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Generate GERBER and Drill files normally
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Upload all files
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Generate BOM CSV with ./bom2csv.xsl
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Use script to replace values in kicad_pcb file with part numbers
python ../macrofab-bom-in-pcbnew-values.py ../kbox.kicad_pcb ../kbox.csv kbox-macrofab.kicad_pcb --substitute ../bom-substitutions.csv
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Upload kicad_pcb file
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Remove DNP parts as well as VIA and graphics (make them do not populate) They should all have the value DNP and be pre-selected.
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Make P1,P2,P3,P6 DNP
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Manually fix inventory parts (need to re-input their value and select inventory)