Ichoran

A Common Format for Worm Tracking Data

Michael Currie (1a), Rex A. Kerr (2), Chee Wai Lee (1b), Jim Hokanson(1c), and Andrew E.X. Brown (3).

Many labs, including ours, have built a wide variety of worm trackers.

	/> using scala 3.6.4

	package examplecontextmacro

	object DoNotUse {
	def __do_not_use__ : Nothing = throw new Exception("Do not use!")
	}

	object MacroImpl {
	import scala.quoted.*

	//> using scala 3.5.0
	//> using dep com.github.ichoran::kse3-basics:0.3.11
	//> using dep com.github.ichoran::kse3-flow:0.3.11

	// Run with scala-cli --power --jmh --jvm=21 ThreadLocalLoom.scala
	// If you change the classes that have to be benchmarked, you may have to rm -r .scala_build


	package threadlocalloom.bench

	// Begin Gist Information
	// Original code by Stefan Zieger (see https://github.com/szeiger/zinc/blob/1d296b2fbeaae1cf14e4c00db0bbc2203f9783a4/internal/zinc-persist/src/main/scala/sbt/internal/inc/consistent/ParallelGzipOutputStream.scala)
	// Modified by Rex Kerr to use Java threads directly rather than Future
	// Probably Apache Commons License? Whatever the original one was is fine.
	// NOT HEAVILY TESTED! (I did verify binary-identical results on one test data file.)
	// End Gist Information


	import java.io.{ ByteArrayOutputStream, FilterOutputStream, OutputStream }
	import java.util.zip.{ CRC32, Deflater, DeflaterOutputStream }

	//> using scala 3.5.0

	// Run with scala-cli --power --jmh --jvm=21 BenchHashVsAnyRef.scala
	// If you change the classes that have to be benchmarked, you may have to rm -r .scala_build


	package bhvar

	import org.openjdk.jmh.annotations._
	import org.openjdk.jmh.infra.Blackhole

	/*
	* Copyright 2020-2024 Typelevel
	*
	* Licensed under the Apache License, Version 2.0 (the "License");
	* you may not use this file except in compliance with the License.
	* You may obtain a copy of the License at
	*
	* http://www.apache.org/licenses/LICENSE-2.0
	*
	* Unless required by applicable law or agreed to in writing, software

	class Simple {
	import scala.util.boundary
	import kse.flow.{given, _}

	def exists[T](xs: Iterable[T], fn: T => Boolean) =
	boundary:
	iFor(xs.iterator): (x, _) =>
	if fn(x) then boundary.break(true)
	false
	}

	package bench

	import scala.language.implicitConversions

	import ichi.bench._

	object Implicits {
	final class ChainingOps[A](private val self: A) extends AnyVal {
	@inline def tap[U](f: A => U): A = { f(self); self }
	@inline def pipe[B](f: A => B): B = f(self)

	def cuml(wt: Array[Double]) = {
	val l = wt.length
	val base = if ((l & (l-1)) == 0) l else java.lang.Integer.highestOneBit(l)*2
	val tree = new Array[Double](base*2)
	System.arraycopy(wt, 0, tree, 0, wt.length)
	var in = 0
	var out = base
	var n = base
	while (in + 1 < out) {
	while (in + 1 < n) {

	// Autogenerated test for collection List with element type String

	package laws

	class Test_Imm_List_Str(numb: Numbers, oper: Ops[String, Option[String]], inst: Instance[String, scala.collection.immutable.List[String]], lln: Int)
	extends StrTest[scala.collection.immutable.List[String], Test_Imm_List_Str](numb, oper, inst, lln) {
	import Test.ComparesTo
	import Test.Logic
	def renumber(numb: Numbers) = new Test_Imm_List_Str(numb, ops, instance, lawLine)
	def reinstance(inst: Instance[String, scala.collection.immutable.List[String]]) = new Test_Imm_List_Str(num, ops, inst, lawLine)