Merge pull request #3 from broadinstitute/docs

create jupyterbook stub for docs

docs/.github/workflows/deploy.yml

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+name: deploy-documentation
+
+# Only run this when the master branch changes
+on:
+  push:
+    branches:
+    - main
+    # Only run if edits in documentation
+    paths:
+    - docs/starrynight-docs/**
+    - docs/.github/workflows/deploy.yml
+
+# This job installs dependencies, builds the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    # Install dependencies
+    - name: Set up Python
+      uses: actions/[email protected]
+      with:
+        python-version: 3.10
+
+    - name: Install dependencies
+      run: |
+        pip install jupyter-book
+
+    # Build the book
+    - name: Build the book
+      run: |
+        jupyter-book build starrynight-docs/
+
+    # Push the book's HTML to github-pages
+    - name: GitHub Pages action
+      uses: peaceiris/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./starrynight-docs/_build/html

docs/_config.yml

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+# Book settings
+
+# Learn more at https://jupyterbook.org/customize/config.html
+title: starrynight Documentation
+author: Broad Institute
+copyright: "2025"
+#logo: img/logo.svg
+
+# Only build files that are in the ToC
+only_build_toc_files: true
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/broadinstitute/starrynight
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+  path_to_book: starrynight-docs
+
+html:
+  baseurl: broadinstitute.github.io
+  use_repository_button: true
+  use_issues_button: true
+  use_edit_page_button: true
+  comments:
+    hypothesis: true
+
+parse:
+  myst_enable_extensions:
+    # Only required if you use html <img>
+    - html_image

docs/_toc.yml

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+# Table of contents
+
+format: jb-book
+root: overview
+parts:
+- caption: FAQ
+  chapters:
+  - file: costs
+- caption: Running starrynight
+  chapters:
+  - file: step_0_creating_project
+  - file: step_1_creating_inventory_index
+  - file: step_2_creating_pipeline
+- caption: Technical Guides
+  chapters:
+  - file: troubleshooting_runs
+  - file: versions

docs/starrynight-docs/costs.md

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+# starrynight Costs
+
+TODO

docs/starrynight-docs/intro.md

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+# What is starrynight?
+
+TODO
+
+## What do I need to have to run this?
+
+TODO
+
+## Can I contribute code to starrynight?
+
+Feel free!  We welcome contributions.
+
+## Who made this?
+
+starrynight is a project from the Imaging Platform at the Broad Institute in Cambridge, MA, USA.

docs/starrynight-docs/overview.md

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+# starrynight Overview
+
+## Projects
+
+In starrynight, a project is TODO.
+The first step in starrynight is creating a project.
+See [how to create a project](step_0_creating_project.md).
+
+## Index and Inventory
+
+In starrynight, after a project is created, an index and inventory are made from the project files.
+An index is TODO.
+An inventory is TODO.
+See [how to create an index and inventory](step_1_creating_inventory_index).

docs/starrynight-docs/step_0_creating_project.md

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+# Creating a Project in starrynight
+
+Go to the starrynight home page and click on the `Create Project` button.
+
+![Create a new project](./images/screen_1.png)
+
+Then fill the details of your project.
+
+![Project creation form](./images/screen_2.png)
+
+- Name: The name of your project.
+- Description: A short description of your project.
+- Dataset: S3 URL of the dataset. It can also be a local path if you are running starrynight locally.
+- Workspace: S3 URL where you want to save intermediate files. It can also be a local path if you are running starrynight locally.
+- Parser: Select the appropriate parser according to your dataset file naming convention. More information on individual parsers can be found here.
+- Project Type: Select a project template. This will help you setup a default workflow for your project. You can also change this later after project creation.
+
+Click on create project.

docs/starrynight-docs/step_1_creating_inventory_index.md

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+# Creating an Inventory and Index in starrynight
+
+TODO

docs/starrynight-docs/step_2_creating_pipeline.md

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+# Creating a Pipeline in starrynight
+
+TODO

docs/starrynight-docs/troubleshooting_runs.md

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+# Troubleshooting starrynight Runs
+
+TODO

docs/starrynight-docs/versions.md

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+# Versions
+
+TODO

docs/user.md

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 # User guide
 
-## Create a new project
-
-Go to the starrynight home page and click on the `Create Project` button.
-
-![Create a new project](./images/screen_1.png)
-
-Then fill the details of your project.
-
-![Project creation form](./images/screen_2.png)
-
-- Name: The name of your project.
-- Description: A short description of your project.
-- Dataset: S3 URL of the dataset. It can also be a local path if you are running starrynight locally.
-- Workspace: S3 URL where you want to save intermediate files. It can also be a local path if you are running starrynight locally.
-- Parser: Select the appropriate parser according to your dataset file naming convention. More information on individual parsers can be found here.
-- Project Type: Select a project template. This will help you setup a default workflow for your project. You can also change this later after project creation.
-
-Click on create project.
 
 ## Add your aws credentials to view project outputs