 2024 10:12:48 -0700
Subject: [PATCH 3/3] (chore) removed unused imports

---
 src/aggregation/dbscan/denseframe_dbscan.rs | 7 +------
 src/aggregation/ms_denoise.rs               | 1 -
 src/main.rs                                 | 1 -
 src/ms/frames/dense_frame_window.rs         | 2 --
 src/ms/frames/frame_slice.rs                | 4 ----
 5 files changed, 1 insertion(+), 14 deletions(-)

diff --git a/src/aggregation/dbscan/denseframe_dbscan.rs b/src/aggregation/dbscan/denseframe_dbscan.rs
index 03b4268..a0be7a6 100644
--- a/src/aggregation/dbscan/denseframe_dbscan.rs
+++ b/src/aggregation/dbscan/denseframe_dbscan.rs
@@ -1,8 +1,4 @@
-use timsrust::{
-    AcquisitionType,
-    MSLevel,
-    QuadrupoleSettings,
-};
+use timsrust::MSLevel;
 
 use crate::aggregation::aggregators::TimsPeakAggregator;
 use crate::aggregation::converters::{
@@ -12,7 +8,6 @@ use crate::aggregation::converters::{
 use crate::aggregation::dbscan::dbscan::dbscan_generic;
 use crate::ms::frames::{
     DenseFrame,
-    SingleQuadrupoleSettings,
     TimsPeak,
 };
 use crate::space::space_generics::{
diff --git a/src/aggregation/ms_denoise.rs b/src/aggregation/ms_denoise.rs
index 31b3cb2..e82465d 100644
--- a/src/aggregation/ms_denoise.rs
+++ b/src/aggregation/ms_denoise.rs
@@ -39,7 +39,6 @@ use crate::ms::frames::{
     DenseFrameWindow,
     ExpandedFrameSlice,
     FrameSlice,
-    SingleQuadrupoleSettings,
     TimsPeak,
 };
 use crate::space::space_generics::{
diff --git a/src/main.rs b/src/main.rs
index 2a39caf..b0a12e4 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -18,7 +18,6 @@ extern crate log;
 extern crate pretty_env_logger;
 
 use std::fs;
-use std::io::Error;
 use std::path::Path;
 
 use clap::Parser;
diff --git a/src/ms/frames/dense_frame_window.rs b/src/ms/frames/dense_frame_window.rs
index 9b25e53..f49938e 100644
--- a/src/ms/frames/dense_frame_window.rs
+++ b/src/ms/frames/dense_frame_window.rs
@@ -1,5 +1,3 @@
-use std::sync::Arc;
-
 use log::info;
 use serde::Serialize;
 use timsrust::converters::{
diff --git a/src/ms/frames/frame_slice.rs b/src/ms/frames/frame_slice.rs
index c034708..0e2b828 100644
--- a/src/ms/frames/frame_slice.rs
+++ b/src/ms/frames/frame_slice.rs
@@ -1,17 +1,13 @@
 use std::fmt;
-use std::sync::Arc;
 
 use serde::Serialize;
 use timsrust::{
     AcquisitionType,
     Frame,
     MSLevel,
-    QuadrupoleSettings,
 };
 
 use super::SingleQuadrupoleSettings;
-use crate::aggregation::ms_denoise;
-use crate::space::quad;
 use crate::space::space_generics::{
     AsNDPointsAtIndex,
     IntenseAtIndex,