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‎.github/workflows/check.yml‎

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# adapted from https://github.com/jonhoo/rust-ci-conf/blob/fabb82abd53e0052c8b70ae197a80e6203ede26d/.github/workflows/check.yml
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# This workflow runs whenever a PR is opened or updated, or a commit is pushed to main. It runs
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# several checks:
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# - fmt: checks that the code is formatted according to rustfmt
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# - clippy: checks that the code does not contain any clippy warnings
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# - doc: checks that the code can be documented without errors
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# - hack: check combinations of feature flags
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# - msrv: check that the msrv specified in the crate is correct
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permissions:
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contents: read
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# This configuration allows maintainers of this repo to create a branch and pull request based on
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# the new branch. Restricting the push trigger to the main branch ensures that the PR only gets
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# built once.
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on:
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push:
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branches: [ main ]
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pull_request:
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# If new code is pushed to a PR branch, then cancel in progress workflows for that PR. Ensures that
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# we don't waste CI time, and returns results quicker https://github.com/jonhoo/rust-ci-conf/pull/5
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concurrency:
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group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
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cancel-in-progress: true
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name: check
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jobs:
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fmt:
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runs-on: ubuntu-latest
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name: stable / fmt
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- name: Install stable
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uses: dtolnay/rust-toolchain@stable
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with:
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components: rustfmt
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- name: cargo fmt --check
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run: cargo fmt --check
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clippy:
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runs-on: ubuntu-latest
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name: ${{ matrix.toolchain }} / clippy
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permissions:
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contents: read
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checks: write
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strategy:
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fail-fast: false
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matrix:
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# Get early warning of new lints which are regularly introduced in beta channels.
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toolchain: [ stable, beta ]
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- name: Install ${{ matrix.toolchain }}
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uses: dtolnay/rust-toolchain@master
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with:
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toolchain: ${{ matrix.toolchain }}
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components: clippy
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- name: cargo clippy
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uses: giraffate/clippy-action@v1
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with:
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reporter: 'github-pr-check'
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github_token: ${{ secrets.GITHUB_TOKEN }}
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hack:
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# cargo-hack checks combinations of feature flags to ensure that features are all additive
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# which is required for feature unification
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runs-on: ubuntu-latest
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name: ubuntu / stable / features
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- name: Install stable
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uses: dtolnay/rust-toolchain@stable
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- name: cargo install cargo-hack
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uses: taiki-e/install-action@cargo-hack
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# intentionally no target specifier; see https://github.com/jonhoo/rust-ci-conf/pull/4
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# --feature-powerset runs for every combination of features
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- name: cargo hack
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run: cargo hack --feature-powerset check
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msrv:
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# check that we can build using the minimal rust version that is specified by this crate
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runs-on: ubuntu-latest
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# we use a matrix here just because env can't be used in job names
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# https://docs.github.com/en/actions/learn-github-actions/contexts#context-availability
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strategy:
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matrix:
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msrv: [ "1.87.0" ] # obtained from cargo-msrv 24/01/2026
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name: ubuntu / ${{ matrix.msrv }}
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- name: Install ${{ matrix.msrv }}
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uses: dtolnay/rust-toolchain@master
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with:
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toolchain: ${{ matrix.msrv }}
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- name: cargo +${{ matrix.msrv }} check
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run: cargo check

‎.github/workflows/release.yml‎

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# inspried by https://github.com/mbhall88/lrge/blob/main/.github/workflows/release.yml
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name: Release
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on:
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push:
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tags:
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- "[0-9]+.[0-9]+.[0-9]+"
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env:
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CICD_INTERMEDIATES_DIR: "_release-intermediates"
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jobs:
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upload:
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name: ${{ matrix.job.os }} (${{ matrix.job.target }})
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permissions:
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contents: write
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runs-on: ${{ matrix.job.os }}
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strategy:
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fail-fast: false
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matrix:
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job:
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- { os: ubuntu-latest, target: x86_64-unknown-linux-gnu, use-cross: true }
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- { os: ubuntu-latest, target: aarch64-unknown-linux-gnu, use-cross: true }
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- { os: macos-13, target: x86_64-apple-darwin, use-cross: true }
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- { os: macos-latest, target: aarch64-apple-darwin, use-cross: true }
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steps:
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- name: Checkout source code
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uses: actions/checkout@v4
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- name: Extract crate information
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shell: bash
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run: |
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echo "PROJECT_NAME=hashfasta" >> $GITHUB_ENV
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echo "PROJECT_VERSION=$(sed -n 's/^version = "\(.*\)"/\1/p' lrge/Cargo.toml | head -n1)" >> $GITHUB_ENV
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echo "PROJECT_MAINTAINER=$(sed -n 's/^authors = \["\(.*\)"\]/\1/p' Cargo.toml)" >> $GITHUB_ENV
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echo "PROJECT_HOMEPAGE=$(sed -n 's/^homepage = "\(.*\)"/\1/p' Cargo.toml)" >> $GITHUB_ENV
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- name: Install toolchain
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uses: dtolnay/rust-toolchain@stable
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with:
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targets: ${{ matrix.job.target }}
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- name: Show version information (Rust, cargo, GCC)
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shell: bash
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run: |
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gcc --version || true
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rustup -V
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rustup toolchain list
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rustup default
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cargo -V
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rustc -V
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- name: Install cross
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uses: taiki-e/install-action@v2
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with:
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tool: cross@0.2.5
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- name: Build with cross
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run: cross build --release --target=${{ matrix.job.target }}
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- name: Set binary name & path
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id: bin
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shell: bash
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run: |
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# Figure out suffix of binary
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EXE_suffix=""
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case ${{ matrix.job.target }} in
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*-pc-windows-*) EXE_suffix=".exe" ;;
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esac;
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# Setup paths
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BIN_NAME="${{ env.PROJECT_NAME }}${EXE_suffix}"
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BIN_PATH="target/${{ matrix.job.target }}/release/${BIN_NAME}"
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# Let subsequent steps know where to find the binary
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echo "BIN_PATH=${BIN_PATH}" >> $GITHUB_OUTPUT
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echo "BIN_NAME=${BIN_NAME}" >> $GITHUB_OUTPUT
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- name: Create tarball
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id: package
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shell: bash
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run: |
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PKG_suffix=".tar.gz" ; case ${{ matrix.job.target }} in *-pc-windows-*) PKG_suffix=".zip" ;; esac;
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PKG_BASENAME=${PROJECT_NAME}-${PROJECT_VERSION}-${{ matrix.job.target }}
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PKG_NAME=${PKG_BASENAME}${PKG_suffix}
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echo "PKG_NAME=${PKG_NAME}" >> $GITHUB_OUTPUT
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PKG_STAGING="${{ env.CICD_INTERMEDIATES_DIR }}/package"
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ARCHIVE_DIR="${PKG_STAGING}/${PKG_BASENAME}/"
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mkdir -p "${ARCHIVE_DIR}"
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# Binary
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cp "${{ steps.bin.outputs.BIN_PATH }}" "$ARCHIVE_DIR"
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# README, LICENSE and CHANGELOG files
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cp "README.md" "LICENSE" "CHANGELOG.md" "$ARCHIVE_DIR"
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# base compressed package
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pushd "${PKG_STAGING}/" >/dev/null
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case ${{ matrix.job.target }} in
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*-pc-windows-*) 7z -y a "${PKG_NAME}" "${PKG_BASENAME}"/* | tail -2 ;;
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*) tar czf "${PKG_NAME}" "${PKG_BASENAME}"/* ;;
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esac;
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popd >/dev/null
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# Let subsequent steps know where to find the compressed package
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echo "PKG_PATH=${PKG_STAGING}/${PKG_NAME}" >> $GITHUB_OUTPUT
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- name: "Artifact upload: tarball"
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uses: actions/upload-artifact@master
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with:
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name: ${{ steps.package.outputs.PKG_NAME }}
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path: ${{ steps.package.outputs.PKG_PATH }}
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- name: Check for release
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id: is-release
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shell: bash
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run: |
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unset IS_RELEASE ; if [[ $GITHUB_REF =~ ^refs/tags/[0-9].* ]]; then IS_RELEASE='true' ; fi
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echo "IS_RELEASE=${IS_RELEASE}" >> $GITHUB_OUTPUT
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- name: Publish archives and packages
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uses: softprops/action-gh-release@v2
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if: steps.is-release.outputs.IS_RELEASE
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with:
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files: |
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${{ steps.package.outputs.PKG_PATH }}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/test.yml‎

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# adapted from https://github.com/jonhoo/rust-ci-conf/blob/fabb82abd53e0052c8b70ae197a80e6203ede26d/.github/workflows/test.yml
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# This is the main CI workflow that runs the test suite on all pushes to main and all pull requests.
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# It runs the following jobs:
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# - required: runs the test suite on ubuntu with stable and beta rust toolchains
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# - minimal: runs the test suite with the minimal versions of the dependencies that satisfy the
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# requirements of this crate, and its dependencies
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# - os-check: runs the test suite on mac and windows
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# See check.yml for information about how the concurrency cancellation and workflow triggering works
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permissions:
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contents: read
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on:
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push:
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branches: [ main ]
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pull_request:
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concurrency:
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group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
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cancel-in-progress: true
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name: test
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jobs:
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required:
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runs-on: ubuntu-latest
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name: ubuntu / ${{ matrix.toolchain }}
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strategy:
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matrix:
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# run on stable and beta to ensure that tests won't break on the next version of the rust
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# toolchain
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toolchain: [ stable, beta ]
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- name: Install ${{ matrix.toolchain }}
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uses: dtolnay/rust-toolchain@master
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with:
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toolchain: ${{ matrix.toolchain }}
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- name: cargo generate-lockfile
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# enable this ci template to run regardless of whether the lockfile is checked in or not
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if: hashFiles('Cargo.lock') == ''
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run: cargo generate-lockfile
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# https://twitter.com/jonhoo/status/1571290371124260865
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- name: cargo test --locked
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run: cargo test --locked --all-features --all-targets
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os-check:
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# run cargo test on mac and windows
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runs-on: ${{ matrix.os }}
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name: ${{ matrix.os }} / stable
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strategy:
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fail-fast: false
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matrix:
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os: [ macos-latest ]
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steps:
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# if your project needs OpenSSL, uncomment this to fix Windows builds.
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# it's commented out by default as the install command takes 5-10m.
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# - run: echo "VCPKG_ROOT=$env:VCPKG_INSTALLATION_ROOT" | Out-File -FilePath $env:GITHUB_ENV -Append
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# if: runner.os == 'Windows'
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# - run: vcpkg install openssl:x64-windows-static-md
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# if: runner.os == 'Windows'
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- uses: actions/checkout@v4
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with:
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submodules: true
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- name: Install stable
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uses: dtolnay/rust-toolchain@stable
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- name: cargo generate-lockfile
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if: hashFiles('Cargo.lock') == ''
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run: cargo generate-lockfile
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- name: cargo test
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run: cargo test --locked --all-features --all-targets

‎CHANGELOG.md‎

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# Changelog
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [1.0.0] - 2026-01-24
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### Added
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- GitHub Actions workflows for `check`, `test`, and `release`
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- Rewrite of entire core functionality:
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- New subcommands: `hash`, `unique`, `duplicate`, replacing previous flag-based interface.
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- Multi-threaded parsing
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- Ability to read FASTX from stdin, http/https URLs, and ssh paths.
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- Quiet mode (`--quiet`) to suppress per-record output in `hash` subcommand.
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- JSON output mode (`--json`)
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- Strict mode (`--strict`) to fail on non-ACGTUN- bases.
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### Changed
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- CLI interface is now subcommand-based
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- Hashing now uses `xxhash3_64`
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- Parsing switched from `noodles` to `paraseq` with parallel processing.
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### Removed
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- Selectable hash algorithms (`--seqhash`, `--finalhash`).
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- CLI flags `--individual`, `--duplicates`, `--fasta`, and `--fastq` (replaced by subcommands).

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