seqpro 0.18.0__tar.gz → 0.19.0__tar.gz

{seqpro-0.18.0 → seqpro-0.19.0}/CHANGELOG.md

@@ -1,3 +1,15 @@
+## 0.19.0 (2026-06-23)
+
+### Feat
+
+- **rag**: port reverse_complement to seqpro-core Rust; rag layer numba-free
+- **rag**: port to_padded to seqpro-core Rust, drop numba kernel
+
+### Refactor
+
+- **rag**: truthful _ops docstring; guard reverse_complement_inplace empty offsets
+- **rust**: extract pyo3-free seqpro-core crate owning the Ragged layout
+
 ## 0.18.0 (2026-06-23)
 
 ### Feat

{seqpro-0.18.0 → seqpro-0.19.0}/Cargo.lock

@@ -59,12 +59,6 @@ version = "0.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5e764a1d40d510daf35e07be9eb06e75770908c27d411ee6c92109c9840eaaf7"
 
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
-
 [[package]]
 name = "bitflags"
 version = "2.11.1"
@@ -470,12 +464,6 @@ version = "0.17.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ed5909b6e89a2db4456e54cd5f673791d7eca6732202bbf2a9cc504fe2f9b84a"
 
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
-
 [[package]]
 name = "heck"
 version = "0.5.0"
@@ -512,12 +500,6 @@ dependencies = [
  "serde_core",
 ]
 
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
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-
 [[package]]
 name = "is-terminal"
 version = "0.4.17"
@@ -579,16 +561,6 @@ version = "0.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32a66949e030da00e8c7d4434b251670a91556f4144941d37452769c25d58a53"
 
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-checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45"
-dependencies = [
- "autocfg",
- "scopeguard",
-]
-
 [[package]]
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 version = "0.4.29"
@@ -611,25 +583,18 @@ version = "2.8.0"
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 checksum = "f8ca58f447f06ed17d5fc4043ce1b10dd205e060fb3ce5b979b8ed8e59ff3f79"
 
-[[package]]
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-dependencies = [
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-]
-
 [[package]]
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 dependencies = [
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  "num-complex",
  "num-integer",
  "num-traits",
+ "portable-atomic",
+ "portable-atomic-util",
  "rawpointer",
  "rayon",
 ]
@@ -640,7 +605,7 @@ version = "0.31.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "cf20d2fde8ff38632c426f1165ed7436270b44f199fc55284c38276f9db47c3d"
 dependencies = [
- "bitflags 2.11.1",
+ "bitflags",
  "cfg-if",
  "cfg_aliases",
  "libc",
@@ -676,9 +641,9 @@ dependencies = [
 
 [[package]]
 name = "numpy"
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 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bef41cbb417ea83b30525259e30ccef6af39b31c240bda578889494c5392d331"
+checksum = "778da78c64ddc928ebf5ad9df5edf0789410ff3bdbf3619aed51cd789a6af1e2"
 dependencies = [
  "libc",
  "ndarray",
@@ -686,14 +651,15 @@ dependencies = [
  "num-integer",
  "num-traits",
  "pyo3",
+ "pyo3-build-config",
  "rustc-hash",
 ]
 
 [[package]]
 name = "once_cell"
-version = "1.19.0"
+version = "1.21.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
+checksum = "9f7c3e4beb33f85d45ae3e3a1792185706c8e16d043238c593331cc7cd313b50"
 
 [[package]]
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@@ -701,29 +667,6 @@ version = "11.1.5"
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 checksum = "d6790f58c7ff633d8771f42965289203411a5e5c68388703c06e14f24770b41e"
 
-[[package]]
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- "redox_syscall",
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-]
-
 [[package]]
 name = "pin-project-lite"
 version = "0.2.17"
@@ -758,6 +701,21 @@ dependencies = [
  "plotters-backend",
 ]
 
+[[package]]
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+version = "1.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c33a9471896f1c69cecef8d20cbe2f7accd12527ce60845ff44c153bb2a21b49"
+
+[[package]]
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+version = "0.2.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c2a106d1259c23fac8e543272398ae0e3c0b8d33c88ed73d0cc71b0f1d902618"
+dependencies = [
+ "portable-atomic",
+]
+
 [[package]]
 name = "ppv-lite86"
 version = "0.2.17"
@@ -791,7 +749,7 @@ checksum = "4b45fcc2344c680f5025fe57779faef368840d0bd1f42f216291f0dc4ace4744"
 dependencies = [
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  "bit-vec",
- "bitflags 2.11.1",
+ "bitflags",
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  "rand_chacha 0.9.0",
@@ -804,36 +762,32 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.20.1"
+version = "0.28.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e82ad98ce1991c9c70c3464ba4187337b9c45fcbbb060d46dca15f0c075e14e2"
+checksum = "91fd8e38a3b50ed1167fb981cd6fd60147e091784c427b8f7183a7ee32c31c12"
 dependencies = [
- "cfg-if",
- "indoc",
  "libc",
- "memoffset",
- "parking_lot",
+ "once_cell",
+ "portable-atomic",
  "pyo3-build-config",
  "pyo3-ffi",
  "pyo3-macros",
- "unindent",
 ]
 
 [[package]]
 name = "pyo3-build-config"
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-checksum = "5503d0b3aee2c7a8dbb389cd87cd9649f675d4c7f60ca33699a3e3859d81a891"
+checksum = "e368e7ddfdeb98c9bca7f8383be1648fd84ab466bf2bc015e94008db6d35611e"
 dependencies = [
- "once_cell",
  "target-lexicon",
 ]
 
 [[package]]
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-version = "0.20.1"
+version = "0.28.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "18a79e8d80486a00d11c0dcb27cd2aa17c022cc95c677b461f01797226ba8f41"
+checksum = "7f29e10af80b1f7ccaf7f69eace800a03ecd13e883acfacc1e5d0988605f651e"
 dependencies = [
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@@ -841,9 +795,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.20.1"
+version = "0.28.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1f4b0dc7eaa578604fab11c8c7ff8934c71249c61d4def8e272c76ed879f03d4"
+checksum = "df6e520eff47c45997d2fc7dd8214b25dd1310918bbb2642156ef66a67f29813"
 dependencies = [
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  "pyo3-macros-backend",
@@ -853,12 +807,13 @@ dependencies = [
 
 [[package]]
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-version = "0.20.1"
+version = "0.28.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "816a4f709e29ddab2e3cdfe94600d554c5556cad0ddfeea95c47b580c3247fa4"
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 dependencies = [
- "heck 0.4.1",
+ "heck",
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+ "pyo3-build-config",
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 ]
@@ -984,15 +939,6 @@ dependencies = [
  "crossbeam-utils",
 ]
 
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
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-dependencies = [
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-]
-
 [[package]]
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@@ -1024,9 +970,9 @@ checksum = "dc897dd8d9e8bd1ed8cdad82b5966c3e0ecae09fb1907d58efaa013543185d0a"
 
 [[package]]
 name = "rustc-hash"
-version = "1.1.0"
+version = "2.1.2"
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-checksum = "08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2"
+checksum = "94300abf3f1ae2e2b8ffb7b58043de3d399c73fa6f4b73826402a5c457614dbe"
 
 [[package]]
 name = "rustix"
@@ -1034,7 +980,7 @@ version = "1.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b6fe4565b9518b83ef4f91bb47ce29620ca828bd32cb7e408f0062e9930ba190"
 dependencies = [
- "bitflags 2.11.1",
+ "bitflags",
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  "libc",
  "linux-raw-sys",
@@ -1068,12 +1014,6 @@ dependencies = [
  "winapi-util",
 ]
 
-[[package]]
-name = "scopeguard"
-version = "1.2.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
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-
 [[package]]
 name = "semver"
 version = "1.0.28"
@@ -1093,10 +1033,20 @@ dependencies = [
  "pyo3",
  "rand 0.8.5",
  "rayon",
+ "seqpro-core",
  "thiserror",
  "xxhash-rust",
 ]
 
+[[package]]
+name = "seqpro-core"
+version = "0.1.0"
+dependencies = [
+ "ndarray",
+ "proptest",
+ "rayon",
+]
+
 [[package]]
 name = "serde"
 version = "1.0.228"
@@ -1152,12 +1102,6 @@ version = "0.4.12"
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-[[package]]
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-
 [[package]]
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 version = "0.18.0"
@@ -1198,9 +1142,9 @@ dependencies = [
 
 [[package]]
 name = "target-lexicon"
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+checksum = "adb6935a6f5c20170eeceb1a3835a49e12e19d792f6dd344ccc76a985ca5a6ca"
 
 [[package]]
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@@ -1263,12 +1207,6 @@ version = "0.2.6"
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-
 [[package]]
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@@ -1385,7 +1323,7 @@ version = "0.244.0"
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 dependencies = [
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+ "bitflags",
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@@ -1422,7 +1360,7 @@ version = "0.59.0"
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 dependencies = [
- "windows-targets 0.52.6",
+ "windows-targets",
 ]
 
 [[package]]
@@ -1434,67 +1372,34 @@ dependencies = [
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 ]
 
-[[package]]
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 dependencies = [
- "windows_aarch64_gnullvm 0.52.6",
- "windows_aarch64_msvc 0.52.6",
- "windows_i686_gnu 0.52.6",
+ "windows_aarch64_gnullvm",
+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
  "windows_i686_gnullvm",
- "windows_i686_msvc 0.52.6",
- "windows_x86_64_gnu 0.52.6",
- "windows_x86_64_gnullvm 0.52.6",
- "windows_x86_64_msvc 0.52.6",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
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-
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-
 [[package]]
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@@ -1507,48 +1412,24 @@ version = "0.52.6"
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 checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
 
-[[package]]
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-
 [[package]]
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 checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
 
-[[package]]
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 [[package]]
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-[[package]]
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-
 [[package]]
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 checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
 
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
-
 [[package]]
 name = "windows_x86_64_msvc"
 version = "0.52.6"
@@ -1577,7 +1458,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ea61de684c3ea68cb082b7a88508a8b27fcc8b797d738bfc99a82facf1d752dc"
 dependencies = [
  "anyhow",
- "heck 0.5.0",
+ "heck",
  "wit-parser",
 ]
 
@@ -1588,7 +1469,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b7c566e0f4b284dd6561c786d9cb0142da491f46a9fbed79ea69cdad5db17f21"
 dependencies = [
  "anyhow",
- "heck 0.5.0",
+ "heck",
  "indexmap",
  "prettyplease",
  "syn 2.0.106",
@@ -1619,7 +1500,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9d66ea20e9553b30172b5e831994e35fbde2d165325bec84fc43dbf6f4eb9cb2"
 dependencies = [
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- "bitflags 2.11.1",
+ "bitflags",
  "indexmap",
  "log",
  "serde",

{seqpro-0.18.0 → seqpro-0.19.0}/Cargo.toml

@@ -1,3 +1,6 @@
+[workspace]
+members = ["crates/seqpro-core"]
+
 [package]
 name = "seqpro"
 version = "0.1.0"
@@ -11,16 +14,17 @@ name = "seqpro"
 crate-type = ["cdylib", "rlib"]
 
 [dependencies]
+seqpro-core = { path = "crates/seqpro-core" }
 anyhow = "1.0.99"
-ndarray = { version = "0.15.6", features = ["rayon"] }
-numpy = "0.20.0"
+ndarray = { version = "0.17", features = ["rayon"] }
+numpy = "0.28.0"
 rand = { version = "0.8.5", features = ["small_rng"] }
 rayon = "1.11.0"
 thiserror = "1.0.69"
 xxhash-rust = { version = "0.8.15", features = ["xxh3"] }
 
 [dependencies.pyo3]
-version = "0.20"
+version = "0.28"
 features = ["abi3-py39"]
 
 [dev-dependencies]

{seqpro-0.18.0 → seqpro-0.19.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seqpro
-Version: 0.18.0
+Version: 0.19.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy

seqpro-0.19.0/crates/seqpro-core/Cargo.toml

@@ -0,0 +1,14 @@
+[package]
+name = "seqpro-core"
+version = "0.1.0"
+edition = "2021"
+
+[lib]
+name = "seqpro_core"
+
+[dependencies]
+ndarray = { version = "0.17", features = ["rayon"] }
+rayon = "1.11.0"
+
+[dev-dependencies]
+proptest = "1.4"

seqpro-0.19.0/crates/seqpro-core/src/lib.rs

@@ -0,0 +1,2 @@
+pub mod ragged;
+pub use ragged::Ragged;