OpenMS Documentation Gets a New Home

[timosachsenberg]

This issue tracks:

1. Movement of Doxygen pages to OpenMS-docs.
2. Movement of Wiki Pages to OpenMS API Reference, OpenMS-docs, and pyopenms-docs.
3. Addition of Tutorials to OpenMS-docs.
4. Addition of References in OpenMS-docs and updated information present in:
   • updateHMDB
   • usage_plots
   • dockerfiles
   • build-scripts
   • autowrap
   • contrib
   • PDCommunityNodes

[tapaswenipathak]

1. Installation instructions:
   • Installation on GNU/Linux
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/tree/develop/doc
   • Installation on MacOS
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/tree/develop/doc
   • Installation on Windows
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/tree/develop/doc
2. Documentation:
   • User Quickstart Guide
     • C+U in https://github.com/OpenMS/OpenMS-docs
       • www.openms.de/BUGS: Dead link
     • D from https://github.com/OpenMS/OpenMS/tree/develop/doc
   • TOPP tutorial
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/tree/develop/doc
   • TOPPAS tutorial
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/tree/develop/doc
3. Misc:
   • Support
     • C in https://github.com/OpenMS/OpenMS-docs
   • Github
     • C in https://github.com/OpenMS/OpenMS-docs
   • Gitter chat
     • C in https://github.com/OpenMS/OpenMS-docs
   • Mailing List
     • C in https://github.com/OpenMS/OpenMS-docs
   • FAQ
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/tree/develop/doc
   • Known Issues
     • ?
4. Development:
   • Developer FAQ (online)
     • U in https://github.com/OpenMS/OpenMS/tree/develop/doc
5. Documentation:
   • Developer Python Quickstart Guide (online)
     • D from https://github.com/OpenMS/OpenMS/tree/develop/doc
   • External Code using OpenMS
     • C+R+U in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/tree/develop/doc
6. OpenMS Wiki: https://github.com/OpenMS/OpenMS/wiki
   • About
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki#about
   • For Users
     • C+R+U in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki#for_users
   • Getting in Contact
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki#for_users
   • Reporting Bugs/Issues
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • For Developers
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Adding your own tool to the TOPP suite
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Build an installer and KNIME package from an own branch
     • C in https://github.com/OpenMS/OpenMS-docs: Quick Start Guide
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Build pyOpenMS on Windows
     • C/U in https://github.com/OpenMS/pyopenms-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Build your own OpenMS KNIME package
     • C in https://github.com/OpenMS/OpenMS-docs: Quick Start Guide
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Building OpenMS
     • C/U/Merge in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Code Examples
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Coding conventions
     • C in https://github.com/OpenMS/OpenMS/tree/develop/doc
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Comparison Scripts
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Compiling with self built compilers and non default standard libraries
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • ConsensusMap and ConsensusFeature whitepaper
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Conversion Scripts
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Cpp Guide
     • C+U in https://github.com/OpenMS/OpenMS/tree/develop/doc
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Developer FAQ
     • C+U in https://github.com/OpenMS/OpenMS/tree/develop/doc
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Developer Guidelines for adding new dependent libraries
     • C+U in Developer Quick Start Guide in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Discussion: Classification of proteins and peptides and protein groups
     • C+U in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Exporting a KNIME workflow as a Docker container
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • External Tools
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • HowTo Write Commit Messages
     • C in https://github.com/OpenMS/OpenMS/tree/develop/doc
     • D from https://github.com/OpenMS/OpenMS/wiki
   • How to setup new agents for Jenkins
     • U in Jenkins https://github.com/OpenMS/OpenMS/wiki
   • Jenkins CI CD system
     • U in Jenkins https://github.com/OpenMS/OpenMS/wiki
   • NewBuildUnit
     • C in https://github.com/OpenMS/OpenMS/wiki ?
   • OpenMS 2.0 Kernel Whitepaper
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • OpenMS 2.0 Planing
     • ?
   • OpenMS 2.0 Planing Interfaces MSExperiment
     • ?
   • OpenMS Docker Containers
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • OpenMS Git Workflow
     • C in https://github.com/OpenMS/OpenMS-docs
     • U in https://github.com/OpenMS/OpenMS/wiki
   • OpenMS missing core functionality
     • ?
   • OpenMS workflow parameters for Q Exactive
     • C in https://github.com/OpenMS/OpenMS-docs
     • U in https://github.com/OpenMS/OpenMS/wiki
   • Preparation of a new OpenMS release
     • C in https://github.com/OpenMS/OpenMS-docs
     • U in https://github.com/OpenMS/OpenMS/wiki
   • Preparation of OpenMS 2.3 release
     • U in https://github.com/OpenMS/OpenMS/wiki
     • U in https://github.com/OpenMS/OpenMS-docs
   • Pull Request Checklist
     • C in https://github.com/OpenMS/OpenMS-docs
     • U in https://github.com/OpenMS/OpenMS/wiki
     • U in https://github.com/OpenMS/OpenMS-docs
   • pyOpenMS
     • U in https://github.com/OpenMS/pyopenms-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Regarding notarization of the macOS dmg
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Release Preparation
     • D from https://github.com/OpenMS/OpenMS/wiki
   • ScreenCasts
     • ?
   • Supported Compilers
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Testing an OpenMS release candidate
     • C in https://github.com/OpenMS/OpenMS/tree/develop/doc
     • U in https://github.com/OpenMS/OpenMS/wiki ?
   • Thirdparty dependencies
     • C+U in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Update check
     • C in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Useful Scripts
     • C+U in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Workflow Collection
     • C+U in https://github.com/OpenMS/OpenMS-docs
     • D from https://github.com/OpenMS/OpenMS/wiki
   • Write tests
     • C in Developer Guide in https://github.com/OpenMS/OpenMS/tree/develop/doc
     • D from https://github.com/OpenMS/OpenMS/wiki
7. Tutorials/Handouts: https://github.com/OpenMS/Tutorials
   • C+U in https://github.com/OpenMS/OpenMS-docs
   • D https://github.com/OpenMS/Tutorials
8. updateHMDB
   • Reference in https://github.com/OpenMS/OpenMS-docs
   • U https://github.com/OpenMS/updateHMDB
9. usage_plots
   • Reference in https://github.com/OpenMS/OpenMS-docs
   • U https://github.com/OpenMS/updateHMDB
10. dockerfiles
    • Reference in https://github.com/OpenMS/OpenMS-docs
    • U https://github.com/OpenMS/dockerfiles
11. build-scripts
    • Reference in https://github.com/OpenMS/OpenMS-docs
    • U https://github.com/OpenMS/build-scripts
12. autowrap
    • Reference in https://github.com/OpenMS/OpenMS-docs
    • U https://github.com/OpenMS/autowrap
13. contrib
    • Reference in https://github.com/OpenMS/OpenMS-docs
    • U https://github.com/OpenMS/autowrap
14. PDCommunityNodes
    • C in https://github.com/OpenMS/OpenMS-docs
    • U+D in https://github.com/OpenMS/PDCommunityNodes

Note: CRUD stands for Create | Replace | Update | Delete

[jpfeuffer]

can we rename this issue? @timosachsenberg can you update your text?

[timosachsenberg]

Sure feel free to rename or update.

[tapaswenipathak]

cc @axelwalter @enetz @jpfeuffer @KyowonJeong @poshul @OpenMS/doc-team.

[jpfeuffer]

I thought we decided that internal discussions stay in the wiki?
E.g. Openms 2.0 kernel white paper and meeting summaries

[tapaswenipathak]

On Sat, May 14, 2022 at 3:01 PM Julianus Pfeuffer ***@***.***> wrote: I thought we decided that internal discussions stay in the wiki? E.g. Openms 2.0 kernel white paper and meeting summaries

I was thinking papers could go to OpenMS/OpenMS-docs, just not visible on https://openms.readthedocs.io/en/latest/? Say, `docs/research/whitepapers`. Meeting summaries, I'll just see for any content and maybe add them under one category in the wiki. Meeting summaries for sure remains in the wiki.

…

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