Support SPI flash chips for CIRCUITPY, using non-DMA SPI for now.

23 files changed, 355 insertions, 206 deletions

diff --git a/ports/atmel-samd/Makefile b/ports/atmel-samd/Makefile
index 3ac4cde9a..486df28c2 100644
--- a/ports/atmel-samd/Makefile
+++ b/ports/atmel-samd/Makefile
@@ -218,6 +218,7 @@ SRC_C = \
 	mphalport.c \
 	reset.c \
 	$(CHIP_FAMILY)_peripherals.c \
+	peripherals.c \
 	$(CHIP_FAMILY)_pins.c \
 	tick.c \
 	usb.c \
@@ -260,6 +261,7 @@ SRC_COMMON_HAL = \
 	microcontroller/Processor.c \
 	neopixel_write/__init__.c \
 	os/__init__.c \
+	storage/__init__.c \
 	time/__init__.c \
 #	analogio/__init__.c \
 	analogio/AnalogIn.c \
@@ -276,7 +278,6 @@ SRC_COMMON_HAL = \
 	pulseio/PulseIn.c \
 	pulseio/PulseOut.c \
 	pulseio/PWMOut.c \
-	storage/__init__.c \
 	touchio/__init__.c \
 	touchio/TouchIn.c \
 	usb_hid/__init__.c \
diff --git a/ports/atmel-samd/asf4 b/ports/atmel-samd/asf4
-Subproject 72f76894ba08c9de2ec3ae231fb71daaf3eafb1
+Subproject 0efc3407dd97ef617a5655674a3516693897a96
diff --git a/ports/atmel-samd/boards/feather_m0_express/mpconfigboard.h b/ports/atmel-samd/boards/feather_m0_express/mpconfigboard.h
index 83c681061..448c6c52b 100644
--- a/ports/atmel-samd/boards/feather_m0_express/mpconfigboard.h
+++ b/ports/atmel-samd/boards/feather_m0_express/mpconfigboard.h
@@ -3,25 +3,35 @@
 
 #define MICROPY_HW_NEOPIXEL (&pin_PA06)
 
-// Salae reads 12mhz which is the limit even though we set it to the safer 8mhz.
+// Clock rates are off: Salae reads 12MHz which is the limit even though we set it to the safer 8MHz.
 #define SPI_FLASH_BAUDRATE  (8000000)
 
-#define SPI_FLASH_MUX_SETTING SPI_SIGNAL_MUX_SETTING_C
-#define SPI_FLASH_PAD0_PINMUX PINMUX_PA08D_SERCOM2_PAD0 // MOSI
-// Use default pinmux for the chip select since we manage it ourselves.
-#define SPI_FLASH_PAD1_PINMUX PINMUX_PA09D_SERCOM2_PAD1 // SCK
-#define SPI_FLASH_PAD2_PINMUX PINMUX_PA14C_SERCOM2_PAD2 // MISO
-#define SPI_FLASH_PAD3_PINMUX PINMUX_UNUSED // SCK
-#define SPI_FLASH_SERCOM      SERCOM2
-
-#define SPI_FLASH_CS          PIN_PA13
-
-#define MICROPY_PORT_A        (PORT_PA06 | PORT_PA08 | PORT_PA09 | PORT_PA14 | PORT_PA13 | PORT_PA14 | PORT_PA24 | PORT_PA25)
+#define SPI_FLASH_MOSI_PIN          PIN_PA08
+#define SPI_FLASH_MISO_PIN          PIN_PA14
+#define SPI_FLASH_SCK_PIN           PIN_PA09
+#define SPI_FLASH_CS_PIN            PIN_PA13
+#define SPI_FLASH_MOSI_PIN_FUNCTION PINMUX_PA08D_SERCOM2_PAD0
+#define SPI_FLASH_MISO_PIN_FUNCTION PINMUX_PA14C_SERCOM2_PAD2
+#define SPI_FLASH_SCK_PIN_FUNCTION  PINMUX_PA09D_SERCOM2_PAD1
+#define SPI_FLASH_SERCOM            SERCOM2
+#define SPI_FLASH_SERCOM_INDEX      2
+#define SPI_FLASH_MOSI_PAD          0
+#define SPI_FLASH_MISO_PAD          2
+#define SPI_FLASH_SCK_PAD           1
+// <o> Transmit Data Pinout
+// <0x0=>PAD[0,1]_DO_SCK
+// <0x1=>PAD[2,3]_DO_SCK
+// <0x2=>PAD[3,1]_DO_SCK
+// <0x3=>PAD[0,3]_DO_SCK
+#define SPI_FLASH_DOPO              0
+#define SPI_FLASH_DIPO              2   // same as MISO pad
+
+// These are pins not to reset.
+#define MICROPY_PORT_A        (PORT_PA06 | PORT_PA08 | PORT_PA09 | PORT_PA13 | PORT_PA14 | PORT_PA24 | PORT_PA25)
 #define MICROPY_PORT_B        ( 0 )
 #define MICROPY_PORT_C        ( 0 )
 
-#include "internal_flash.h"
-//#include "spi_flash.h"
+#include "spi_flash.h"
 
 // If you change this, then make sure to update the linker scripts as well to
 // make sure you don't overwrite code.
diff --git a/ports/atmel-samd/boards/feather_m0_express/mpconfigboard.mk b/ports/atmel-samd/boards/feather_m0_express/mpconfigboard.mk
index 820ec4eca..5e3a97493 100644
--- a/ports/atmel-samd/boards/feather_m0_express/mpconfigboard.mk
+++ b/ports/atmel-samd/boards/feather_m0_express/mpconfigboard.mk
@@ -4,8 +4,7 @@ USB_PID = 0x8023
 USB_PRODUCT = "Feather M0 Express"
 USB_MANUFACTURER = "Adafruit Industries LLC"
 
-#SPI_FLASH_FILESYSTEM = 1
-INTERNAL_FLASH_FILESYSTEM = 1
+SPI_FLASH_FILESYSTEM = 1
 
 CHIP_VARIANT = SAMD21G18A
 CHIP_FAMILY = samd21
diff --git a/ports/atmel-samd/boards/metro_m0_express/mpconfigboard.h b/ports/atmel-samd/boards/metro_m0_express/mpconfigboard.h
index e3b67de4b..023beb688 100644
--- a/ports/atmel-samd/boards/metro_m0_express/mpconfigboard.h
+++ b/ports/atmel-samd/boards/metro_m0_express/mpconfigboard.h
@@ -1,5 +1,3 @@
-#define USB_REPL
-
 #define MICROPY_HW_BOARD_NAME "Adafruit Metro M0 Express"
 #define MICROPY_HW_MCU_NAME "samd21g18"
 
@@ -8,24 +6,35 @@
 
 #define MICROPY_HW_NEOPIXEL (&pin_PA30)
 
-// Salae reads 12mhz which is the limit even though we set it to the safer 8mhz.
+// Clock rates are off: Salae reads 12MHz which is the limit even though we set it to the safer 8MHz.
 #define SPI_FLASH_BAUDRATE  (8000000)
 
-#define SPI_FLASH_MUX_SETTING SPI_SIGNAL_MUX_SETTING_F
-#define SPI_FLASH_PAD0_PINMUX PINMUX_UNUSED // CS
-// Use default pinmux for the chip select since we manage it ourselves.
-#define SPI_FLASH_PAD1_PINMUX PINMUX_PB03D_SERCOM5_PAD1 // MISO
-#define SPI_FLASH_PAD2_PINMUX PINMUX_PB22D_SERCOM5_PAD2 // MOSI
-#define SPI_FLASH_PAD3_PINMUX PINMUX_PB23D_SERCOM5_PAD3 // SCK
-#define SPI_FLASH_CS          PIN_PA13
-#define SPI_FLASH_SERCOM      SERCOM5
-
+#define SPI_FLASH_MOSI_PIN          PIN_PB22
+#define SPI_FLASH_MISO_PIN          PIN_PB03
+#define SPI_FLASH_SCK_PIN           PIN_PB23
+#define SPI_FLASH_CS_PIN            PIN_PA13
+#define SPI_FLASH_MOSI_PIN_FUNCTION PINMUX_PB22D_SERCOM5_PAD2
+#define SPI_FLASH_MISO_PIN_FUNCTION PINMUX_PB03D_SERCOM5_PAD1
+#define SPI_FLASH_SCK_PIN_FUNCTION  PINMUX_PB23D_SERCOM5_PAD3
+#define SPI_FLASH_SERCOM            SERCOM5
+#define SPI_FLASH_SERCOM_INDEX      5
+#define SPI_FLASH_MOSI_PAD          2
+#define SPI_FLASH_MISO_PAD          1
+#define SPI_FLASH_SCK_PAD           3
+// <o> Transmit Data Pinout
+// <0x0=>PAD[0,1]_DO_SCK
+// <0x1=>PAD[2,3]_DO_SCK
+// <0x2=>PAD[3,1]_DO_SCK
+// <0x3=>PAD[0,3]_DO_SCK
+#define SPI_FLASH_DOPO              1
+#define SPI_FLASH_DIPO              1   // same as MISO pad
+
+// These are pins not to reset.
 #define MICROPY_PORT_A        (PORT_PA13 |PORT_PA24 | PORT_PA25 | PORT_PA27 | PORT_PA30 | PORT_PA31)
 #define MICROPY_PORT_B        (PORT_PB03 | PORT_PB22 | PORT_PB23)
 #define MICROPY_PORT_C        (0)
 
-#include "internal_flash.h"
-//#include "spi_flash.h"
+#include "spi_flash.h"
 
 // If you change this, then make sure to update the linker scripts as well to
 // make sure you don't overwrite code.
diff --git a/ports/atmel-samd/boards/metro_m0_express/mpconfigboard.mk b/ports/atmel-samd/boards/metro_m0_express/mpconfigboard.mk
index 7d63321af..d624b8191 100644
--- a/ports/atmel-samd/boards/metro_m0_express/mpconfigboard.mk
+++ b/ports/atmel-samd/boards/metro_m0_express/mpconfigboard.mk
@@ -4,8 +4,7 @@ USB_PID = 0x8014
 USB_PRODUCT = "Metro M0 Express"
 USB_MANUFACTURER = "Adafruit Industries LLC"
 
-#SPI_FLASH_FILESYSTEM = 1
-INTERNAL_FLASH_FILESYSTEM = 1
+SPI_FLASH_FILESYSTEM = 1
 
 CHIP_VARIANT = SAMD21G18A
 CHIP_FAMILY = samd21
diff --git a/ports/atmel-samd/boards/metro_m0_express/pins.c b/ports/atmel-samd/boards/metro_m0_express/pins.c
index bafd0bc9f..58510faab 100644
--- a/ports/atmel-samd/boards/metro_m0_express/pins.c
+++ b/ports/atmel-samd/boards/metro_m0_express/pins.c
@@ -29,6 +29,5 @@ STATIC const mp_rom_map_elem_t board_global_dict_table[] = {
     { MP_ROM_QSTR(MP_QSTR_SCK),  MP_ROM_PTR(&pin_PB11) },
     { MP_ROM_QSTR(MP_QSTR_MOSI), MP_ROM_PTR(&pin_PB10) },
     { MP_ROM_QSTR(MP_QSTR_MISO), MP_ROM_PTR(&pin_PA12) },
-    { MP_ROM_QSTR(MP_QSTR_FLASH_CS),   MP_ROM_PTR(&pin_PA13) },
 };
 MP_DEFINE_CONST_DICT(board_module_globals, board_global_dict_table);
diff --git a/ports/atmel-samd/boards/metro_m4_express/mpconfigboard.h b/ports/atmel-samd/boards/metro_m4_express/mpconfigboard.h
index 34a681607..1af18ecbc 100644
--- a/ports/atmel-samd/boards/metro_m4_express/mpconfigboard.h
+++ b/ports/atmel-samd/boards/metro_m4_express/mpconfigboard.h
@@ -8,29 +8,46 @@
 
 #define MICROPY_HW_NEOPIXEL (&pin_PB17)
 
-#define SPI_FLASH_BAUDRATE  (1000000)
-
-// Rev F
-#define SPI_FLASH_MUX_SETTING SPI_SIGNAL_MUX_SETTING_F
-#define SPI_FLASH_PAD0_PINMUX PINMUX_PB08 // MOSI
-// Use default pinmux for the chip select since we manage it ourselves.
-#define SPI_FLASH_PAD1_PINMUX PINMUX_PB09 // SCK
-#define SPI_FLASH_PAD2_PINMUX PINMUX_DEFAULT // CS
-#define SPI_FLASH_PAD3_PINMUX PINMUX_PB11 // MISO
-#define SPI_FLASH_CS          PIN_PB10
-#define SPI_FLASH_SERCOM      SERCOM5
-
+#define SPI_FLASH_BAUDRATE  (8000000)
+
+// Rev B: single channel SPI
+// Rev C will be QSPI
+#define SPI_FLASH_MOSI_PIN          PIN_PB08
+#define SPI_FLASH_MISO_PIN          PIN_PB11
+#define SPI_FLASH_SCK_PIN           PIN_PB09
+#define SPI_FLASH_CS_PIN            PIN_PB10
+#define SPI_FLASH_MOSI_PIN_FUNCTION PINMUX_PB08D_SERCOM4_PAD0
+#define SPI_FLASH_MISO_PIN_FUNCTION PINMUX_PB11D_SERCOM4_PAD3
+#define SPI_FLASH_SCK_PIN_FUNCTION  PINMUX_PB09D_SERCOM4_PAD1
+#define SPI_FLASH_SERCOM            SERCOM4
+#define SPI_FLASH_SERCOM_INDEX      4
+#define SPI_FLASH_MOSI_PAD          0
+#define SPI_FLASH_MISO_PAD          3
+#define SPI_FLASH_SCK_PAD           1
+// <o> Transmit Data Pinout
+// <0x0=>PAD[0,1]_DO_SCK
+// <0x1=>PAD[2,3]_DO_SCK
+// <0x2=>PAD[3,1]_DO_SCK
+// <0x3=>PAD[0,3]_DO_SCK
+#define SPI_FLASH_DOPO              0
+#define SPI_FLASH_DIPO              3   // same as MISO pad
+
+// These are pins not to reset.
 #define MICROPY_PORT_A        (PORT_PA27)
-#define MICROPY_PORT_B        (PORT_PB06 | PORT_PB08 | PORT_PB09 | PORT_PB11 | PORT_PB17)
+#define MICROPY_PORT_B        (PORT_PB06 | PORT_PB08 | PORT_PB09 | PORT_PB10 | PORT_PB11 | PORT_PB17)
 #define MICROPY_PORT_C        (0)
 #define MICROPY_PORT_D        (0)
 
 #define AUTORESET_DELAY_MS 500
 
-#include "internal_flash.h"
+#include "spi_flash.h"
 
 // If you change this, then make sure to update the linker scripts as well to
-// make sure you don't overwrite code.
+// make sure you don't overwrite code
+// #define CIRCUITPY_INTERNAL_NVM_SIZE 256
 #define CIRCUITPY_INTERNAL_NVM_SIZE 0
 
-#define BOARD_FLASH_SIZE (FLASH_SIZE - 0x4000)
+#define BOARD_FLASH_SIZE (FLASH_SIZE - 0x4000 - CIRCUITPY_INTERNAL_NVM_SIZE)
+
+#include "flash_S25FL216K.h"
+#include "flash_GD25Q16C.h"
diff --git a/ports/atmel-samd/boards/metro_m4_express/mpconfigboard.mk b/ports/atmel-samd/boards/metro_m4_express/mpconfigboard.mk
index 194116545..0369a7dd2 100644
--- a/ports/atmel-samd/boards/metro_m4_express/mpconfigboard.mk
+++ b/ports/atmel-samd/boards/metro_m4_express/mpconfigboard.mk
@@ -4,8 +4,7 @@ USB_PID = 0x8021
 USB_PRODUCT = "Metro M4 Express"
 USB_MANUFACTURER = "Adafruit Industries LLC"
 
-#SPI_FLASH_FILESYSTEM = 1
-INTERNAL_FLASH_FILESYSTEM = 1
+SPI_FLASH_FILESYSTEM = 1
 
 CHIP_VARIANT = SAMD51J19A
 CHIP_FAMILY = samd51
diff --git a/ports/atmel-samd/common-hal/busio/I2C.c b/ports/atmel-samd/common-hal/busio/I2C.c
index 31b5767e7..4182c8651 100644
--- a/ports/atmel-samd/common-hal/busio/I2C.c
+++ b/ports/atmel-samd/common-hal/busio/I2C.c
@@ -72,7 +72,7 @@ void common_hal_busio_i2c_construct(busio_i2c_obj_t *self,
 
 
     // Set up I2C clocks on sercom.
-    samd_peripheral_sercom_clock_init(sercom, sercom_index);
+    samd_peripherals_sercom_clock_init(sercom, sercom_index);
 
     if (i2c_m_sync_init(&self->i2c_desc, sercom) != ERR_NONE) {
             mp_raise_OSError(MP_EIO);
diff --git a/ports/atmel-samd/common-hal/busio/SPI.c b/ports/atmel-samd/common-hal/busio/SPI.c
index 21fed5d12..cb6a165de 100644
--- a/ports/atmel-samd/common-hal/busio/SPI.c
+++ b/ports/atmel-samd/common-hal/busio/SPI.c
@@ -37,17 +37,7 @@
 
 #include "peripherals.h"
 #include "pins.h"
-#include "shared_dma.h"
-
-// Convert frequency to clock-speed-dependent value. Return 0 if out of range.
-static uint8_t baudrate_to_baud_reg_value(const uint32_t baudrate) {
-    uint32_t baud_reg_value = (uint32_t) (((float) PROTOTYPE_SERCOM_SPI_M_SYNC_CLOCK_FREQUENCY /
-                                           (2 * baudrate)) + 0.5f);
-    if (baud_reg_value > 0xff) {
-        return 0;
-    }
-    return (uint8_t) baud_reg_value;
-}
+//#include "shared_dma.h"
 
 void common_hal_busio_spi_construct(busio_spi_obj_t *self,
         const mcu_pin_obj_t * clock, const mcu_pin_obj_t * mosi,
@@ -78,7 +68,7 @@ void common_hal_busio_spi_construct(busio_spi_obj_t *self,
         }
         clock_pinmux = PINMUX(clock->pin, (i == 0) ? MUX_C : MUX_D);
         clock_pad = clock->sercom[i].pad;
-        if (!samd_peripheral_valid_spi_clock_pad(clock_pad)) {
+        if (!samd_peripherals_valid_spi_clock_pad(clock_pad)) {
             continue;
         }
         for (int j = 0; j < NUM_SERCOMS_PER_PIN; j++) {
@@ -86,7 +76,7 @@ void common_hal_busio_spi_construct(busio_spi_obj_t *self,
                 if(potential_sercom == mosi->sercom[j].sercom) {
                     mosi_pinmux = PINMUX(mosi->pin, (j == 0) ? MUX_C : MUX_D);
                     mosi_pad = mosi->sercom[j].pad;
-                    dopo = samd_peripheral_get_spi_dopo(clock_pad, mosi_pad);
+                    dopo = samd_peripherals_get_spi_dopo(clock_pad, mosi_pad);
                     if (dopo > 0x3) {
                         continue;  // pad combination not possible
                     }
@@ -121,7 +111,7 @@ void common_hal_busio_spi_construct(busio_spi_obj_t *self,
     }
 
     // Set up SPI clocks on SERCOM.
-    samd_peripheral_sercom_clock_init(sercom, sercom_index);
+    samd_peripherals_sercom_clock_init(sercom, sercom_index);
     
     if (spi_m_sync_init(&self->spi_desc, sercom) != ERR_NONE) {
         mp_raise_OSError(MP_EIO);
@@ -132,7 +122,7 @@ void common_hal_busio_spi_construct(busio_spi_obj_t *self,
 
     // Always start at 250khz which is what SD cards need. They are sensitive to
     // SPI bus noise before they are put into SPI mode.
-    uint8_t baud_value = baudrate_to_baud_reg_value(250000);
+    uint8_t baud_value = samd_peripherals_baudrate_to_baud_reg_value(250000);
     if (baud_value == 0) {
         mp_raise_RuntimeError("SPI initial baudrate out of range.");
     }
@@ -142,6 +132,7 @@ void common_hal_busio_spi_construct(busio_spi_obj_t *self,
         mp_raise_OSError(MP_EIO);
     }
         
+    gpio_set_pin_direction(clock->pin, GPIO_DIRECTION_OUT);
     gpio_set_pin_pull_mode(clock->pin, GPIO_PULL_OFF);
     gpio_set_pin_function(clock->pin, clock_pinmux);
     claim_pin(clock);
@@ -150,6 +141,7 @@ void common_hal_busio_spi_construct(busio_spi_obj_t *self,
     if (mosi_none) {
         self->MOSI_pin = NO_PIN;
     } else {
+        gpio_set_pin_direction(mosi->pin, GPIO_DIRECTION_OUT);
         gpio_set_pin_pull_mode(mosi->pin, GPIO_PULL_OFF);
         gpio_set_pin_function(mosi->pin, mosi_pinmux);
         self->MOSI_pin = mosi->pin;
@@ -159,6 +151,7 @@ void common_hal_busio_spi_construct(busio_spi_obj_t *self,
     if (miso_none) {
         self->MISO_pin = NO_PIN;
     } else {
+        gpio_set_pin_direction(miso->pin, GPIO_DIRECTION_IN);
         gpio_set_pin_pull_mode(miso->pin, GPIO_PULL_OFF);
         gpio_set_pin_function(miso->pin, miso_pinmux);
         self->MISO_pin = miso->pin;
@@ -186,7 +179,7 @@ void common_hal_busio_spi_deinit(busio_spi_obj_t *self) {
 
 bool common_hal_busio_spi_configure(busio_spi_obj_t *self,
         uint32_t baudrate, uint8_t polarity, uint8_t phase, uint8_t bits) {
-    uint8_t baud_reg_value = baudrate_to_baud_reg_value(baudrate);
+    uint8_t baud_reg_value = samd_peripherals_baudrate_to_baud_reg_value(baudrate);
     if (baud_reg_value == 0) {
         mp_raise_ValueError("baudrate out of range");
     }
@@ -248,7 +241,7 @@ bool common_hal_busio_spi_write(busio_spi_obj_t *self,
         spi_m_sync_get_io_descriptor(&self->spi_desc, &spi_io);
         status = spi_io->write(spi_io, data, len);
 //    }
-        return status > 0; // Status is number of chars read or an error code < 0.
+        return status >= 0; // Status is number of chars read or an error code < 0.
 }
 
 bool common_hal_busio_spi_read(busio_spi_obj_t *self,
@@ -267,5 +260,5 @@ bool common_hal_busio_spi_read(busio_spi_obj_t *self,
 
         status = spi_io->read(spi_io, data, len);
 //    }
-        return status > 0; // Status is number of chars read or an error code < 0.
+        return status >= 0; // Status is number of chars read or an error code < 0.
 }
diff --git a/ports/atmel-samd/common-hal/storage/__init__.c b/ports/atmel-samd/common-hal/storage/__init__.c
index 184184b8b..c4cb83142 100644
--- a/ports/atmel-samd/common-hal/storage/__init__.c
+++ b/ports/atmel-samd/common-hal/storage/__init__.c
@@ -30,6 +30,7 @@
 #include "py/mperrno.h"
 #include "py/runtime.h"
 #include "shared-bindings/storage/__init__.h"
+#include "usb.h"
 
 extern volatile bool mp_msc_enabled;
 
@@ -38,7 +39,9 @@ void common_hal_storage_remount(const char* mount_path, bool readonly) {
         mp_raise_OSError(MP_EINVAL);
     }
 
-    if (mp_msc_enabled) {
+    // TODO(dhalbert): is this is a good enough check? It checks for
+    // CDC enabled. There is no "MSC enabled" check.
+    if (usb_connected()) {
         mp_raise_RuntimeError("Cannot remount '/' when USB is active.");
     }
 
diff --git a/ports/atmel-samd/mpconfigport.h b/ports/atmel-samd/mpconfigport.h
index 1db2d5a67..f15efca96 100644
--- a/ports/atmel-samd/mpconfigport.h
+++ b/ports/atmel-samd/mpconfigport.h
@@ -215,7 +215,6 @@ extern const struct _mp_obj_module_t usb_hid_module;
 
 //    { MP_OBJ_NEW_QSTR(MP_QSTR_gamepad),(mp_obj_t)&gamepad_module },
 //    { MP_OBJ_NEW_QSTR(MP_QSTR_usb_hid),(mp_obj_t)&usb_hid_module },
-//    { MP_OBJ_NEW_QSTR(MP_QSTR_storage), (mp_obj_t)&storage_module },
 
 
 #define MICROPY_PORT_BUILTIN_MODULES \
@@ -226,6 +225,7 @@ extern const struct _mp_obj_module_t usb_hid_module;
     { MP_OBJ_NEW_QSTR(MP_QSTR_neopixel_write),(mp_obj_t)&neopixel_write_module }, \
     { MP_OBJ_NEW_QSTR(MP_QSTR_os), (mp_obj_t)&os_module }, \
     { MP_OBJ_NEW_QSTR(MP_QSTR_random), (mp_obj_t)&random_module }, \
+    { MP_OBJ_NEW_QSTR(MP_QSTR_storage), (mp_obj_t)&storage_module }, \
     { MP_OBJ_NEW_QSTR(MP_QSTR_struct), (mp_obj_t)&struct_module }, \
     { MP_OBJ_NEW_QSTR(MP_QSTR_supervisor), (mp_obj_t)&supervisor_module }, \
     { MP_OBJ_NEW_QSTR(MP_QSTR_math), (mp_obj_t)&math_module }, \
diff --git a/ports/atmel-samd/peripherals.c b/ports/atmel-samd/peripherals.c
new file mode 100644
index 000000000..6de813cca
--- /dev/null
+++ b/ports/atmel-samd/peripherals.c
@@ -0,0 +1,43 @@
+/*
+ * This file is part of the Micro Python project, http://micropython.org/
+ *
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2017 Dan Halbert for Adafruit Industries
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+#include "peripherals.h"
+
+#include "hpl_sercom_config.h"
+
+// Routines that are the same across all samd variants.
+
+
+// Convert frequency to clock-speed-dependent value. Return 0 if out of range.
+uint8_t samd_peripherals_baudrate_to_baud_reg_value(const uint32_t baudrate) {
+    uint32_t baud_reg_value = (uint32_t) (((float) PROTOTYPE_SERCOM_SPI_M_SYNC_CLOCK_FREQUENCY /
+                                           (2 * baudrate)) + 0.5f);
+    if (baud_reg_value > 0xff) {
+        return 0;
+    }
+    return (uint8_t) baud_reg_value;
+}
+
diff --git a/ports/atmel-samd/peripherals.h b/ports/atmel-samd/peripherals.h
index 03828ae74..95bc1ec53 100644
--- a/ports/atmel-samd/peripherals.h
+++ b/ports/atmel-samd/peripherals.h
@@ -27,8 +27,13 @@
 #ifndef MICROPY_INCLUDED_ATMEL_SAMD_PERIPHERALS_H
 #define MICROPY_INCLUDED_ATMEL_SAMD_PERIPHERALS_H
 
+#include <stdint.h>
+
 #include "mpconfigport.h"
 
+// Routines common across chip families.
+uint8_t samd_peripherals_baudrate_to_baud_reg_value(const uint32_t baudrate);
+
 #ifdef SAMD21
 #include "samd21_peripherals.h"
 #endif
diff --git a/ports/atmel-samd/samd21_peripherals.c b/ports/atmel-samd/samd21_peripherals.c
index 0ddc3be52..484c787cb 100644
--- a/ports/atmel-samd/samd21_peripherals.c
+++ b/ports/atmel-samd/samd21_peripherals.c
@@ -58,7 +58,7 @@ static const uint8_t SERCOMx_GCLK_ID_SLOW[] = {
 
     
 // Clock initialization as done in Atmel START.
-void samd_peripheral_sercom_clock_init(Sercom* sercom, uint8_t sercom_index) {
+void samd_peripherals_sercom_clock_init(Sercom* sercom, uint8_t sercom_index) {
     _pm_enable_bus_clock(PM_BUS_APBC, sercom);
     _gclk_enable_channel(SERCOMx_GCLK_ID_CORE[sercom_index], GCLK_CLKCTRL_GEN_GCLK0_Val);
     _gclk_enable_channel(SERCOMx_GCLK_ID_SLOW[sercom_index], GCLK_CLKCTRL_GEN_GCLK3_Val);
@@ -70,7 +70,7 @@ void samd_peripheral_sercom_clock_init(Sercom* sercom, uint8_t sercom_index) {
 // <0x1=>PAD[2,3]_DO_SCK
 // <0x2=>PAD[3,1]_DO_SCK
 // <0x3=>PAD[0,3]_DO_SCK
-uint8_t samd_peripheral_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad) {
+uint8_t samd_peripherals_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad) {
     if (clock_pad == 1) {
         if (mosi_pad == 0) {
             return 0;
@@ -87,6 +87,6 @@ uint8_t samd_peripheral_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad) {
     return 255;
 }
 
-bool samd_peripheral_valid_spi_clock_pad(uint8_t clock_pad) {
+bool samd_peripherals_valid_spi_clock_pad(uint8_t clock_pad) {
     return clock_pad == 1 || clock_pad == 3;
 }
diff --git a/ports/atmel-samd/samd21_peripherals.h b/ports/atmel-samd/samd21_peripherals.h
index a317d3ddc..7a4477891 100644
--- a/ports/atmel-samd/samd21_peripherals.h
+++ b/ports/atmel-samd/samd21_peripherals.h
@@ -29,8 +29,8 @@
 
 #include "include/sam.h"
 
-void samd_peripheral_sercom_clock_init(Sercom* sercom, uint8_t sercom_index);
-uint8_t samd_peripheral_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad);
-bool samd_peripheral_valid_spi_clock_pad(uint8_t clock_pad);
+void samd_peripherals_sercom_clock_init(Sercom* sercom, uint8_t sercom_index);
+uint8_t samd_peripherals_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad);
+bool samd_peripherals_valid_spi_clock_pad(uint8_t clock_pad);
 
 #endif  // MICROPY_INCLUDED_ATMEL_SAMD_SAMD21_PERIPHERALS_H
diff --git a/ports/atmel-samd/samd51_peripherals.c b/ports/atmel-samd/samd51_peripherals.c
index f1528f3c1..e06f7f9df 100644
--- a/ports/atmel-samd/samd51_peripherals.c
+++ b/ports/atmel-samd/samd51_peripherals.c
@@ -62,7 +62,7 @@ static const uint8_t SERCOMx_GCLK_ID_SLOW[] = {
 
     
 // Clock initialization as done in Atmel START.
-void samd_peripheral_sercom_clock_init(Sercom* sercom, uint8_t sercom_index) {
+void samd_peripherals_sercom_clock_init(Sercom* sercom, uint8_t sercom_index) {
 	hri_gclk_write_PCHCTRL_reg(GCLK,
                                    SERCOMx_GCLK_ID_CORE[sercom_index],
                                    GCLK_PCHCTRL_GEN_GCLK1_Val | (1 << GCLK_PCHCTRL_CHEN_Pos));
@@ -113,7 +113,7 @@ void samd_peripheral_sercom_clock_init(Sercom* sercom, uint8_t sercom_index) {
 // <0x1=>PAD[2,3]_DO_SCK [RESERVED]
 // <0x2=>PAD[3,1]_DO_SCK
 // <0x3=>PAD[0,3]_DO_SCK [RESERVED]
-uint8_t samd_peripheral_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad) {
+uint8_t samd_peripherals_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad) {
     if (clock_pad != 1) {
         return 255;
     }
@@ -126,6 +126,6 @@ uint8_t samd_peripheral_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad) {
     return 255;
 }
 
-bool samd_peripheral_valid_spi_clock_pad(uint8_t clock_pad) {
+bool samd_peripherals_valid_spi_clock_pad(uint8_t clock_pad) {
     return clock_pad == 1;
 }
diff --git a/ports/atmel-samd/samd51_peripherals.h b/ports/atmel-samd/samd51_peripherals.h
index 3e8097c87..c47e3bee7 100644
--- a/ports/atmel-samd/samd51_peripherals.h
+++ b/ports/atmel-samd/samd51_peripherals.h
@@ -29,9 +29,9 @@
 
 #include "sam.h"
 
-void samd_peripheral_sercom_clock_init(Sercom* sercom, uint8_t sercom_index);
-uint8_t samd_peripheral_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad);
-bool samd_peripheral_valid_spi_clock_pad(uint8_t clock_pad);
+void samd_peripherals_sercom_clock_init(Sercom* sercom, uint8_t sercom_index);
+uint8_t samd_peripherals_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad);
+bool samd_peripherals_valid_spi_clock_pad(uint8_t clock_pad);
 
 #endif  // MICROPY_INCLUDED_ATMEL_SAMD_SAMD51_PERIPHERALS_H
 
diff --git a/ports/atmel-samd/samd_peripherals.h b/ports/atmel-samd/samd_peripherals.h
new file mode 100644
index 000000000..7a4477891
--- /dev/null
+++ b/ports/atmel-samd/samd_peripherals.h
@@ -0,0 +1,36 @@
+/*
+ * This file is part of the MicroPython project, http://micropython.org/
+ *
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2017 by Dan Halbert for Adafruit Industries
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+#ifndef MICROPY_INCLUDED_ATMEL_SAMD_SAMD21_PERIPHERALS_H
+#define MICROPY_INCLUDED_ATMEL_SAMD_SAMD21_PERIPHERALS_H
+
+#include "include/sam.h"
+
+void samd_peripherals_sercom_clock_init(Sercom* sercom, uint8_t sercom_index);
+uint8_t samd_peripherals_get_spi_dopo(uint8_t clock_pad, uint8_t mosi_pad);
+bool samd_peripherals_valid_spi_clock_pad(uint8_t clock_pad);
+
+#endif  // MICROPY_INCLUDED_ATMEL_SAMD_SAMD21_PERIPHERALS_H
diff --git a/ports/atmel-samd/shared_dma.c b/ports/atmel-samd/shared_dma.c
index a2914c3cf..f8cef0992 100644
--- a/ports/atmel-samd/shared_dma.c
+++ b/ports/atmel-samd/shared_dma.c
@@ -43,28 +43,33 @@ void init_shared_dma(void) {
     struct dma_resource_config config;
     dma_get_config_defaults(&config);
 
-    // This allocates the lowest channel first so make sure the audio is first
-    // so it gets the highest priority.
-    config.peripheral_trigger = DAC_DMAC_ID_EMPTY;
-    config.trigger_action = DMA_TRIGGER_ACTION_BEAT;
-    config.event_config.input_action = DMA_EVENT_INPUT_TRIG;
-    config.event_config.event_output_enable = true;
-    dma_allocate(&audio_dma, &config);
+    // See asf4_conf/hpl_dmac_config.h for initial settings for DMA channels
+    // DMA Channel 0: audio, highest priority,
+    // normal transfer on input, DAC 0 empty is trigger source, trigger on each beat, beat is one byte
+    // output enable true.
+    // asf3 settings:
+    //config.peripheral_trigger = DAC_DMAC_ID_EMPTY;
+    //config.trigger_action = DMA_TRIGGER_ACTION_BEAT;
+    //config.event_config.input_action = DMA_EVENT_INPUT_TRIG;
+    //config.event_config.event_output_enable = true;
+
     // Turn on the transfer complete interrupt so that the job_status changes to done.
     g_chan_interrupt_flag[audio_dma.channel_id] |= (1UL << DMA_CALLBACK_TRANSFER_DONE);
 
     // Prioritize the RX channel over the TX channel because TX can cause an RX
     // overflow.
-    dma_get_config_defaults(&config);
-    config.trigger_action = DMA_TRIGGER_ACTION_BEAT;
-    config.event_config.input_action = DMA_EVENT_INPUT_TRIG;
+    
+    // DMA Channel 1: rx channel,
+    // normal transfer on input, trigger on each beat, beat is one byte
+    //config.trigger_action = DMA_TRIGGER_ACTION_BEAT;
+    //config.event_config.input_action = DMA_EVENT_INPUT_TRIG;
     dma_allocate(&general_dma_rx, &config);
     g_chan_interrupt_flag[general_dma_rx.channel_id] |= (1UL << DMA_CALLBACK_TRANSFER_DONE);
 
-    dma_get_config_defaults(&config);
-    config.trigger_action = DMA_TRIGGER_ACTION_BEAT;
-    config.event_config.input_action = DMA_EVENT_INPUT_TRIG;
-    dma_allocate(&general_dma_tx, &config);
+    // DMA Channel 1: rx channel,
+    // normal transfer on input, trigger on each beat, beat is one byte
+    //config.trigger_action = DMA_TRIGGER_ACTION_BEAT;
+    //config.event_config.input_action = DMA_EVENT_INPUT_TRIG;
     g_chan_interrupt_flag[general_dma_tx.channel_id] |= (1UL << DMA_CALLBACK_TRANSFER_DONE);
 
     // Be sneaky and reuse the active descriptor memory.
diff --git a/ports/atmel-samd/spi_flash.c b/ports/atmel-samd/spi_flash.c
index 8191887e4..a64c0ed33 100644
--- a/ports/atmel-samd/spi_flash.c
+++ b/ports/atmel-samd/spi_flash.c
@@ -28,20 +28,19 @@
 #include <stdint.h>
 #include <string.h>
 
-<<<<<<< HEAD
-#include "asf/sam0/drivers/sercom/spi/spi.h"
-
 #include "extmod/vfs.h"
 #include "extmod/vfs_fat.h"
-=======
->>>>>>> WIP
 #include "py/gc.h"
 #include "py/obj.h"
 #include "py/runtime.h"
 #include "lib/oofatfs/ff.h"
+#include "peripherals.h"
+#include "supervisor/shared/rgb_led_status.h"
+
+//#include "shared_dma.h"
 
-#include "rgb_led_status.h"
-#include "shared_dma.h"
+#include "hal_gpio.h"
+#include "hal_spi_m_sync.h"
 
 #define SPI_FLASH_PART1_START_BLOCK (0x1)
 
@@ -60,7 +59,7 @@
 
 static bool spi_flash_is_initialised = false;
 
-struct spi_module spi_flash_instance;
+struct spi_m_sync_descriptor spi_flash_desc;
 
 // The currently cached sector in the cache, ram or flash based.
 static uint32_t current_sector;
@@ -74,35 +73,37 @@ static uint32_t dirty_mask;
 
 // Enable the flash over SPI.
 static void flash_enable(void) {
-    port_pin_set_output_level(SPI_FLASH_CS, false);
+    gpio_set_pin_level(SPI_FLASH_CS_PIN, false);
 }
 
 // Disable the flash over SPI.
 static void flash_disable(void) {
-    port_pin_set_output_level(SPI_FLASH_CS, true);
+    gpio_set_pin_level(SPI_FLASH_CS_PIN, true);
 }
 
 // Wait until both the write enable and write in progress bits have cleared.
 static bool wait_for_flash_ready(void) {
-    uint8_t status_request[2] = {CMD_READ_STATUS, 0x00};
-    uint8_t response[2] = {0x00, 0x01};
-    enum status_code status = STATUS_OK;
+    uint8_t read_status_request[2] = {CMD_READ_STATUS, 0x00};
+    uint8_t read_status_response[2] = {0x00, 0x00};
+    struct spi_xfer read_status_xfer = {read_status_request, read_status_response, 2};
+    int32_t status;
     // Both the write enable and write in progress bits should be low.
-    while (status == STATUS_OK && (response[1] & 0x3) != 0) {
+    do {
         flash_enable();
-        status = spi_transceive_buffer_wait(&spi_flash_instance, status_request, response, 2);
+        status = spi_m_sync_transfer(&spi_flash_desc, &read_status_xfer);
         flash_disable();
-    }
-    return status == STATUS_OK;
+    } while (status >= 0 && (read_status_response[1] & 0x3) != 0);
+    return status >= 0;         // status is number of chars read or a negative error code.
 }
 
 // Turn on the write enable bit so we can program and erase the flash.
 static bool write_enable(void) {
     flash_enable();
-    uint8_t command = CMD_ENABLE_WRITE;
-    enum status_code status = spi_write_buffer_wait(&spi_flash_instance, &command, 1);
+    uint8_t enable_write_request[1] = {CMD_ENABLE_WRITE};
+    struct spi_xfer enable_write_xfer = {enable_write_request, 0, 1};
+    int32_t status = spi_m_sync_transfer(&spi_flash_desc, &enable_write_xfer);
     flash_disable();
-    return status == STATUS_OK;
+    return status >= 0;         // status is number of chars read or a negative error code.
 }
 
 // Pack the low 24 bits of the address into a uint8_t array.
@@ -120,17 +121,19 @@ static bool read_flash(uint32_t address, uint8_t* data, uint32_t data_length) {
     if (!wait_for_flash_ready()) {
         return false;
     }
-    enum status_code status;
     // We can read as much as we want sequentially.
-    uint8_t read_request[4] = {CMD_READ_DATA, 0x00, 0x00, 0x00};
-    address_to_bytes(address, read_request + 1);
+    uint8_t read_data_request[4] = {CMD_READ_DATA, 0x00, 0x00, 0x00};
+    struct spi_xfer read_data_xfer = {read_data_request, 0, 4};
+    // Write the SPI flash read address into the bytes following the command byte.
+    address_to_bytes(address, read_data_request + 1);
     flash_enable();
-    status = spi_write_buffer_wait(&spi_flash_instance, read_request, 4);
-    if (status == STATUS_OK) {
-        status = shared_dma_read(spi_flash_instance.hw, data, data_length, 0x00);
+    int32_t status = spi_m_sync_transfer(&spi_flash_desc, &read_data_xfer);
+    struct spi_xfer read_data_buffer_xfer = {0, data, data_length};
+    if (status >= 0) {
+        status = spi_m_sync_transfer(&spi_flash_desc, &read_data_buffer_xfer);
     }
     flash_disable();
-    return status == STATUS_OK;
+    return status >= 0;
 }
 
 // Writes data_length's worth of bytes starting at address from data. Assumes
@@ -159,26 +162,29 @@ static bool write_flash(uint32_t address, const uint8_t* data, uint32_t data_len
         if (!wait_for_flash_ready() || !write_enable()) {
             return false;
         }
-        enum status_code status;
+        int32_t status;
 
         #ifdef SPI_FLASH_SECTOR_PROTECTION
         // Print out the protection status.
         // uint8_t protect_check[5] = {0x3C, 0x00, 0x00, 0x00, 0x00};
         // address_to_bytes(address + bytes_written, protect_check + 1);
         // flash_enable();
-        // status = spi_write_buffer_wait(&spi_flash_instance, protect_check, 5);
+        // status = spi_write_buffer_wait(&spi_flash_desc, protect_check, 5);
         // flash_disable();
         #endif
 
         flash_enable();
-        uint8_t command[4] = {CMD_PAGE_PROGRAM, 0x00, 0x00, 0x00};
-        address_to_bytes(address + bytes_written, command + 1);
-        status = spi_write_buffer_wait(&spi_flash_instance, command, 4);
-        if (status == STATUS_OK) {
-            status = shared_dma_write(spi_flash_instance.hw, data + bytes_written, SPI_FLASH_PAGE_SIZE);
+        uint8_t page_program_request[4] = {CMD_PAGE_PROGRAM, 0x00, 0x00, 0x00};
+        // Write the SPI flash write address into the bytes following the command byte.
+        address_to_bytes(address + bytes_written, page_program_request + 1);
+        struct spi_xfer page_program_xfer = {page_program_request, 0, 4};
+        status = spi_m_sync_transfer(&spi_flash_desc, &page_program_xfer);
+        if (status >= 0) {
+            struct spi_xfer write_data_buffer_xfer = {(uint8_t*) data + bytes_written, 0, SPI_FLASH_PAGE_SIZE};
+            status = spi_m_sync_transfer(&spi_flash_desc, &write_data_buffer_xfer);
         }
         flash_disable();
-        if (status != STATUS_OK) {
+        if (status < 0) {
             return false;
         }
     }
@@ -224,11 +230,11 @@ static bool erase_sector(uint32_t sector_address) {
 
     uint8_t erase_request[4] = {CMD_SECTOR_ERASE, 0x00, 0x00, 0x00};
     address_to_bytes(sector_address, erase_request + 1);
-
+    struct spi_xfer erase_xfer = {erase_request, 0, 4};
     flash_enable();
-    enum status_code status = spi_write_buffer_wait(&spi_flash_instance, erase_request, 4);
+    int32_t status = spi_m_sync_transfer(&spi_flash_desc, &erase_xfer);
     flash_disable();
-    return status == STATUS_OK;
+    return status >= 0;
 }
 
 // Sector is really 24 bits.
@@ -247,82 +253,103 @@ static bool copy_block(uint32_t src_address, uint32_t dest_address) {
 }
 
 void spi_flash_init(void) {
-    if (!spi_flash_is_initialised) {
-        struct spi_config config_spi_master;
-        spi_get_config_defaults(&config_spi_master);
-        config_spi_master.mux_setting = SPI_FLASH_MUX_SETTING;
-        config_spi_master.pinmux_pad0 = SPI_FLASH_PAD0_PINMUX;
-        config_spi_master.pinmux_pad1 = SPI_FLASH_PAD1_PINMUX;
-        config_spi_master.pinmux_pad2 = SPI_FLASH_PAD2_PINMUX;
-        config_spi_master.pinmux_pad3 = SPI_FLASH_PAD3_PINMUX;
-        config_spi_master.mode_specific.master.baudrate = SPI_FLASH_BAUDRATE;
-        spi_init(&spi_flash_instance, SPI_FLASH_SERCOM, &config_spi_master);
-        spi_enable(&spi_flash_instance);
-
-        // Manage chip select ourselves.
-        struct port_config pin_conf;
-        port_get_config_defaults(&pin_conf);
-
-        pin_conf.direction  = PORT_PIN_DIR_OUTPUT;
-        port_pin_set_config(SPI_FLASH_CS, &pin_conf);
-        flash_disable();
+    if (spi_flash_is_initialised) {
+        return;
+    }
+        
+    samd_peripherals_sercom_clock_init(SPI_FLASH_SERCOM, SPI_FLASH_SERCOM_INDEX);
 
-        // Activity LED for flash writes.
-        #ifdef MICROPY_HW_LED_MSC
-            port_pin_set_config(MICROPY_HW_LED_MSC, &pin_conf);
-            port_pin_set_output_level(MICROPY_HW_LED_MSC, false);
-        #endif
+    // Set up with defaults, then change.
+    spi_m_sync_init(&spi_flash_desc, SPI_FLASH_SERCOM);
+        
+    hri_sercomspi_write_CTRLA_DOPO_bf(SPI_FLASH_SERCOM, SPI_FLASH_DOPO);
+    hri_sercomspi_write_CTRLA_DIPO_bf(SPI_FLASH_SERCOM, SPI_FLASH_DIPO);
 
-        uint8_t jedec_id_request[4] = {CMD_READ_JEDEC_ID, 0x00, 0x00, 0x00};
-        uint8_t response[4] = {0x00, 0x00, 0x00, 0x00};
-        flash_enable();
-        spi_transceive_buffer_wait(&spi_flash_instance, jedec_id_request, response, 4);
-        flash_disable();
-        uint8_t manufacturer = response[1];
-        if ((response[1] == SPI_FLASH_JEDEC_MANUFACTURER
-            #ifdef SPI_FLASH_JEDEC_MANUFACTURER_2
-             || response[1] == SPI_FLASH_JEDEC_MANUFACTURER_2
-            #endif
-            ) &&
-            response[2] == SPI_FLASH_JEDEC_MEMORY_TYPE &&
-            response[3] == SPI_FLASH_JEDEC_CAPACITY) {
-            spi_flash_is_initialised = true;
-        } else {
-            // Unknown flash chip!
-            spi_flash_is_initialised = false;
-            return;
-        }
+    gpio_set_pin_direction(SPI_FLASH_SCK_PIN, GPIO_DIRECTION_OUT);
+    gpio_set_pin_pull_mode(SPI_FLASH_SCK_PIN, GPIO_PULL_OFF);
+    gpio_set_pin_function(SPI_FLASH_SCK_PIN, SPI_FLASH_SCK_PIN_FUNCTION);
 
-        if ((manufacturer == SPI_FLASH_JEDEC_MANUFACTURER && SPI_FLASH_SECTOR_PROTECTION)
-           #ifdef SPI_FLASH_JEDEC_MANUFACTURER_2
-           || (manufacturer == SPI_FLASH_JEDEC_MANUFACTURER_2 && SPI_FLASH_SECTOR_PROTECTION_2)
-           #endif
-            )  {
-            write_enable();
-
-            // Turn off sector protection
-            uint8_t disable_protect_request[2] = {CMD_WRITE_STATUS_BYTE1, 0x00};
-            uint8_t disable_protect_response[2] = {0x00, 0x00};
-            flash_enable();
-            spi_transceive_buffer_wait(&spi_flash_instance, disable_protect_request, disable_protect_response, 2);
-            flash_disable();
-        }
+    gpio_set_pin_direction(SPI_FLASH_MOSI_PIN, GPIO_DIRECTION_OUT);
+    gpio_set_pin_pull_mode(SPI_FLASH_MOSI_PIN, GPIO_PULL_OFF);
+    gpio_set_pin_function(SPI_FLASH_MOSI_PIN, SPI_FLASH_MOSI_PIN_FUNCTION);
 
-        // Turn off writes in case this is a microcontroller only reset.
-        uint8_t disable_write_request[1] = {CMD_DISABLE_WRITE};
-        uint8_t disable_response[1] = {0x00};
-        flash_enable();
-        spi_transceive_buffer_wait(&spi_flash_instance, disable_write_request, disable_response, 1);
-        flash_disable();
+    gpio_set_pin_direction(SPI_FLASH_MISO_PIN, GPIO_DIRECTION_IN);
+    gpio_set_pin_pull_mode(SPI_FLASH_MISO_PIN, GPIO_PULL_OFF);
+    gpio_set_pin_function(SPI_FLASH_MISO_PIN, SPI_FLASH_MISO_PIN_FUNCTION);
 
-        wait_for_flash_ready();
+    hri_sercomspi_write_CTRLA_DOPO_bf(SPI_FLASH_SERCOM, SPI_FLASH_DOPO);
+    hri_sercomspi_write_CTRLA_DIPO_bf(SPI_FLASH_SERCOM, SPI_FLASH_DIPO);
 
-        current_sector = NO_SECTOR_LOADED;
-        dirty_mask = 0;
-        MP_STATE_VM(flash_ram_cache) = NULL;
+    spi_m_sync_set_baudrate(&spi_flash_desc, samd_peripherals_baudrate_to_baud_reg_value(SPI_FLASH_BAUDRATE));
 
+    gpio_set_pin_direction(SPI_FLASH_CS_PIN, GPIO_DIRECTION_OUT);
+    // There's already a pull-up on the board.
+    gpio_set_pin_pull_mode(SPI_FLASH_CS_PIN, GPIO_PULL_OFF);
+    gpio_set_pin_function(SPI_FLASH_CS_PIN, GPIO_PIN_FUNCTION_OFF);
+
+    // Set CS high (disabled).
+    flash_disable();
+
+    spi_m_sync_enable(&spi_flash_desc);
+
+    // Activity LED for flash writes.
+#ifdef MICROPY_HW_LED_MSC
+    gpio_set_pin_function(SPI_FLASH_CS_PIN, GPIO_PIN_FUNCTION_OFF);
+    gpio_set_pin_direction(MICROPY_HW_LED_MSC, GPIO_DIRECTION_OUT);
+    // There's already a pull-up on the board.
+    gpio_set_pin_level(MICROPY_HW_LED_MSC, false);
+#endif
+
+    uint8_t jedec_id_request[4] = {CMD_READ_JEDEC_ID, 0x00, 0x00, 0x00};
+    uint8_t jedec_id_response[4] = {0x00, 0x00, 0x00, 0x00};
+    struct spi_xfer jedec_id_xfer = { jedec_id_request, jedec_id_response, 4 };
+    flash_enable();
+    spi_m_sync_transfer(&spi_flash_desc, &jedec_id_xfer);
+    flash_disable();
+    uint8_t manufacturer = jedec_id_response[1];
+    if ((jedec_id_response[1] == SPI_FLASH_JEDEC_MANUFACTURER
+#ifdef SPI_FLASH_JEDEC_MANUFACTURER_2
+         || jedec_id_response[1] == SPI_FLASH_JEDEC_MANUFACTURER_2
+#endif
+         ) &&
+        jedec_id_response[2] == SPI_FLASH_JEDEC_MEMORY_TYPE &&
+        jedec_id_response[3] == SPI_FLASH_JEDEC_CAPACITY) {
         spi_flash_is_initialised = true;
+    } else {
+        // Unknown flash chip!
+        spi_flash_is_initialised = false;
+        return;
     }
+
+    if ((manufacturer == SPI_FLASH_JEDEC_MANUFACTURER && SPI_FLASH_SECTOR_PROTECTION)
+#ifdef SPI_FLASH_JEDEC_MANUFACTURER_2
+        || (manufacturer == SPI_FLASH_JEDEC_MANUFACTURER_2 && SPI_FLASH_SECTOR_PROTECTION_2)
+#endif
+        )  {
+        write_enable();
+
+        // Turn off sector protection
+        uint8_t disable_protect_request[2] = {CMD_WRITE_STATUS_BYTE1, 0x00};
+        struct spi_xfer disable_protect_xfer = { disable_protect_request, 0, 4 };
+        flash_enable();
+        spi_m_sync_transfer(&spi_flash_desc, &disable_protect_xfer);
+        flash_disable();
+    }
+
+    // Turn off writes in case this is a microcontroller only reset.
+    uint8_t disable_write_request[1] = {CMD_DISABLE_WRITE};
+    struct spi_xfer disable_write_xfer = { disable_write_request, 0, 1 };
+    flash_enable();
+    spi_m_sync_transfer(&spi_flash_desc, &disable_write_xfer);
+    flash_disable();
+
+    wait_for_flash_ready();
+
+    current_sector = NO_SECTOR_LOADED;
+    dirty_mask = 0;
+    MP_STATE_VM(flash_ram_cache) = NULL;
+
+    spi_flash_is_initialised = true;
 }
 
 // The size of each individual block.
diff --git a/ports/atmel-samd/usb_mass_storage.c b/ports/atmel-samd/usb_mass_storage.c
index 85c662e77..818736a78 100644
--- a/ports/atmel-samd/usb_mass_storage.c
+++ b/ports/atmel-samd/usb_mass_storage.c
@@ -271,7 +271,11 @@ int32_t usb_msc_xfer_done(uint8_t lun) {
     return ERR_NONE;
 }
 
-// The start_read callback begins a read transaction which we accept but delay our response until the "main thread" calls usb_msc_background. Once it does, we read immediately from the drive into our cache and trigger the USB DMA to output the sector. Once the sector is transmitted, xfer_done will be called.
+// The start_read callback begins a read transaction which we accept
+// but delay our response until the "main thread" calls
+// usb_msc_background. Once it does, we read immediately from the
+// drive into our cache and trigger the USB DMA to output the
+// sector. Once the sector is transmitted, xfer_done will be called.
 void usb_msc_background(void) {
     if (active_read && !usb_busy) {
         if (active_nblocks == 0) {
@@ -290,7 +294,7 @@ void usb_msc_background(void) {
             fs_user_mount_t * vfs = get_vfs(active_lun);
             disk_write(vfs, sector_buffer, active_addr, 1);
             // Since by getting here we assume the mount is read-only to
-            // MicroPython lets update the cached FatFs sector if its the one
+            // MicroPython let's update the cached FatFs sector if it's the one
             // we just wrote.
             #if _MAX_SS != _MIN_SS
             if (vfs->ssize == FILESYSTEM_BLOCK_SIZE) {