Merge pull request #2 from thompsonmj/setup-mkdocs

Setup mkdocs

.github/workflows/deploy.yaml

@@ -0,0 +1,33 @@
+name: Deploy MkDocs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        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@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site

.gitignore

@@ -1,2 +1,6 @@
 # Mac System
 .DS_Store
+
+# Additional
+__pycache__
+

CODE_OF_CONDUCT.md → docs/CODE_OF_CONDUCT.md

@@ -3,6 +3,7 @@
 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. 
@@ -16,23 +17,23 @@ We abide by these principles in all Imageomics spaces, including but not limited
 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 Sam Stevens, Diane, or Tanya.
+3. Report the incident to Diane Boghrat.
 
 Privacy will be protected to the greatest extent possible.
 
-# JEDI Framework
+## JEDI Framework
 
-[Full text](https://docs.google.com/document/d/1zHghf5bCsDsw1n0s_Nxt5wu_GYIbj9to/edit?usp=sharing&ouid=114612552367385014086&rtpof=true&sd=true)
+[Full text](pdfs/Imageomics_Equity_Tool.pdf)
 
-## VALUES
-### TRANSPARENCY
+### VALUES
+#### TRANSPARENCY
 We ensure our efforts are clear about assumptions, uncertainty, and limits, and provide open sources of information, processes, and discovery.
-### ACCOUNTABILITY
+#### 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
+#### 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
+#### 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

@@ -0,0 +1,40 @@
+# 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)"

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

@@ -29,8 +29,8 @@ See also [GitHub's Markdown Guide](https://docs.github.com/en/get-started/writin
 | `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:
+#### Usual Process
+After making changes to a file on a branch, 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>
@@ -41,10 +41,10 @@ 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.
+!!! note Note
+    If you need to update your branch with changes from the remote `main`, first switch to the branch, then set pull from `main` instead of the current branch, as below.
+    ```bash
+    git checkout <branch>		
 
-```bash
-git checkout <branch>		
-
-git pull origin main
-```
+    git pull origin main
+    ```