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According to Section 6.1.2 of an official ECP5 manual, only the on-chip oscillator MCLK is available as the SPI clock when in Master SPI mode by default. To use any user clock as the SPI clock, a USRMCLK Instance must be instantiated and there is no need to request for the clock from Ball U3. Requesting for such clock will lead to an error as reported by @xobs on the nextpnr repo.
Therefore, I would like to suggest modification on memory.py such that there is an option to add the SPI flash resources to a platform (not only ECP5) without the clock. Although this modification has been used to successfully build and flash a bitstream on an ECP5 board (the example was an SPI reader module on my nmigen-stdio fork), I cannot deny that there is room for improvement on my code for this pull request.
I look forward to seeing further comments, thanks.
See also: my pull request on nmigen-stdio for a SPI controller.
Note that sometimes such primitives combine many unrelated signals (and you can always count on Xilinx for doing that, see STARTUPE3), so this needs some thought. Maybe a central place where all those primitives are managed and where the user can access them (e.g. connect additional signals, modify their parameters) if required.