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Run Snakemake with --rerun-incomplete

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CI on: pull_request 46

lint

test-source (python=3.8 os=ubuntu-latest)

test-source (python=3.9 os=ubuntu-latest)

test-source (python=3.10 os=ubuntu-latest)

test-source (python=3.11 os=ubuntu-latest)

test-source (python=3.12 os=ubuntu-latest)

test-source (python=3.13 os=ubuntu-latest)

test-source (python=3.8 os=macos-latest)

test-source (python=3.9 os=macos-latest)

test-source (python=3.10 os=macos-latest)

test-source (python=3.11 os=macos-latest)

test-source (python=3.12 os=macos-latest)

test-source (python=3.13 os=macos-latest)

test-source (python=3.8 os=windows-latest)

test-source (python=3.9 os=windows-latest)

test-source (python=3.10 os=windows-latest)

test-source (python=3.11 os=windows-latest)

test-source (python=3.12 os=windows-latest)

test-source (python=3.13 os=windows-latest)

build-dist

doc / build

build-standalone (ubuntu-22.04, x86_64-unknown-linux-gnu, nextstrain)

build-standalone (ubuntu-22.04-arm, aarch64-unknown-linux-gnu, nextstrain)

build-standalone (macos-15-intel, x86_64-apple-darwin, nextstrain)

build-standalone (macos-14, aarch64-apple-darwin, nextstrain)

build-standalone (windows-2022, x86_64-pc-windows-msvc, nextstrain.exe)

test-dist (python=3.8 os=ubuntu-latest)

test-dist (python=3.9 os=ubuntu-latest)

test-dist (python=3.10 os=ubuntu-latest)

test-dist (python=3.11 os=ubuntu-latest)

test-dist (python=3.12 os=ubuntu-latest)

test-dist (python=3.13 os=ubuntu-latest)

test-dist (python=3.8 os=macos-latest)

test-dist (python=3.9 os=macos-latest)

test-dist (python=3.10 os=macos-latest)

test-dist (python=3.11 os=macos-latest)

test-dist (python=3.12 os=macos-latest)

test-dist (python=3.13 os=macos-latest)

test-dist (python=3.8 os=windows-latest)

test-dist (python=3.9 os=windows-latest)

test-dist (python=3.10 os=windows-latest)

test-dist (python=3.11 os=windows-latest)

test-dist (python=3.12 os=windows-latest)

test-dist (python=3.13 os=windows-latest)

write-install-commands

test-standalone (os=ubuntu-22.04, target=x86_64-unknown-linux-gnu)

test-standalone (os=ubuntu-24.04, target=x86_64-unknown-linux-gnu)

test-standalone (os=ubuntu-22.04-arm, target=aarch64-unknown-linux-gnu)

test-standalone (os=ubuntu-24.04-arm, target=aarch64-unknown-linux-gnu)

test-standalone (os=macos-15-intel, target=x86_64-apple-darwin)

test-standalone (os=macos-14, target=x86_64-apple-darwin)

test-standalone (os=macos-15, target=x86_64-apple-darwin)

test-standalone (os=macos-14, target=aarch64-apple-darwin)

test-standalone (os=macos-15, target=aarch64-apple-darwin)

test-standalone (os=windows-2022, target=x86_64-pc-windows-msvc)

test-standalone (os=windows-2025, target=x86_64-pc-windows-msvc)

release

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