v1.9 Consolidated GHA and OTTR-fying beta

[cansavvy]

Wiki/Documentation updates

• ottrfying has been documented: https://www.ottrproject.org/ottr-fy.html though it still needs more testing
• Customizing Docker has more details added: https://www.ottrproject.org/customize-docker.html
• Issue templates have been updated to reflect ottrproject.org links instead of Wiki

Template/style changes:

• A Fred Hutch style set has been added with funfetti!

Github action changes:

• The Github checks are now consolidated on their own repository so that less code is needed in pull_request.yml
• This will also mean less syncs will be needed because as changes to https://github.com/jhudsl/ottr-reports they will be published and accessible without changes to an OTTR repository's code.
• URL checker wasn't properly identifying all 404s but now it should!

Docker image updates:

• All docker images related files are are now stored in https://github.com/jhudsl/ottr_docker
• jhudsl/course_template has now been renamed jhudsl/base_ottr

What's Changed

• Update Staging branch with what's in main by @cansavvy in Update Staging branch with what's in main #438
• Consolidate and config a pull request GHA by @cansavvy in Consolidate and config a pull request GHA  #448
• Consolidate and config a rendering GHA by @cansavvy in Consolidate and config a rendering GHA  #449
• Fix false URL finds by @cansavvy in Fix false URL finds #521
• Update sync.yml for AnviL Template script accomodation by @cansavvy in Update sync.yml for AnviL Template script accomodation #522
• Polishing url-check.R by @cansavvy in Polishing url-check.R #523
• Boxes by @carriewright11 in Boxes #524
• Boxes by @carriewright11 in Boxes #525
• make an AnVIL_Template group in sync.yml by @KatherineCox in make an AnVIL_Template group in sync.yml #527
• Boxes by @carriewright11 in Boxes #529
• Update sync.yml by @cansavvy in Update sync.yml #526
• Update sync.yml to have jhudsl/Choosing_Genomics_Tools by @cansavvy in Update sync.yml to have jhudsl/Choosing_Genomics_Tools #530
• Update sync list for AnVIL_Template by @KatherineCox in Update sync list for AnVIL_Template #538
• Branches sometimes overwrite each other - trying to fix by @cansavvy in Branches sometimes overwrite each other - trying to fix #537
• clean and consolidate styling for callout boxes by @KatherineCox in clean and consolidate styling for callout boxes #541
• Update transfer-rendered-files.yml - specify docker image by @cansavvy in Update transfer-rendered-files.yml - specify docker image  #542
• Style documentation update for boxes by @carriewright11 in Style documentation update for boxes #544
• Add styler to render all workflow by @avahoffman in Add styler to render all workflow #546
• Bump create-issue-from-file action by @avahoffman in Bump create-issue-from-file action #552
• Delete style-sets/AnVIL directory by @KatherineCox in Delete style-sets/AnVIL directory #553
• Remove AnVIL repos from sync by @avahoffman in Remove AnVIL repos from sync #555
• Update sync.yml by @KatherineCox in Update sync.yml #554
• remove GDSCN style-set by @KatherineCox in remove GDSCN style-set #560
• Create super bare bones theme for fhdasl stuff by @avahoffman in Create super bare bones theme for fhdasl stuff #556
• Get 404s properly by @cansavvy in Get 404s properly #564
• Add pull-request.yml to use report-maker.yml here by @cansavvy in Add pull-request.yml to use report-maker.yml here #513
• Call report-maker.yml from here by @cansavvy in Call report-maker.yml from here #565
• Update links in automatic issues by @KatherineCox in Update links in automatic issues #567
• switch the name and refs of course_template to base_ottr by @cansavvy in switch the name and refs of course_template to base_ottr #569
• Clear out newly unneeded files by @cansavvy in Clear out newly unneeded files #571
• Add funfetti themeing by @avahoffman in Add funfetti themeing #566
• Refresh preview branch each time by @cansavvy in Refresh preview branch each time #573
• Have transfer-rendered-files.yml transfer the _bookdown.yml file by @cansavvy in Have transfer-rendered-files.yml transfer the _bookdown.yml file #574

Full Changelog: 1.8.1...1.9

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This discussion was created from the release v1.9 Consolidated GHA and OTTR-fying beta .