Set custom shipping rates programmatically in Woocommerce 3

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As this is a filter and as the data is cached, you can’t get any output with print_r().

The correct way to make it work is the following:

add_filter( 'woocommerce_package_rates', 'custom_shipping_costs', 20, 2 );
function custom_shipping_costs( $rates, $package ) {
    // New shipping cost (can be calculated)
    $new_cost = 1000;
    $tax_rate = 0.2;

    foreach( $rates as $rate_key => $rate ){
        // Excluding free shipping methods
        if( $rate->method_id != 'free_shipping'){

            // Set rate cost
            $rates[$rate_key]->cost = $new_cost;

            // Set taxes rate cost (if enabled)
            $taxes = array();
            foreach ($rates[$rate_key]->taxes as $key => $tax){
                if( $rates[$rate_key]->taxes[$key] > 0 )
                    $taxes[$key] = $new_cost * $tax_rate;
            }
            $rates[$rate_key]->taxes = $taxes;

        }
    }
    return $rates;
}

Code goes in function.php file of your active child theme (active theme).

Tested and works.

Sometimes, you should may be need to refresh shipping methods:
1) Empty cart first.
2) Go to shipping Zones settings, then disable/save and re-enable/save the related shipping methods.

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