Merge pull request #397 from openaps/dev

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openaps · Oct 2, 2016 · 782ad1b · 782ad1b
2 parents a948ead + 2d2c874
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diff --git a/docs/api/openaps/openaps.rst b/docs/api/openaps/openaps.rst
@@ -8,12 +8,9 @@ Subpackages
 
     openaps.alias
     openaps.cli
-    openaps.controllers
     openaps.devices
     openaps.glucose
-    openaps.monitors
     openaps.reports
-    openaps.suggesters
     openaps.uses
     openaps.vendors
 

diff --git a/docs/docs/README.md b/docs/docs/README.md
@@ -1,3 +1,3 @@
 # Docs / Docs
 
-This is not the main OpenAPS documentation directory. To switch to main Readme please click [here](../../README.md)
+This is not the main OpenAPS documentation directory. To switch to main Readme please click [here](../)
diff --git a/docs/docs/Resources/faq.md b/docs/docs/Resources/faq.md
@@ -15,14 +15,14 @@ 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](other-projects.md#commercial-aps-efforts) for more
+[Commercial APS Efforts](../Resources/other-projects#commercial-aps-efforts) for more
 information.
 
 
 \#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
 mealtime insulin. For background on #OpenAPS, review the [\#OpenAPS Reference
-Design](http://openaps.org/open-artificial-pancreas-system-openaps-reference-design/)
+Design](https://openaps.org/reference-design/)
 page.
 
 ## What does an OpenAPS closed loop look like?

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](../Resources/resources.md) section for a list of those sharing their experiences publicly.
+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.
 
 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
@@ -9,6 +9,7 @@ Resources
    my-first-pr
    technical-resources
    troubleshooting
+   wifi
    history
    other-projects
    faq

diff --git a/docs/docs/Resources/other-projects.md b/docs/docs/Resources/other-projects.md
@@ -42,7 +42,7 @@ Notably, work on Boston University iLet UI (https://github.com/tidepool-org/bion
 
 There are currently several commercial closed-loop products in development by old and new companies in the diabetes treatment space. These include:
 
-* [Medtronic MiniMed 640G](https://www.medtronic-diabetes.com.au/insulin-pumps/640g)
+* [Medtronic MiniMed 640G](https://www.medtronic-diabetes.com.au/pump-therapy/640g)
 * [Medtronic MiniMed 670G](http://diatribe.org/drugdevice-name/medtronic-minimed-670g)
 * [TypeZero Technologies](http://www.typezero.com/)
 * [Bigfoot Biomedical](http://www.bigfootbiomedical.com/)

diff --git a/docs/docs/Resources/technical-resources.md b/docs/docs/Resources/technical-resources.md
@@ -43,8 +43,6 @@ These represent a small selection of guides, tutorials, and quick references for
 
 [Fing](http://www.overlooksoft.com/download) (Android and Apple): Identify IP address of devices on a network. Useful for finding the IP address of RPi on new networks.
 
-[Hotspot Manager](https://play.google.com/store/apps/details?id=com.etustudio.android.hotspotmanager&hl=en) (Android):  Identify IP address of devices on a hotspot. Useful for finding the IP address of RPi on hotspots.
-
 [JuiceSSH](https://play.google.com/store/apps/details?id=com.sonelli.juicessh&hl=en) (Android): SSH client for Android devices
 
 ## Markdown syntax

diff --git a/docs/Resources/wifi.md → docs/docs/Resources/wifi.md b/docs/Resources/wifi.md → docs/docs/Resources/wifi.md
diff --git a/docs/docs/introduction/index.rst b/docs/docs/introduction/index.rst
@@ -12,7 +12,6 @@ Introduction section includes:
    :maxdepth: 4
 
    understand-this-guide
-   conventions
    contribute
    communication-support-channels
 

diff --git a/docs/docs/openaps-guide/core/vendors.md b/docs/docs/openaps-guide/core/vendors.md
diff --git a/docs/docs/openaps-guide/index.rst b/docs/docs/openaps-guide/index.rst
@@ -1,6 +1,6 @@
 
 Guide to understanding the openaps toolkit
------------------------------
+------------------------------------------
 
 Welcome to openaps
 
@@ -14,12 +14,3 @@ Welcome to openaps
    core/reports
    core/alias
 
-.. ::
-
-   core/vendors
-   tutorial
-   
-
-
-
-
diff --git a/docs/docs/openaps-guide/tutorial.md b/docs/docs/openaps-guide/tutorial.md
diff --git a/docs/docs/walkthrough/phase-0/hardware.md b/docs/docs/walkthrough/phase-0/hardware.md
@@ -192,7 +192,7 @@ charged, it will stay charged when connected to the Pi.
 Your OpenAPS implementation can also pull CGM data from a Nightscout site in
 addition to pulling from the CGM directly. You can find more documentation about
 pulling CGM data from a Nightscout site
-[here](../phase-1/using-openaps-tools.html#pulling-blood-glucose-levels-from-nightscout).
+[here](../phase-1/using-openaps-tools#pulling-blood-glucose-levels-from-nightscout).
 
 * If you have an Android phone, you can use the xDrip app to get your data from
   the Dexcom to Nightscout, to then be used in OpenAPS.
@@ -287,7 +287,7 @@ the Raspberry Pi.
 
 [TeckNet® POWER BANK 9000mAh USB External Battery Backup Pack](http://www.amazon.com/gp/product/B00FBD3O2M)
 
-[Zendure® 2nd Gen A3 Portable Charger 10000mAh - 2.1a Dual USB - in-line charging](www.amazon.com/Zendure-2nd-Portable-Charger-10000mAh/dp/B014RBEAQC/ref=sr_1_1)
+[Zendure® 2nd Gen A3 Portable Charger 10000mAh - 2.1a Dual USB - in-line charging](http://www.amazon.com/Zendure-2nd-Portable-Charger-10000mAh/dp/B014RBEAQC/ref=sr_1_1)
 
 ### USB Cables
 

diff --git a/...walkthrough/phase-1/analyze-existing-data → ...kthrough/phase-1/analyze-existing-data.md b/...walkthrough/phase-1/analyze-existing-data → ...kthrough/phase-1/analyze-existing-data.md
diff --git a/docs/docs/walkthrough/phase-1/index.rst b/docs/docs/walkthrough/phase-1/index.rst
@@ -8,8 +8,8 @@ Phase 1: Monitoring and Visualization
    log-clean-analyze
    analyze-existing-data
    using-openaps-tools
-
    visualization
+   openaps-to-nightscout
    offline-monitoring
 
 

diff --git a/docs/docs/walkthrough/phase-1/openaps-to-nightscout.md b/docs/docs/walkthrough/phase-1/openaps-to-nightscout.md
@@ -1,3 +1,5 @@
+# Alternate Nightscout OpenAPS Instructions
+
 To get your OpenAPS viewed onto your Nightscout site, start by using the following tool:(It would be a good idea to be disconnected from your pump and do a Bolus Wizard so you can check the status of your Nightscout uploading.)
 $nightscout autoconfigure-device-crud
 To view your data on your Nightscout site, start by doing the following:

diff --git a/docs/docs/walkthrough/phase-3/index.rst b/docs/docs/walkthrough/phase-3/index.rst
@@ -8,6 +8,7 @@ Phase 3: Automated Control
 
    considerations
    Understand-determine-basal
+   Open-Loop-Testing
 
 
 
diff --git a/docs/docs/walkthrough/phase-5/tuning-targets.md b/docs/docs/walkthrough/phase-5/tuning-targets.md
@@ -2,7 +2,7 @@
 
 After you adjust your max iob and go beyond low glucose suspend mode, run the system overnight under close observation with the following considerations around targets:
 
-* You should start with high targets and a good safety margin. For example, you might start with your target at 150 to see how the system does. OpenAPS has a "min" target floor which prevents you from setting it below 90.
+* You should start with high targets and a good safety margin. For example, you might start with your target at 150 to see how the system does. OpenAPS has a "min" target floor which prevents you from setting it below 80.
 
 * Before adjusting your target, you should have at least one night with zero low alarms (in three days) before considering dropping the max target below 160.
 

diff --git a/docs/docs/walkthrough/phase-6/index.rst b/docs/docs/walkthrough/phase-6/index.rst
@@ -12,6 +12,7 @@ Phase 6: Iterate and Improve the Closed Loop
    daytime-testing
    advanced-features
    Configure-Automatic-Sensitivity-Mode
+   Usability-considerations
 
 
 

diff --git a/docs/reference/mm/index.rst b/docs/reference/mm/index.rst
@@ -1,6 +1,4 @@
 
-
-.. _mm-tools
 mm
 ==
 .. toctree::

diff --git a/docs/reference/openaps/openaps-device-pump.md b/docs/reference/openaps/openaps-device-pump.md
@@ -3,13 +3,13 @@ This device contains the information requied to connect to your pump, such as yo
 ##### Setup code
 `openaps device add pump mmeowlink subg_rfspy /dev/mmeowlink [YOUR PUMP SERIAL]`
 ##### Sample contents
-`
+```
 [device "pump"]
 serial = [YOUR PUMP SERIAL]
 port = /dev/mmeowlink
 radio_type = subg_rfspy
 model = [YOUR PUMP MODEL]
 expires = 2016-05-23T23:02:36.168762
-'
+```
 ##### Dependencies
 None
diff --git a/docs/reference/openaps/openaps-report-monitor-battery.md b/docs/reference/openaps/openaps-report-monitor-battery.md
@@ -3,9 +3,11 @@ This report contains the current status and voltage of the battery in your pump.
 ##### Setup code
 `openaps report add monitor/battery.json JSON pump read_battery_status`
 ##### Sample contents
-`{
+```
+{
   "status": "normal",
   "voltage": 1.56
-}`
+}
+```
 ##### Dependencies
 None
diff --git a/docs/reference/openaps/openaps-report-monitor-clock.md b/docs/reference/openaps/openaps-report-monitor-clock.md
@@ -5,4 +5,4 @@ This report contains the date and time that is set on your pump, but does **NOT*
 ##### Sample contents
 `"2016-05-22T00:18:41"`
 ##### Dependencies
-* [`pump.ini`](openaps-device-pump.md)
+* [`pump.ini`](./openaps-device-pump.md)
diff --git a/docs/reference/openaps/openaps-report-monitor-glucose.md b/docs/reference/openaps/openaps-report-monitor-glucose.md
@@ -3,7 +3,8 @@ This report contains multiple glucose entries from either your CGM or Nightscout
 ##### Setup code
 `openaps report add monitor/glucose.json JSON cgm oref0_glucose --hours "25.0" --threshold "100"`
 ##### Sample contents
-`[
+```
+[
   {
     "trend_arrow": "FLAT",.
     "display_time": "2016-05-22T00:22:27",.
@@ -19,6 +20,7 @@ This report contains multiple glucose entries from either your CGM or Nightscout
     "type": "sgv",.
     "glucose": 149
   },
-]`
+]
+```
 ##### Dependencies
-* [`cgm.ini`](openaps-device-cgm.md)
+* [`cgm.ini`](./openaps-device-cgm.md)
diff --git a/docs/reference/openaps/openaps-report-monitor-iob.md b/docs/reference/openaps/openaps-report-monitor-iob.md
@@ -3,7 +3,8 @@ This report contains several entries detailing the levels of IOB (Insulin On Boa
 ##### Setup code
 `openaps report add monitor/iob.json text iob shell monitor/pumphistory-zoned.json settings/profile.json monitor/clock-zoned.json`
 ##### Sample contents
-`[
+```
+[
   {
     "iob": 1.908,
     "activity": 0.0009,
@@ -13,8 +14,9 @@ This report contains several entries detailing the levels of IOB (Insulin On Boa
     "hightempinsulin": 3.2,
     "time": "2016-05-22T04:43:33.000Z"
   },
-]`
+]
+```
 ##### Dependencies
-* [`monitor/pumphistory-zoned.json`](openaps-report-monitor-pumphistory-zoned.md)
-* [`settings/profile.json`](openaps-report-settings-profile.md)
-* [`monitor/clock-zoned.json`](openaps-report-monitor-clock-zoned.md)
+* [`monitor/pumphistory-zoned.json`](./openaps-report-monitor-pumphistory-zoned.md)
+* [`settings/profile.json`](./openaps-report-settings-profile.md)
+* [`monitor/clock-zoned.json`](./openaps-report-monitor-clock-zoned.md)
diff --git a/docs/reference/openaps/openaps-report-monitor-pumphistory-zoned.md b/docs/reference/openaps/openaps-report-monitor-pumphistory-zoned.md
@@ -3,7 +3,8 @@ This report is the same as your `pumphistory.json` report, but adjusted for your
 ##### Setup code
 `openaps use tz rezone --timezone "[YOUR TIMEZONE]" --adjust "missing" --date "timestamp dateString start_at end_at created_at" --astimezone monitor/pumphistory.json`
 ##### Sample contents
-`[
+```
+[
   {
     "_type": "TempBasalDuration",.
     "_description": "TempBasalDuration 2016-05-23T22:15:28 head[2], body[0] op[0x16]",.
@@ -13,6 +14,7 @@ This report is the same as your `pumphistory.json` report, but adjusted for your
     "duration (min)": 30,.
     "_date": "5c4f165710"
   },
-]`
+]
+```
 ##### Dependencies
-* [`monitor/pumphistory.json`](openaps-report-monitor-pumphistory.md)
+* [`monitor/pumphistory.json`](./openaps-report-monitor-pumphistory.md)
diff --git a/docs/reference/openaps/openaps-report-monitor-pumphistory.md b/docs/reference/openaps/openaps-report-monitor-pumphistory.md
@@ -3,7 +3,8 @@ This report gathers the last 5 hours of history directly from your pump.
 ##### Setup code
 `openaps report add monitor/pumphistory.json JSON pump iter_pump_hours 5`
 ##### Sample contents
-`[
+```
+[
   {
     "_type": "TempBasalDuration",.
     "duration (min)": 30,.
@@ -13,6 +14,7 @@ This report gathers the last 5 hours of history directly from your pump.
     "_head": "1601",.
     "_date": "5c4f165710"
   },
-]`
+]
+```
 ##### Dependencies
-* [`pump.ini`](openaps-device-pump.md)
+* [`pump.ini`](./openaps-device-pump.md)
diff --git a/docs/reference/openaps/openaps-report-settings-auto-sens.md b/docs/reference/openaps/openaps-report-settings-auto-sens.md
@@ -5,8 +5,8 @@ This report contains an automatically determined, temporary modification to your
 ##### Sample contents
 `{"ratio":0.78}`
 ##### Dependencies
-* [`monitor/glucose.json`](openaps-report-monitor-glucose.md)
-* [`settings/pumphistory-24h-zoned.json`](openaps-report-settings-pumphistory-24h-zoned.md)
-* [`settings/insulin_sensitivities.json`](openaps-report-settings-insulin_sensitivities.md)
-* [`settings/basal_profile.json`](openaps-report-settings-basal_profile.md)
-* [`settings/profile.json`](openaps-report-settings-profile.md)
+* [`monitor/glucose.json`](./openaps-report-monitor-glucose.md)
+* [`settings/pumphistory-24h-zoned.json`](./openaps-report-settings-pumphistory-24h-zoned.md)
+* [`settings/insulin_sensitivities.json`](./openaps-report-settings-insulin_sensitivities.md)
+* [`settings/basal_profile.json`](./openaps-report-settings-basal_profile.md)
+* [`settings/profile.json`](./openaps-report-settings-profile.md)
diff --git a/docs/reference/openaps/openaps-report-settings-basal_profile.md b/docs/reference/openaps/openaps-report-settings-basal_profile.md
@@ -3,7 +3,8 @@ This report contains the basal rates that are set up in your pump.
 ##### Setup code
 `openaps report add settings/basal_profile.json JSON pump read_selected_basal_profile`
 ##### Sample contents
-`[
+```
+[
   {
     "i": 0,
     "start": "00:00:00",
@@ -22,6 +23,7 @@ This report contains the basal rates that are set up in your pump.
     "rate": 1.8,
     "minutes": 480
   }
-]`
+]
+```
 ##### Dependencies
-* [`pump.ini`](openaps-device-pump.md)
+* [`pump.ini`](./openaps-device-pump.md)
diff --git a/docs/reference/openaps/openaps-report-settings-bg_targets.md b/docs/reference/openaps/openaps-report-settings-bg_targets.md
@@ -3,7 +3,8 @@ This report contains the high/low glucose targets set up in your pump. OpenAPS h
 ##### Setup code
 `openaps report add settings/bg_targets.json JSON pump read_bg_targets`
 ##### Sample contents
-`{
+```
+{
   "units": "mg/dL",
   "raw": "0x01 0x00 0x64 0x78 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00",
   "targets": [
@@ -17,6 +18,7 @@ This report contains the high/low glucose targets set up in your pump. OpenAPS h
     }
   ],
   "first": 1
-}`
+}
+```
 ##### Dependencies
-* [`pump.ini`](openaps-device-pump.md)
+* [`pump.ini`](./openaps-device-pump.md)
diff --git a/docs/reference/openaps/openaps-report-settings-carb_ratios.md b/docs/reference/openaps/openaps-report-settings-carb_ratios.md
@@ -3,7 +3,8 @@ This report contains your carb ratios.
 ##### Setup code
 `openaps report add settings/carb-ratios.json JSON pump read_carb_ratios`
 ##### Sample contents
-`{
+```
+{
   "units": "grams",
   "raw": "0x01 0x00 0x05 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00",
   "first": 1,
@@ -17,6 +18,7 @@ This report contains your carb ratios.
       "x": 0
     }
   ]
-}`
+}
+```
 ##### Dependencies
-* [`pump.ini`](openaps-device-pump.md)
+* [`pump.ini`](./openaps-device-pump.md)
diff --git a/docs/reference/openaps/openaps-report-settings-insulin_sensitivities.md b/docs/reference/openaps/openaps-report-settings-insulin_sensitivities.md
@@ -3,7 +3,8 @@ This report contains the insulin sensitivity levels stored in your pump.
 ##### Setup code
 `openaps report add settings/insulin_sensitivities.json JSON pump read_insulin_sensitivities`
 ##### Sample contents
-`{
+```
+{
   "units": "mg/dL",
   "sensitivities": [
     {
@@ -15,6 +16,7 @@ This report contains the insulin sensitivity levels stored in your pump.
     }
   ],
   "first": 1
-}`
+}
+```
 ##### Dependencies
-* [`pump.ini`](openaps-device-pump.md)
+* [`pump.ini`](./openaps-device-pump.md)