Unicode and DNA regexes + more benchmarker improvements

Sources/RegexBenchmark/Benchmark.swift

@@ -69,11 +69,12 @@ struct CrossBenchmark {
   /// TODO: Probably better ot have a whole-line vs search anywhere, maybe
   /// accomodate multi-line matching, etc.
   var isWhole: Bool = false
+
+  /// Whether or not to do firstMatch as well or just allMatches
+  var includeFirst: Bool = false
 
   func register(_ runner: inout BenchmarkRunner) {
     let swiftRegex = try! Regex(regex)
-
-    let nsPattern = isWhole ? "^" + regex + "$" : regex
     let nsRegex: NSRegularExpression
     if isWhole {
       nsRegex = try! NSRegularExpression(pattern: "^" + regex + "$")
@@ -95,30 +96,32 @@ struct CrossBenchmark {
           type: .first,
           target: input))
     } else {
-      runner.register(
-        Benchmark(
-          name: baseName + "First",
-          regex: swiftRegex,
-          type: .first,
-          target: input))
       runner.register(
         Benchmark(
           name: baseName + "All",
           regex: swiftRegex,
           type: .allMatches,
           target: input))
-      runner.register(
-        NSBenchmark(
-          name: baseName + "First_NS",
-          regex: nsRegex,
-          type: .first,
-          target: input))
       runner.register(
         NSBenchmark(
           name: baseName + "All_NS",
           regex: nsRegex,
           type: .allMatches,
           target: input))
+      if includeFirst {
+        runner.register(
+          Benchmark(
+            name: baseName + "First",
+            regex: swiftRegex,
+            type: .first,
+            target: input))
+        runner.register(
+          NSBenchmark(
+            name: baseName + "First_NS",
+            regex: nsRegex,
+            type: .first,
+            target: input))
+      }
     }
   }
 }

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/CLI.swift

@@ -2,7 +2,7 @@ import ArgumentParser
 
 @main
 struct Runner: ParsableCommand {
-  @Argument(help: "Names of benchmarks to run")
+  @Argument(help: "Patterns for benchmarks to run")
   var specificBenchmarks: [String] = []
 
   @Flag(help: "Run only once for profiling purposes")
@@ -20,19 +20,30 @@ struct Runner: ParsableCommand {
   @Flag(help: "Should the results be saved")
   var save = false
 
-  @Flag(help: "Compare this result with the latest saved result")
+  @Flag(help: "Compare this result with a saved result")
   var compare = false
 
   @Option(help: "The result file to compare against, if this flag is not set it will compare against the most recent result file")
   var compareFile: String?
 
+  @Flag(help: "Exclude the comparisons to NSRegex")
+  var excludeNs = false
+
   mutating func run() throws {
     var runner = BenchmarkRunner.makeRunner(samples, outputPath)
-
-    // todo: regex based filter 
+
     if !self.specificBenchmarks.isEmpty {
-      runner.suite = runner.suite.filter { b in specificBenchmarks.contains(b.name) }
+      runner.suite = runner.suite.filter { b in
+        specificBenchmarks.contains { pattern in
+          try! Regex(pattern).wholeMatch(in: b.name) != nil
+        }
+      }
     }
+
+    if excludeNs {
+      runner.suite = runner.suite.filter { b in !b.name.contains("NS") }
+    }
+
     switch (profile, debug) {
     case (true, true): print("Cannot run both profile and debug")
     case (true, false): runner.profile()

Sources/RegexBenchmark/Suite/CssRegex.swift

@@ -6,7 +6,7 @@ extension BenchmarkRunner {
     let r = #"--([a-zA-Z0-9_-]+)\s*:\s*(.*?);"#
 
     let css = CrossBenchmark(
-      baseName: "css", regex: r, input: Inputs.swiftOrgCSS)
+      baseName: "Css", regex: r, input: Inputs.swiftOrgCSS)
     css.register(&self)
   }
 }

Sources/RegexBenchmark/Suite/CustomCharacterClasses.swift

@@ -13,37 +13,37 @@ extension BenchmarkRunner {
     let input = Inputs.graphemeBreakData
 
     register(Benchmark(
-      name: "basicCCC",
+      name: "BasicCCC",
       regex: try! Regex(basic),
       type: .allMatches,
       target: input))
 
     register(Benchmark(
-      name: "basicRangeCCC",
+      name: "BasicRangeCCC",
       regex: try! Regex(basicRange),
       type: .allMatches,
       target: input))
 
     register(Benchmark(
-      name: "caseInsensitiveCCC",
+      name: "CaseInsensitiveCCC",
       regex: try! Regex(caseInsensitive),
       type: .allMatches,
       target: input))
 
     register(Benchmark(
-      name: "invertedCCC",
+      name: "InvertedCCC",
       regex: try! Regex(inverted),
       type: .allMatches,
       target: input))
 
     register(Benchmark(
-      name: "subtractionCCC",
+      name: "SubtractionCCC",
       regex: try! Regex(subtraction),
       type: .allMatches,
       target: input))
 
     register(Benchmark(
-      name: "intersectionCCC",
+      name: "IntersectionCCC",
       regex: try! Regex(intersection),
       type: .allMatches,
       target: input))

Sources/RegexBenchmark/Suite/Dna.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/Suite/EmailRegex.swift

@@ -13,22 +13,22 @@ extension BenchmarkRunner {
     let emailWithLookaheads = #"(?=[A-z0-9][A-z0-9@._%+-]{5,253})[A-z0-9._%+-]{1,64}@(?:(?=[A-z0-9-]{1,63}\.)[A-z0-9]+(?:-[A-z0-9]+)*\.){1,8}[A-z]{2,63}"#
 
     let emailRFCValid = CrossBenchmark(
-      baseName: "emailRFC", regex: emailRFC, input: Inputs.validEmails)
+      baseName: "EmailRFC", regex: emailRFC, input: Inputs.validEmails)
 
     let emailRFCInvalid = CrossBenchmark(
-      baseName: "emailRFCNoMatches",
+      baseName: "EmailRFCNoMatches",
       regex: emailRFC,
       input: Inputs.graphemeBreakData
     )
 
     let emailValid = CrossBenchmark(
-      baseName: "emailLookahead",
+      baseName: "EmailLookahead",
       regex: emailWithLookaheads,
       input: Inputs.validEmails
     )
 
     let emailInvalid = CrossBenchmark(
-      baseName: "emailLookaheadNoMatches",
+      baseName: "EmailLookaheadNoMatches",
       regex: emailWithLookaheads,
       input: Inputs.graphemeBreakData
     )

Sources/RegexBenchmark/Suite/GraphemeBreak.swift

@@ -18,7 +18,7 @@ extension BenchmarkRunner {
     let regex = #"HANGUL SYLLABLE [A-Z]+(?:\.\.HANGUL SYLLABLE [A-Z]+)?"#
 
     let benchmark = CrossBenchmark(
-      baseName: "HangulSyllable", regex: regex, input: input)
+      baseName: "HangulSyllable", regex: regex, input: input, includeFirst: true)
     benchmark.register(&self)
   }
 }

Sources/RegexBenchmark/Suite/HtmlRegex.swift

@@ -6,7 +6,7 @@ extension BenchmarkRunner {
     let r = #"<(\w*)\b[^>]*>(.*?)<\/\1>"#
 
     let html = CrossBenchmark(
-      baseName: "html", regex: r, input: Inputs.swiftOrgHTML)
+      baseName: "Html", regex: r, input: Inputs.swiftOrgHTML)
     html.register(&self)
   }
 }

Sources/RegexBenchmark/Suite/NotFound.swift

@@ -6,11 +6,11 @@ extension BenchmarkRunner {
     let input = String(repeating: " ", count: 100_000)
 
     let notFound = CrossBenchmark(
-      baseName: "notFound", regex: "a", input: input)
+      baseName: "NotFound", regex: "a", input: input)
     notFound.register(&self)
 
     let anchoredNotFound = CrossBenchmark(
-      baseName: "notFound", regex: "^ +a", input: input)
+      baseName: "AnchoredNotFound", regex: "^ +a", input: input)
     anchoredNotFound.register(&self)
   }
 }

Sources/RegexBenchmark/Suite/Unicode.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)
+  }
+}

Utils/benchmark-generators/generateFasta.py

@@ -0,0 +1,99 @@
+# DnaFasta.swift was generated with python3 Utils/generateFasta.py 100000
+
+# 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()