[OpenMS-docs/main branch] Prep for 3.0.0 Pre-Release of OpenMS Documentation

[tapaswenipathak]

TODOs

• Add links to OpenMS RTD Documentation OpenMS#6197 @tapaswenipathak
• Rearrange/Revisit OpenMS API Reference Doxygen Documentation OpenMS#6198
• Update pinned repositories of OpenMS #116 @jpfeuffer @timosachsenberg
• [DOXYGEN] Change to Doxygen Awesome theme OpenMS#6110
• Update pyopenms.readthedocs.io theme to furo pyopenms-docs#284 @greengypsy
• Handouts for training #2
• URLs should be clickable #18 @greengypsy
• American or British spelling? #29 @greengypsy
• Add announcement banner to redirect to OpenMS API Doxygen Documentation #56 @tapaswenipathak
• Ordering of sections #59 @greengypsy
  • Tutorials for TOPP shell and TOPPView #69 @greengypsy
  • Update or delete Shipping external code to a new machine section #80 @jpfeuffer
  • "TOPP For Advanced Users" section requires clarity #100 @greengypsy
  • TOPPView and scripting information has been combined in one section #103 @greengypsy
  • TOPP concepts page needs work #104 @greengypsy
• Add tooltips to glossary terms #68
• Use of variable for the current version number #91
• Internal links broken #93 @tapaswenipathak
• Dozens of warnings #94
• Tabs not rendering properly on Introduction page #96
• Installation instructions wrong #98
• [maintenance] Setup GitHub automation permissions for openms-docs #106 @timosachsenberg
• Remove references to OMSSA #109 @greengypsy
• TOPPView - Add detailed instructions including gifs #113 @greengypsy
• Archive/Rename OpenMS/Tutorials repository? Tutorials#205 @jpfeuffer @timosachsenberg

Review Iterations

• Alpha of staging: [alpha-testing] To go live on OpenMS develop documentation: https://openms.readthedocs.io/en/develop #65: @tapaswenipathak
• OpenMS Documentation Gets a New Home #4
• Wiki pages archived: https://github.com/OpenMS/OpenMS/wiki @tapaswenipathak
• Alpha of develop: @OpenMS/collaborators @OpenMS/core @OpenMS/developers

References/Documents

• https://docs.google.com/document/d/1SEDf93uXPQuYC9SXaJiu-IBD4-VkX0H88qJ5kUuJK2E/edit?disco=AAAAbJkxrYM @greengypsy @axelwalter @jpfeuffer @timosachsenberg
• https://docs.google.com/document/d/1adohUF3ehmCzf1q_igst2js8Vyj52nL_zvm3gG3SxY8/edit @jpfeuffer

[tapaswenipathak]

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