Cache Rust builds and remove ineffective thin LTO

.github/workflows/release.yml

@@ -127,6 +127,10 @@ jobs:
             curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
             echo "$HOME/.cargo/bin" >> $GITHUB_PATH
           fi
+      - uses: swatinem/rust-cache@v2
+        with:
+          key: ${{ join(matrix.targets, '-') }}
+          cache-provider: ${{ matrix.cache_provider }}
       - name: Install dist
         run: ${{ matrix.install_dist.run }}
       # Get the dist-manifest

.github/workflows/test_simpleaf.yml

@@ -21,14 +21,21 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2.4.2
+        uses: actions/checkout@v6
 
       - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1
+        uses: dtolnay/rust-toolchain@stable
         with:
-          toolchain: stable
-          override: true
           components: rustfmt
+
+      # simpleaf has a large, stable dependency graph (notably Polars and
+      # HDF5). Cache dependency artifacts separately for each runner/toolchain;
+      # rust-cache derives the remaining key from Cargo.lock and the Rust
+      # environment, and deliberately excludes simpleaf itself.
+      - name: Cache Rust dependencies
+        uses: Swatinem/rust-cache@v2
+        with:
+          cache-on-failure: true
 
       # Cheap and compiles nothing, so it runs first.
       - name: Check formatting
@@ -38,9 +45,9 @@ jobs:
         run: cargo build --verbose --release
 
       # Deliberately `--release`: it reuses the artifacts the Build step just
-      # produced, which makes this ~30s. A debug `cargo test` would rebuild the
-      # whole dependency graph in a second profile — including HDF5, which is
-      # compiled from source — and cost minutes.
+      # produced. A debug `cargo test` would rebuild the whole dependency graph
+      # in a second profile — including HDF5, which is compiled from source —
+      # and cost minutes.
       #
       # This job previously ran neither this nor `cargo fmt`, which is how a
       # test that did not compile, and a stale CLI snapshot, both reached main.
@@ -54,7 +61,7 @@ jobs:
         run: cargo doc --no-deps
 
       - name: Install conda env
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v4
         with:
           channels: conda-forge,default,bioconda
           channel-priority: true

Cargo.toml

@@ -36,8 +36,6 @@ categories = ["command-line-utilities", "science"]
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [dependencies]
-cc = "1.2.20"
-
 # seq_geom_parser (chumsky-based, from the piscem-rs workspace) — used for
 # geometry validation and multiplex-quant. Published on crates.io; the
 # `.cargo/config.toml` patch this comment used to describe is long gone (there
@@ -107,11 +105,6 @@ tempfile = "3.19.1"
 ureq = { version = "3.0.11", features = ["json"] }
 file-requirements = "0.1.0"
 
-[profile.release]
-lto = "thin"
-opt-level = 3
-
 # The profile that 'cargo dist' will build with
 [profile.dist]
 inherits = "release"
-lto = "thin"

dist-workspace.toml

@@ -13,6 +13,10 @@ installers = ["shell"]
 targets = ["aarch64-apple-darwin", "aarch64-unknown-linux-gnu", "x86_64-apple-darwin", "x86_64-unknown-linux-gnu"]
 # Which actions to run on pull requests
 pr-run-mode = "plan"
+# Preserve compiled dependency artifacts between release builds. This is most
+# useful when rerunning a failed release or when dependencies stay fixed across
+# patch releases; cargo-dist keys each target independently.
+cache-builds = true
 # Whether to install an updater program
 install-updater = true
 # Path that installers should place binaries in