Add unicode and dna benchmarks

Author: rctcwyvrn

Sources/RegexBenchmark/BenchmarkRegistration.swift

@@ -16,6 +16,8 @@ extension BenchmarkRunner {
     benchmark.addHTML()
     benchmark.addEmail()
     benchmark.addCustomCharacterClasses()
+    benchmark.addDna()
+    benchmark.addUnicode()
     // -- end of registrations --
     return benchmark
   }

Sources/RegexBenchmark/Inputs/DnaFASTA.swift

@@ -0,0 +1,25 @@
+import _StringProcessing
+
+extension BenchmarkRunner {
+  mutating func addDna() {
+    // regex-redux from the benchmarks game
+    // https://benchmarksgame-team.pages.debian.net/benchmarksgame/description/regexredux.html#regexredux
+    let dna = "agg[act]taaa|ttta[agt]cct"
+    let ends = "aND|caN|Ha[DS]|WaS"
+    
+    let dnaMatching = CrossBenchmark(
+      baseName: "DnaMatch",
+      regex: dna,
+      input: Inputs.dnaFASTA,
+      includeFirst: true)
+    
+    let sequenceEnds = CrossBenchmark(
+      baseName: "DnaEndsMatch",
+      regex: ends,
+      input: Inputs.dnaFASTA,
+      includeFirst: true)
+    
+    dnaMatching.register(&self)
+    sequenceEnds.register(&self)
+  }
+}

Sources/RegexBenchmark/Inputs/TaggedUnicode.swift

@@ -0,0 +1,24 @@
+import _StringProcessing
+
+extension BenchmarkRunner {
+  mutating func addUnicode() {
+    // tagged unicode: unicode characters surrounded by html tags
+    // use the same html regex, uses backreference + reluctant quantification
+    let tags = #"<(\w*)\b[^>]*>(.*?)<\/\1>"#
+    let taggedEmojis = CrossBenchmark(
+      baseName: "TaggedEmojis",
+      regex: tags,
+      input: Inputs.taggedEmojis)
+
+    // Now actually matching emojis
+    let emoji = #"(😃|😀|😳|😲|😦|😊|🙊|😘|😏|😳|😒){2,5}"#
+    
+    let emojiRegex = CrossBenchmark(
+      baseName: "EmojiRegex",
+      regex: emoji,
+      input: Inputs.taggedEmojis)
+
+    taggedEmojis.register(&self)
+    emojiRegex.register(&self)
+  }
+}

Sources/RegexBenchmark/Suite/Dna.swift

@@ -0,0 +1,97 @@
+# The Computer Language Benchmarks Game
+# https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
+#
+# modified by Ian Osgood
+# modified again by Heinrich Acker
+# modified by Justin Peel
+# 2to3
+
+"""Copyright © 2004-2008 Brent Fulgham, 2005-2022 Isaac Gouy
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name "The Computer Language Benchmarks Game" nor the name "The Benchmarks Game" nor the name "The Computer Language Shootout Benchmarks" nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."""
+
+import sys, bisect
+
+alu = (
+   'GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG'
+   'GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA'
+   'CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT'
+   'ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA'
+   'GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG'
+   'AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC'
+   'AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA')
+
+iub = list(zip('acgtBDHKMNRSVWY', [0.27, 0.12, 0.12, 0.27] + [0.02]*11))
+
+homosapiens = [
+    ('a', 0.3029549426680),
+    ('c', 0.1979883004921),
+    ('g', 0.1975473066391),
+    ('t', 0.3015094502008),
+]
+
+
+def genRandom(ia = 3877, ic = 29573, im = 139968):
+    seed = 42
+    imf = float(im)
+    while 1:
+        seed = (seed * ia + ic) % im
+        yield seed / imf
+
+Random = genRandom()
+
+def makeCumulative(table):
+    P = []
+    C = []
+    prob = 0.
+    for char, p in table:
+        prob += p
+        P += [prob]
+        C += [char]
+    return (P, C)
+
+def repeatFasta(src, n):
+    width = 60
+    r = len(src)
+    s = src + src + src[:n % r]
+    for j in range(n // width):
+        i = j*width % r
+        print(s[i:i+width])
+    if n % width:
+        print(s[-(n % width):])
+
+def randomFasta(table, n):
+    width = 60
+    r = range(width)
+    gR = Random.__next__
+    bb = bisect.bisect
+    jn = ''.join
+    probs, chars = makeCumulative(table)
+    for j in range(n // width):
+        x = jn([chars[bb(probs, gR())] for i in r])
+        print(x)
+    if n % width:
+        print(jn([chars[bb(probs, gR())] for i in range(n % width)]))
+
+def main():
+    n = int(sys.argv[1])
+
+    print('>ONE Homo sapiens alu')
+    repeatFasta(alu, n*2)
+
+    print('>TWO IUB ambiguity codes')
+    randomFasta(iub, n*3)
+
+    print('>THREE Homo sapiens frequency')
+    randomFasta(homosapiens, n*5)
+
+main()

Sources/RegexBenchmark/Suite/Unicode.swift

@@ -0,0 +1,24 @@
+# Generates lines of junk unicode wrapped in html tags
+import random
+
+# devanagari
+#low = 0x0900
+#high = 0x097F
+
+# emojis only
+low = 0x1F600
+high = 0x1F64F
+
+numLines = 1000
+
+start = "<data> "
+end = " </data>"
+minLine = 10
+maxLine = 100
+
+def get_random(i):
+   return "".join([chr(random.randint(low, high)) for _ in range(i)])
+   
+lines = [start + get_random(random.randint(minLine, maxLine)) + end for _ in range(numLines)]
+
+print("\n".join(lines))