Minimappers 0.1.4

.github/workflows/build-test-rust-fakeminimap2.yaml

@@ -1,4 +1,4 @@
-name: Rust
+name: fakeminimap2
 
 on:
   pull_request:

.github/workflows/build-test-rust-minimap2-sys.yml

@@ -1,4 +1,4 @@
-name: Rust
+name: minimap2-sys
 
 on:
   pull_request:

.github/workflows/build-test-rust-minimap2.yaml

@@ -1,4 +1,4 @@
-name: Rust
+name: minimap2-rs
 
 on:
   pull_request:

.github/workflows/build-test-rust-minimappers2.yaml

@@ -1,4 +1,4 @@
-name: Rust
+name: minimappers2
 
 on:
   pull_request:
@@ -34,7 +34,7 @@ jobs:
         env:
           RUSTFLAGS: -C target-feature=+fxsr,+sse,+sse2,+sse3,+ssse3,+sse4.1,+sse4.2,+popcnt,+avx,+fma
         with:
-          rust-toolchain: nightly-2023-01-19
-          maturin-version: '0.14.10'
+          rust-toolchain: nightly-2023-10-15
+          maturin-version: '1.4.0'
           command: build
           args: -m minimappers2/Cargo.toml

Cargo.toml

@@ -22,13 +22,12 @@ exclude = [
 
 [workspace]
 
-members = [
-    "fakeminimap2",
-    "minimap2-sys"
-]
+members = []
 
 exclude = [
-    "minimappers2"
+    "minimappers2",
+    "fakeminimap2",
+    "minimap2-sys"
 ]
 
 [dependencies]
@@ -38,8 +37,8 @@ flate2 = { version = "1.0.27", default-features = false }
 fffx = { version = "0.1.3", optional = true }
 
 # Dep for development
-minimap2-sys = { path = "./minimap2-sys" }
-#minimap2-sys = "0.1.16"
+#minimap2-sys = { path = "./minimap2-sys" }
+minimap2-sys = "0.1.16"
 rust-htslib = { version = "0.44.1", optional = true }
 
 # [profile.release]

fakeminimap2/Cargo.toml

@@ -6,14 +6,13 @@ edition = "2021"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-minimap2 = { path = ".."}
-# minimap2 = { git = "https://github.com/jguhlin/minimap2-rs", branch = "static", features = ["static"] }
+minimap2 = "0.1.16+minimap2.2.26"
 crossbeam = "0.8.2"
 needletail = "0.5.1"
 fern = { version = "0.6.2", features = ["colored", "chrono"] }
 humantime = "2.1.0"
-log = "0.4.17"
-colored = { version = "2.0.0", features = ["no-color"] }
+log = "0.4.20"
+colored = { version = "2.0.4", features = ["no-color"] }
 
 [profile.release]
 opt-level = 3

minimap2-sys/Cargo.toml

@@ -40,7 +40,7 @@ pkg-config = "0.3.27"
 
 [build-dependencies.bindgen]
 optional = true
-version = "0.68.1"
+version = "0.69.1"
 default-features = false
 features = ["which-rustfmt", "runtime"]
 

minimappers2/Cargo.toml

@@ -8,18 +8,14 @@ name = "minimappers2"
 crate-type = ["cdylib", "rlib"]
 
 [dependencies]
-# fffx = "0.1.2"
-
 minimap2 = { version = "0.1.16", features = ["simde"] }
 minimap2-sys = { version = "0.1.16", features = ["simde"] }
-#minimap2 = { path = "../", features = ["simde"] }
-#minimap2-sys = { path = "../minimap2-sys", features = ["simde"] }
 crossbeam = "0.8.2"
-mimalloc = {version = "0.1.34", default-features = false }
+mimalloc = {version = "0.1.39", default-features = false }
 
-pyo3 = { version = "0.19.2" }
-polars = "0.32.1"
-pyo3-polars = "0.6.0"
+pyo3 = { version = "0.20.0" }
+polars = "0.35.4"
+pyo3-polars = "0.9.0"
 
 [profile.release]
 opt-level = 3

minimappers2/README.md

@@ -86,15 +86,15 @@ As this is a very-early stage library, error checking is not yet implemented. Wh
 
 ## Compatability
 
-* Windows: Unlikely
-* Linux: Likely
+* Linux: Yes
 * Mac: Unknown
+* Windows: Unlikely
 
-* x86_64: Likely
-* aarch64: Unknown
+* x86_64: Yes
+* aarch64: Unknown (open an issue)
 * neon: No (Open an issue)
 
-* Google Colab: No, not sure why though.
+* Google Colab: Yes
 
 # Performance
 Effort has been made to make this as performant as possible, but if you need more performance, please use minimap2 directly and import the results.
@@ -112,7 +112,8 @@ and/or:
 
 # Changelog
 ## 0.1.4 
-* Update pyo3, polars, and minimap2-rs deps
+* Update pyo3, polars, minimap2-rs, and mimalloc deps
+
 ## 0.1.1
 * Update pyo3 and polars deps
 * Add with_seq for indexing TODO