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Merge pull request #1003 from COMBINE-lab/codex/develop-refactor
Refactor, index update
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‎.codex/REFRACTOR_BOOKMARK.md‎

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# Refactor Checkpoint (2026-03-08)
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Branch: `codex/develop-refactor`
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## Completed in this checkpoint
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- Continued module ownership cleanup under `src/{io,model,util,tests}`.
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- Kept `AlignmentIO` as the sole htslib boundary layer with more wrapper logic moved out of headers.
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- Continued FASTQ/FASTA modernization around FQFeeder:
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- switched call sites to `salmon_fqfeeder::ParserConfig`.
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- retained lightweight compatibility aliases in `FastxReader.hpp` required by `SAMWriter`/`SalmonMappingUtils`.
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- Simplified dependency resolution toward modern CMake package-first behavior.
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- Added dependency floor checks for:
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- `spdlog/fmt`
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- `parallel_hashmap`
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- `nlohmann/json`
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- `Eigen >= 3.4`
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## Verified at checkpoint
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- Configure: `cmake -S . -B build/codex-check`
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- Build: `cmake --build build/codex-check -j8 --target salmon unitTests`
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- Tests: `ctest --test-dir build/codex-check --output-on-failure -R "unit_tests|salmon_read_test_quasi|salmon_alevin_stub"`
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## Resume From Here
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1. Remove remaining Staden-era compatibility artifacts after confirming no remaining call paths.
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2. Keep shrinking heavy headers (`ReadExperiment.hpp`, `AlignmentLibrary.hpp`) by moving non-template logic into `.cpp`/`.inl`.
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3. Continue top-level include shim removal only where include-policy and unit/integration tests remain green.
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4. Quant hot-path optimization pass (read-based mode):
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- parser chunking + queue contention
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- mapping-stage allocations and temporary buffers
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- log/progress overhead in worker loops
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- merge/reduce behavior across mini-batches

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
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**Describe the bug**
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A clear and concise description of what the bug is.
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‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches:
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- "**"
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workflow_dispatch:
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permissions:
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contents: read
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jobs:
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precheck:
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runs-on: ubuntu-latest
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outputs:
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run_ci: ${{ steps.decide.outputs.run_ci }}
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steps:
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- id: decide
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shell: bash
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run: |
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set -euo pipefail
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msg="$(jq -r '.head_commit.message // ""' "$GITHUB_EVENT_PATH")"
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ref="${GITHUB_REF#refs/heads/}"
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run_ci=false
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if [[ "${GITHUB_EVENT_NAME}" == "workflow_dispatch" ]]; then
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run_ci=true
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fi
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if [[ "$ref" == "main" ]]; then
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run_ci=true
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fi
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if [[ "$msg" == *"[run-ci]"* ]]; then
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run_ci=true
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fi
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{
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echo "run_ci=$run_ci"
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} >> "$GITHUB_OUTPUT"
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build-test:
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needs: precheck
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if: ${{ needs.precheck.outputs.run_ci == 'true' }}
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runs-on: ${{ matrix.os }}
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timeout-minutes: 120
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strategy:
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fail-fast: false
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matrix:
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include:
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- os: ubuntu-22.04
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target_id: linux-x86_64
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build_parallel: 2
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- os: ubuntu-24.04-arm
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target_id: linux-aarch64
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build_parallel: 2
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- os: macos-15-intel
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target_id: macos-x86_64
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build_parallel: 3
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- os: macos-14
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target_id: macos-arm64
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build_parallel: 3
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steps:
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- uses: actions/checkout@v4
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- name: Install Linux Build Dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get install -y \
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build-essential \
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cmake \
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git \
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curl \
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libcurl4-openssl-dev \
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libbz2-dev \
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liblzma-dev
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- name: Configure
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run: |
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cmake -S . -B build-ci \
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-DCMAKE_BUILD_TYPE=Release \
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-DSALMON_ENABLE_TESTS=ON \
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-DSALMON_USE_SYSTEM_DEPS=OFF \
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-DSALMON_FETCH_MISSING_DEPS=ON \
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-DSALMON_BOOST_USE_STATIC_LIBS=ON
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- name: Build
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run: cmake --build build-ci --target salmon unitTests --parallel ${{ matrix.build_parallel }}
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- name: Run Unit Tests
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run: ./build-ci/src/unitTests
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- name: CLI Smoke
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run: ./build-ci/src/salmon -h
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- name: Prepare Sample Data
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shell: bash
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run: |
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set -euo pipefail
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if [[ ! -d sample_data ]]; then
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tar -xzf sample_data.tgz
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fi
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- name: Sample Data Smoke (Mapping)
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run: |
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./build-ci/src/salmon index \
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-t sample_data/transcripts.fasta \
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-i build-ci/sample_index
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./build-ci/src/salmon quant \
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-l A \
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-i build-ci/sample_index \
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-1 sample_data/reads_1.fastq \
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-2 sample_data/reads_2.fastq \
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-o build-ci/sample_quant_mapping
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- name: Sample Data Smoke (Alignment)
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run: |
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./build-ci/src/salmon quant \
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-l A \
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-t sample_data/transcripts.fasta \
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-a sample_data/sample_alignments.bam \
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-o build-ci/sample_quant_alignment
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- name: Package Binary Artifact
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shell: bash
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run: |
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set -euo pipefail
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pkg_dir="release/salmon-${{ matrix.target_id }}"
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mkdir -p "$pkg_dir/bin"
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cp build-ci/src/salmon "$pkg_dir/bin/"
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cp LICENSE "$pkg_dir/"
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cp README.md "$pkg_dir/"
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tar -C release -czf "salmon-${{ matrix.target_id }}.tar.gz" "salmon-${{ matrix.target_id }}"
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- name: Upload Binary Artifact
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uses: actions/upload-artifact@v4
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with:
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name: salmon-${{ matrix.target_id }}
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path: salmon-${{ matrix.target_id }}.tar.gz
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if-no-files-found: error

‎.github/workflows/release.yml‎

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name: Release
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on:
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workflow_run:
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workflows: ["CI"]
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types: [completed]
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permissions:
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contents: write
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actions: read
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jobs:
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release:
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if: ${{ github.event.workflow_run.conclusion == 'success' && github.event.workflow_run.head_branch == 'main' }}
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runs-on: ubuntu-latest
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steps:
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- name: Determine Release Tag From Commit Message
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id: tag
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shell: bash
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run: |
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set -euo pipefail
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msg="$(jq -r '.workflow_run.head_commit.message // ""' "$GITHUB_EVENT_PATH")"
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if [[ "$msg" =~ \[release[[:space:]]+v?([0-9]+\.[0-9]+\.[0-9]+)\] ]]; then
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echo "release_tag=v${BASH_REMATCH[1]}" >> "$GITHUB_OUTPUT"
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echo "should_release=true" >> "$GITHUB_OUTPUT"
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else
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echo "No [release vX.Y.Z] token found; skipping release."
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echo "release_tag=" >> "$GITHUB_OUTPUT"
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echo "should_release=false" >> "$GITHUB_OUTPUT"
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fi
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- name: Checkout Repository
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if: ${{ steps.tag.outputs.should_release == 'true' }}
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Download CI Artifacts
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if: ${{ steps.tag.outputs.should_release == 'true' }}
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uses: actions/download-artifact@v4
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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run-id: ${{ github.event.workflow_run.id }}
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path: release-assets
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merge-multiple: true
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- name: Create and Push Tag
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if: ${{ steps.tag.outputs.should_release == 'true' }}
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env:
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RELEASE_TAG: ${{ steps.tag.outputs.release_tag }}
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RELEASE_SHA: ${{ github.event.workflow_run.head_sha }}
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run: |
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set -euo pipefail
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git fetch --tags
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if git rev-parse -q --verify "refs/tags/${RELEASE_TAG}" >/dev/null; then
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echo "Tag ${RELEASE_TAG} already exists"
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else
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git tag -a "${RELEASE_TAG}" "${RELEASE_SHA}" -m "Release ${RELEASE_TAG}"
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git push origin "${RELEASE_TAG}"
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fi
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- name: Create GitHub Release
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if: ${{ steps.tag.outputs.should_release == 'true' }}
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uses: softprops/action-gh-release@v2
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with:
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tag_name: ${{ steps.tag.outputs.release_tag }}
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target_commitish: ${{ github.event.workflow_run.head_sha }}
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generate_release_notes: true
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files: release-assets/*.tar.gz

‎.readthedocs.yaml‎

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# Read the Docs configuration file for Salmon
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html
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version: 2
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build:
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os: ubuntu-22.04
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tools:
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python: "3.12"
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sphinx:
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configuration: doc/source/conf.py
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python:
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install:
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- requirements: doc/requirements.txt

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