v0.31.0: S3 staging + Peptide types + sequence-derived rescore features

.github/workflows/release.yml

@@ -45,7 +45,7 @@ jobs:
             artifact_name: windows-x64
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Install Rust
         uses: actions-rust-lang/setup-rust-toolchain@v1
@@ -60,6 +60,12 @@ jobs:
         if: matrix.target == 'x86_64-unknown-linux-musl'
         run: sudo apt-get update && sudo apt-get install -y musl-tools
 
+      - name: Apply crate patches (rustyms gnome.dat stub)
+        shell: bash
+        run: |
+          cargo install --git https://github.com/jspaezp/cargo-patch-crate patch-crate --locked
+          cargo patch-crate
+
       - name: Build Binaries
         shell: bash
         run: |

.github/workflows/rust.yml

@@ -21,6 +21,10 @@ jobs:
           - "--no-default-features"  # serial
     steps:
       - uses: actions/checkout@v6
+      - name: Apply crate patches (rustyms gnome.dat stub)
+        run: |
+          cargo install --git https://github.com/jspaezp/cargo-patch-crate patch-crate --locked
+          cargo patch-crate
       - name: Build
         run: cargo build --verbose -p timsseek ${{ matrix.features }}
       - name: Run tests

.gitignore

@@ -52,6 +52,9 @@ bench.bash
 bench_*.bash
 quichbench*.bash
 run_instrument.bash
+run_remote.bash
+stage.bash
+here.toml
 *.log
 results.tsv
 config_use.json