openaps · bewest · Dec 30, 2015 · Jan 19, 2016 · Jan 26, 2016 · Jan 28, 2016
diff --git a/README.md b/README.md
@@ -1,16 +1,18 @@
 # Introduction 
 
 ### Read the Docs
-* [Latest production docs](http://openaps.readthedocs.org/en/latest/index.html)
-* [Dev docs](http://openaps.readthedocs.org/en/dev/index.html)
-* [Dana's docs](http://openaps.readthedocs.org/en/dana-dev/index.html)
+* [Latest production docs](https://openaps.readthedocs.org/en/latest/index.html)
+* [Dev docs](https://openaps.readthedocs.org/en/dev/index.html)
+* [Dana's docs](https://openaps.readthedocs.org/en/dana-dev/index.html)
 
 ## Welcome
 
 Welcome to the [openaps](https://github.com/openaps/) documentation!
 
 openaps is part of a set of tools to 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/). 
 
+Here are two visuals to show you what the physical hardware components of an OpenAPS setup look like - ![version A](./docs/docs/IMG_1112.jpg) is without labels; ![version B](docs/Images/piSetup.jpg) contains labels to describe the parts.
+
 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. 
 
 The tools may be categorized as: 1)  **monitor** collecting data and

diff --git a/docs/Images/basal_profile.png b/docs/Images/basal_profile.png
diff --git a/docs/Images/nightscout.png b/docs/Images/nightscout.png
diff --git a/docs/Images/ns_app_settings.png b/docs/Images/ns_app_settings.png
diff --git a/docs/Images/ns_version.png b/docs/Images/ns_version.png
diff --git a/docs/Images/piSetup.jpg b/docs/Images/piSetup.jpg
diff --git a/docs/Images/profile_editor.png b/docs/Images/profile_editor.png
diff --git a/docs/_static/openaps-logo.png b/docs/_static/openaps-logo.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -60,8 +60,8 @@
 
 # General information about the project.
 project = u'OpenAPS'
-copyright = u'2016, Ben West'
-author = u'Ben West'
+copyright = u'2016, Ben West, Dana Lewis, and openaps contributors'
+author = u'Ben West, Dana Lewis, Scott Leibrand, 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
@@ -123,18 +123,43 @@
 # a list of builtin themes.
 html_theme = 'alabaster'
 
+
+extra_nav_links = {
+  'docs': 'https://github.com/openaps/docs',
+  'openaps': 'https://github.com/openaps/openaps',
+  'dexcom_reader': 'https://github.com/openaps/dexcom_reader',
+  'decocare': 'https://github.com/bewest/decoding-carelink',
+  'openaps.org': 'https://openaps.org/',
+}
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
 # alabaster
+theme_github_user = 'openaps'
+theme_github_repo = 'docs'
 html_theme_options = {
   'show_related': True,
+  'github_user': theme_github_user,
+  'github_repo': theme_github_repo,
+  'logo': 'openaps-logo.png',
+  # TODO: ???? doesn't work?
+  'extra_nav_links': extra_nav_links,
+}
+
+"""
+html_theme = 'sphinx_rtd_theme'
+html_theme_options = {
+  'display_github': True,
+  'github_user': 'openaps',
+  'github_repo': 'docs',
 }
+import sphinx_rtd_theme
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path( )]
+"""
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-html_theme_path = [alabaster.get_path( )]
+html_theme_path = []
+html_theme_path = [alabaster.get_path( ),]
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
@@ -146,6 +171,7 @@
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
 #html_logo = None
+html_logo = '_static/openaps-logo.png'
 
 # The name of an image file (relative to this directory) to use as a favicon of
 # the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -165,6 +191,7 @@
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
 #html_last_updated_fmt = '%b %d, %Y'
+html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
@@ -173,6 +200,7 @@
 # Custom sidebar templates, maps document names to template names.
 #html_sidebars = {}
 # for alabaster
+"""
 html_sidbars = {
   '**': [
       'about.html',
@@ -182,6 +210,9 @@
       'donate.html',
   ]
 }
+"""
+
+html_sidbars = { }
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
@@ -251,7 +282,7 @@
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
     (master_doc, 'OpenAPS.tex', u'OpenAPS Documentation',
-     u'Ben West', 'manual'),
+     author, 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of

diff --git a/docs/docs/Overview/index.rst b/docs/docs/Overview/index.rst
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/troubleshooting.md b/docs/docs/Resources/troubleshooting.md
@@ -58,7 +58,7 @@ Warning: do not run any  openaps commands with sudo in front of it `sudo openaps
 
 ### Environment variables
 
-If you are getting your BG from Nightscout or you want to upload loop status/resuts to Nightscout, among other things you'll need to set 2 environment variabled: `NIGHTSCOUT_HOST` and `API_SECRET`. If you do not set and export these variables you will receive errors while running `openaps report invoke monitor/ns-glucose.json` and while executing `ns-upload.sh` script which is most probably part of your `upload-recent-treatments` alias.Make sure your `API_SECRET` is in hashed format. Please see [this page](https://github.com/openaps/oref0#ns-upload-entries) for details. Additionally, your `NIGHTSCOUT_HOST` should be in a format like `http://yourname.herokuapp.com` (without trailing slash). For the complete visualization guide use [this page](https://github.com/openaps/docs/blob/master/docs/Automate-system/vizualization.md) from the OopenAPS documentation.
+If you are getting your BG from Nightscout or you want to upload loop status/resuts to Nightscout, among other things you'll need to set 2 environment variabled: `NIGHTSCOUT_HOST` and `API_SECRET`. If you do not set and export these variables you will receive errors while running `openaps report invoke monitor/ns-glucose.json` and while executing `ns-upload.sh` script which is most probably part of your `upload-recent-treatments` alias.Make sure your `API_SECRET` is in hashed format. Please see [this page](https://github.com/openaps/oref0#ns-upload-entries) for details. Additionally, your `NIGHTSCOUT_HOST` should be in a format like `http://yourname.herokuapp.com` (without trailing slash). See also [Openaps complete visualization guide](../walkthrough/phase-1/visualization.md) for more details.
 
 ### Common error messages
 
@@ -74,5 +74,7 @@ json: error: input is not JSON: Unexpected '<' at line 1, column 1:
 
   This error usually comes up when you have pulled a file down from Nightscount that was an invalid file. Typcially you might see this when trying to pull down treatments. Make sure that you have your HOST and API_KEY set correctly at the top of your cron, in your ~/.profile
 
+### Wifi and hotspot issues
+See [wifi troubleshooting page](wifi.md)
 
 
diff --git a/docs/docs/Resources/wifi.md b/docs/docs/Resources/wifi.md
@@ -0,0 +1,25 @@
+# Wifi Troubleshooting
+
+## My wifi connection keeps dropping and/or I keep getting kicked out of ssh
+There is a script that you can add to your root cron that will test your connection and reset it if it is down. Here is an example that runs every two minuntes (odd minutes). You could also do it every 5 minutes or less. Note, this does not have to be for an Edison, you can set this up for a Pi, etc as well.
+
+```
+cd ~/src
+git clone https://github.com/TC2013/edison_wifi
+cd edison_wifi
+chmod 0755 /home/edison/src/edison_wifi/wifi.sh
+```
+Next, add the script to your root cron. Note this is a different cron that what your loops runs on, so when you open it don't expect to see your loop and other items you've added.
+  * Log in as root ```su root```
+  * Edit your root cron ```crontab -e```
+  * Add the following line ```1-59/2 * * * * /home/edison/src/edison_wifi/wifi.sh google.com 2>&1 | logger -t wifi-reset```
+
+## I forget to switch back to home wifi and it runs up my data plan
+You can add a line to your cron that will check to see if <YOURWIFINAME> is avaiable and automatically switch to it if you are on a different network.
+  * Log in as root ```su root```
+  * Edit your root cron ```crontab -e```
+  * Add the following line ```*/2 * * * * ( (wpa_cli status | grep <YOURWIFINAME> > /dev/null && echo already on <YOURWIFINAME>) || (wpa_cli scan > /dev/null && wpa_cli scan_results | egrep <YOURWIFINAME> > /dev/null && udo pa_cli select_network $(wpa_clilist_networks | grep jsqrd | cut -f 1) && echo switched to <YOURWIFINAME> && sleep 15 && (for i in $(wpa_cli list_networks | grep DISABLED | cut -f 1); do wpa_cli enable_network $i > /dev/null; done) && echo and re-enabled other networks) ) 2>&1 | logger -t wifi-select```
+
+## I am having trouble consistently connecting to my wifi hotspot when I leave the house (iPhone)
+1. When you turn on your hotspot it will only broadcast for 90 seconds and then stop (even if it is flipped on). So, when you leave your house you need to go into the hotspot setting screen (and flip on if needed). Leave this screen open until you see your rig has connected.
+2. If your phone knows about wifi networks that your rig does not, your phone may connect to that wifi and in turn drop the hotspot. Make sure your phone does not connect to other wifi networks (coffee shops, a friends house, etc). You man need to forget the networks. This can also be tricky if your computer and iPhone share a network list.
diff --git a/docs/docs/introduction/communication-support-channels.md b/docs/docs/introduction/communication-support-channels.md
@@ -1,6 +1,6 @@
 # Where to go for help with your implementation
 
-There are several ways to communicate with other participants and contributors in the #OpenAPS project. See also the [Resources](../Resources/) section for additional assistance.
+There are several ways to communicate with other participants and contributors in the #OpenAPS project. See also the [Resources](../Resources/index.rst) section for additional assistance.
 
 **Note:** It's best practice not to share your pump's serial number, so make sure not to include it in pictures or pasted text output when seeking help on pump communication.
 

diff --git a/docs/docs/walkthrough/phase-0/baseline-data.md b/docs/docs/walkthrough/phase-0/baseline-data.md
@@ -12,4 +12,7 @@ Go ahead and document your most recent A1c and keep it somewhere handy. This wil
 
 ## Get comfortable making a PR
 
-You should be comfortable making a PR to this documentation. If you haven't ever done this, [click here](../../Resources/my-first-pr.html) and try it out.
+You should be comfortable making a PR to this documentation. If you haven't
+ever done this, take a look at
+[my first pull request guide](../../Resources/my-first-pr.md)
+and try it out.
diff --git a/...ocs/walkthrough/phase-0/loops-in-progress → .../walkthrough/phase-0/loops-in-progress.md b/...ocs/walkthrough/phase-0/loops-in-progress → .../walkthrough/phase-0/loops-in-progress.md
diff --git a/docs/docs/walkthrough/phase-1/visualization.md b/docs/docs/walkthrough/phase-1/visualization.md
@@ -114,7 +114,9 @@ $ openaps alias add format-latest-nightscout-treatments '! bash -c "nightscout c
 $ openaps alias add upload-recent-treatments '! bash -c "openaps format-latest-nightscout-treatments && test $(json -f upload/latest-treatments.json -a created_at eventType | wc -l ) -gt 0 && (ns-upload $NIGHTSCOUT_HOST $API_SECRET treatments.json upload/latest-treatments.json ) || echo \"No recent treatments to upload\""' || die "Can't add upload-recent-treatments"
 ```
 
-Note that a pumphistory-zoned.json report is required, which can be generated from pumphistory.json using `tz`, following the approach described above for clock-zoned.json. After running your loop from command line, you may try executing `openaps upload-recent-treatments` manually from command line. Upon successful upload, the recent treatments will show up automatically on the Nightscount page.  
+Note that a pumphistory-zoned.json report is required, which can be generated from pumphistory.json using `tz`, following the approach described above for clock-zoned.json, including making sure to add it to your monitor-pump alias. In addition, if you haven't already created a settings/model.json report, you should create that report and invoke it since it is required for format-latest-nightscout-treatments.
+
+After running your loop from command line, you may try executing `openaps upload-recent-treatments` manually from command line. Upon successful upload, the recent treatments will show up automatically on the Nightscount page.  
 
 Note:  Currently extended boluses are not handled well and depending on the timing of the upload are either missed entirely or have incorrect information.
 

diff --git a/docs/docs/walkthrough/phase-2/Using-oref0-tools.md b/docs/docs/walkthrough/phase-2/Using-oref0-tools.md
@@ -1,4 +1,4 @@
-#Using oref0 Tools
+# Using oref0 Tools
 
 ## Add the oref0 Virtual Devices
 In Phase 1, you added two physical medical devices to openaps—your pump and your cgm. This was done using the command `$ openaps device add` and then specifying the device name, type, and parameters. OpenAPS tools to gather system profile parameters such as pump settings, calculate the current insulin on board (IOB), and determine if the pump temp basal should be updated or not, are contained in the OpenAPS reference system oref0. Since there is no physical oref0 device, you are essentially adding it to the openaps environment as a virtual device or plugin.

diff --git a/docs/docs/walkthrough/phase-2/building-preflight-safety-checks.md b/docs/docs/walkthrough/phase-2/building-preflight-safety-checks.md
@@ -37,7 +37,7 @@ returns the current pump time stamp, such as "2016-01-09T10:47:56", if the syste
 Collecting all the error checking, a `preflight` alias could be defined as follows:
 
 ```
-$ openaps alias add preflight '! bash -c "rm -f monitor/clock.json && openaps report invoke monitor/clock.json 2>/dev/null && grep -q T monitor/clock.json && echo PREFLIGHT OK || (mm-stick warmup || (sudo oref0-reset-usb && echo PREFLIGHT SLEEP && sleep 120); echo PREFLIGHT FAIL; exit 1)"'
+$ openaps alias add preflight '! bash -c "rm -f monitor/clock.json && openaps report invoke monitor/clock.json 2>/dev/null && grep -q T monitor/clock.json && echo PREFLIGHT OK || (mm-stick warmup || (sudo oref0-reset-usb; echo PREFLIGHT SLEEP; sleep 120); echo PREFLIGHT FAIL; exit 1)"'
 ```
 
 In this `preflight` example, a wait period of 120 seconds is added using `sleep` bash command if the USB ports have been reset in an attempt to revive the MM CareLink stick. This `preflight` example also shows how bash commands can be chained together with the bash && ("and") or || ("or") operators to execute different subsequent commands depending on the output code of a previous command (interpreted as "true" or "false").

diff --git a/docs/docs/walkthrough/phase-2/loop-and-retry-logic.md b/docs/docs/walkthrough/phase-2/loop-and-retry-logic.md
@@ -3,3 +3,27 @@
 To pull all of oref0 together, you could create a "loop" alias that looks something like `openaps alias add loop '! bash -c "openaps monitor-cgm 2>/dev/null && ( openaps preflight && openaps gather && openaps enact) || echo No CGM data."'`. If you want to also add some retry logic to try again if something failed, you could then do something like `openaps alias add retry-loop '! bash -c "openaps preflight && until( ! mm-stick warmup || openaps loop); do sleep 5; done"'`.
 
 Once all that is working and tested, you will have a command that can be run manually or on a schedule to collect data from the pump and cgm, calculate IOB and a temp basal suggestion, and then enact that on the pump. 
+
+## A barebones loop
+
+- Make sure all dirs that have new files generated are cleaned out
+- Get CGM data
+- Get pump data
+- Get Basal Suggestions
+- Check if you need to put suggestions in place and if you do, then run them
+
+## A more advanced loop
+**Pull pump settings once an hour**
+
+**Log everything!**
+- Make sure only one loop runs at a time
+- Verify you can talk to the pump, you can't reset the USB carelink connection
+- Make sure all dirs that have new files generated are cleaned out
+- Get CGM data
+- Get pump data
+- Get Basal Suggestions
+- Check if you need to put suggestions in place and if you do, then run them
+	- Pull pump settings again since you just modified the pump
+	- get latest ns treatment time
+	- format latest nightscout treatments
+	- upload recent treatments
diff --git a/docs/docs/walkthrough/phase-2/using-openaps-tools.md b/docs/docs/walkthrough/phase-2/using-openaps-tools.md
@@ -136,6 +136,8 @@ Then, you can add your pump again with a different name or serial number.
 
 ### Check that you can communicate with your pump
 
+Ensure that you have the CareLink USB stick plugged into the Pi using the USB extension
+
 Now that you have added these devices, let's see if we can establish communication with them. First, the pump:
 
 `$ openaps use <my_pump_name> model`
@@ -362,8 +364,17 @@ repository" box checked. Once created, you will be directed to a "Repository
 setup" page. Under the "Command line" section, click on the "I have an existing
 project" option and follow the instructions.
 
+In order to eliminate being
+prompted for your Bitbucket password every time you `$ git push`, change the
+origin field provided by Bitbucket from `https://USERNAME@bitbucket.org...` to
+`https://USERNAME:PASSWORD@bitbucket.org...`.  PASSWORD is the same password
+you use to log-in to your Bitbucket account.
+
 Once you have completed this step, all of the files in your `<my_openaps>`
 directory will be saved in your online Bitbucket repository. Whenever you would
 like to update your backup, simply go into your `<my_openaps>` directory and `$
 git push`. This process can be automated, but we'll save that for another day.
 
+[Github mkimg tool](https://github.com/zymbit/rpi-mkimg) has the ability to create a full SD card image with the advantage to shrink it to its minimum size quite different from the windows Win32DiskImager which always creates an image which is as large as the card.  Using Win32DiskImager it might not be possible to restore an image on a new card with the same size. Using Github mkimg tool instead 
+for example a 32 GB size card can be reduced to approximately 1.9 GB.
+
diff --git a/docs/piSetup.jpg b/docs/piSetup.jpg
diff --git a/docs/reference/nightscout/index.rst b/docs/reference/nightscout/index.rst
@@ -1,5 +1,5 @@
 
-.. _nightscout-tools
+.. _nightscout-tools:
 
 Nightscout
 ==========