HuMoN-Research-Lab · kileyhartigan · Oct 6, 2022 · Oct 6, 2022 · Oct 6, 2022 · Oct 6, 2022
diff --git a/Works_in_progress/Knowledge_base_organization.md b/Works_in_progress/Knowledge_base_organization.md
@@ -0,0 +1,11 @@
+# How do we want to organize this knowledge base? 
+
+## Literature Library  
+1. Harder but classier: 
+- Embed actual pdf's using absolute/relative paths to uploaded pdfs in the repo itself? 
+- [Here's a guide to do this](https://stackoverflow.com/questions/69237778/how-to-embed-a-local-pdf-file-in-mkdocs-generated-website-on-github-pages)
+2. Easier but less classy? 
+- Write a summary of the article using [this workflow](../docs/Contributing_to_this_knowledge_base/Literature_Reviews.md).
+- Simply add a webpage link to the article. (potential problem with this is journal access).
+3. An In between option, seams easy-ish: 
+- Link the web version of the original publication and then Embed snippets of it into our docs using [this guide](https://facelessuser.github.io/pymdown-extensions/extensions/snippets/)
diff --git a/.../Contributing_to_this_knowledge_base/How_to_Contribute_to_Literature_Reviews.md b/.../Contributing_to_this_knowledge_base/How_to_Contribute_to_Literature_Reviews.md
@@ -0,0 +1,14 @@
+# How To Contribute to Literature Reviews  
+Let's capture the important pieces of papers we read. Below is a flexible framework for you to capture notes after you read them. As you write this, keep in mind making this searchable for our future selves.
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
+
+<p>&nbsp;</p>
+
+### What about including images?
+Add screenshots/images of graphs/data using [this guide](https://squidfunk.github.io/mkdocs-material/reference/images/?h=images) from mkdocs. 
diff --git a/...ontributing_to_this_knowledge_base/How_to_Contribute_to_Troubleshooting_docs.md b/...ontributing_to_this_knowledge_base/How_to_Contribute_to_Troubleshooting_docs.md
@@ -0,0 +1,43 @@
+## Workflow for contributing to Troubleshooting  
+
+- When you run into any issue that you eventually solve and you think someone else in the lab would benefit from knowing how you solved it, you should add it to the Troubleshooting folder. Here's a rough workflow to follow so we can attempt to have a standard-ish way of doing things. When making this workflow, I used this reference: [New Relic Troubleshooting Docs Guide](https://docs.newrelic.com/docs/style-guide/writing-docs/article-templates/troubleshooting-docs-guide/). 
+
+<p>&nbsp;</p>
+
+**First:**  
+
+1. Check out the troubleshooting folder in this repository to see if there is already a .md file in there with the category of error you're experiencing (like 'Mkdocs Errors' or 'running a freemocap session errors' or 'Blender Errors'). If there is already a file with your error category, simply add to the current file and just add a line (---) and a new secondary header (##) with your specific error problem. 
+    - Add your troubleshooting solution following the loose framework below.
+
+2. If there isn't a file with your error category, just create a new .md file inside the 'Troubleshooting' folder. In that new file, give it a reasonable header (#) so we all can understand the error category. 
+    -  Add your troubleshooting solution following the loose framework below.
+
+<p>&nbsp;</p>
+
+See this [mkdocs errors troubleshooting doc](../Troubleshooting/Mkdocs_Errors.md) as an example of how to structure your contribution. 
+
+<p>&nbsp;</p>
+
+
+    # General Error Category
+
+    ## More Specific Description of Error
+
+    ### 1. Problem
+
+    - Provide a clear, concise description of the problem the user is trying to solve. Who, what, when, where?  
+
+    ### 2. Solution(s)
+
+    - Provide an ordered list of steps to guide someone through the solution. Copy and paste useful parts of the error codes. (No screen shots. Ideally, we want to be able to search the error codes themselves).
+
+    ### 3. Cause(s)
+
+    - A highlevel paragraph of why the error happened. 
+
+    ### 4. Related info
+
+    - A more indepth reason why the error occured. Jon, this one's for you :)  
+
+    ---
+
diff --git a/docs/Contributing_to_this_knowledge_base/Start_Here.md b/docs/Contributing_to_this_knowledge_base/Start_Here.md
@@ -0,0 +1,69 @@
+# Start Here
+
+## Here's how this is all structured
+<p>&nbsp;</p> 
+This knowledge base is a github repository. We update it like any codebase using github, with branches, commits, pull requests, approvals, merges, etc. 
+
+- We're updating the docs that live on [this repository](https://github.com/HuMoN-Research-Lab/HuMoN-Research-Lab.github.io)
+and are hosted via Github Pages at [this URL](https://humon-research-lab.github.io/).
+
+- The page is built via the `material` theme of [mkdocs](https://www.mkdocs.org/).
+
+- Specifically, [this is the theme we are using](https://squidfunk.github.io/mkdocs-material/).
+
+This workflow is very similar to the one we will use to update the freemocap docs, except that the HuMoN Lab docs will be hosted via Github Pages while the freemocap docs are hosted via `readthedocs.io`
+<p>&nbsp;</p> 
+
+## How to guide - Update the humon research lab docs  
+<p>&nbsp;</p> 
+
+### Method 1: Using the Terminal  
+
+ Clone the repository on your computer using a terminal (I'm going to use a Windows Terminal, but it would look the same from any Command Prompt or powershell or whatever)
+    - this assumes you gave `git` installed. If you don't google "how to install git"  
+
+- in the terminal
+    -  `cd` to the location you want to store the docs
+    -  type `git clone https://github.com/HuMoN-Research-Lab/HuMoN-Research-Lab.github.io
+- open that folder in PyCharm
+    - make sure to open the ENTIRE FOLDER, not  a file inside of it
+- make a branch off the `main` branch
+    - call it [your_name]/[some_description_of_what_youre_doing]
+        - no spaces
+        - keep it short, it doesn't matter
+- Make a change to a document in the `/docs/` folder OR the configuration file `mkdocs.yml`
+- You can PREVIEW your changes by entering the command `mkdocs serve` in the terminal
+    - after you've installed `mkdocs-material` via `pip install -r requirements.txt`
+- add new pages by adding them to `nav` in the `mkdocs.yml` file
+    - detailed instructions here - https://www.mkdocs.org/getting-started/#adding-pages
+- When you are happy with your changes:
+  - commit your branch to Github
+  - make a Pull Request (PR) onto the `main` branch
+- When that PR is approved, it will automatically update the live docs site
+
+### Method 2: GitHub Desktop
+- Have Jon give you access to the freemocap foundation. This will allow you to make branches to the Humon Research Lab github repo. 
+
+- Install Github Desktop and add make this repo be the 'Current Repository': https://github.com/HuMoN-Research-Lab/HuMoN-Research-Lab.github.io
+
+- Create a new branch with your name and 'dev' in the title. Push the new branch. 
+
+- Now you can start making changes to the repo...using Vscode, PyCharm, Obsidian, etc. Make a change to a document in the `/docs/` folder OR the configuration file `mkdocs.yml`.  
+
+    - I (Kiley) personally use VsCode as my IDE, and I found [this resource](https://code.visualstudio.com/docs/languages/markdown) to be incredibly helpful for organizing markdown projects in VsCode. There are many helpful IDE specific shortcuts. 
+
+- You can PREVIEW your changes by entering the command `mkdocs serve` in the terminal
+    - after you've installed `mkdocs-material` via `pip install -r requirements.txt`
+- add new pages by adding them to `nav` in the `mkdocs.yml` file
+    - detailed instructions here - https://www.mkdocs.org/getting-started/#adding-pages
+- When you are happy with your changes:
+  - commit your branch to Github. Try to do this farely regularly so you don't commit a whole bucket of changes all at once, but rather a few at a time. 
+  - make a Pull Request (PR) onto the `main` branch
+- When that PR is approved, it will automatically update the live docs site
+<p>&nbsp;</p>
+
+---
+<p>&nbsp;</p>
+
+
+
diff --git a/docs/Our_Research/Retinal_Optic_Flow_During_Natural_Locomotion.md b/docs/Our_Research/Retinal_Optic_Flow_During_Natural_Locomotion.md
diff --git a/docs/Spinal_Level_Reflexes/Beam_walking_H-Reflex.md b/docs/Spinal_Level_Reflexes/Beam_walking_H-Reflex.md
@@ -0,0 +1,16 @@
+
+
+## 1. Title (linked to original publication)  
+
+[Human H-reflexes are smaller in difficult beam walking than in normal treadmill walking](https://pubmed.ncbi.nlm.nih.gov/2073943/)
+
+## 2. Date, Authors, Universities
+1990
+
+M Llewellyn, J F Yang, A Prochazka
+
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Deep_Tendon_Reflexes.md b/docs/Spinal_Level_Reflexes/Deep_Tendon_Reflexes.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Dynamic_Sensorimotor_Interactions.md b/docs/Spinal_Level_Reflexes/Dynamic_Sensorimotor_Interactions.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Evolution_of_Motor_Control_Review.md b/docs/Spinal_Level_Reflexes/Evolution_of_Motor_Control_Review.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Force_Spinal_Cord_Regulation_of_Limb_Mechanics.md b/docs/Spinal_Level_Reflexes/Force_Spinal_Cord_Regulation_of_Limb_Mechanics.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Fusimotor_Control_of_Spindle_Sensitivity.md b/docs/Spinal_Level_Reflexes/Fusimotor_Control_of_Spindle_Sensitivity.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/H-Reflex_methodology.md b/docs/Spinal_Level_Reflexes/H-Reflex_methodology.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Muscle_Function_Review.md b/docs/Spinal_Level_Reflexes/Muscle_Function_Review.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Muscle_Spindles_Postural_Control.md b/docs/Spinal_Level_Reflexes/Muscle_Spindles_Postural_Control.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Neuromechanics_Review.md b/docs/Spinal_Level_Reflexes/Neuromechanics_Review.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Predictive_and_Reactive_Tuning_Locomotor_CPG.md b/docs/Spinal_Level_Reflexes/Predictive_and_Reactive_Tuning_Locomotor_CPG.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Reflex_Circuit_Modulation_in_Motor_Control.md b/docs/Spinal_Level_Reflexes/Reflex_Circuit_Modulation_in_Motor_Control.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Spinal_Level_Reflexes/Titin_and_Winding_Filament_Theory.md b/docs/Spinal_Level_Reflexes/Titin_and_Winding_Filament_Theory.md
@@ -0,0 +1,7 @@
+## 1. Title
+## 2. Date, Authors, Universities
+## 3. General research category
+## 4. What question(s) were they trying to answer?
+## 5. How did they attempt to answer their question?
+## 6. Any noteworthy results?
+## 7. How could this research be relevant to ours?
diff --git a/docs/Troubleshooting/Mkdocs_Errors.md b/docs/Troubleshooting/Mkdocs_Errors.md
@@ -0,0 +1,72 @@
+# Mkdocs_Errors  
+
+
+## Unable to publish static site with 'mkdocs serve' command
+
+<p>&nbsp;</p>
+
+### Problem: 
+When trying to preview changes made to freemocap documentation repo using the command `mkdocs serve` in the terminal, I got the following error:
+
+
+
+    (base) kileyhartigan@Kileys-MacBook-Pro documentation % mkdocs serve
+    INFO     -  Building documentation...
+    ERROR    -  Config value: 'theme'. Error: Unrecognised theme name: 'material'. The available installed themes are: mkdocs, readthedocs
+    ERROR    -  Config value: 'markdown_extensions'. Error: Failed to load extension 'pymdownx.snippets'.
+            ModuleNotFoundError: No module named 'pymdownx'
+    Aborted with 2 Configuration Errors!
+<p>&nbsp;</p>
+
+### Solution(s)
+Skipping to the end of many things I tried:  
+1. Make sure you're operating in a virtual environment. 
+2. Once you're in your v-env, Update mkdocs and then install the server theme. To do these, enter these commands into the terminal: 
+`pip install -U mkdocs`  (This command updates mkdocs)   
+`pip install mkdocs-material` (This command installs the theme for the mkdocs server)
+3. Now typing the command  
+`mkdocs serve`  
+into the terminal should give you a url that renders a static local site for you to check your changes. 
+<p>&nbsp;</p>
+
+### Cause(s)
+1. The first problem was that I had an out of date version of mkdocs, so it didn't recognize the version of markdown my system was using.  
+2. The second problem was that I hadn't installed the right theme.
+<p>&nbsp;</p>
+
+### Related info
+The original error had a line that said: `...failed to load extension 'pymdownx.snippets'.`
+  Stackoverflow and google helped me with a suggestion to force install pymdown like this...
+
+    (base) kileyhartigan@Kileys-MacBook-Pro documentation % pip install pymdown-extensions --force
+    Collecting pymdown-extensions
+    Downloading pymdown_extensions-9.5-py3-none-any.whl (217 kB)
+        |████████████████████████████████| 217 kB 517 kB/s 
+    Collecting markdown>=3.2
+    Downloading Markdown-3.4.1-py3-none-any.whl (93 kB)
+        |████████████████████████████████| 93 kB 3.1 MB/s 
+    Collecting importlib-metadata>=4.4
+    Using cached importlib_metadata-4.12.0-py3-none-any.whl (21 kB)
+    Collecting zipp>=0.5
+    Downloading zipp-3.8.1-py3-none-any.whl (5.6 kB)
+    Installing collected packages: zipp, importlib-metadata, markdown, pymdown-extensions
+    Attempting uninstall: zipp
+        Found existing installation: zipp 3.4.1
+        Uninstalling zipp-3.4.1:
+        Successfully uninstalled zipp-3.4.1
+    Attempting uninstall: importlib-metadata
+        Found existing installation: importlib-metadata 4.12.0
+        Uninstalling importlib-metadata-4.12.0:
+        Successfully uninstalled importlib-metadata-4.12.0
+    Attempting uninstall: markdown
+        Found existing installation: Markdown 3.3.7
+        Uninstalling Markdown-3.3.7:
+        Successfully uninstalled Markdown-3.3.7
+    ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
+    mkdocs 1.3.1 requires Markdown<3.4,>=3.2.1, but you have markdown 3.4.1 which is incompatible.
+    Successfully installed importlib-metadata-4.12.0 markdown-3.4.1 pymdown-extensions-9.5 zipp-3.8.1
+
+This helped me start looking at what version of markdown I was using and ultimately realized I could simply upgrade mkdocs to the newest version, which ultimately solved the markdown version issue.  
+
+
+
diff --git a/docs/assets/Lab_Logo.png b/docs/assets/Lab_Logo.png
diff --git a/docs/assets/skelly_freemocap_favicon.ico b/docs/assets/skelly_freemocap_favicon.ico
diff --git a/docs/assets/skelly_freemocap_logo.png b/docs/assets/skelly_freemocap_logo.png
diff --git a/docs/how-to-update-these-docs.md b/docs/how-to-update-these-docs.md
diff --git a/docs/index.md b/docs/index.md
@@ -1,4 +1,7 @@
-# Welcome to the Knowledge Base for the HuMon Research Lab 
+# Home  
+
+## Welcome to the Knowledge Base for the HuMon Research Lab 
+<p>&nbsp;</p>
 
 The page is built via the `material` theme of mkdocs
 

diff --git a/docs/meeting-notes.md b/docs/meeting-notes.md
@@ -1,3 +1,5 @@
-# 2022-09-02 -  FreeMoCap Pair Programming 
+# Meeting_Notes
+
+## 2022-09-02 -  FreeMoCap Pair Programming 
 
 [![hackmd-github-sync-badge](https://hackmd.io/OoHK-ZoRTXS27lC_xS2JVw/badge)](https://hackmd.io/OoHK-ZoRTXS27lC_xS2JVw)
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css