Create mkdocs website for guide material

.github/workflows/deploy.yaml

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+name: Deploy MkDocs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Build MkDocs site
+        run: |
+          mkdocs build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site

.gitignore

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 # Mac System
 .DS_Store
+
+# Python
+__pycache__/

docs/CODE_OF_CONDUCT.md

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+# Imageomics Institute Principles of Engagement
+
+As members of the Imageomics community, we agree to maintain an environment where every participant feels welcome to be their true self and speak from the heart.
+
+To this end, we agree as individuals and as a group to:
+
+- **Listen to understand.** When one person talks, others listen.
+- **Speak to be understood.** We use lay terms and are patient with people who are not experts in our specific field. We are all learning, no matter who we are.
+- Embrace **“Yes and…”** Focus on possibilities instead of obstacles. Be inclusive of other people’s ideas. Honor divergence. 
+- **Take space / make space.** Those who tend to talk a lot are intentional about letting others talk first, while those who tend to hold back are intentional about contributing.
+- **Beware of blind spots.** We do not know what we do not know. We are vigilant for differences among our experiences and positions. 
+- **Respect time.** When a session is over, we need to move on. There is designated time for in-depth follow up and continuing conversations. 
+- **Care** for each other. We bring our full selves to the community, and we look out for each other wholeheartedly. 
+
+We abide by these principles in all Imageomics spaces, including but not limited to digital and in-person meetings, formal and informal gatherings, online discussion forums and chat spaces, and field and lab work. 
+
+Discrimination, bullying or harassment–sexual or otherwise–is misconduct. Those found to engage in misconduct will be subject to dismissal from the project and further actions as directed by the guidelines of the employers and the place of incidence.
+
+If you believe you have experienced or witnessed misconduct in an Imageomics setting, please take these steps:
+
+1. Document the incident;
+2. Tell someone you trust;
+3. Report the incident to Diane Boghrat.
+
+Privacy will be protected to the greatest extent possible.
+
+## JEDI Framework
+
+[Full text](pdfs/Imageomics_Equity_Tool.pdf)
+
+### VALUES
+#### TRANSPARENCY
+We ensure our efforts are clear about assumptions, uncertainty, and limits, and provide open sources of information, processes, and discovery.
+#### ACCOUNTABILITY
+We are responsible, individually and collectively, for the outcomes we produce and ensure, to the best of our abilities, that the methods outcome matches intended use.
+#### INCLUSION & COLLABORATION
+We create and nurture inclusive environments and welcome, value, and affirm all members of our community. We also consider how and for whom solutions are created and promote the diversification of perspectives in the creation process. We actively engage others’ perspectives, recognize everyone’s potential to contribute new ideas, and work together to find creative solutions to complex problems.
+#### SAFETY
+We ensure our practices are ethical and unbiased to the best of our ability. We address biases when we discover it and practice good data governance.  We work to improve practices and dismantle existing structures that create harm to people or the environment. 

docs/index.md

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+# Welcome to the Imageomics Institute!
+
+This wiki is intended to host internal documentation, making the information needed to get started with and use institute resources readily available to all members. It will evolve continuously with the institute.
+
+## Highlights
+There are many pages of useful information contained in this wiki covering a range of topics from institute hardware, to repositories and archives, to a glossary of _imageomics-related_ terms.
+
+### Just starting a project?
+Check out our guides to get your project off on the right foot!
+
+- [The GitHub Repo Guide](wiki-guide/GitHub-Repo-Guide.md): This page reviews expected and suggested GitHub repository contents, as well as structural considerations. 
+
+- [The Hugging Face Repo Guide](wiki-guide/Hugging-Face-Repo-Guide.md): Analogous expected and suggested repository contents for Hugging Face repositories; there are notable differences from GitHub in both content and structure.
+
+- [Metadata Guide](wiki-guide/Metadata-Guide.md): Guide to metadata collection and documentation. This closely follows the [HF Dataset Card Template](wiki-guide/HF_DatasetCard_Template_mkdocs.md) sections.
+
+### Project repo up, what's next?
+Check out our workflow guides for how to interact with your new repo:
+
+- [The GitHub Workflow](wiki-guide/The-GitHub-Workflow.md): This page mainly focuses on branching and the PR process.
+
+- [The Hugging Face Workflow](wiki-guide/The-Hugging-Face-Workflow.md): Analogous workflow directions for Hugging Face; there are notable differences from GitHub in how this process works practically, though the concept is the same.
+
+### Project management or organization got you down?
+Discover new tools to help:
+
+- [Guide to GitHub Projects](wiki-guide/Guide-to-GitHub-Projects.md): This page focuses on GitHub's project management tool, Projects, which integrates issues and pull requests into a unified task board to keep tabs on how your project is progressing. Labels, milestones, and assignee tags provide improved organization, and allow for more focused views.
+
+- [Helpful Tools for your Workflow](wiki-guide/Helpful-Tools-for-your-Workflow.md): Collection of useful tools to facilitate and improve workflows. Comments and recommendations encouraged!
+
+- [Virtual Environments](wiki-guide/Virtual-Environments.md): Summary of `conda` and `pip` environments: how to make, use, and share them.
+
+### Other pages of note
+- [Glossary for Imageomics](wiki-guide/Glossary-for-Imageomics.md): Collection of terms used in imageomics. The goal is to ensure all participating domains are represented, thus facilitating interdisciplinary communication. This is a group effort, please check it out and add terms you think should be there!
+- [Command Line Cheat Sheet](wiki-guide/Command-Line-Cheat-Sheet.md): Collection of useful bash, emacs, and git commands.
+
+<br>
+<br>
+
+!!! question "[Questions, Comments, or Concerns?](https://github.com/Imageomics/Imageomics-guide/issues)"

docs/wiki-guide/Command-Line-Cheat-Sheet.md

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+# Command Line Cheat Sheet
+
+See also [GitHub's Markdown Guide](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax).
+
+## Useful bash, emacs, and git:
+| Command | Action |
+| --- | --- |
+| `<cmd> -h` |          print the help documentation for a command, showing usage information and options |
+| `cd`	|		change directory |
+|`cd ..` |		up one directory |
+| `pwd` | 		current working directory |
+| `ls` | 		list everything in current directory (use `-a` to also show **a**ll files including hidden, `-l` for a **l**ong list including permissions and ownership info, `-1` ("dash one") to display the output with **1** item on each line) |
+| `wc -l <file>` |      use the **w**ord **c**ount command with the `-l` **l**ines option to list the number of lines in a file |
+| `du <dirname>/`|      calculate and show how much **d**isk **u**sage is consumed by a directory (use `-h` to make it **h**uman-readable, i.e. report in MB, GB or whatever units are most appropriate, and `-s` for **s**ummary of all the contents together rather than each item individually) |        
+| `ctrl r` |		search for command (will pop up `bck-i-search:`) |
+| `rm <target>` |       remove a file (or folder with `-r`). Beware when using `rm -rf <folder>` to **f**orce the **r**ecursive removal of all contents in a folder, which cannot be undone unless there is a backup. |
+| `<cmd1> \| <cmd2>` |   The "pipe" operator (`\|`) feeds the output of the first command (`cmd1`) to the input of the second command (`cmd2`). For example, show the total number of files in a directory with `ls -1 <dir> \| wc -l`|
+
+### Git-Specific
+| Command | Action |
+| --- | --- |
+| `git log`   | 		list of commits with author, date, time (type `q` to leave) |
+| `git log --oneline` | 		list of just commits (ID, location, message), type `q` to leave |
+| `git status`  | 	status of local vs remote repo (commits, ignored files, etc), <br> shows changed files that git is tracking and that git is not tracking   |
+| `git rm <target>`   | 		remove file (or folder with `-r`) from repo and filesystem (or just from the repo and not filesystem with `--cached`) <br>cache file ex: `git rm -r --cached __pycache__` |
+| `git mv <file> <folder>`   | 			move file to folder <br>or rename: `git mv <filename> <new_filename>` |
+| `git branch`   | 				list branches, current branch has `*` in front and is green |
+| `git checkout -b <branch>`   | 		create new branch and check it out |
+| `git checkout <branch>`   |			checkout branch |
+| `git branch -d <branch>`   | 			delete branch |
+
+**Usual Process:**
+After making changes to a file, check the status of your current working branch (with `git status`). Then, you "add" the file, state what is new about the file ("commit the change"), and `push` the file from your local copy of the repo to the remote copy:
+
+```bash
+git add <filename>
+
+git commit -m "Changed x,y,z"
+
+git push
+
+```
+
+**Note:** If you need to update your branch with changes from `main`, first switch to the branch, then set pull from `main` instead of the current branch, as below.
+
+```bash
+git checkout <branch>		
+
+git pull origin main
+```