Integrating isotope with custom post types - the HTML

portfolio-template.php

<!-- Begin filter links -->
<div class="portfolio-filters">

<ul id="filters">
  <li><a href="#" data-filter="*">All</a></li>
	<!-- Begin filter loop -->
	<?php
	// Create an array and assign the projects taxonomy to it
	$args = array( 'taxonomy' => 'skills' );
	// Call the categories from this array
	$categories=get_categories($args);
	// Now, loop through them and...
	foreach ($categories as $category) {

		echo '<li><a href="#" data-filter=".'.$category->category_nicename.'">'.$category->cat_name;
		echo '</a></li>';

	} ?>
	<!-- End filter loop -->
</ul>

</div>
<!-- End filter links -->


<!-- Begin portfolio loop -->
<section class="portfolio">

	<div id="container">

	<?php

	  // The Query
	  $the_query = new WP_Query( 'post_type=portfolio&posts_per_page=-1');

	  // The Loop
	  while ( $the_query->have_posts() ) :
	  	$the_query->the_post(); ?>
	
	  	<article class="<?php echo custom_taxonomies_terms_links(); ?>">

	      <!-- Your Portfolio Loop Content -- Example Below -->
      
        <?php if ( has_post_thumbnail() ) { the_post_thumbnail() } ?>
      
        <?php the_title(); ?>

		  </article>

	<?php endwhile; ?>

	<?php wp_reset_postdata(); ?>

	</div>

</section>
<!-- End portfolio loop -->