In an embodiment, a methodology for automating the generation of a programmable logic device implementation of at least a portion of an integrated circuit is contemplated. The methodology may operate on one or more hardware description language (HDL) files which describe the integrated circuit as an input. Additionally, one or more user-generated control files may be input to the methodology. The methodology may process the one or more HDL files, generating a bitstream to program one or more programmable logic devices to implement the described design. The methodology may include automated modification of the HDL files to prepare them for programmable logic device implementation, automated pad ring generation, automated pin multiplexing, daughter card definition, partitioning, etc.