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‎.github/workflows/build_and_upload_wheels.yml‎

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name: Build and upload to PyPI
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# Source: https://raw.githubusercontent.com/pypa/cibuildwheel/main/examples/github-deploy.yml
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env:
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CIBW_SKIP: "cp36-*"
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# Build on every branch push, tag push, and pull request change:
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on:
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workflow_dispatch:
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jobs:
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build_wheels:
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name: Build wheels on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-20.04, windows-2019, macos-11]
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steps:
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- uses: actions/checkout@v3
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- name: Build wheels
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uses: pypa/cibuildwheel@v2.12.3
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- uses: actions/upload-artifact@v3
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with:
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path: ./wheelhouse/*.whl
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Build sdist
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run: pipx run build --sdist
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- uses: actions/upload-artifact@v3
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with:
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path: dist/*.tar.gz
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upload_pypi:
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needs: [build_wheels, build_sdist]
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runs-on: ubuntu-latest
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# upload to PyPI on every tag starting with 'v'
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# if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
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# alternatively, to publish when a GitHub Release is created, use the following rule:
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# if: github.event_name == 'release' && github.event.action == 'published'
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steps:
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- uses: actions/download-artifact@v3
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with:
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# unpacks default artifact into dist/
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# if `name: artifact` is omitted, the action will create extra parent dir
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name: artifact
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path: dist
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- uses: pypa/gh-action-pypi-publish@v1.5.0
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with:
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user: ${{ secrets.PYPI_USER }}
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password: ${{ secrets.PYPI_PROD_PASSWORD }}
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verbose: true
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# To test: repository_url: https://test.pypi.org/legacy/

‎.github/workflows/install_doctest_lint_typecheck.yml‎

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name: Install, test, doctest, lint, typecheck ncls
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# Source: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#using-multiple-python-versions
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on: [pull_request, workflow_dispatch]
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jobs:
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install_and_test:
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runs-on: ubuntu-latest
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strategy:
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# You can use PyPy versions in python-version.
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# For example, pypy2.7 and pypy3.9
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matrix:
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python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- run:
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pip install pytest
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- name: Install
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run: |
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pip install .
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pytest tests/*.py
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isort:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python environment
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uses: actions/setup-python@v4
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with:
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python-version: "3.11"
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- run: pip install isort
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- run: isort --profile black -l 120 --check --diff ncls tests
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black:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python environment
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uses: actions/setup-python@v4
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with:
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python-version: "3.11.0"
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- run: pip install black
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- run: black -l 120 --check --diff ncls tests
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flake8:
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runs-on: ubuntu-latest
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name: Lint
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steps:
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- name: Check out source repository
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uses: actions/checkout@v3
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- name: Set up Python environment
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uses: actions/setup-python@v4
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- name: flake8 Lint install
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run: pip install flake8
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- name: flake8 Lint
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run: flake8 --max-line-length=120 --ignore E203,E501,W503 ncls tests
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mypy:
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runs-on: ubuntu-latest
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name: Mypy
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steps:
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- name: Check out source repository
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uses: actions/checkout@v3
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- name: Set up Python environment
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uses: actions/setup-python@v4
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with:
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python-version: "3.11"
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- name: Install mypy
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run: pip install mypy
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- name: mypy
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run: |
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pip install numpy # for the typing stubs
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python -m pip install pandas-stubs types-setuptools
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mypy ncls

‎CHANGELOG‎

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<<<<<<< HEAD
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# 0.0.67/68 (12.05.23)
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- Remove .c files that should be regenerated (@starsareintherose)
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=======
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# 0.0.67 (12.05.23)
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- Remove .c files that should be regenerated
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>>>>>>> 6f7f5f27f2d9117ce9dfab58edee183a04da135a
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# 0.0.66 (09.01.23)
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- fix more deprecated stuff

‎examples/test_all_overlaps_both.py‎

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from ncls import NCLS
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import pickle

‎examples/test_find_overlap_list.py‎

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from ncls import NCLS
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import pickle

‎examples/test_fncls.py‎

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from ncls import FNCLS
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import numpy as np
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np.random.seed(0)
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import pandas as pd
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size = int(1e4)
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starts = np.random.randint(0, high=int(1e6), size=size) + np.random.random()

‎ncls/__init__.py‎

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from ncls.src.ncls import NCLS64
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from ncls.src.ncls32 import NCLS32
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import numpy as np
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import pkg_resources
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__version__ = pkg_resources.get_distribution("ncls").version
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from ncls.src.ncls import NCLS64 # type: ignore
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from ncls.src.ncls32 import NCLS32 # type: ignore
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def NCLS(starts, ends, ids):
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def NCLS(starts, ends, ids):
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if isinstance(starts, list) or "pandas" in str(type(starts)):
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starts, ends, ids = [np.array(s) for s in [starts, ends, ids]]
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def FNCLS(starts, ends, ids):
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from ncls.src.fncls import FNCLS
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from ncls.src.fncls import FNCLS # type: ignore
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if isinstance(starts, list) or "pandas" in str(type(starts)):
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starts, ends, ids = [np.array(s) for s in [starts, ends, ids]]
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return FNCLS(starts, ends.astype(np.double), ids)
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else:
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raise Exception("Starts/Ends not double: " + str(starts.dtype))
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from ncls.version import __version__

‎ncls/src/cncls32.pxd‎

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from libc.stdint cimport int32_t, int64_t
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cdef extern from "stdlib.h":
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void free(void *)
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void *malloc(size_t)

‎ncls/src/fncls.pyx‎

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cimport ncls.src.cfncls as cn
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cimport cython
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from libc.stdint cimport int64_t
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from libc.stdlib cimport malloc
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cimport ncls.src.cfncls as cn
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cimport ncls.src.cncls as cn
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from libc.stdlib cimport malloc
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import numpy as np
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cdef inline int int_max(int a, int b): return a if a >= b else b
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cdef inline int int_min(int a, int b): return a if a <= b else b
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# import ctypes as c

‎ncls/src/ncls.pyx‎

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# import numpy as cnp
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import sys
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cimport cython
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from libc.stdint cimport int64_t
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from libc.stdlib cimport malloc
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cimport ncls.src.cncls as cn
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from libc.stdlib cimport malloc
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import numpy as np
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cdef inline int int_max(int a, int b): return a if a >= b else b
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cdef inline int int_min(int a, int b): return a if a <= b else b
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# import ctypes as c

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