how fade in a flex box?

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>

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