Merge pull request #3 from kabilar/main

Create documentation framework

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = .git,*.pdf,*.svg,venvs,venv,site
+ignore-words-list = Weill

.github/workflows/build-docs.yaml

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+name: Build MkDocs
+on:
+  push:
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v1
+
+      - name: Install version of Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11' 
+
+      - name: Install requirements
+        run: pip install -r requirements.txt
+
+      - name: Build docs
+        run: mkdocs build

.github/workflows/codespell.yml

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+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/publishdocs.yaml

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+name: Publish docs via GitHub Pages
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v1
+
+      - name: Deploy docs
+        uses: mhausenblas/mkdocs-deploy-gh-pages@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

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+.DS_Store
+.idea/
+activities/.DS_Store
+protocols/.DS_Store
+node_modules
+local_data
+
+site/

.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.0.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 19.3b0
+    hooks:
+    -   id: black
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.5
+  hooks:
+  - id: codespell

README.md

@@ -1,2 +1,3 @@
-# linc-docs
-[Uploading data to lincbrain.org](upload.md)
+# LINC Documentation
+
+Docs for the LINC project which can be found at lincbrain.org/docs

docs/about.md

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+# About this doc
+
+## Acknowledgements
+
+Thank you to the DANDI Archive project for setting up the documentation framework that is utilized here.  See the [DANDI Handbook](https://www.dandiarchive.org/handbook/) for more information.
+
+## License
+
+<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a>
+
+This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/).
+

docs/contribute.md

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+# Contribute to this documentation
+
+If you find an issue with this documentation please file an issue or submit a pull request on the [linc-docs repository](https://github.com/lincbrain/linc-docs).
+
+If you would like to contribute to the LINC documentation and render the documentation locally as you make edits, please follow the steps below:
+
+1. Fork the [linc-docs repository](https://github.com/lincbrain/linc-docs) and clone it to your computer.
+2. Set up a Python environment with the dependencies in the [requirements.txt file](https://github.com/lincbrain/linc-docs/blob/main/requirements.txt).
+3. Within the Python environment, run `mkdocs serve`.  This will build the website and start a local webserver (e.g. at http://127.0.0.1:8000) with your documentation.
+4. As you continue to edit the markdown files or configuration file, your documentation will be automatically re-built and rendered locally.
+5. Commit your changes and submit a pull request.

docs/index.md

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+# Welcome to the LINC Documentation
+
+<img
+src="./img/linc.logo.color+white.png"
+alt="linc_banner"
+style="width: 75%; height: auto; display: block; margin-left: auto; margin-right: auto;"/>
+
+The center for [Large-scale Imaging of Neural Circuits (LINC)](https://connects.mgh.harvard.edu/)
+ (PIs: Haber, Hillman, Yendiki) is funded by the
+ [NIH BRAIN Initiative CONNECTS program](https://www.ninds.nih.gov/news-events/highlights-announcements/nih-brain-initiative-launches-projects-develop-innovative-technologies-map-brain-incredible-detail).
+Its goal is to develop novel technologies for imaging brain connections down to 
+the microscopic scale, and deploy these technologies to image 
+cortico-subcortical projections that are relevant to deep brain stimulation for 
+motor and psychiatric disorders.
+
+## About this doc
+
+The LINC documentation is meant to share information across the LINC project investigators.  If you are new to the LINC project, you can start on the [Upload data](upload.md) page for a description of how to interact with the LINC data sharing platform.
+
+## Quick Links
+
+- [LINC Homepage](https://connects.mgh.harvard.edu/)
+- [LINC Data Sharing Platform](https://lincbrain.org/)
+- [LINC Project Code on GitHub](https://github.com/lincbrain)
+
+## Support
+
+For questions, bug reports, and feature requests, please:
+
+- File an issue on the relevant [GitHub repository](https://github.com/lincbrain)
+- Reach out on the [LINC Slack](https://mit-lincbrain.slack.com/)
+- Send an email to kabi@mit.edu

mkdocs.yml

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+site_name: LINC Documentation
+repo_name: "lincbrain/linc-docs"
+repo_url: "https://github.com/lincbrain/linc-docs"
+copyright: "CC-BY 4.0"
+use_directory_urls: true
+site_url: https://www.lincbrain.org/docs/
+
+# Material theme
+theme:
+  name: "material"
+  language: "en"
+  favicon: img/linc.logo.color+white.notext+square.png
+  logo: img/linc.logo.color+black.alpha.notext.png
+  palette:
+    primary: "deep purple"
+    accent: "purple"
+  features:
+    - toc.integrate
+
+# Pages
+nav:
+  - Welcome: "index.md"
+  - Upload data: "upload.md"
+  - Contribute documentation: "contribute.md"
+  - About this doc: "about.md"
+
+# List of extensions
+markdown_extensions:
+  - admonition
+  - pymdownx.details
+  - pymdownx.critic
+  - pymdownx.magiclink
+  - toc:
+      permalink: True
+
+# List of plugins
+plugins:
+  - search
+  - open-in-new-tab
+
+# Customize theme
+extra:
+  generator: false
+  social:
+    - icon: material/home
+      link: https://connects.mgh.harvard.edu/
+      name: Homepage
+    - icon: fontawesome/brands/slack
+      link: https://mit-lincbrain.slack.com/
+      name: Slack
+    - icon: fontawesome/brands/github
+      link: https://github.com/lincbrain
+      name: GitHub

requirements.txt

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+mkdocs-material>=9.5.10
+pymdown-extensions
+mkdocs-open-in-new-tab