how fade in a flex box?

How do I get a flex box to not be part of the page until I fade it in? I used to do this with 'display: 0;' and then use jQuery .fadeIn(). But now if I set display to 0, when I fade it in, of course I lose the flex-iness of the box. If I use jQuery to set display to flex, then it will just appear, not fade in.

HTML

<div class="" id="popupContainer">
    <div class="flex-item-popup" id="popup">
		<div class="close"><i class="fa fa-2x fa-times-circle"></i></div>
		<h2></h2>
		<div class='text'></div>
		<div class="videos"></div>
		<div class="flex-container images"></div>
	</div>
</div>

CSS

#popupContainer {
  	position: absolute;
  	left: 0;
  	top: 0;
  	width: 100%;
  	height: 100%;
	display:flex;
    flex-direction: row;
    flex-wrap: wrap;
    justify-content: center;
    align-content: flex-start;
    align-items: center;
    z-index: 15;
}

jQuery

$(document).ready(function() {
    //???
});

It seems a bit odd, but what you can do is in the css, set it to display: none. Then the trick is to set the display to flex in your jquery and then hide it again, then fadeIn:

CSS:

#popupContainer {
    /* ... */

    display:none;
    flex-direction: row;
    flex-wrap: wrap;

    /* ... */
}

JS:

$("#popupContainer")
    .css("display", "flex")
    .hide()
    .fadeIn();

This works because fadeIn() will set the item back to its previous non-hidden display value. So setting flex and re-hiding it will set this "default" for it to be set back to.

http://jsfiddle.net/z2kxyjcq/1/

$("#popupContainer")
    .css("display", "flex")
    .hide()
    .fadeIn(2000);

#popupContainer {
    position: absolute;
    left: 0;
    top: 0;
    width: 100%;
    height: 100%;
    display:none;
    flex-direction: row;
    flex-wrap: wrap;
    justify-content: center;
    align-content: flex-start;
    align-items: center;
    z-index: 15;
    background-color: red;
}
#popupContainer *{
    border: 1px solid blue;
background-color: white;    
}

<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
<div class="" id="popupContainer">
<div class="flex-item-popup" id="popup">
    <div class="close"><i class="fa fa-2x fa-times-circle">1</i></div>
    <h2>2</h2>
    <div class='text'>a</div>
    <div class="videos">b</div>
    <div class="flex-container images">c</div>
</div>

Easiest and most clean way (if you can edit DOM) is to wrap the element, and fade the wrapper while having div with flex inside

<div class="popup" id="popupContainer">
  <div class="popup__flexbox">
    <div class="popup__flex-item" id="popup">
    <div class="popup__close">
       <i class="fa fa-2x fa-times-circle"></i>
    </div>
    <h2></h2>
    <div class='popup__text'></div>
    <div class="popup__videos"></div>
    <div class="popup__images"></div>
  </div>
</div>

css:

.popup {
  display: none;
}

.popup__flexbox {
  display: flex;
}

js:

$("#popupContainer").fadeIn();

You can set the opacity as 0 and animate:

$('#popupContainer').animate({
    opacity: 1
}, 'fast');

var flex = $('#flex');

console.log(flex.css('display'));

flex.hide();

flex.velocity('fadeIn', {duration: 100, display: 'flex'});

setTimeout(function(){
  console.log(flex.css('display'));
 }, 100);

#flex{
  display: 'flex'
}

<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/velocity/1.5.0/velocity.min.js"></script>

<div id="flex"></div>