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CSS

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JavaScript

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Babel includes JSX processing.

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HTML 

              
                <div class="wrapper">
	<div class="box-top"></div>
	<div class="box"></div>
</div>

<!--  WHAT DO I EXPECT? 

First start
1. Orange box appears
2. Red box move
3. Orange box disappear
Now the yoyo return and...
4. Do not repeat reversed step 3
5. Move(reversed) red box
6. Do not repeat reversed step 1
And now the loop starts again
7. go back to 1st step...
-->
!

CSS 

              
                .wrapper {
	max-width: 500px;
	height: 500px;
	margin: 0 auto;
	padding: 100px;
}

.box {
	position: relative;
	width: 150px;
	height: 150px;
	background: red;
}
.box-top {
	width: 50px;
	height: 50px;
	background: orange;
}
!

JS 

              
                const mainTL = gsap.timeline({
	onRepeat: TL_REPEAT,
	yoyo: true,
	repeat: -1,
	repeatDelay: 1
});

if (mainTL.progress() !== 1) {
	// i would like it to skip this on yoyo return
	mainTL.add(MOVE_TOP_BOX_ON_BEGINING());
}

// This should always run
mainTL.add(MOVE_MAIN_BOX());

if (mainTL.progress() === 0) {
	// i would like it to skip this on yoyo begining
	mainTL.add(HIDE_TOP_BOX_ON_COMEBACK());
}

// This should trigger only when timeline starts (yoyo begin) but when timeline goes back it should skip this step and turn around again
function MOVE_TOP_BOX_ON_BEGINING() {
	const top_box = document.querySelector(".box-top");

	const tl = gsap.timeline();
	tl.fromTo(
		top_box,
		{ opacity: 0, x: "-=50" },
		{
			x: 0,
			opacity: 1
		}
	);

	return tl;
}

// HIDE TOP BOX WHEN TIMELINE FINISHED (with repeat&yoyo - progres = 0)
function HIDE_TOP_BOX_ON_COMEBACK() {
	const boxTop = document.querySelector(".box-top");

	const tl = gsap.timeline();
	tl.to(boxTop, {
		y: "+=30",
		opacity: 0,
		duration: 1
	});

	return tl;
}

function MOVE_MAIN_BOX() {
	const box = document.querySelector(".box");

	const tl = gsap.timeline();
	tl.to(box, {
		y: "+=30",
		duration: 1
	});

	return tl;
}

function TL_REPEAT() {
	// const isTimelineGoingBack = mainTL.progress() === 1;
	// if (isTimelineGoingBack) {
	// 	console.log(`🔙 Timeline is going back`);
	// 	HIDE_TOP_BOX_ON_COMEBACK();
	// } else {
	// 	console.log(`🛫 Timeline begin`);
	// }
}
!
999px

Console