fix(openchallenges): restructure docs site (#2441)

Sage-Bionetworks · Feb 13, 2024 · 6343bd6 · 6343bd6
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diff --git a/docs/angular-universal.md → docs/_archive/angular-universal.md b/docs/angular-universal.md → docs/_archive/angular-universal.md
diff --git a/docs/app-styles-themes-assets.md → docs/_archive/app-styles-themes-assets.md b/docs/app-styles-themes-assets.md → docs/_archive/app-styles-themes-assets.md
diff --git a/docs/changelog.md → docs/_archive/changelog.md b/docs/changelog.md → docs/_archive/changelog.md
diff --git a/docs/cheat-sheet.md → docs/_archive/cheat-sheet.md b/docs/cheat-sheet.md → docs/_archive/cheat-sheet.md
diff --git a/...lect-challenge-logs-and-system-metrics.md → ...lect-challenge-logs-and-system-metrics.md b/...lect-challenge-logs-and-system-metrics.md → ...lect-challenge-logs-and-system-metrics.md
diff --git a/docs/coverage.md → docs/_archive/coverage.md b/docs/coverage.md → docs/_archive/coverage.md
diff --git a/docs/create-a-new-angular-component.md → ...archive/create-a-new-angular-component.md b/docs/create-a-new-angular-component.md → ...archive/create-a-new-angular-component.md
diff --git a/docs/devcontainer.md → docs/_archive/devcontainer.md b/docs/devcontainer.md → docs/_archive/devcontainer.md
diff --git a/docs/develop-on-a-remote-host.md → docs/_archive/develop-on-a-remote-host.md b/docs/develop-on-a-remote-host.md → docs/_archive/develop-on-a-remote-host.md
diff --git a/docs/developing-in-python.md → docs/_archive/developing-in-python.md b/docs/developing-in-python.md → docs/_archive/developing-in-python.md
diff --git a/docs/enable-sso-with-keycloak.md → docs/_archive/enable-sso-with-keycloak.md b/docs/enable-sso-with-keycloak.md → docs/_archive/enable-sso-with-keycloak.md
diff --git a/docs/faq.md → docs/_archive/faq.md b/docs/faq.md → docs/_archive/faq.md
diff --git a/docs/figma-to-code.md → docs/_archive/figma-to-code.md b/docs/figma-to-code.md → docs/_archive/figma-to-code.md
diff --git a/docs/_archive/index.md b/docs/_archive/index.md
@@ -0,0 +1,65 @@
+
+
+- [Overview of Sage Monorepo]
+- Cheat Sheet (coming soon)
+- [Docs](docs)
+
+## Development Setup
+
+### Requirements
+
+- [Docker Engine] OR [GitHub Codespace]
+- [Visual Studio Code]
+
+### Open Sage Monorepo in VS Code
+
+**Option 1**: Click on the button shown below to open Sage Monorepo in its [development container]
+with VS Code. This option is suitable if you want to explore the content of Sage Monorepo.
+
+[![Open in Dev Containers](https://img.shields.io/static/v1?label=Dev%20Containers&message=Open&color=blue&logo=visualstudiocode&style=for-the-badge)](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/Sage-Bionetworks/sage-monorepo 'Open in VS Code Dev Containers')
+
+**Option 2**: If you plan to contribute to this project, please [create a fork] and use its URL for
+cloning. For more information on contributing and/or our Forking Workflow, see
+[CONTRIBUTING.md](CONTRIBUTING.md).
+
+<!-- termynal -->
+```console
+$ git clone --filter=blob:none <fork url>
+---> 100%
+Resolving deltas: 100% (...), done.
+```
+
+Then open your fork repo inside our dev container using these instructions:
+
+- [Developing inside a Container](./docs/devcontainer.md)
+- [Develop on a remote host](./docs/develop-on-a-remote-host.md) (optional)
+
+## Ecosystem
+
+- Java
+- Node.js
+- Python
+- R
+
+
+## Projects
+
+- OpenChallenges
+- Schematic (evaluation)
+- Synapse (evaluation)
+
+---
+
+Love Sage Monorepo and its projects? Give our repo a star ⭐.
+
+<!-- Links -->
+
+[docker engine]: https://docs.docker.com/get-docker/
+[visual studio code]: https://code.visualstudio.com/
+[apache license 2.0]: https://github.com/Sage-Bionetworks/sage-monorepo/blob/main/LICENSE.txt
+[GitHub Codespace]: https://github.com/features/codespaces
+[Overview of Sage Monorepo]: https://docs.google.com/document/d/12oA-Uol_NsWUtC9LHlAlpcgZXXY9jkxFXqK2EMF96XM
+[Code of Conduct]: CODE_OF_CONDUCT.md
+[contributing]: CONTRIBUTING.md
+[development container]: https://containers.dev/
+[create a fork]: https://github.com/Sage-Bionetworks/sage-monorepo/fork
diff --git a/docs/java-cheat-sheet.md → docs/_archive/java-cheat-sheet.md b/docs/java-cheat-sheet.md → docs/_archive/java-cheat-sheet.md
diff --git a/docs/legacy-repositories.md → docs/_archive/legacy-repositories.md b/docs/legacy-repositories.md → docs/_archive/legacy-repositories.md
diff --git a/docs/libraries.md → docs/_archive/libraries.md b/docs/libraries.md → docs/_archive/libraries.md
diff --git a/docs/linters-and-formatters.md → docs/_archive/linters-and-formatters.md b/docs/linters-and-formatters.md → docs/_archive/linters-and-formatters.md
diff --git a/docs/nx-readme.md → docs/_archive/nx-readme.md b/docs/nx-readme.md → docs/_archive/nx-readme.md
diff --git a/docs/nx-tags.md → docs/_archive/nx-tags.md b/docs/nx-tags.md → docs/_archive/nx-tags.md
diff --git a/docs/projects.md → docs/_archive/projects.md b/docs/projects.md → docs/_archive/projects.md
diff --git a/docs/references.md → docs/_archive/references.md b/docs/references.md → docs/_archive/references.md
diff --git a/docs/search-engine-optimization.md → docs/_archive/search-engine-optimization.md b/docs/search-engine-optimization.md → docs/_archive/search-engine-optimization.md
diff --git a/docs/stack-monitoring.md → docs/_archive/stack-monitoring.md b/docs/stack-monitoring.md → docs/_archive/stack-monitoring.md
diff --git a/docs/update-dependencies.md → docs/_archive/update-dependencies.md b/docs/update-dependencies.md → docs/_archive/update-dependencies.md
diff --git a/docs/using-nx.md → docs/_archive/using-nx.md b/docs/using-nx.md → docs/_archive/using-nx.md
diff --git a/docs/vscode-cheat-sheet.md → docs/_archive/vscode-cheat-sheet.md b/docs/vscode-cheat-sheet.md → docs/_archive/vscode-cheat-sheet.md
diff --git a/docs/bug-report.md b/docs/bug-report.md
diff --git a/docs/code-of-conduct.md b/docs/code-of-conduct.md
diff --git a/docs/contributing-guidelines.md b/docs/contributing-guidelines.md
diff --git a/docs/contributions/bug-report.md b/docs/contributions/bug-report.md
@@ -0,0 +1,8 @@
+Issues should be used to report problems with this project, request a new feature, or to discuss
+potential changes before a pull request (PR) is created. When you create a new issue, a template
+will be loaded that will guide you through collecting and providing the information we need to
+investigate.
+
+If you find an issue that addresses the problem you're having, please add your own reproduction
+information to the existing issue rather than creating a new one. Adding a reaction can also help
+be indicating to our maintainers that a particular problem is affecting more than just the reporter.
diff --git a/docs/contributing.md → docs/contributions/guidelines.md b/docs/contributing.md → docs/contributions/guidelines.md
diff --git a/docs/contributions/overview.md b/docs/contributions/overview.md
@@ -0,0 +1,14 @@
+Thank you contributing to the Sage Monorepo!  We welcome any and all feedback, ideas, and
+suggestions.
+
+Contributions can be made via issues and pull eequests (PRs).
+
+* [Reporting a bug](/bug-report)
+* [Adding a feature](/contributing)
+
+
+### Code of Conduct
+
+We take our open source community seriously and hold ourselves and other contributors to high
+standards of communication. By participating and contributing to this project, you agree to uphold
+our [Code of Conduct](https://github.com/Sage-Bionetworks/sage-monorepo/blob/main/CODE_OF_CONDUCT.md).
diff --git a/docs/developers-guide/faq.md b/docs/developers-guide/faq.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/getting-started/local-dev.md b/docs/getting-started/local-dev.md
@@ -0,0 +1 @@
+!!!note "Content comming soon!"
diff --git a/docs/getting-started/remote-dev.md b/docs/getting-started/remote-dev.md
@@ -0,0 +1 @@
+!!!note "Content comming soon!"
diff --git a/docs/getting-started/what-is-angular.md b/docs/getting-started/what-is-angular.md
@@ -0,0 +1 @@
+!!!note "Content comming soon!"
diff --git a/docs/getting-started/what-is-devcontainer.md b/docs/getting-started/what-is-devcontainer.md
@@ -0,0 +1 @@
+!!!note "Content comming soon!"
diff --git a/docs/getting-started/what-is-nx.md b/docs/getting-started/what-is-nx.md
@@ -0,0 +1 @@
+!!!note "Content comming soon!"
diff --git a/docs/index.md b/docs/index.md
@@ -1,72 +1,34 @@
-![cnb-tools](images/logo-1.png)
+![sage-mono-repo](images/logo-1.png)
 
-<img src="https://img.shields.io/github/actions/workflow/status/Sage-Bionetworks/sage-monorepo/ci.yml?branch=main&color=007acc&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github&label=CI/CD" alt="Sage Monorepo CI/CD" />
-<img src="https://img.shields.io/github/license/Sage-Bionetworks/sage-monorepo.svg?color=007acc&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/Sage-Bionetworks/sage-monorepo/blob/main/LICENSE" alt="Sage Monorepo License" />
+# Sage Monorepo
+_Build robust apps faster_
 
 ---
 
-Get started with Sage Monorepo, learn the fundamentals and explore advanced topics.
-
-- [Overview of Sage Monorepo]
-- Cheat Sheet (coming soon)
-- [Docs](docs)
-
-## Development Setup
-
-### Requirements
-
-- [Docker Engine] OR [GitHub Codespace]
-- [Visual Studio Code]
-
-### Open Sage Monorepo in VS Code
-
-**Option 1**: Click on the button shown below to open Sage Monorepo in its [development container]
-with VS Code. This option is suitable if you want to explore the content of Sage Monorepo.
-
-[![Open in Dev Containers](https://img.shields.io/static/v1?label=Dev%20Containers&message=Open&color=blue&logo=visualstudiocode&style=for-the-badge)](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/Sage-Bionetworks/sage-monorepo 'Open in VS Code Dev Containers')
-
-**Option 2**: If you plan to contribute to this project, please [create a fork] and use its URL for
-cloning. For more information on contributing and/or our Forking Workflow, see
-[CONTRIBUTING.md](CONTRIBUTING.md).
-
-<!-- termynal -->
-```console
-$ git clone --filter=blob:none <fork url>
----> 100%
-Resolving deltas: 100% (...), done.
-```
-
-Then open your fork repo inside our dev container using these instructions:
-
-- [Developing inside a Container](./docs/devcontainer.md)
-- [Develop on a remote host](./docs/develop-on-a-remote-host.md) (optional)
-
-## Ecosystem
+<img src="https://img.shields.io/github/actions/workflow/status/Sage-Bionetworks/sage-monorepo/ci.yml?branch=main&color=007acc&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github&label=CI/CD" alt="Sage Monorepo CI/CD" />
+<img src="https://img.shields.io/github/license/Sage-Bionetworks/sage-monorepo.svg?color=007acc&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/Sage-Bionetworks/sage-monorepo/blob/main/LICENSE" alt="Sage Monorepo License" />
 
-- Java
-- Node.js
-- Python
-- R
+---
 
+Developers building components in silos can lead to a number of problems, including duplicated
+components, increased maintenance, and reduced visibility.
 
-## Projects
+Sage Monorepo addresses these problems by providing a centralized repository for standardized,
+reusable components. This solution also improves the developer experience (DX), which can lead to
+increased morale, productivity, retention, and knowledge transfer.
 
-- OpenChallenges
-- Schematic (evaluation)
-- Synapse (evaluation)
+## Key Features
 
----
+* Build apps faster
+* Use latest technologies
+* Open-source
 
-Love Sage Monorepo and its projects? Give our repo a star ⭐.
 
-<!-- Links -->
+## Current Projects
 
-[docker engine]: https://docs.docker.com/get-docker/
-[visual studio code]: https://code.visualstudio.com/
-[apache license 2.0]: https://github.com/Sage-Bionetworks/sage-monorepo/blob/main/LICENSE.txt
-[GitHub Codespace]: https://github.com/features/codespaces
-[Overview of Sage Monorepo]: https://docs.google.com/document/d/12oA-Uol_NsWUtC9LHlAlpcgZXXY9jkxFXqK2EMF96XM
-[Code of Conduct]: CODE_OF_CONDUCT.md
-[contributing]: CONTRIBUTING.md
-[development container]: https://containers.dev/
-[create a fork]: https://github.com/Sage-Bionetworks/sage-monorepo/fork
+Name | Description 
+--|--
+[Agora](https://agora.adknowledgeportal.org/genes) | Agora hosts high-dimensional human transcriptomic, proteomic, and metabolomic evidence for whether or not genes are associated with Alzheimer’s disease (AD).
+[iAtlas](https://isb-cgc.shinyapps.io/iatlas/) | The iAtlas portal serves as an interactive tool for exploring and analyzing immuno-oncology data.
+[OpenChallenges](https://openchallenges.io/home) | OpenChallenges (OC) aggregates biomedical challenges to accelerate citizen science and data benchmarking
+[Schematic](https://github.com/Sage-Bionetworks/schematic) | SCHEMATIC (Schema Engine for Manifest Ingress and Curation) is a novel schema-based, metadata ingress ecosystem, meant to streamline the process of biomedical dataset annotation, metadata validation and submission to a data repository for various data contributors.
diff --git a/docs/news.md b/docs/news.md
@@ -0,0 +1,25 @@
+## General
+
+### Jan 2024
+
+We're kicking off the new year with our new-and-improved docs site!  We are continuously looking
+to improve, so if you have any feedback, [please us know](https://github.com/Sage-Bionetworks/sage-monorepo/issues/new?assignees=&labels=type%3A+docs&projects=&template=3-documentation.yml&title=%5BDocs%5D+%3Ctitle%3E)!
+
+### Sept 2023
+
+Introducing a new product we support: [Agora](https://agora.adknowledgeportal.org/genes)!
+
+### June 2023
+
+We now support the schematic API! [Check them out](https://schematicpy.readthedocs.io/en/latest/cli_reference.html).
+
+### Jan 2023
+
+Kicking off the Sage Monorepo with our first product: [OpenChallenges](https://openchallenges.io/home)
+
+## Agora
+
+## OpenChallenges
+
+## Schematic
+
diff --git a/docs/reference/agora.md b/docs/reference/agora.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/reference/oc-microservices.md b/docs/reference/oc-microservices.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/reference/oc-schemas.md b/docs/reference/oc-schemas.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/reference/schematic.md b/docs/reference/schematic.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/tutorials/angular/add-api-client.md b/docs/tutorials/angular/add-api-client.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/tutorials/angular/add-app.md b/docs/tutorials/angular/add-app.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/tutorials/angular/add-component.md b/docs/tutorials/angular/add-component.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/tutorials/angular/add-library.md b/docs/tutorials/angular/add-library.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/tutorials/docker/new-project.md b/docs/tutorials/docker/new-project.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/tutorials/java/add-library.md b/docs/tutorials/java/add-library.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/tutorials/java/add-rest-api.md b/docs/tutorials/java/add-rest-api.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/docs/tutorials/python/add-rest-api.md b/docs/tutorials/python/add-rest-api.md
@@ -0,0 +1 @@
+
diff --git a/docs/tutorials/r/new-project.md b/docs/tutorials/r/new-project.md
@@ -0,0 +1 @@
+!!!note "Content coming soon!"
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -9,50 +9,59 @@ repo_name: sage-monorepo
 
 # Navigation
 nav:
-  - Home:
-    - Home: index.md
-    - Changelog: changelog.md
+  - Home: 
+    - Sage Monorepo: index.md
+    - What's new: news.md
     - Contributing:
-      - Overview: contributing-guidelines.md
-      - Reporting a bug: bug-report.md
-      - Adding a feature: contributing.md
-      - Code of conduct: code-of-conduct.md
+      - Overview: contributions/overview.md
+      - Reporting a bug: contributions/bug-report.md
+      - Adding a feature: contributions/guidelines.md
   - Getting Started:
-    - Angular Universal: angular-universal.md
-    - Devcontainer: devcontainer.md
-    - Nx: using-nx.md
-    - Remote host: develop-on-a-remote-host.md
-  - Setup:
-    - Figma-to-Code: figma-to-code.md
-    - Using styles/themes: app-styles-themes-assets.md
-    - Create a new library: libraries.md
-    - Create a new component: create-a-new-angular-component.md
-    - Monitor the stack: stack-monitoring.md
-    - Collect logs and system metrics: collect-challenge-logs-and-system-metrics.md
-    - Update tools and dependencies: update-dependencies.md
-    - Code coverage: coverage.md
-  - Cheat Sheets:
-    - VSCode: vscode-cheat-sheet.md
-    - Java: java-cheat-sheed.md
-    - OpenChallenges: cheat-sheet.md
-  - References:
-    - references.md
-    - Linters and formatters: linters-and-formatters.md
-  - FAQ: faq.md
+    - What is Angular Universal?: getting-started/what-is-angular.md
+    - What is a devcontainer?: getting-started/what-is-devcontainer.md
+    - What is Nx?: getting-started/what-is-nx.md
+    - Setup: 
+      - Develop Locally: getting-started/local-dev.md
+      - Develop On a Remote Host: getting-started/remote-dev.md
+  - Tutorials:
+    - Angular:
+      - Create an Angular app: tutorials/angular/add-app.md
+      - Add an Angular API client: tutorials/angular/add-api-client.md
+      - Add an Angular component: tutorials/angular/add-component.md
+      - Add an Angular library: tutorials/angular/add-library.md
+    - Docker:
+      - Create a Docker-based project: tutorials/docker/new-project.md
+    - Java:
+      - Add a Java library: tutorials/java/add-library.md
+      - Add a Java REST API: tutorials/java/add-rest-api.md
+    - Python:
+      - Add a Python REST API: tutorials/python/add-rest-api.md
+    - R:
+      - Add an R project: tutorials/r/new-project.md
+  - Developers Guide:
+    - Common Issues: developers-guide/faq.md
+  - Reference:
+    - Agora:
+      - API: reference/agora.md
+    - OpenChallenges:
+      - Microservices: reference/oc-microservices.md
+      - Schemas: reference/oc-schemas.md
+    - Schematic:
+      - API: reference/schematic.md
 
 # Theme configuration
 theme:
   name: material
   palette:
     - media: "(prefers-color-scheme: light)" 
       scheme: default
-      primary: teal
+      primary: blue
       toggle:
         icon: material/toggle-switch-off-outline
         name: Switch to dark mode
     - media: "(prefers-color-scheme: dark)" 
       scheme: slate
-      primary: deep purple
+      primary: blue
       toggle:
         icon: material/toggle-switch
         name: Switch to light mode