From ce2d6b641a2dfe760e25643556b94f1ba81fcb60 Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmail.com>
Date: Thu, 13 Aug 2026 15:06:41 -0700
Subject: [PATCH] ci: cache cargo artifacts, parallelize jobs and tests

- Swatinem/rust-cache in the compiling jobs: every run previously
  cold-compiled the full dependency tree (including rust-htslib's C
  build) three times.
- Drop 'needs: Formatting' so Testing no longer queues behind a
  10-second job.
- Drop --test-threads=1: it dates to the original 2022 CI template,
  predating the tempfile-based regression harness; current tests are
  parallel-safe (unique tempfiles, read-only fixtures).
- Replace archived actions-rs/toolchain with dtolnay/rust-toolchain and
  bump checkout to v4.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 .github/workflows/CI.yml | 28 +++++++++++++---------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index ff2aee33..28eddc52 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -11,13 +11,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1
+        uses: dtolnay/rust-toolchain@stable
         with:
-          toolchain: stable
-          override: true
           components: rustfmt
 
       - name: Check format
@@ -27,33 +25,33 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1
+        uses: dtolnay/rust-toolchain@stable
         with:
-          toolchain: stable
-          override: true
           components: clippy
 
+      - name: Cache cargo artifacts
+        uses: Swatinem/rust-cache@v2
+
       - name: Lint with clippy
         run: cargo clippy -p fibertools-rs
 
   Testing:
-    needs: Formatting
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          override: true
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache cargo artifacts
+        uses: Swatinem/rust-cache@v2
 
       - name: Run test
-        run: cargo test -p fibertools-rs -- --test-threads=1
+        run: cargo test -p fibertools-rs
 
       - name: Run molecular-annotation tests
         run: cargo test -p molecular-annotation --features htslib