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📦 Add infer and new pipeline infrastructure

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- Update Cargo.lock with dependency additions (bumpalo, byteorder, cfb, fnv, infer, js-sys, uuid wasm-bindgen)
- Refactor obikseq::superkmer: reorder imports and improve formatting
  - Add `obipipeline` crate with scheduler, error handling & macros (WIP)
- Replace obiread::expand_paths logic with PathIter and path_iterator module
  - Add mimetype detection using `infer` crate via PeekReader wrapper
This commit is contained in:
Eric Coissac
2026-04-23 21:03:48 +02:00
parent 664d0216b5
commit 3f8880a7e5
15 changed files with 893 additions and 86 deletions
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src/Cargo.lock
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+110
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@@ -103,6 +103,18 @@ version = "0.9.25"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "0b8d4b90317451025bfa1f7d359a5fa698a5f745927ff27696429b7fbd7c0c48"
[[package]]
name = "bumpalo"
version = "3.20.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "5d20789868f4b01b2f2caec9f5c4e0213b41e3e5702a50157d699ae31ced2fcb"
[[package]]
name = "byteorder"
version = "1.5.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
[[package]]
name = "bytes"
version = "1.11.1"
@@ -147,6 +159,17 @@ dependencies = [
"shlex",
]
[[package]]
name = "cfb"
version = "0.7.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "d38f2da7a0a2c4ccf0065be06397cc26a81f4e528be095826eee9d4adbb8c60f"
dependencies = [
"byteorder",
"fnv",
"uuid",
]
[[package]]
name = "cfg-if"
version = "1.0.4"
@@ -326,6 +349,12 @@ dependencies = [
"miniz_oxide",
]
[[package]]
name = "fnv"
version = "1.0.7"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
[[package]]
name = "form_urlencoded"
version = "1.2.2"
@@ -484,6 +513,15 @@ dependencies = [
"icu_properties",
]
[[package]]
name = "infer"
version = "0.19.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "a588916bfdfd92e71cacef98a63d9b1f0d74d6599980d11894290e7ddefffcf7"
dependencies = [
"cfb",
]
[[package]]
name = "is_terminal_polyfill"
version = "1.70.2"
@@ -506,6 +544,16 @@ dependencies = [
"libc",
]
[[package]]
name = "js-sys"
version = "0.3.95"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "2964e92d1d9dc3364cae4d718d93f227e3abb088e747d92e0395bfdedf1c12ca"
dependencies = [
"once_cell",
"wasm-bindgen",
]
[[package]]
name = "lazy_static"
version = "1.5.0"
@@ -648,6 +696,7 @@ dependencies = [
name = "obiread"
version = "0.1.0"
dependencies = [
"infer",
"niffler",
"obikrope",
"tracing",
@@ -825,6 +874,12 @@ dependencies = [
"untrusted",
]
[[package]]
name = "rustversion"
version = "1.0.22"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "b39cdef0fa800fc44525c84ccb54a029961a8215f9619753635a9c0d2538d46d"
[[package]]
name = "same-file"
version = "1.0.6"
@@ -1102,6 +1157,16 @@ version = "0.2.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
[[package]]
name = "uuid"
version = "1.23.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "ddd74a9687298c6858e9b88ec8935ec45d22e8fd5e6394fa1bd4e99a87789c76"
dependencies = [
"js-sys",
"wasm-bindgen",
]
[[package]]
name = "valuable"
version = "0.1.1"
@@ -1133,6 +1198,51 @@ dependencies = [
"wit-bindgen",
]
[[package]]
name = "wasm-bindgen"
version = "0.2.118"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "0bf938a0bacb0469e83c1e148908bd7d5a6010354cf4fb73279b7447422e3a89"
dependencies = [
"cfg-if",
"once_cell",
"rustversion",
"wasm-bindgen-macro",
"wasm-bindgen-shared",
]
[[package]]
name = "wasm-bindgen-macro"
version = "0.2.118"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "eeff24f84126c0ec2db7a449f0c2ec963c6a49efe0698c4242929da037ca28ed"
dependencies = [
"quote",
"wasm-bindgen-macro-support",
]
[[package]]
name = "wasm-bindgen-macro-support"
version = "0.2.118"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9d08065faf983b2b80a79fd87d8254c409281cf7de75fc4b773019824196c904"
dependencies = [
"bumpalo",
"proc-macro2",
"quote",
"syn",
"wasm-bindgen-shared",
]
[[package]]
name = "wasm-bindgen-shared"
version = "0.2.118"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "5fd04d9e306f1907bd13c6361b5c6bfc7b3b3c095ed3f8a9246390f8dbdee129"
dependencies = [
"unicode-ident",
]
[[package]]
name = "webpki-roots"
version = "0.26.11"