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Warnings from CustomGroup and CustomField create functions
Both CustomGroup and CustomField seem to treat create as a method only for creating new entities. Although updates do work, a few places in the code expect that you have included some value in the params that you don't intend to update.
For example:
$params = ['id' => 1, 'is_active' => 0];
civicrm_api3('CustomField', 'create', $params);Will produce a warning (from a test I wrote for this):
Failure in api call for CustomGroup create: Undefined index: extends
#0 /repos/civicrm-core/CRM/Core/BAO/CustomGroup.php(64): PHPUnit_Util_ErrorHandler::handleError(8, 'Undefined index...', '/repos/civicrm-...', 64, Array)