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Enhance peak mapping, FFT alignment, and improve documentation #12

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Merged
singjc merged 14 commits into from
May 7, 2026
Merged

Enhance peak mapping, FFT alignment, and improve documentation #12

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fbb1a26
feat: update create_fft_dtw_rt_mapping to use DTW path for alignment …
singjc May 7, 2026
fbaff57
feat: add peak mapping candidate inspection and flattening functions
singjc May 7, 2026
debf00b
feat: add methods for fetching precursors and processing peak mapping…
singjc May 7, 2026
24423c9
feat: refactor from_arguments to use from_config_path for loading par…
singjc May 7, 2026
0884172
add: debug cli tool
singjc May 7, 2026
705a84d
feat: update build process to include arycal-debug-alignment binary a…
singjc May 7, 2026
88fa413
feat: enhance peak mapping functionality and improve transition filte…
singjc May 7, 2026
18f3c3c
Refactor FFT cross-correlation in arycal
singjc May 7, 2026
f4ade09
refactor: improve code readability and consistency in alignment modules
singjc May 7, 2026
e0d036e
Implement stratified shuffling for peak tuples and enhance decoy peak…
singjc May 7, 2026
db7918d
Merge branch 'master' into debugging
singjc May 7, 2026
9e59001
refactor: remove unused imports from main.rs
singjc May 7, 2026
8566f6a
refactor: remove unused rlimit import from main.rs
singjc May 7, 2026
8cfbc74
refactor: update thread handling to use map and unwrap_or for safer d…
singjc May 7, 2026
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30 changes: 23 additions & 7 deletions .github/workflows/rust-release.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,9 @@ jobs:
bin: arycal
os: ubuntu-latest
build: |
cargo build --release
cargo build --release --bin arycal --bin arycal-debug-alignment
cp target/release/arycal artifacts/arycal
cp target/release/arycal-debug-alignment artifacts/arycal-debug-alignment

# CLI: fully static musl via cross (with Rust 1.85.0 in container)
- name: x86_64-linux-musl
Expand All @@ -46,8 +47,9 @@ jobs:
os: ubuntu-latest
build: |
cargo install cross --version 0.2.5 --locked
CROSS_CONTAINER_ENGINE=docker cross build --release --target=x86_64-unknown-linux-musl
CROSS_CONTAINER_ENGINE=docker cross build --release --target=x86_64-unknown-linux-musl --bin arycal --bin arycal-debug-alignment
cp target/x86_64-unknown-linux-musl/release/arycal artifacts/arycal
cp target/x86_64-unknown-linux-musl/release/arycal-debug-alignment artifacts/arycal-debug-alignment

# CLI: glibc + MPI
- name: x86_64-linux-gnu-mpi
Expand All @@ -56,8 +58,9 @@ jobs:
os: ubuntu-latest
build: |
sudo apt-get update && sudo apt-get install -y libopenmpi-dev openmpi-bin
cargo build --release --target=x86_64-unknown-linux-gnu --features mpi
cargo build --release --target=x86_64-unknown-linux-gnu --features mpi --bin arycal --bin arycal-debug-alignment
cp target/x86_64-unknown-linux-gnu/release/arycal artifacts/arycal
cp target/x86_64-unknown-linux-gnu/release/arycal-debug-alignment artifacts/arycal-debug-alignment

# macOS + Windows
- name: x86_64-darwin
Expand All @@ -66,17 +69,19 @@ jobs:
os: macos-latest
build: |
rustup target add x86_64-apple-darwin
cargo build --release --target=x86_64-apple-darwin
cargo build --release --target=x86_64-apple-darwin --bin arycal --bin arycal-debug-alignment
cp target/x86_64-apple-darwin/release/arycal artifacts/arycal
cp target/x86_64-apple-darwin/release/arycal-debug-alignment artifacts/arycal-debug-alignment

- name: x86_64-windows
bin: arycal
target: x86_64-pc-windows-msvc
os: windows-latest
build: |
rustup target add x86_64-pc-windows-msvc
cargo build --release --target=x86_64-pc-windows-msvc
cargo build --release --target=x86_64-pc-windows-msvc --bin arycal --bin arycal-debug-alignment
cp target/x86_64-pc-windows-msvc/release/arycal.exe artifacts/arycal.exe
cp target/x86_64-pc-windows-msvc/release/arycal-debug-alignment.exe artifacts/arycal-debug-alignment.exe

steps:
- uses: actions/checkout@v4
Expand Down Expand Up @@ -112,7 +117,7 @@ jobs:
- name: Build
run: bash -lc "${{ matrix.build }}"

- name: Upload Binaries to Release
- name: Upload arycal to Release
if: startsWith(github.ref, 'refs/tags/')
uses: taiki-e/upload-rust-binary-action@v1
with:
Expand All @@ -124,10 +129,21 @@ jobs:
zip: windows
token: ${{ secrets.GITHUB_TOKEN }}

- name: Upload arycal-debug-alignment to Release
if: startsWith(github.ref, 'refs/tags/')
uses: taiki-e/upload-rust-binary-action@v1
with:
bin: arycal-debug-alignment
archive: arycal-debug-alignment-${{ steps.version.outputs.version }}-${{ matrix.name }}
target: ${{ matrix.target || '' }}
include: LICENSE,README.md
tar: unix
zip: windows
token: ${{ secrets.GITHUB_TOKEN }}

- name: Upload Artifacts (manual run)
if: ${{ !startsWith(github.ref, 'refs/tags/') }}
uses: actions/upload-artifact@v4
with:
name: arycal-${{ steps.version.outputs.version }}-${{ matrix.name }}
path: artifacts/*

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