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.
Files changed (42) hide show
  1. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/.github/workflows/build-release.yml +23 -17
  2. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/Cargo.lock +413 -395
  3. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/Cargo.toml +15 -6
  4. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/PKG-INFO +1 -1
  5. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/README.md +1 -1
  6. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/pyproject.toml +1 -5
  7. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/lib.rs +10 -2
  8. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/strkit/aligned_coords.rs +27 -6
  9. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/strkit/cigar.rs +20 -20
  10. strkit_rust_ext-0.26.0/src/strkit/consensus/best_representatives.rs +78 -0
  11. strkit_rust_ext-0.26.0/src/strkit/consensus/poa.rs +238 -0
  12. strkit_rust_ext-0.26.0/src/strkit/consensus.rs +107 -0
  13. strkit_rust_ext-0.26.0/src/strkit/coords.rs +2 -0
  14. strkit_rust_ext-0.26.0/src/strkit/exceptions.rs +32 -0
  15. strkit_rust_ext-0.26.0/src/strkit/locus.rs +656 -0
  16. strkit_rust_ext-0.26.0/src/strkit/reads.rs +708 -0
  17. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/strkit/repeats.rs +2 -2
  18. strkit_rust_ext-0.26.0/src/strkit/snvs.rs +693 -0
  19. strkit_rust_ext-0.26.0/src/strkit/utils.rs +88 -0
  20. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/src/strkit.rs +2 -0
  21. strkit_rust_ext-0.26.0/strkit_rust_ext.pyi +315 -0
  22. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/cigar.py +3 -3
  23. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/common.py +2 -1
  24. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_aligned_coords.py +10 -0
  25. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_consensus.py +2 -1
  26. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_locus.py +21 -2
  27. strkit_rust_ext-0.26.0/tests/test_utils.py +18 -0
  28. strkit_rust_ext-0.24.2/src/strkit/consensus.rs +0 -240
  29. strkit_rust_ext-0.24.2/src/strkit/locus.rs +0 -426
  30. strkit_rust_ext-0.24.2/src/strkit/reads.rs +0 -332
  31. strkit_rust_ext-0.24.2/src/strkit/snvs.rs +0 -544
  32. strkit_rust_ext-0.24.2/src/strkit/utils.rs +0 -53
  33. strkit_rust_ext-0.24.2/strkit_rust_ext.pyi +0 -214
  34. strkit_rust_ext-0.24.2/tests/test_utils.py +0 -10
  35. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/.gitignore +0 -0
  36. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/LICENSE +0 -0
  37. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/rust_ext_logo.png +0 -0
  38. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/__init__.py +0 -0
  39. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/benchmark.py +0 -0
  40. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_cigar.py +0 -0
  41. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_repeats.py +0 -0
  42. {strkit_rust_ext-0.24.2 → strkit_rust_ext-0.26.0}/tests/test_snvs.py +0 -0
@@ -14,20 +14,20 @@ jobs:
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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@v5
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+ - uses: actions/checkout@v6
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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: 1.85.0
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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>=1.9.6,<1.10' pytest numpy
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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
@@ -36,15 +36,15 @@ jobs:
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  runs-on: ubuntu-24.04
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  strategy:
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  matrix:
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- target: [x86_64, aarch64, armv7] # x86 disabled for now
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+ target: [x86_64, aarch64] # x86, armv7 disabled for now
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  steps:
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- - uses: actions/checkout@v5
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+ - uses: actions/checkout@v6
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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: 1.85.0
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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 python3.12 -i python3.13
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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
@@ -90,9 +90,11 @@ jobs:
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  fi
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  - name: Upload wheels
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  uses: actions/upload-artifact@v4
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+ if: ${{ github.event_name == 'release' || github.event_name == 'workflow_dispatch' }}
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  with:
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  name: wheels-linux-${{ matrix.target }}
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  path: dist
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+ retention-days: 1
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  # windows:
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  # runs-on: ubuntu-24.04
@@ -100,7 +102,7 @@ jobs:
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  # matrix:
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  # target: [x86_64-pc-windows-gnu]
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  # steps:
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- # - uses: actions/checkout@v5
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+ # - uses: actions/checkout@v6
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  # # - name: Install OpenSSL (Windows)
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  # # shell: powershell
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  # # run: |
@@ -109,9 +111,9 @@ jobs:
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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: 1.85.0
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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 python3.12 -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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  # before-script-linux: |
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  # sudo apt-get update -y && sudo apt-get install -y g++-mingw-w64-x86-64 gcc-mingw-w64-x86-64
@@ -130,7 +132,7 @@ jobs:
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  # - { sys: ucrt64, env: ucrt-x86_64 }
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  # steps:
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- # - uses: actions/checkout@v5
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+ # - uses: actions/checkout@v6
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  # - name: Set up MSYS2 MinGW-W64
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  # uses: msys2/setup-msys2@v2
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  # with:
@@ -185,35 +187,39 @@ jobs:
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  matrix:
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  target: [x86_64, aarch64]
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  steps:
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- - uses: actions/checkout@v5
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+ - uses: actions/checkout@v6
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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: 1.85.0
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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 python3.12 -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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  - name: Upload wheels
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  uses: actions/upload-artifact@v4
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+ if: ${{ github.event_name == 'release' || github.event_name == 'workflow_dispatch' }}
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  with:
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  name: wheels-macos-${{ matrix.target }}
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  path: dist
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+ retention-days: 1
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  sdist:
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  runs-on: ubuntu-24.04
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  steps:
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- - uses: actions/checkout@v5
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+ - uses: actions/checkout@v6
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  - name: Build sdist
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  uses: PyO3/maturin-action@v1
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  with:
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- rust-toolchain: 1.85.0
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+ rust-toolchain: 1.88.0
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  command: sdist
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  args: --out dist
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  - name: Upload sdist
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  uses: actions/upload-artifact@v4
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+ if: ${{ github.event_name == 'release' || github.event_name == 'workflow_dispatch' }}
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  with:
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  name: wheels-sdist
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  path: dist
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+ retention-days: 1
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  release:
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  name: Release
@@ -233,4 +239,4 @@ jobs:
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  with:
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  command: upload
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  args: --non-interactive --skip-existing wheels/*
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- rust-toolchain: 1.85.0
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+ rust-toolchain: 1.88.0