Add cython example

.circleci/config.yml

@@ -121,6 +121,12 @@ commands:
             make allchecks
             python -m pytest -n2
 
+      - run:
+          name: Build cython example LWT interface code and run
+          command: |
+            cd python/lwt_interface/cython_example
+            make
+
       - run:
           name: Generate coverage
           command: |

python/lwt_interface/cython_example/Makefile

@@ -0,0 +1,13 @@
+all: compile run
+
+compile:
+	pip install -e . --use-pep517
+
+run:
+	PYTHONPATH=../.. python -c "import example; example.main()"
+
+clean:
+	rm -rf build/
+	rm -rf tskit_cython_example.egg-info/
+	rm -f example.c
+	rm -f *.so

python/lwt_interface/cython_example/_lwtc.c

@@ -0,0 +1,64 @@
+/*
+ * MIT License
+ *
+ * Copyright (c) 2019-2020 Tskit Developers
+ * Copyright (c) 2015-2018 University of Oxford
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+// Turn off clang-formatting for this file as turning off formatting
+// for specific bits will make it more confusing.
+// clang-format off
+
+#define PY_SSIZE_T_CLEAN
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+
+#include <Python.h>
+#include <structmember.h>
+#include <numpy/arrayobject.h>
+
+#include "kastore.h"
+#include "tskit.h"
+
+#include "tskit_lwt_interface.h"
+
+static PyMethodDef lwt_methods[] = {
+    { NULL, NULL, 0, NULL } /* sentinel */
+};
+
+static struct PyModuleDef lwt_module = {
+    .m_base = PyModuleDef_HEAD_INIT,
+    .m_name = "_lwt",
+    .m_doc = "tskit LightweightTableCollection",
+    .m_size = -1,
+    .m_methods = lwt_methods };
+
+PyMODINIT_FUNC
+PyInit__lwtc(void)
+{
+    PyObject *module = PyModule_Create(&lwt_module);
+    if (module == NULL) {
+        return NULL;
+    }
+    import_array();
+    if (register_lwt_class(module) != 0) {
+        return NULL;
+    }
+    return module;
+}

python/lwt_interface/cython_example/example.pyx

@@ -0,0 +1,63 @@
+from libc.stdint cimport uint32_t
+import _lwtc
+import tskit
+
+cdef extern from "tskit.h" nogil:
+    ctypedef uint32_t tsk_flags_t
+    ctypedef struct tsk_table_collection_t:
+        pass
+    ctypedef struct tsk_treeseq_t:
+        pass
+    int tsk_treeseq_init(tsk_treeseq_t *self, const tsk_table_collection_t *tables, tsk_flags_t options)
+    int tsk_treeseq_free(tsk_treeseq_t *self)
+    int tsk_table_collection_build_index(tsk_table_collection_t *self, tsk_flags_t options)
+    ctypedef struct tsk_tree_t:
+        pass
+    int tsk_tree_init(tsk_tree_t *self, const tsk_treeseq_t *ts, tsk_flags_t options)
+    int tsk_tree_first(tsk_tree_t *self)
+    int tsk_tree_next(tsk_tree_t *self)
+    int tsk_tree_last(tsk_tree_t *self)
+    int tsk_tree_prev(tsk_tree_t *self)
+    int tsk_tree_get_num_roots(tsk_tree_t *self)
+    int tsk_tree_free(tsk_tree_t *self)
+    const char *tsk_strerror(int err)
+
+cdef extern:
+    ctypedef class _lwtc.LightweightTableCollection [object LightweightTableCollection]:
+        cdef tsk_table_collection_t *tables
+
+def check_tsk_error(val):
+    if val < 0:
+        raise RuntimeError(tsk_strerror(val))
+
+def iterate_trees(pyts: tskit.TreeSequence):
+    lwtc = LightweightTableCollection()
+    lwtc.fromdict(pyts.dump_tables().asdict())        
+    cdef tsk_treeseq_t ts
+    err = tsk_treeseq_init(&ts, lwtc.tables, 0)
+    check_tsk_error(err)
+    cdef tsk_tree_t tree
+    ret = tsk_tree_init(&tree, &ts, 0)
+    check_tsk_error(ret)
+
+    print("Iterate forwards")
+    cdef int tree_iter = tsk_tree_first(&tree)
+    while tree_iter == 1:
+        print("\ttree has %d roots" % (tsk_tree_get_num_roots(&tree)))
+        tree_iter = tsk_tree_next(&tree)
+    check_tsk_error(tree_iter)
+
+    print("Iterate backwards")
+    tree_iter = tsk_tree_last(&tree)
+    while tree_iter == 1:
+        print("\ttree has %d roots" % (tsk_tree_get_num_roots(&tree)))
+        tree_iter = tsk_tree_prev(&tree)
+    check_tsk_error(tree_iter)
+
+    tsk_tree_free(&tree)
+    tsk_treeseq_free(&ts)
+
+def main():
+    import msprime as msp  # (msprime could be compiled against a different version of tskit)
+    ts = msp.simulate(sample_size=5, length=100, recombination_rate=.01)  
+    iterate_trees(ts)

python/lwt_interface/cython_example/pyproject.toml

@@ -0,0 +1,13 @@
+[build-system]
+requires = ["setuptools>=64", "wheel", "Cython", "numpy"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tskit_cython_example"
+version = "0.0.1"
+description = "Cython example for tskit"
+authors = [{name = "tskit developers"}]
+dependencies = ["numpy", "Cython"]
+
+[tool.setuptools]
+packages = []

python/lwt_interface/cython_example/setup.py

@@ -0,0 +1,40 @@
+import glob
+import os
+
+import numpy as np
+from Cython.Build import cythonize
+from setuptools import setup
+from setuptools.extension import Extension
+
+TSKIT_BASE = os.path.join(os.path.dirname(__file__), "..", "..", "..")
+TSKIT_C_PATH = os.path.join(TSKIT_BASE, "c")
+TSKIT_PY_PATH = os.path.join(TSKIT_BASE, "python/lwt_interface")
+KASTORE_PATH = os.path.join(TSKIT_BASE, "c", "subprojects", "kastore")
+include_dirs = [TSKIT_C_PATH, TSKIT_PY_PATH, KASTORE_PATH, np.get_include()]
+
+tskit_sourcefiles = list(glob.glob(os.path.join(TSKIT_C_PATH, "tskit", "*.c"))) + [
+    os.path.join(KASTORE_PATH, "kastore.c")
+]
+
+extensions = [
+    Extension(
+        "_lwtc",
+        ["_lwtc.c"] + tskit_sourcefiles,
+        language="c",
+        include_dirs=include_dirs,
+    ),
+    Extension(
+        "example",
+        ["example.pyx"] + tskit_sourcefiles,
+        language="c",
+        include_dirs=include_dirs,
+    ),
+]
+
+extensions = cythonize(extensions, language_level=3)
+
+setup(
+    name="tskit_cython_example",
+    version="0.0.1",
+    ext_modules=extensions,
+)