documentation!

7 files changed, 715 insertions, 41 deletions

diff --git a/Doxyfile b/Doxyfile
new file mode 100644
index 00000000..da710195
--- /dev/null
+++ b/Doxyfile
@@ -0,0 +1,384 @@
+# Doxyfile 1.9.1
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+DOXYFILE_ENCODING      = UTF-8
+PROJECT_NAME           = "Sensor Watch"
+PROJECT_NUMBER         = "0.0.0"
+PROJECT_BRIEF          = "A board replacement for the classic Casio F-91W wristwatch, powered by a Microchip SAM L22 microcontroller."
+PROJECT_LOGO           =
+OUTPUT_DIRECTORY       = "../Sensor-Watch-Documentation"
+CREATE_SUBDIRS         = NO
+ALLOW_UNICODE_NAMES    = NO
+OUTPUT_LANGUAGE        = English
+OUTPUT_TEXT_DIRECTION  = None
+BRIEF_MEMBER_DESC      = YES
+REPEAT_BRIEF           = YES
+ABBREVIATE_BRIEF       = "The $name class" \
+                         "The $name widget" \
+                         "The $name file" \
+                         is \
+                         provides \
+                         specifies \
+                         contains \
+                         represents \
+                         a \
+                         an \
+                         the
+ALWAYS_DETAILED_SEC    = NO
+INLINE_INHERITED_MEMB  = NO
+FULL_PATH_NAMES        = YES
+STRIP_FROM_PATH        =
+STRIP_FROM_INC_PATH    =
+SHORT_NAMES            = NO
+JAVADOC_AUTOBRIEF      = NO
+JAVADOC_BANNER         = NO
+QT_AUTOBRIEF           = NO
+MULTILINE_CPP_IS_BRIEF = NO
+PYTHON_DOCSTRING       = YES
+INHERIT_DOCS           = YES
+SEPARATE_MEMBER_PAGES  = NO
+TAB_SIZE               = 4
+ALIASES                =
+OPTIMIZE_OUTPUT_FOR_C  = YES
+OPTIMIZE_OUTPUT_JAVA   = NO
+OPTIMIZE_FOR_FORTRAN   = NO
+OPTIMIZE_OUTPUT_VHDL   = NO
+OPTIMIZE_OUTPUT_SLICE  = NO
+EXTENSION_MAPPING      =
+MARKDOWN_SUPPORT       = YES
+TOC_INCLUDE_HEADINGS   = 5
+AUTOLINK_SUPPORT       = YES
+BUILTIN_STL_SUPPORT    = NO
+CPP_CLI_SUPPORT        = NO
+SIP_SUPPORT            = NO
+IDL_PROPERTY_SUPPORT   = YES
+DISTRIBUTE_GROUP_DOC   = YES
+GROUP_NESTED_COMPOUNDS = NO
+SUBGROUPING            = YES
+INLINE_GROUPED_CLASSES = NO
+INLINE_SIMPLE_STRUCTS  = NO
+TYPEDEF_HIDES_STRUCT   = NO
+LOOKUP_CACHE_SIZE      = 0
+NUM_PROC_THREADS       = 1
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+EXTRACT_ALL            = NO
+EXTRACT_PRIVATE        = NO
+EXTRACT_PRIV_VIRTUAL   = NO
+EXTRACT_PACKAGE        = NO
+EXTRACT_STATIC         = NO
+EXTRACT_LOCAL_CLASSES  = YES
+EXTRACT_LOCAL_METHODS  = NO
+EXTRACT_ANON_NSPACES   = NO
+RESOLVE_UNNAMED_PARAMS = YES
+HIDE_UNDOC_MEMBERS     = NO
+HIDE_UNDOC_CLASSES     = NO
+HIDE_FRIEND_COMPOUNDS  = NO
+HIDE_IN_BODY_DOCS      = NO
+INTERNAL_DOCS          = NO
+CASE_SENSE_NAMES       = NO
+HIDE_SCOPE_NAMES       = NO
+HIDE_COMPOUND_REFERENCE= NO
+SHOW_INCLUDE_FILES     = YES
+SHOW_GROUPED_MEMB_INC  = NO
+FORCE_LOCAL_INCLUDES   = NO
+INLINE_INFO            = YES
+SORT_MEMBER_DOCS       = YES
+SORT_BRIEF_DOCS        = NO
+SORT_MEMBERS_CTORS_1ST = NO
+SORT_GROUP_NAMES       = NO
+SORT_BY_SCOPE_NAME     = NO
+STRICT_PROTO_MATCHING  = NO
+GENERATE_TODOLIST      = YES
+GENERATE_TESTLIST      = YES
+GENERATE_BUGLIST       = YES
+GENERATE_DEPRECATEDLIST= YES
+ENABLED_SECTIONS       =
+MAX_INITIALIZER_LINES  = 30
+SHOW_USED_FILES        = YES
+SHOW_FILES             = YES
+SHOW_NAMESPACES        = YES
+FILE_VERSION_FILTER    =
+LAYOUT_FILE            =
+CITE_BIB_FILES         =
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+QUIET                  = NO
+WARNINGS               = YES
+WARN_IF_UNDOCUMENTED   = YES
+WARN_IF_DOC_ERROR      = YES
+WARN_NO_PARAMDOC       = NO
+WARN_AS_ERROR          = NO
+WARN_FORMAT            = "$file:$line: $text"
+WARN_LOGFILE           =
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+INPUT                  = ./watch-library/watch
+INPUT_ENCODING         = UTF-8
+FILE_PATTERNS          = *.c \
+                         *.cc \
+                         *.cxx \
+                         *.cpp \
+                         *.c++ \
+                         *.java \
+                         *.ii \
+                         *.ixx \
+                         *.ipp \
+                         *.i++ \
+                         *.inl \
+                         *.idl \
+                         *.ddl \
+                         *.odl \
+                         *.h \
+                         *.hh \
+                         *.hxx \
+                         *.hpp \
+                         *.h++ \
+                         *.cs \
+                         *.d \
+                         *.php \
+                         *.php4 \
+                         *.php5 \
+                         *.phtml \
+                         *.inc \
+                         *.m \
+                         *.markdown \
+                         *.md \
+                         *.mm \
+                         *.dox \
+                         *.py \
+                         *.pyw \
+                         *.f90 \
+                         *.f95 \
+                         *.f03 \
+                         *.f08 \
+                         *.f18 \
+                         *.f \
+                         *.for \
+                         *.vhd \
+                         *.vhdl \
+                         *.ucf \
+                         *.qsf \
+                         *.ice
+RECURSIVE              = YES
+EXCLUDE                =
+EXCLUDE_SYMLINKS       = NO
+EXCLUDE_PATTERNS       =
+EXCLUDE_SYMBOLS        =
+EXAMPLE_PATH           =
+EXAMPLE_PATTERNS       = *
+EXAMPLE_RECURSIVE      = NO
+IMAGE_PATH             =
+INPUT_FILTER           =
+FILTER_PATTERNS        =
+FILTER_SOURCE_FILES    = NO
+FILTER_SOURCE_PATTERNS =
+USE_MDFILE_AS_MAINPAGE =
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+SOURCE_BROWSER         = NO
+INLINE_SOURCES         = NO
+STRIP_CODE_COMMENTS    = YES
+REFERENCED_BY_RELATION = NO
+REFERENCES_RELATION    = NO
+REFERENCES_LINK_SOURCE = YES
+SOURCE_TOOLTIPS        = YES
+USE_HTAGS              = NO
+VERBATIM_HEADERS       = YES
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+ALPHABETICAL_INDEX     = YES
+IGNORE_PREFIX          =
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+GENERATE_HTML          = YES
+HTML_OUTPUT            = docs
+HTML_FILE_EXTENSION    = .html
+HTML_HEADER            =
+HTML_FOOTER            =
+HTML_STYLESHEET        =
+HTML_EXTRA_STYLESHEET  =
+HTML_EXTRA_FILES       =
+HTML_COLORSTYLE_HUE    = 220
+HTML_COLORSTYLE_SAT    = 100
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+HTML_TIMESTAMP         = NO
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+HTML_INDEX_NUM_ENTRIES = 100
+GENERATE_DOCSET        = NO
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+DOCSET_PUBLISHER_NAME  = Publisher
+GENERATE_HTMLHELP      = NO
+CHM_FILE               =
+HHC_LOCATION           =
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+CHM_INDEX_ENCODING     =
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+DISABLE_INDEX          = NO
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+TREEVIEW_WIDTH         = 250
+EXT_LINKS_IN_WINDOW    = NO
+HTML_FORMULA_FORMAT    = png
+FORMULA_FONTSIZE       = 10
+FORMULA_TRANSPARENT    = YES
+FORMULA_MACROFILE      =
+USE_MATHJAX            = NO
+MATHJAX_FORMAT         = HTML-CSS
+MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax@2
+MATHJAX_EXTENSIONS     =
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+SERVER_BASED_SEARCH    = NO
+EXTERNAL_SEARCH        = NO
+SEARCHENGINE_URL       =
+SEARCHDATA_FILE        = searchdata.xml
+EXTERNAL_SEARCH_ID     =
+EXTRA_SEARCH_MAPPINGS  =
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+GENERATE_LATEX         = FALSE
+LATEX_OUTPUT           = latex
+LATEX_CMD_NAME         =
+MAKEINDEX_CMD_NAME     = makeindex
+LATEX_MAKEINDEX_CMD    = makeindex
+COMPACT_LATEX          = NO
+PAPER_TYPE             = a4
+EXTRA_PACKAGES         =
+LATEX_HEADER           =
+LATEX_FOOTER           =
+LATEX_EXTRA_STYLESHEET =
+LATEX_EXTRA_FILES      =
+PDF_HYPERLINKS         = YES
+USE_PDFLATEX           = YES
+LATEX_BATCHMODE        = NO
+LATEX_HIDE_INDICES     = NO
+LATEX_SOURCE_CODE      = NO
+LATEX_BIB_STYLE        = plain
+LATEX_TIMESTAMP        = NO
+LATEX_EMOJI_DIRECTORY  =
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+GENERATE_RTF           = NO
+RTF_OUTPUT             = rtf
+COMPACT_RTF            = NO
+RTF_HYPERLINKS         = NO
+RTF_STYLESHEET_FILE    =
+RTF_EXTENSIONS_FILE    =
+RTF_SOURCE_CODE        = NO
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+GENERATE_MAN           = NO
+MAN_OUTPUT             = man
+MAN_EXTENSION          = .3
+MAN_SUBDIR             =
+MAN_LINKS              = NO
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+GENERATE_XML           = NO
+XML_OUTPUT             = xml
+XML_PROGRAMLISTING     = YES
+XML_NS_MEMB_FILE_SCOPE = NO
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+GENERATE_DOCBOOK       = NO
+DOCBOOK_OUTPUT         = docbook
+DOCBOOK_PROGRAMLISTING = NO
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+GENERATE_AUTOGEN_DEF   = NO
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+GENERATE_PERLMOD       = NO
+PERLMOD_LATEX          = NO
+PERLMOD_PRETTY         = YES
+PERLMOD_MAKEVAR_PREFIX =
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+ENABLE_PREPROCESSING   = YES
+MACRO_EXPANSION        = NO
+EXPAND_ONLY_PREDEF     = NO
+SEARCH_INCLUDES        = YES
+INCLUDE_PATH           =
+INCLUDE_FILE_PATTERNS  =
+PREDEFINED             =
+EXPAND_AS_DEFINED      =
+SKIP_FUNCTION_MACROS   = YES
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+TAGFILES               =
+GENERATE_TAGFILE       =
+ALLEXTERNALS           = NO
+EXTERNAL_GROUPS        = YES
+EXTERNAL_PAGES         = YES
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+CLASS_DIAGRAMS         = YES
+DIA_PATH               =
+HIDE_UNDOC_RELATIONS   = YES
+HAVE_DOT               = NO
+DOT_NUM_THREADS        = 0
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+DOT_WRAP_THRESHOLD     = 17
+TEMPLATE_RELATIONS     = NO
+INCLUDE_GRAPH          = YES
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+GRAPHICAL_HIERARCHY    = YES
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+DOT_IMAGE_FORMAT       = png
+INTERACTIVE_SVG        = NO
+DOT_PATH               =
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+PLANTUML_JAR_PATH      =
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+DOT_GRAPH_MAX_NODES    = 50
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+DOT_TRANSPARENT        = NO
+DOT_MULTI_TARGETS      = NO
+GENERATE_LEGEND        = YES
+DOT_CLEANUP            = YES
diff --git a/Sensor Watch BME280 Project/app.c b/Sensor Watch BME280 Project/app.c
index bcbd3080..e84e5760 100644
--- a/Sensor Watch BME280 Project/app.c
+++ b/Sensor Watch BME280 Project/app.c
@@ -1,7 +1,6 @@
 #include <stdio.h>
 #include <string.h>
 #include "watch.h"
-#include "app.h"
 #include "bme280.h"
 
 typedef enum ApplicationMode {
diff --git a/Sensor Watch Starter Project/app.c b/Sensor Watch Starter Project/app.c
index c3eddcbc..a180f0ea 100644
--- a/Sensor Watch Starter Project/app.c
+++ b/Sensor Watch Starter Project/app.c
@@ -1,7 +1,6 @@
 #include <stdio.h>
 #include <string.h>
 #include "watch.h"
-#include "app.h"
 
 //////////////////////////////////////////////////////////////////////////////////////////
 // This section sets up types and storage for our application state.
diff --git a/watch-library/app.h b/watch-library/app.h
deleted file mode 100644
index df40a30f..00000000
--- a/watch-library/app.h
+++ /dev/null
@@ -1,33 +0,0 @@
-/**
-  * Header file for Sensor Watch application
-  *
-  * You should be able to write a watch app by simply implementing these functions
-  * and declaring callbacks for various GPIO and peripheral interrupts. The main.c
-  * file takes care of calling these functions for you. The general flow:
-  *
-  * 1. Your app_init() function is called.
-  *      - This method should only be used to set your initial application state.
-  * 2. If your app is waking from BACKUP, app_wake_from_deep_sleep()  is called.
-  *      - If you saved state in the RTC's backup registers, you can restore it here.
-  * 3. Your app_setup() method is called.
-  *      - You may wish to enable some functionality and peripherals here.
-  *      - You should definitely set up some interrupts here.
-  * 4. The main run loop begins: your app_loop() function is called.
-  *      - Run code and update your UI here.
-  *      - Return true if your app is prepared to enter STANDBY mode.
-  * 5. This step differs depending on the value returned by app_loop:
-  *      - If you returned false, execution resumes at (4).
-  *      - If you returned true, app_prepare_for_sleep() is called; execution moves on to (6).
-  * 6. The microcontroller enters the STANDBY sleep mode.
-  *      - No user code will run, and the watch will enter a low power mode.
-  *      - The watch will remain in this state until an interrupt wakes it.
-  * 7. Once woken from STANDBY, your app_wake_from_sleep() function is called.
-  *      - After this, execution resumes at (4).
-  */
-
-void app_init();
-void app_wake_from_deep_sleep();
-void app_setup();
-bool app_loop();
-void app_prepare_for_sleep();
-void app_wake_from_sleep();
diff --git a/watch-library/main.c b/watch-library/main.c
index 42d0b56a..dd0822ad 100755
--- a/watch-library/main.c
+++ b/watch-library/main.c
@@ -39,7 +39,6 @@
 #include "hal_gpio.h"
 #include "atmel_start_pins.h"
 #include "watch.h"
-#include "app.h"
 
 //-----------------------------------------------------------------------------
 HAL_GPIO_PIN(UART_TX,   B, 0)
@@ -101,7 +100,7 @@ int main(void) {
     }
 
     // Watch library code. Set initial parameters for the device and enable the RTC.
-    watch_init();
+    _watch_init();
 
     // User code. Give the app a chance to enable and set up peripherals.
     app_setup();
diff --git a/watch-library/watch/watch.c b/watch-library/watch/watch.c
index b569c13d..6931a73a 100644
--- a/watch-library/watch/watch.c
+++ b/watch-library/watch/watch.c
@@ -4,7 +4,7 @@
 //////////////////////////////////////////////////////////////////////////////////////////
 // Initialization
 
-void watch_init() {
+void _watch_init() {
     // Use switching regulator for lower power consumption.
     SUPC->VREG.bit.SEL = 1;
     while(!SUPC->STATUS.bit.VREGRDY);
diff --git a/watch-library/watch/watch.h b/watch-library/watch/watch.h
index 04f1e486..64fc5355 100644
--- a/watch-library/watch/watch.h
+++ b/watch-library/watch/watch.h
@@ -1,3 +1,5 @@
+/// @file watch.h
+
 #ifndef WATCH_H_
 #define WATCH_H_
 #include <stdint.h>
@@ -5,54 +7,378 @@
 #include "hpl_calendar.h"
 #include "hal_ext_irq.h"
 
-void watch_init();
+/** @mainpage Sensor Watch Documentation
+ *  @brief This documentation covers most of the functions you will use to interact with the Sensor Watch
+           hardware. It is divided into the following sections:
+            - @ref app - This section covers the functions that you will implement in your app.c file when designing a
+                         Sensor Watch app.
+            - @ref slcd - This section covers functions related to the Segment LCD display driver, which is responsible
+                          for displaying strings of characters and indicators on the main watch display.
+            - @ref led - This section covers functions related to the bi-color red/green LED mounted behind the LCD.
+            - @ref rtc - This section covers functions related to the SAM L22's real-time clock peripheral, including
+                         date, time and alarm functions.
+            - @ref adc - This section covers functions related to the SAM L22's analog-to-digital converter, as well as
+                         configuring and reading values from the three analog-capable pins on the 9-pin connector.
+            - @ref buttons - This section covers functions related to the three buttons: Light, Mode and Alarm.
+            - @ref gpio - This section covers functions related to general-purpose input and output signals.
+            - @ref i2c - This section covers functions related to the SAM L22's built-I2C driver, including configuring
+                         the I2C bus, putting values directly on the bus and reading data from registers on I2C devices.
+            - @ref deepsleep - This section covers functions related to preparing for and entering BACKUP mode, the
+                               deepest sleep mode available on the SAM L22.
+ */
+
+/** @addtogroup app Application Framework
+  * @brief This section covers the functions that you will implement in your app.c file when designing a Sensor Watch app.
+  * @details You should be able to write a watch app by simply implementing these functions and declaring callbacks for
+  *          various GPIO and peripheral interrupts. The main.c file takes care of calling these functions for you. The
+  *          general flow:
+  *
+  *            1. Your app_init() function is called.
+  *               - This method should only be used to set your initial application state.
+  *            2. If your app is waking from BACKUP, app_wake_from_deep_sleep()  is called.
+  *               - If you saved state in the RTC's backup registers, you can restore it here.
+  *            3. Your app_setup() method is called.
+  *               - You may wish to enable some functionality and peripherals here.
+  *               - You should definitely set up some interrupts here.
+  *            4. The main run loop begins: your app_loop() function is called.
+  *               - Run code and update your UI here.
+  *               - Return true if your app is prepared to enter STANDBY mode.
+  *            5. This step differs depending on the value returned by app_loop:
+  *               - If you returned false, execution resumes at (4).
+  *               - If you returned true, app_prepare_for_sleep() is called; execution moves on to (6).
+  *            6. The microcontroller enters the STANDBY sleep mode.
+  *               - No user code will run, and the watch will enter a low power mode.
+  *               - The watch will remain in this state until an interrupt wakes it.
+  *            7. Once woken from STANDBY, your app_wake_from_sleep() function is called.
+  *               - After this, execution resumes at (4).
+  */
+/// @{
+/** @brief A function you will implement to initialize your application state. The app_init function is called before
+  *        anything else. Use it to set up any internal data structures or application state required by your app,
+  *        but don't configure any peripherals just yet.
+  */
+void app_init();
+
+/** @brief A function you will implement to wake from deep sleep mode. The app_wake_from_deep_sleep function is only
+  *        called if your app is waking from the ultra-low power BACKUP sleep mode. You may have chosen to store some
+  *        state in the RTC's backup registers prior to entering this mode. You may restore that state here.
+  */
+void app_wake_from_deep_sleep();
+
+/** @brief A function you will implement to set up your application. The app_setup function is like setup() in Arduino.
+  *        It is called once when the program begins. You should set pin modes and enable any peripherals you want to
+  *        set up (real-time clock, I2C, etc.) Depending on your application, you may or may not want to configure
+  *        sensors on your sensor board here. For example, a low-power accelerometer that will run at all times should
+  *        be configured here, whereas you may want to enable a more power-hungry sensor only when you need it.
+  * @note If your app enters the ultra-low power BACKUP sleep mode, this function will be called again when it wakes
+  *       from that deep sleep state. In this state, the RTC will still be configured with the correct date and time.
+  */
+void app_setup();
+
+/** @brief A function you will implement to serve as the app's main run loop. This method will be called repeatedly,
+           or if you enter STANDBY sleep mode, as soon as the device wakes from sleep.
+  * @return You should return true if your app is prepared to enter STANDBY sleep mode. If you return false, your
+  *         app's app_loop method will be called again immediately.
+  * @note Only the RTC, the segment LCD controller and the external interrupt controller run in STANDBY mode. If you
+  *       are using, e.g. the PWM function to set a custom LED color, you should return false here until you are
+  *       finished with that operation. Note however that the peripherals will continue running after waking up,
+  *       so e.g. the I2C controller, if configured, will sleep in STANDBY. But you can use it again as soon as your
+  *       app wakes up.
+  */
+bool app_loop();
+
+/** @brief A function you will implement to prepare to enter STANDBY sleep mode. The app_prepare_for_sleep function is
+ *         called before the watch goes into the  STANDBY sleep mode. In STANDBY mode, most peripherals are shut down,
+ *         and no code will run until the watch receives an interrupt (generally either the 1Hz tick or a press on one
+ *         of the buttons).
+ */
+void app_prepare_for_sleep();
 
+/** @brief A method you will implement to configure the app after waking from STANDBY sleep mode.
+  */
+void app_wake_from_sleep();
+
+/// Called by main.c while setting up the app. You should not call this from your app.
+void _watch_init();
+/// @}
+
+
+/** @addtogroup slcd Segment LCD Display
+  * @brief This section covers functions related to the Segment LCD display driver, which is responsible
+  *        for displaying strings of characters and indicators on the main watch display.
+  */
+/// @{
+/** @brief Enables the Segment LCD display.
+  * Call this before attempting to set pixels or display strings.
+  */
 void watch_enable_display();
+
+/** @brief Sets a pixel. Use this to manually set a pixel with a given common and segment number.
+  * @param com the common pin, numbered from 0-2
+  * @param seg the segment pin, numbered from 0-23
+  */
 void watch_set_pixel(uint8_t com, uint8_t seg);
+
+/** @brief Clears a pixel. Use this to manually clear a pixel with a given common and segment number.
+  * @param com the common pin, numbered from 0-2
+  * @param seg the segment pin, numbered from 0-23
+  * Use this to manually set a pixel with a common and a segment number.
+  */
+
 void watch_clear_pixel(uint8_t com, uint8_t seg);
+
+/** @brief Displays a string at the given position, starting from the top left. There are ten digits.
+           A space in any position will clear that digit.
+  * @param string A null-terminated string.
+  * @param position The position to start. The day of week digits are positions 0 and 1, the day of
+                    month digits are positions 2 and 3, and the main clock line is positions 4-9.
+  * @note This method does not clear the display; if for example you display a two-character string at
+          position 0, positions 2-9 will retain whatever state they were previously displaying.
+  */
 void watch_display_string(char *string, uint8_t position);
+/// @}
+
 
+/** @addtogroup led LED Control
+  * @brief This section covers functions related to the bi-color red/green LED mounted behind the LCD.
+  */
+/// @{
+/** @brief Enables the LED.
+  * @param pwm if true, enables PWM output for brightness control (required to use @ref watch_set_led_color).
+               If false, configures the LED pins as digital outputs.
+  * @note The TC driver required for PWM mode does not run in STANDBY mode. You should keep your app awake
+          while PWM'ing the LED's, and disable them before going to sleep.
+  */
 void watch_enable_led(bool pwm);
+
+/** @brief Disables the LED.
+  * @param pwm if true, disables the PWM output. If false, disables the digital outputs.
+  */
 void watch_disable_led(bool pwm);
+
+/** @brief Sets the LED to a custom color by modulating each output's duty cycle.
+  * @param red The red value.
+  * @param green The green value.
+  * @note still working on this, 0-65535 works now but these values may change.
+  */
 void watch_set_led_color(uint16_t red, uint16_t green);
+/** @brief Sets the red LED to full brightness, and turns the green LED off.
+  */
 void watch_set_led_red();
+
+/** @brief Sets the green LED to full brightness, and turns the red LED off. */
 void watch_set_led_green();
+
+/** @brief Sets both red and green LEDs to full brightness. */
 void watch_set_led_yellow();
+
+/** @brief Sets both red and green LEDs to full brightness. */
 void watch_set_led_off();
+/// @}
+
+
+/** @addtogroup rtc Real-Time Clock
+  * @brief This section covers functions related to the SAM L22's real-time clock peripheral, including
+  *        date, time and alarm functions.
+  */
+/// @{
+/// Called by main.c to check if the RTC is enabled.
+bool _watch_rtc_is_enabled();
 
-bool watch_rtc_is_enabled();
+/** @brief Sets the system date and time.
+  * @param date_time A struct representing the date and time you wish to set.
+  */
 void watch_set_date_time(struct calendar_date_time date_time);
+
+/** @brief Returns the system date and time in the provided struct.
+  * @param date_time A pointer to a calendar_date_time struct.
+                     It will be populated with the correct date and time on return.
+  */
 void watch_get_date_time(struct calendar_date_time *date_time);
 
+/** @brief Registers a "tick" callback that will be called once per second.
+  * @param callback The function you wish to have called when the clock ticks.
+  */
 void watch_register_tick_callback(ext_irq_cb_t callback);
+/// @}
+
 
+/** @addtogroup adc Analog Input
+  * @brief This section covers functions related to the SAM L22's analog-to-digital converter, as well as
+  *        configuring and reading values from the three analog-capable pins on the 9-pin connector.
+  */
+/// @{
+/** @brief Enables the ADC peripheral, and configures the selected pin for analog input.
+  * @param pin One of pins A0, A1 or A2.
+  */
 void watch_enable_analog(const uint8_t pin);
+/// @}
+
 
+/** @addtogroup buttons Buttons
+  * @brief This section covers functions related to the three buttons: Light, Mode and Alarm.
+  */
+/// @{
+/** @brief Enables the external interrupt controller.
+  */
 void watch_enable_buttons();
+
+/** @brief Configures an external interrupt
+  * @param pin One of pins BTN_LIGHT, BTN_MODE or BTN_ALARM.
+  * @param callback The function you wish to have called when the button is pressed.
+  * @todo Make the alarm interrupt use the RTC tamper interrupt instead of the EIC.
+  */
 void watch_register_button_callback(const uint32_t pin, ext_irq_cb_t callback);
+/// @}
+
 
+/** @addtogroup gpio Digital Input and Output
+  * @brief This section covers functions related to general-purpose input and output signals.
+  */
+/// @{
+/** @brief Configures the selected pin for digital input.
+  * @param pin The pin that you wish to act as an input.
+  */
 void watch_enable_digital_input(const uint8_t pin);
+
+/** @brief Enables a pull-up resistor on the selected pin.
+  * @param pin The pin that you wish to configure.
+  */
 void watch_enable_pull_up(const uint8_t pin);
+
+/** @brief Enables a pull-down resistor on the selected pin.
+  * @param pin The pin that you wish to configure.
+  */
 void watch_enable_pull_down(const uint8_t pin);
+
+/** @brief Gets the level of the selected pin.
+  * @param pin The pin whose value you wish to read.
+  * @return true if the pin was logic high; otherwise, false.
+  */
 bool watch_get_pin_level(const uint8_t pin);
 
+/** @brief Configures the selected pin for digital output.
+  * @param pin The pin that you wish to act as an output.
+  */
 void watch_enable_digital_output(const uint8_t pin);
+
+/** @brief Disables digital output on the selected pin.
+  * @param pin The pin that you wish disable.
+  */
 void watch_disable_digital_output(const uint8_t pin);
+
+/** @brief Sets the level of the selected pin.
+  * @param pin The pin whose value you wish to set.
+  * @param level The level you wish to set: true for high, false for low.
+  */
 void watch_set_pin_level(const uint8_t pin, const bool level);
+/// @}
 
-struct io_descriptor *I2C_0_io;
 
+/** @addtogroup i2c I2C Controller Driver
+  * @brief This section covers functions related to the SAM L22's built-I2C driver, including
+  *        configuring the I2C bus, putting values directly on the bus and reading data from
+  *        registers on I2C devices.
+  */
+/// @{
+/** @brief Enables the I2C peripheral. Call this before attempting to interface with I2C devices.
+  */
 void watch_enable_i2c();
+
+/** @brief Sends a series of values to a device on the I2C bus.
+  * @param addr The address of the device you wish to talk to.
+  * @param buf A series of unsigned bytes; the data you wish to transmit.
+  * @param length The number of bytes in buf that you wish to send.
+  */
 void watch_i2c_send(int16_t addr, uint8_t *buf, uint16_t length);
+
+/** @brief Receives a series of values from a device on the I2C bus.
+  * @param addr The address of the device you wish to hear from.
+  * @param buf Storage for the incoming bytes; on return, it will contain the received data.
+  * @param length The number of bytes that you wish to receive.
+  */
 void watch_i2c_receive(int16_t addr, uint8_t *buf, uint16_t length);
+
+/** @brief Writes a byte to a register in an I2C device.
+  * @param addr The address of the device you wish to address.
+  * @param reg The register on the device that you wish to set.
+  * @param data The value that you wish to set the register to.
+  */
 void watch_i2c_write8(int16_t addr, uint8_t reg, uint8_t data);
+
+/** @brief Reads a byte from a register in an I2C device.
+  * @param addr The address of the device you wish to address.
+  * @param reg The register on the device that you wish to read.
+  * @return An unsigned byte representing the value of the register that was read.
+  */
 uint8_t watch_i2c_read8(int16_t addr, uint8_t reg);
+
+/** @brief Reads an unsigned little-endian word from a register in an I2C device.
+  * @param addr The address of the device you wish to address.
+  * @param reg The register on the device that you wish to read.
+  * @return An unsigned word representing the value of the register that was read.
+  * @note This reads two bytes into the word in bus order. If the device returns
+          the LSB first and then the MSB, you can use this value as returned.
+          If the device returns the data in big-endian order or uses some other
+          kind of fancy bit packing, you may need to shuffle some bits around.
+  */
 uint16_t watch_i2c_read16(int16_t addr, uint8_t reg);
+
+/** @brief Reads three bytes as an unsigned little-endian int from a register in an I2C device.
+  * @param addr The address of the device you wish to address.
+  * @param reg The register on the device that you wish to read.
+  * @return An unsigned word representing the value of the register that was read.
+  * @note This reads three bytes into the word in bus order. If the device returns
+          these bytes LSB first, you can use this value as returned. If there is a
+          sign bit, the device returns the data in big-endian order, or it uses some
+          other kind of fancy bit packing, you may need to shuffle some bits around.
+  */
 uint32_t watch_i2c_read24(int16_t addr, uint8_t reg);
+
+
+/** @brief Reads an unsigned little-endian int from a register in an I2C device.
+  * @param addr The address of the device you wish to address.
+  * @param reg The register on the device that you wish to read.
+  * @return An unsigned word representing the value of the register that was read.
+  * @note This reads three bytes into the word in bus order. If the device returns
+          these bytes LSB first, you can use this value as returned. If the device
+          returns the data in big-endian order, or it uses some other kind of fancy
+          bit packing, you may need to shuffle some bits around.
+  */
 uint32_t watch_i2c_read32(int16_t addr, uint8_t reg);
+/// @}
+
 
+/** @addtogroup deepsleep Deep Sleep Control
+  * @brief This section covers functions related to preparing for and entering BACKUP mode, the
+  *        deepest sleep mode available on the SAM L22
+  */
+/// @{
+/** @brief Stores 32 bits of data in the RTC's backup register, which retains its data in deep sleep.
+  * @param data An unsigned 32 bit integer with the data you wish to store.
+  * @param reg A register from 0-7.
+  */
 void watch_store_backup_data(uint32_t data, uint8_t reg);
+
+/** @brief Gets 32 bits of data from the RTC's backup register, which retains its data in deep sleep.
+  * @param reg A register from 0-7.
+  * @return An unsigned 32 bit integer with the from the backup register.
+  */
 uint32_t watch_get_backup_data(uint8_t reg);
+
+/** @brief Enters the SAM L22's lowest-power mode, BACKUP.
+  * @details This function does some housekeeping before entering BACKUP mode. It first disables all
+  *          peripherals except for the RTC, and disables the tick interrupt (since that would wake)
+  *          us up from deep sleep. It also sets an external wake source on the ALARM button, if one
+  *          was not already set. If you wish to wake from another source, such as one of the external
+  *          wake interrupt pins on the 9-pin connector, set that up prior to calling this function.
+  * @note If you have a callback set for an external wake interrupt, it will be called if triggered while
+  *       in ACTIVE, IDLE or STANDBY modes, but it *will not be called* when waking from BACKUP.
+  *       Waking from backup is effectively like waking from reset, except that your @ref
+  *       app_wake_from_deep_sleep function will be called.
+  * @warning still kind of glitchy!
+  */
 void watch_enter_deep_sleep();
+/// @}
 
 #endif /* WATCH_H_ */
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