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benjefferyjeromekelleher
benjeffery
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Add cython example
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‎.circleci/config.yml‎

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make allchecks
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python -m pytest -n2
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- run:
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name: Build cython example LWT interface code and run
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command: |
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cd python/lwt_interface/cython_example
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make
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- run:
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name: Generate coverage
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command: |

‎python/lwt_interface/cython_example/Makefile‎

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all: compile run
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compile:
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pip install -e . --use-pep517
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run:
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PYTHONPATH=../.. python -c "import example; example.main()"
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clean:
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rm -rf build/
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rm -rf tskit_cython_example.egg-info/
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rm -f example.c
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rm -f *.so

‎python/lwt_interface/cython_example/_lwtc.c‎

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/*
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* MIT License
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*
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* Copyright (c) 2019-2020 Tskit Developers
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* Copyright (c) 2015-2018 University of Oxford
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in all
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* copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*/
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// Turn off clang-formatting for this file as turning off formatting
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// for specific bits will make it more confusing.
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// clang-format off
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#define PY_SSIZE_T_CLEAN
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#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
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#include <Python.h>
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#include <structmember.h>
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#include <numpy/arrayobject.h>
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#include "kastore.h"
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#include "tskit.h"
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#include "tskit_lwt_interface.h"
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static PyMethodDef lwt_methods[] = {
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{ NULL, NULL, 0, NULL } /* sentinel */
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};
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static struct PyModuleDef lwt_module = {
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.m_base = PyModuleDef_HEAD_INIT,
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.m_name = "_lwt",
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.m_doc = "tskit LightweightTableCollection",
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.m_size = -1,
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.m_methods = lwt_methods };
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PyMODINIT_FUNC
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PyInit__lwtc(void)
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{
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PyObject *module = PyModule_Create(&lwt_module);
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if (module == NULL) {
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return NULL;
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}
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import_array();
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if (register_lwt_class(module) != 0) {
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return NULL;
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}
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return module;
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}

‎python/lwt_interface/cython_example/example.pyx‎

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from libc.stdint cimport uint32_t
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import _lwtc
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import tskit
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cdef extern from "tskit.h" nogil:
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ctypedef uint32_t tsk_flags_t
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ctypedef struct tsk_table_collection_t:
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pass
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ctypedef struct tsk_treeseq_t:
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pass
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int tsk_treeseq_init(tsk_treeseq_t *self, const tsk_table_collection_t *tables, tsk_flags_t options)
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int tsk_treeseq_free(tsk_treeseq_t *self)
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int tsk_table_collection_build_index(tsk_table_collection_t *self, tsk_flags_t options)
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ctypedef struct tsk_tree_t:
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pass
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int tsk_tree_init(tsk_tree_t *self, const tsk_treeseq_t *ts, tsk_flags_t options)
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int tsk_tree_first(tsk_tree_t *self)
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int tsk_tree_next(tsk_tree_t *self)
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int tsk_tree_last(tsk_tree_t *self)
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int tsk_tree_prev(tsk_tree_t *self)
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int tsk_tree_get_num_roots(tsk_tree_t *self)
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int tsk_tree_free(tsk_tree_t *self)
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const char *tsk_strerror(int err)
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cdef extern:
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ctypedef class _lwtc.LightweightTableCollection [object LightweightTableCollection]:
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cdef tsk_table_collection_t *tables
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def check_tsk_error(val):
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if val < 0:
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raise RuntimeError(tsk_strerror(val))
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def iterate_trees(pyts: tskit.TreeSequence):
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lwtc = LightweightTableCollection()
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lwtc.fromdict(pyts.dump_tables().asdict())
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cdef tsk_treeseq_t ts
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err = tsk_treeseq_init(&ts, lwtc.tables, 0)
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check_tsk_error(err)
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cdef tsk_tree_t tree
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ret = tsk_tree_init(&tree, &ts, 0)
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check_tsk_error(ret)
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print("Iterate forwards")
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cdef int tree_iter = tsk_tree_first(&tree)
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while tree_iter == 1:
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print("\ttree has %d roots" % (tsk_tree_get_num_roots(&tree)))
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tree_iter = tsk_tree_next(&tree)
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check_tsk_error(tree_iter)
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print("Iterate backwards")
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tree_iter = tsk_tree_last(&tree)
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while tree_iter == 1:
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print("\ttree has %d roots" % (tsk_tree_get_num_roots(&tree)))
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tree_iter = tsk_tree_prev(&tree)
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check_tsk_error(tree_iter)
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tsk_tree_free(&tree)
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tsk_treeseq_free(&ts)
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def main():
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import msprime as msp # (msprime could be compiled against a different version of tskit)
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ts = msp.simulate(sample_size=5, length=100, recombination_rate=.01)
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iterate_trees(ts)

‎python/lwt_interface/cython_example/pyproject.toml‎

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[build-system]
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requires = ["setuptools>=64", "wheel", "Cython", "numpy"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "tskit_cython_example"
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version = "0.0.1"
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description = "Cython example for tskit"
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authors = [{name = "tskit developers"}]
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dependencies = ["numpy", "Cython"]
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[tool.setuptools]
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packages = []

‎python/lwt_interface/cython_example/setup.py‎

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import glob
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import os
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import numpy as np
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from Cython.Build import cythonize
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from setuptools import setup
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from setuptools.extension import Extension
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TSKIT_BASE = os.path.join(os.path.dirname(__file__), "..", "..", "..")
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TSKIT_C_PATH = os.path.join(TSKIT_BASE, "c")
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TSKIT_PY_PATH = os.path.join(TSKIT_BASE, "python/lwt_interface")
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KASTORE_PATH = os.path.join(TSKIT_BASE, "c", "subprojects", "kastore")
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include_dirs = [TSKIT_C_PATH, TSKIT_PY_PATH, KASTORE_PATH, np.get_include()]
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tskit_sourcefiles = list(glob.glob(os.path.join(TSKIT_C_PATH, "tskit", "*.c"))) + [
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os.path.join(KASTORE_PATH, "kastore.c")
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]
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extensions = [
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Extension(
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"_lwtc",
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["_lwtc.c"] + tskit_sourcefiles,
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language="c",
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include_dirs=include_dirs,
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),
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Extension(
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"example",
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["example.pyx"] + tskit_sourcefiles,
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language="c",
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include_dirs=include_dirs,
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),
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]
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extensions = cythonize(extensions, language_level=3)
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setup(
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name="tskit_cython_example",
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version="0.0.1",
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ext_modules=extensions,
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)

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