Merge branch 'master' into use-pdm

setup.py

@@ -0,0 +1,59 @@
+"""
+-------
+License
+-------
+
+It is released under the MIT license.
+
+    Copyright (c) 2013 Hiroyuki Tanaka
+
+    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.
+"""
+
+
+try:
+    from setuptools import Extension, setup
+except:
+    from distutils import Extension, setup
+
+from Cython.Build import cythonize
+
+ext_modules = cythonize("editdistance/bycython.pyx")
+
+with open("README.rst") as readme_file:
+    readme = readme_file.read()
+
+setup(
+    name="editdistance",
+    version="0.7.0",
+    python_requires=">=3.6",
+    description="Fast implementation of the edit distance(Levenshtein distance)",
+    long_description=readme,
+    long_description_content_type="text/x-rst",
+    author="Hiroyuki Tanaka",
+    author_email="aflc0x@gmail.com",
+    url="https://www.github.com/roy-ht/editdistance",
+    ext_modules=ext_modules,
+    packages=["editdistance"],
+    package_data={
+        "editdistance": ["__init__.pxd", "_editdistance.h", "bycython.pxd", "def.h"]
+    },
+    classifiers=[
+        "License :: OSI Approved :: MIT License",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3 :: Only",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: Implementation :: CPython",
+        "Programming Language :: Python :: Implementation :: PyPy",
+    ],
+)

src/editdistance/__init__.pxd

@@ -1,2 +1,2 @@
 # cython: language_level=3
-from editdistance.bycython cimport eval
+from editdistance.bycython cimport eval, eval_criterion

src/editdistance/__init__.py

@@ -1,9 +1,12 @@
-from .bycython import eval
+from .bycython import eval, eval_criterion
 
 
 def distance(*args, **kwargs):
     """"An alias to eval"""
     return eval(*args, **kwargs)
 
+def distance_le_than(*args, **kwargs):
+    """"An alias to eval"""
+    return eval_criterion(*args, **kwargs)
 
-__all__ = ('eval', 'distance')
+__all__ = ('eval', 'distance', "eval_criterion", "distance_le_than")

src/editdistance/_editdistance.cpp

@@ -41,7 +41,7 @@ unsigned int edit_distance_bpv(T &cmap, int64_t const *vec, size_t const &vecsiz
     for(size_t i = 0; i < tlen; ++i) VP[tmax] |= (1LL << i);
     for(size_t i = 0; i < vecsize; ++i) {
         TVALUE &PM = cmap[vec[i]];
-        for(int r = 0; r <= tmax; ++r) {
+        for(unsigned int r = 0; r <= tmax; ++r) {
             uint64_t X = PM[r];
             if(r > 0 && (HN[r - 1] & lmb)) X |= 1LL;
             D0[r] = (((X & VP[r]) + VP[r]) ^ VP[r]) | X | VN[r];
@@ -61,21 +61,43 @@ unsigned int edit_distance_bpv(T &cmap, int64_t const *vec, size_t const &vecsiz
 
 
 /// c.f. http://handasse.blogspot.com/2009/04/c_29.html
-template<typename T>
-unsigned int edit_distance_dp(T const *str1, size_t const size1, T const *str2, size_t const size2) {
+unsigned int edit_distance_dp(int64_t const *str1, size_t const size1, int64_t const *str2, size_t const size2) {
     // vectorより固定長配列の方が速いが、文字列が長い時の保険でのみ呼ばれるのでサイズを決め打ちできない
     vector< vector<uint32_t> > d(2, vector<uint32_t>(size2 + 1));
     d[0][0] = 0;
     d[1][0] = 1;
-    for (int i = 0; i < size2 + 1; i++) d[0][i] = i;
-    for (int i = 1; i < size1 + 1; i++) {
-        for (int j = 1; j < size2 + 1; j++) {
+    for (size_t i = 0; i < size2 + 1; i++) d[0][i] = i;
+    for (size_t i = 1; i < size1 + 1; i++) {
+        d[i&1][0] = d[(i-1)&1][0] + 1;
+        for (size_t j = 1; j < size2 + 1; j++) {
             d[i&1][j] = min(min(d[(i-1)&1][j], d[i&1][j-1]) + 1, d[(i-1)&1][j-1] + (str1[i-1] == str2[j-1] ? 0 : 1));
         }
     }
     return d[size1&1][size2];
 }
 
+template<typename T>
+bool edit_distancec_dp(T const *str1, size_t const size1, T const *str2, size_t const size2, unsigned int const thr) {
+    vector< vector<uint32_t> > d(2, vector<uint32_t>(size2 + 1));
+    d[0][0] = 0;
+    d[1][0] = 1;
+    for (size_t i = 0; i < size2 + 1; i++) d[0][i] = i;
+    for (size_t i = 1; i < size1 + 1; i++) {
+        d[i&1][0] = d[(i-1)&1][0] + 1;
+        bool below_thr = false;
+        for (size_t j = 1; j < size2 + 1; j++) {
+            d[i&1][j] = min(min(d[(i-1)&1][j], d[i&1][j-1]) + 1, d[(i-1)&1][j-1] + (str1[i-1] == str2[j-1] ? 0 : 1));
+            if (d[i%1][j] <= thr) {
+                below_thr = true;
+            }
+        }
+        if (!below_thr) {
+            return false;
+        }
+    }
+    return d[size1&1][size2] <= thr;
+}
+
 template <size_t N>
 struct varr {
     uint64_t arr_[N];
@@ -127,5 +149,30 @@ unsigned int edit_distance(const int64_t *a, const unsigned int asize, const int
     else if(vsize == 8) return edit_distance_map_<8>(ap, *asizep, bp, *bsizep);
     else if(vsize == 9) return edit_distance_map_<9>(ap, *asizep, bp, *bsizep);
     else if(vsize == 10) return edit_distance_map_<10>(ap, *asizep, bp, *bsizep);
-    return edit_distance_dp<int64_t>(ap, *asizep, bp, *bsizep);  // dynamic programmingに任せる
+    return edit_distance_dp(ap, *asizep, bp, *bsizep);  // dynamic programmingに任せる
+}
+
+bool edit_distance_criterion(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize, const unsigned int thr) {
+    if(asize == 0) return bsize <= thr;
+    if(bsize == 0) return asize <= thr;
+    // 要素数の大きいほうがa
+    int64_t const *ap, *bp;
+    unsigned int const *asizep, *bsizep;
+    if(asize < bsize) ap = b, bp = a, asizep = &bsize, bsizep = &asize;
+    else ap = a, bp = b, asizep = &asize, bsizep = &bsize;
+    // 必要な配列サイズを調べる
+    size_t vsize = ((*asizep - 1) >> 6) + 1;  // 64までは1, 128までは2, ...
+    // bit-parallelでできそうな限界を超えたら要素数の小さい方をaとする。
+    if(vsize > 10) {
+        int64_t const *_ = ap;
+        unsigned int const *__ = asizep;
+        ap = bp, bp = _, asizep = bsizep, bsizep = __;
+        vsize = ((*asizep - 1) >> 6) + 1;
+    }
+
+    return edit_distancec_dp<int64_t>(ap, *asizep, bp, *bsizep, thr);  // dynamic programmingに任せる
 }
+
+
+
+

src/editdistance/_editdistance.h

@@ -8,6 +8,8 @@ extern "C" {
 #endif
 
 unsigned int edit_distance(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize);
+bool edit_distance_criterion(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize, const unsigned int thr);
+unsigned int edit_distance_dp(int64_t const *str1, size_t const size1, int64_t const *str2, size_t const size2);
 
 #ifdef __cplusplus
 }

src/editdistance/bycython.pxd

@@ -1,2 +1,3 @@
 # cython: language_level=3
 cpdef unsigned int eval(object a, object b) except 0xffffffffffffffff
+cpdef bint eval_criterion(object a, object b, const unsigned int thr) except 0xffffffffffffffff

src/editdistance/bycython.pyx

@@ -2,11 +2,15 @@
 # distutils: sources = src/editdistance/_editdistance.cpp
 
 from libc.stdlib cimport malloc, free
+from libcpp cimport bool
 # from libc.stdint cimport int64_t
 
 cdef extern from "./_editdistance.h":
     ctypedef int int64_t
     unsigned int edit_distance(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize)
+    bool edit_distance_criterion(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize, const unsigned int thr)
+    unsigned int edit_distance_dp(const int64_t *str1, const size_t size1, const int64_t *str2, const size_t size2)
+
 
 cpdef unsigned int eval(object a, object b) except 0xffffffffffffffff:
     cdef unsigned int i, dist
@@ -20,3 +24,30 @@ cpdef unsigned int eval(object a, object b) except 0xffffffffffffffff:
     free(al)
     free(bl)
     return dist
+
+cpdef bint eval_criterion(object a, object b, const unsigned int thr) except 0xffffffffffffffff:
+    cdef unsigned int i
+    cdef bint ret
+    cdef int64_t *al = <int64_t *>malloc(len(a) * sizeof(int64_t))
+    for i in range(len(a)):
+        al[i] = hash(a[i])
+    cdef int64_t *bl = <int64_t *>malloc(len(b) * sizeof(int64_t))
+    for i in range(len(b)):
+        bl[i] = hash(b[i])
+    ret = edit_distance_criterion(al, len(a), bl, len(b), thr)
+    free(al)
+    free(bl)
+    return ret
+
+  cpdef unsigned int eval_dp(object a, object b) except 0xffffffffffffffff:
+    cdef unsigned int i, dist
+    cdef int64_t *al = <int64_t *>malloc(len(a) * sizeof(int64_t))
+    for i in range(len(a)):
+        al[i] = hash(a[i])
+    cdef int64_t *bl = <int64_t *>malloc(len(b) * sizeof(int64_t))
+    for i in range(len(b)):
+        bl[i] = hash(b[i])
+    dist = edit_distance_dp(al, len(a), bl, len(b))
+    free(al)
+    free(bl)
+    return dist

test/test_editdistance.py

@@ -1,10 +1,31 @@
 import unittest
+import random
+
 
 class TestEditDistance(unittest.TestCase):
     def test_editdistance(self):
         import editdistance
         self.assertEqual(1, editdistance.eval('abc', 'aec'))
-
+
+    def test_editdistance_criterion(self):
+        import editdistance
+        self.assertEqual(False, editdistance.eval_criterion('abcb', 'aeca', 1))
+        self.assertEqual(True, editdistance.eval_criterion('abc', 'aec', 1))
+
+    def test_dp_editdistance(self):
+        from editdistance.bycython import eval_dp
+        self.assertEqual(3, eval_dp('bbb', 'a'))
+        self.assertEqual(3, eval_dp('a', 'bbb'))
+
+    def test_dp_vs_default(self):
+        for _ in range(10):
+            import editdistance
+            from editdistance.bycython import eval_dp
+            seq1 = random.choices([0, 1, 2], k=random.randint(10, 50))
+            seq2 = random.choices([0, 1, 2], k=random.randint(10, 50))
+
+            self.assertEqual(editdistance.eval(seq1, seq2), eval_dp(seq1, seq2))
+
 
 if __name__ == '__main__':
     unittest.main()