Merge pull request #1 from openaps/master

update to latest master
openaps · Jul 1, 2017 · be329b4 · be329b4
2 parents 41b8188 + bb2a6a7
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diff --git a/README.md b/README.md
@@ -1,40 +1,26 @@
 # Introduction
 
-* Easily navigable version of the [latest production docs are here.](https://openaps.readthedocs.org/en/latest/index.html)
-* Easily navigable version of the [in-development or "dev" docs can be found here.](https://openaps.readthedocs.org/en/dev/index.html)
-
-## Welcome
-
 Welcome to the [openaps](https://github.com/openaps/) documentation!
 
-This documentation support a self-driven Do-It-Yourself (DIY) implementation of an artificial pancreas based on the [OpenAPS reference design](http://openaps.org/open-artificial-pancreas-system-openaps-reference-design/). By proceeding to use these tools or any piece within, you agree to the copyright (see LICENSE.txt for more information) and release any contributors from liability, and assume full responsibility for all of your actions and outcomes related to usage of these tools or ideas.
+This documentation supports implementing a self driven, Do It Yourself (DIY) artificial pancreas, based on the [OpenAPS Reference Design](https://openaps.org/reference-design/). By proceeding to use these tools or any [openaps](https://github.com/openaps/) repositories, you agree to abide by the copyright agreement and release any contributors from any liability. You assume full responsibility for all actions and outcomes related to use of these tools or ideas. [Please read the copyright agreement before proceeding](https://github.com/openaps/docs/blob/master/license.txt).
+
+* [The easiest option for reading the documentation is by using this version](https://openaps.readthedocs.org/en/latest/index.html). (You may want to bookmark this link.)
 
 ----------
-### A Note on DIY and the "Open" Part of OpenAPS
-This is a set of development tools to support a self-driven DIY implementation.
-Any person choosing to use these tools is solely responsible for testing and
-implementing these tools independently or together as a system.
-
-The [DIY part of OpenAPS is important](http://bit.ly/1NBbZtO). While formal training
-or experience as an engineer or a developer is not a prerequisite, a growth
-mindset is required to learn to work with the "building blocks" that will help
-you develop your OpenAPS instance. Remember as you consider this project that
-this is not a "set and forget" system; an OpenAPS implementation requires
-diligent and consistent testing and monitoring to ensure each piece of the
-system is monitoring, predicting, and controlling as desired. The performance
-and quality of your system lies solely with you.
-
-This community of contributors believes in "paying it forward," and individuals
-who are implementing these tools are asked to contribute by asking questions,
-[helping improve documentation](docs/docs/Resources/my-first-pr.md), and
-contributing in other ways.
+## A Note on DIY and the Open Part of OpenAPS
+
+This is a set of development tools to support a self driven DIY implementation of an open source artificial pancreas, OpenAPS. Any individual choosing to use these tools is solely responsible for testing, verifying, and implementing each of these tools independently or together as a system.
+
+The [DIY part of OpenAPS is important](http://bit.ly/1NBbZtO). A growth and learning mindset is required to work with the "building blocks" that will help develop your OpenAPS system. **This is not a set and forget system**; an OpenAPS system requires persistent attention. Users must do blood glucose tests frequently and watch continuous glucose monitors vigilantly, in order to ensure each piece of the system is monitoring, predicting, and controlling blood glucose safely, given user defined constraints. The performance and quality of your OpenAPS system relies solely on you.
+
+This community of contributors believes in paying it forward, and individuals who are implementing these tools are asked to contribute by asking questions, [helping improve this documentation](docs/docs/Resources/my-first-pr.md), and contributing in other ways.
 
 
 ----------
-### OpenAPS System Development Phases
+## OpenAPS System Development Phases
+
+This documentation is organized into a series of phases that progressively build upon the openaps development tools towards a working OpenAPS system.
 
-This documentation is organized into a series of phases that progressively
-build upon the openaps development tools towards a working OpenAPS system.
 The phases are as follows:
 
 * **Phase 0: General Setup**<br>
@@ -43,17 +29,22 @@ Get the equipment you need; record baseline data, configure your hardware, insta
 * **Phase 1: Monitoring and Visualization Setup**<br>
 Prepare Nightscout or other visualization tools that are key for monitoring a closed loop.
 
-* **Phase 2: Creating a a PLGM or open loop**<br>
+* **Phase 2: Creating a PLGM or open loop**<br>
 Use the setup script to build a basic loop; you can choose to run the loop manually ("open loop" mode), or automate your loop. At this stage, you should review and refine algorithms, test different scenarios for safety, etc.
 
 * **Phase 3: Understanding Your Loop and Tweaking Settings**<br>
 Analyze the basal recommendations that are outputted from your system; run in a test environment for multiple days to configure safety settings that are right for you before moving forward. 
 
 * **Phase 4: Iterate and Improve the Closed Loop**<br>
-At the end of the previous stages and after 3 consecutive nights with no hardware failures and at least 1 night without low alarms, you can move into advanced features like meal-assist and auto-sensitivity tuning. Also improve the functionality of the system with additional software or hardware development
+At the end of the previous stages and after 3 consecutive nights with no hardware failures and at least 1 night without low alarms, you can move into advanced features like advanced meal assist (AMA) and auto-sensitivity tuning ("autosens" and "autotune"), and improve the functionality of the system with additional software or hardware development.
 
 ----------
-You may be looking for:
-* How to [get help with your implementation](http://openaps.readthedocs.io/en/latest/docs/introduction/communication-support-channels.html) (hint: [go to Gitter here](https://gitter.im/nightscout/intend-to-bolus))
-* The ["old" directions](http://openaps.readthedocs.io/en/latest/docs/walkthrough/manual/index.html)
-* The [OpenAPS Reference Design](https://openaps.org/reference-design/) 
+**You may be looking for:**
+
+* [Live help with your implementation](http://openaps.readthedocs.io/en/latest/docs/introduction/communication-support-channels.html) (Hint: [Check out this Gitter channel](https://gitter.im/nightscout/intend-to-bolus))
+
+* ["Old" setup directions](http://openaps.readthedocs.io/en/latest/docs/walkthrough/manual/index.html)
+
+* [OpenAPS Reference Design](https://openaps.org/reference-design/)
+
+
diff --git a/docs/conf.py b/docs/conf.py
@@ -27,6 +27,9 @@
 
 # -- General configuration ------------------------------------------------
 
+# RTD
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+
 # If your documentation needs a minimal Sphinx version, state it here.
 #needs_sphinx = '1.0'
 
@@ -61,8 +64,8 @@
 
 # General information about the project.
 project = u'OpenAPS'
-copyright = u'2016, Ben West, Dana Lewis, and openaps contributors'
-author = u'Ben West, Dana Lewis, Scott Leibrand, openaps community'
+copyright = u'2017, the #OpenAPS community'
+author = u'the #OpenAPS community'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -122,7 +125,7 @@
 
 # The theme to use for HTML and HTML Help pages. See the documentation for
 # a list of builtin themes.
-html_theme = 'alabaster'
+#html_theme = 'default`
 
 
 extra_nav_links = {
@@ -148,7 +151,7 @@
 }
 
 """
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'default'
 html_theme_options = {
  'display_github': True,
  'github_user': 'openaps',

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diff --git a/docs/docs/Images/versions.jpg b/docs/docs/Images/versions.jpg
diff --git a/docs/docs/Resources/faq.md b/docs/docs/Resources/faq.md
@@ -11,13 +11,7 @@ glucose within the desired range through adjusting hormone doses.
 
 There are numerous different types of closed loop systems, ranging from simple
 basal suspend systems designed to mitigate extreme hypoglycemia to dual
-hormone, fully automated systems. The JDRF [Artificial Pancreas Project
-Plan](http://jdrf.org/research/treat/artificial-pancreas-project/) page
-provides an overview of the current commercial and academic generation-based
-approach. Several commercial systems are currently in development; see
-[Commercial APS Efforts](../Resources/other-projects#commercial-aps-efforts) for more
-information.
-
+hormone, fully automated systems. 
 
 \#OpenAPS is focused on a single-hormone hybrid closed-loop system. This is a
 system that uses only insulin (no glucagon) and still requires user input for
@@ -27,10 +21,16 @@ page.
 
 ## What does an OpenAPS closed loop look like?
 
-While there are numerous variations, this particular setup shows the key components—namely, a continuous glucose monitor, an insulin pump, a method for communicating with the pump (here, a CareLink USB stick), and a controller (here, a Raspberry Pi). Also shown is a Pebble watch, which can be used for monitoring the status of the OpenAPS. Not shown is the power supply (off-screen) and a way to interact with and program the Raspberry Pi, typically a computer or smartphone.
+There are numerous variations of OpenAPS setups. 
+
+This particular setup below is an original setup, similar to what was first used to close the loop by DIYers in late 2014/early 2015. The picture below shows the key components—namely, a continuous glucose monitor, an insulin pump, a method for communicating with the pump (here, a CareLink USB stick), and a controller (here, a Raspberry Pi). Also shown is a Pebble watch, which can be used for monitoring the status of the OpenAPS. Not shown is the power supply (off-screen) and a way to interact with and program the Raspberry Pi, typically a computer or smartphone.
 
 ![Example OpenAPS Setup](../IMG_1112.jpg)
 
+The most common setup as of late 2015/early 2016 has evolved to be a smaller rig, with similar components. The Edison chip is the mini-computer, and the Explorer Board hosts it along with the radio stick to communicate with the CGM and pump.
+
+![Example OpenAPS "Explorer Board" rig](../Images/Explorer_Board_rig.png)
+
 For more details on the exact hardware required to build an OpenAPS, see the
-[Hardware](../walkthrough/phase-0/hardware.md) section.
+[Hardware](../walkthrough/phase-0/hardware/hardware.md) section.
 
diff --git a/docs/docs/Resources/glossary.md b/docs/docs/Resources/glossary.md
@@ -1,6 +1,13 @@
 # Glossary
 
-<b>APS</b> - artificial pancreas system. Sometimes also referred to as "AP"
+
+## AP and OpenAPS high level terminology 
+
+<b>APS or AP</b> - artificial pancreas system. A term for a closed-loop automated insulin delivery system in which temporary basal adjustments are used to maintain BG levels at a user-specified target range. 
+
+<b>closed-loop</b> - closed-loop systems make automatic adjustments to basal delivery, without needing user-approval, based on an algorithm.
+
+<b>open-loop</b> - open-loop systems will suggest recommended adjustments to basal delivery, but will require specific user-approval prior to implementing.
 
 <b>CGM</b> - continuous glucose monitor, a temporary glucose sensor that is injected into your skin (the needle is removed) for 3-7 days and, with twice a day calibrations, provides BG readings approximately every 5 minutes.
 
@@ -10,6 +17,8 @@
 
 <b>openaps</b> - the core suite of software tools under development by this community for use in an OpenAPS implementation
 
+<b>oref0</b> - "reference design implementation version 0" of the OpenAPS reference design. Aka, the key algorithm behind OpenAPS.
+
 <b>BG</b> - Blood Glucose
 
 <b>BGI</b> (BG Impact) - The degree to which BG "should" be rising or falling. OpenAPS calculates this value to determine the 'Eventual BG'. This value can be used to make other high/low basal decisions in advanced implementations of OpenAPS.
@@ -18,22 +27,25 @@
 
 <b>Basal</b> - baseline insulin level that is pre-programmed into your pump and mimics the insulin your pancreas would give throughout the day and night
 
-<b>IOB</b> - Insulin On Board, or insulin active in your body. Note that most commercially available pumps calculate IOB based on bolus activity only. Usually, but not always, Net IOB is what Nightscout displays as 'IOB'.
+<b>IOB</b> - Insulin On Board, or insulin active in your body. Note that most commercially available pumps calculate IOB based on bolus activity only. Usually, but not always, Net IOB is what Nightscout displays as 'IOB'. While what's displayed in your NS IOB pill may match what IOB is in your current loop, it's probably a good practive not to rely on this pill alone for knowing how much IOB.
 
-<b>Net IOB</b> - amount of insulin on board, taking into account any adjusted (higher or lower) basal rates as well as bolus activity. 
+<b>Net IOB</b> - amount of insulin on board, taking into account any adjusted (higher or lower) basal rates (see Basal IOB below) as well as bolus activity. 
 
-<b>Basal IOB</b> - difference (positive or negative) between amount of insulin on board delivered via basal rates, and the amount specified by the profile basal rate.
+<b>Basal IOB</b> - difference (positive or negative) between amount of insulin on board delivered via basal rates (including any temporary basal rates), and the amount specified by your standard profile basal rate.
 
 <b>Treatments IOB</b> - amount of insulin on board delivered via boluses. Reported by some pumps as 'active insulin'.
 
-<b>DIA</b> - duration of insulin action, or how long the insulin is active in your body. (Ranges 3-6 hours typically)
+<b>DIA</b> - duration of insulin action, or how long the insulin is active in your body (Ranges 3-6 hours typically).
 
-<b>CR</b> - carb ratio, or carbohydrate ratio - the amount of carbohydrates for one unit of insulin. Example: 1 u of insulin for 10 carbs
+<b>CR</b> - carb ratio, or carbohydrate ratio - the amount of carbohydrates that are covered by one unit of insulin. Example: 1 u of insulin for 10 carbs.
 
-<b>ISF</b> - insulin sensitivity factor - the amount of insulin that drops your BG by a certain amount. Example: 1 u of insulin for 40 mg/dL (2.2 mmol/L)
+<b>ISF</b> - insulin sensitivity factor - the expected decrease in BG as a result of one unit of insulin. 
+Example: 1 u of insulin for 40 mg/dL (2.2 mmol/L)
 
 <b>NS, or Nightscout</b> - a cloud-based visualization and remote-monitoring tool. 
 
+## OpenAPS specific terminology 
+
 <b>OpenAPS Nightscout Status Messages</b> appear when the OpenAPS plugin is enabled.
  * <b>Looping ↻</b> - Success; Temp basal rate has been suggested.
  * <b>Enacted ⌁</b> - Success; Temp basal rate has been set.
@@ -49,4 +61,6 @@
 
 <b>Exp. Delta</b> - expected BG delta right now, considering all OpenAPS inputs (IOB, COB, etc).
 
-<b>RileyLink (RL)</b> - A custom designed Bluetooth Smart (BLE) to sub-1GHz module - it can be used to bridge any BLE capable smartphone to the world of sub-1GHz devices. This device is focused on talking to Medtronic insulin pumps and sensors.
+<b>snoozeBG</b> - predicted value of blood glucose adjusted for bolussnooze IOB. SnoozeBG will never exceed EventualBG.
+
+<b>predBGs</b> - predicted blood sugars over next N many minutes based on openAPS logic, in 5 minute increments
diff --git a/docs/docs/Resources/history.md b/docs/docs/Resources/history.md
@@ -10,6 +10,6 @@ In light of the success of #DIYPS closed loop and other simple APS systems built
 
 \#OpenAPS is not intended to be a “set and forget” APS system. To maximize safety, a system designed from OpenAPS only doses basal insulin. Users still need to bolus for meals as they do today. However, OpenAPS can identify deviations from predicted blood sugar changes and change basal rates to prevent dangerous drops or rises that deviate from expected behavior.
 
-After launching in early 2015, there are at least 44 known instances of OpenAPS that are live and running (as of March 23, 2016), with several others in development and testing phases. For anecdotal experiences from those running OpenAPS, watch the [#OpenAPS hashtag on Twitter](https://twitter.com/search?f=tweets&vertical=default&q=%23OpenAPS&src=typd) and also check out the [Resources](./index) section for a list of those sharing their experiences publicly.
+After OpenAPS was launched in early 2015, there are now more than ~215 known instances of DIY closed loopers using a variety of open source diabetes technologies (as of Feb 1, 2016). For anecdotal experiences from those running OpenAPS, watch the [#OpenAPS hashtag on Twitter](https://twitter.com/search?f=tweets&vertical=default&q=%23OpenAPS&src=typd) and also check out the [Resources](./index) section for a list of those sharing their experiences publicly.
 
 In early 2016, progress continues to be made with the iteration of several hardware options, in addition to multiple new software features.
diff --git a/docs/docs/Resources/index.rst b/docs/docs/Resources/index.rst
@@ -11,8 +11,6 @@ Resources
  troubleshooting
  wifi
  history
- other-projects
  faq
  glossary
-
-
+ switching-between-DIY-systems