strkit-rust-ext 0.24.2__tar.gz → 0.26.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/.github/workflows/build-release.yml +23 -17
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/Cargo.lock +413 -395
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/Cargo.toml +15 -6
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/PKG-INFO +1 -1
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/README.md +1 -1
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/pyproject.toml +1 -5
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/lib.rs +10 -2
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/strkit/aligned_coords.rs +27 -6
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/strkit/cigar.rs +20 -20
- strkit_rust_ext-0.26.0/src/strkit/consensus/best_representatives.rs +78 -0
- strkit_rust_ext-0.26.0/src/strkit/consensus/poa.rs +238 -0
- strkit_rust_ext-0.26.0/src/strkit/consensus.rs +107 -0
- strkit_rust_ext-0.26.0/src/strkit/coords.rs +2 -0
- strkit_rust_ext-0.26.0/src/strkit/exceptions.rs +32 -0
- strkit_rust_ext-0.26.0/src/strkit/locus.rs +656 -0
- strkit_rust_ext-0.26.0/src/strkit/reads.rs +708 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/strkit/repeats.rs +2 -2
- strkit_rust_ext-0.26.0/src/strkit/snvs.rs +693 -0
- strkit_rust_ext-0.26.0/src/strkit/utils.rs +88 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/strkit.rs +2 -0
- strkit_rust_ext-0.26.0/strkit_rust_ext.pyi +315 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/cigar.py +3 -3
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/common.py +2 -1
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_aligned_coords.py +10 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_consensus.py +2 -1
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_locus.py +21 -2
- strkit_rust_ext-0.26.0/tests/test_utils.py +18 -0
- strkit_rust_ext-0.24.2/src/strkit/consensus.rs +0 -240
- strkit_rust_ext-0.24.2/src/strkit/locus.rs +0 -426
- strkit_rust_ext-0.24.2/src/strkit/reads.rs +0 -332
- strkit_rust_ext-0.24.2/src/strkit/snvs.rs +0 -544
- strkit_rust_ext-0.24.2/src/strkit/utils.rs +0 -53
- strkit_rust_ext-0.24.2/strkit_rust_ext.pyi +0 -214
- strkit_rust_ext-0.24.2/tests/test_utils.py +0 -10
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/.gitignore +0 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/LICENSE +0 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/rust_ext_logo.png +0 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/__init__.py +0 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/benchmark.py +0 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_cigar.py +0 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_repeats.py +0 -0
- {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_snvs.py +0 -0
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test:
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runs-on: ubuntu-24.04
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steps:
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- uses: actions/checkout@
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- uses: actions/setup-python@v6
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with:
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python-version: '3.10'
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- uses: actions-rust-lang/setup-rust-toolchain@v1
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with:
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toolchain: 1.
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toolchain: 1.88.0
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rustflags: ""
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- name: Run tests
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run: |
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export CARGO_PROFILE_DEV_BUILD_OVERRIDE_DEBUG=true
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python -m venv env
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source env/bin/activate
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python -m pip install 'maturin>=1.
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python -m pip install 'maturin>=1.12.2,<1.13' pytest numpy
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python -m maturin develop --jobs 2
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pytest
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cargo test
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strategy:
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matrix:
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target: [x86_64, aarch64
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target: [x86_64, aarch64] # x86, armv7 disabled for now
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- name: Build wheels
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uses: PyO3/maturin-action@v1
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with:
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rust-toolchain: 1.
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rust-toolchain: 1.88.0
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target: ${{ matrix.target }}
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args: --release --verbose --jobs 2 --out dist -i python3.10 -i python3.11 -i python3.
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args: --release --verbose --jobs 2 --out dist -i python3.10 -i python3.11 python3.12 -i python3.13 -i python3.14
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# sccache: 'true'
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manylinux: '2_28'
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# https://github.com/sfackler/rust-openssl/issues/2036#issuecomment-1724324145
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fi
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- name: Upload wheels
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if: ${{ github.event_name == 'release' || github.event_name == 'workflow_dispatch' }}
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name: wheels-linux-${{ matrix.target }}
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path: dist
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# windows:
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# matrix:
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# target: [x86_64-pc-windows-gnu]
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# steps:
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# # - name: Install OpenSSL (Windows)
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# # shell: powershell
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# with:
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# sudo apt-get update -y && sudo apt-get install -y g++-mingw-w64-x86-64 gcc-mingw-w64-x86-64
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# - { sys: ucrt64, env: ucrt-x86_64 }
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# - name: Set up MSYS2 MinGW-W64
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# uses: msys2/setup-msys2@v2
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# with:
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target: ${{ matrix.target }}
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args: --release --verbose --jobs 2 --out dist -i python3.10 -i python3.11 -i python3.12 -i python3.13
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args: --release --verbose --jobs 2 --out dist -i python3.10 -i python3.11 -i python3.12 -i python3.13 -i python3.14
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# sccache: 'true'
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if: ${{ github.event_name == 'release' || github.event_name == 'workflow_dispatch' }}
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name: wheels-macos-${{ matrix.target }}
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sdist:
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name: Release
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args: --non-interactive --skip-existing wheels/*
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