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mandysullimandysulli
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structure update and gh action tweak
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‎.github/workflows/build-binaries.yml‎

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‎.github/workflows/release.yml‎

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name: Release
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on:
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push:
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branches:
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- '**' # Matches all branches for now
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paths:
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- 'CHANGELOG.md'
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permissions: {}
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env:
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CARGO_TERM_COLOR: always
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RELEASE_BIN: mira-oxide
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REGISTRY: ghcr.io
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jobs:
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create-release:
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name: Create New Release
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runs-on: ubuntu-latest
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permissions:
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contents: write
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outputs:
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upload_url: ${{ steps.create_release.outputs.upload_url }}
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steps:
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- uses: actions/checkout@v4
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- name: Extract Changelog
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id: extract_changelog
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shell: bash
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run: perl .github/scripts/last_release_notes.pl > $RUNNER_TEMP/release_notes.md
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- name: Create Release
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id: create_release
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shell: bash
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run: |
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[[ "${{ github.ref_name }}" == "test" ]] && latest="--latest=false" || latest=
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gh release create "${{ github.ref_name }}" \
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--title "${RELEASE_BIN} ${{ github.ref_name }}" \
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--notes-file "$RUNNER_TEMP/release_notes.md" \
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$latest
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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build-release-image-and-linux-artifacts:
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name: Build Linux Artifacts and Images
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needs: [create-release]
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strategy:
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matrix:
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include:
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- arch: x86_64
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runner: ubuntu-latest
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- arch: aarch64
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runner: ubuntu-24.04-arm
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runs-on: ${{ matrix.runner }}
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permissions:
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contents: write
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packages: write
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steps:
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- uses: actions/checkout@v4
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- name: Log in to the Container registry
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uses: docker/login-action@v3
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Extract metadata for Docker
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id: meta
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uses: docker/metadata-action@v5
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with:
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images: ${{ env.REGISTRY }}/${{ github.repository }}
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tags: |
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type=raw,value=latest-${{ matrix.arch }}
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- name: Debug Git ref
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run: |
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echo "GITHUB_REF: $GITHUB_REF"
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echo "GITHUB_REF_NAME: $GITHUB_REF_NAME"
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echo "GITHUB_SHA: $GITHUB_SHA"
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echo "GITHUB_REPOSITORY: $GITHUB_REPOSITORY"
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- name: Build and push Docker image
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uses: docker/build-push-action@v6
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with:
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file: Dockerfile
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context: .
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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- name: Prepare Linux Binary
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shell: bash
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run: |
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IMAGE_TAG=$(echo "${{ steps.meta.outputs.tags }}" | grep -- '-${{ matrix.arch }}$' | head -n 1)
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docker create --name temp-container $IMAGE_TAG \
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&& docker cp temp-container:/app/${RELEASE_BIN} ./${RELEASE_BIN} \
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&& docker rm temp-container \
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&& tar -czf ${RELEASE_BIN}-linux-${{ matrix.arch }}-${{ github.ref_name }}.tar.gz ${RELEASE_BIN}
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- name: Upload Linux Release Asset
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shell: bash
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run: |
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gh release upload "${{ github.ref_name }}" ${RELEASE_BIN}-linux-${{ matrix.arch }}-${{ github.ref_name }}.tar.gz
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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create-image-manifest:
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name: Create Image Manifest
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needs: build-release-image-and-linux-artifacts
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runs-on: ubuntu-latest
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permissions:
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packages: write
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contents: read
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steps:
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- name: Log in to the Container registry
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uses: docker/login-action@v3
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Create and push manifests
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shell: bash
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run: |
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REPO=$(echo "${{ env.REGISTRY }}/${{ github.repository }}" | tr '[A-Z]' '[a-z]')
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VERSION=${REPO}:${{ github.ref_name }}
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LATEST=${REPO}:latest
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docker manifest create $VERSION --amend ${LATEST}-x86_64 --amend ${LATEST}-aarch64 \
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&& docker manifest push $VERSION
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docker manifest create $LATEST --amend ${LATEST}-x86_64 --amend ${LATEST}-aarch64 \
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&& docker manifest push $LATEST
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build-mac-artifacts:
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name: Build Mac Artifacts
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needs: create-release
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runs-on: macos-latest
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- name: Install latest nightly Rust
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run: |
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rustup update nightly
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rustup default nightly
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rustup target add aarch64-apple-darwin x86_64-apple-darwin
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- name: Build
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run: |
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cargo build --release --target aarch64-apple-darwin --target x86_64-apple-darwin
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- name: Package Binary
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shell: bash
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run: |
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lipo -create -output ${{ env.RELEASE_BIN }} \
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target/aarch64-apple-darwin/release/${{ env.RELEASE_BIN }} \
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target/x86_64-apple-darwin/release/${{ env.RELEASE_BIN }}
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tar -czf ${{ env.RELEASE_BIN }}-apple-universal-${{ github.ref_name }}.tar.gz ${{ env.RELEASE_BIN }}
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- name: Upload Release Asset
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shell: bash
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run: |
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gh release upload "${{ github.ref_name }}" ${{ env.RELEASE_BIN }}-apple-universal-${{ github.ref_name }}.*
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎CHANGELOG.md‎

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# cdcgov/mira-oxide: Changelog
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [0.0.0] - 2025-09-19
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### THIS IS A TEST
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## [1.1.2] - 2025-09-19
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- [Amanda Sullivan](https://github.com/mandysulli)
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### `Added`
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- [PR #44](https://github.com/CDCgov/mira-oxide/pull/44) - Added filtering to a single subtype for the variants_of_interest outputs if the virus flu (as "INFLUENZA") is passed to the program.
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- [PR #46](https://github.com/CDCgov/mira-oxide/pull/46) - Added filtering to a single subtype for the positions_of_interest outputs if the virus flu (as "INFLUENZA") is passed to the program.
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## [1.1.1] - 2025-09-11
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- [Sam Wiley](https://github.com/samcwiley)
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### `Fixed`
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- [PR #38](https://github.com/CDCgov/mira-oxide/pull/38) - Fixed issue with `find_chemistry.rs` not being able to handle compressed files
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### `Added`
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- [PR #38](https://github.com/CDCgov/mira-oxide/pull/38) - Adds `utils/read_fastq.rs` with functionality for handling gzipped fastq files
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<!-- Versions -->
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[1.1.1]: https://github.com/CDCgov/mira-oxide/compare/f824940...v1.1.1

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