2.1.0 Quarto compatibility and config bug fixes

Summary

⚠️ Carefully review the config_automation.yml changes. There are critical changes to the config file that are suggested but you will need to incorporate these if you've made any specific options to config_automation.yml for your particular use case

New features:

• Quarto is now compatible with OTTR.
• Website is updated and cleaner.
• In the config automation.yml formerly render-bookdown option is now render-website and options are quarto or rmd.

Bugs addressed:

• make-book-txt should not have been TRUE/FALSE. It should have been yes/no as options.
• Some cleaning up of deprecated files.

What's Changed

• Update sync.yml by @caalo in #762
• Update sync.yml by @kweav in #763
• Update sync.yml with Data Viz Courses by @kweav in #765
• Make GHA yml's compatible with quarto by @cansavvy in #746
• Delete docker workflows by @avahoffman in #767
• Update sync.yml by @caalo in #768
• Update config_automation.yml by @cansavvy in #769

Full Changelog: 2.0.1...2.1.0

2.0.1 Patch for github branch management changes

What's Changed

• Update sync.yml by @kweav in #739
• update sync configuration for OCS_Guide by @carriewright11 in #740
• Add new PR template for sync.yml edits by @kweav in #742
• Automatically open links to new tab by @howardbaek in #743
• add OTTR recognition to footer by @kweav in #745
• add ottr_docker to contributing.md info by @kweav in #752
• Rebase helps with render woes by @avahoffman in #756
• Fixing branch conflicts -- by addressing the folder issue that I think is causing it by @cansavvy in #757
• Update sync.yml by @kweav in #755
• update issue templates, related automatic issue, and include in cleanup by @kweav in #759
• Do rebase for render-all too (put back what @avahoffman had) by @cansavvy in #760
• Transfer bug fixes from Intro_to_R to here by @cansavvy in #761

Full Changelog: 2.0.0...2.0.1

2.0 OTTR

The Big OTTR Changes in this release

• The website has been updated! https://www.ottrproject.org/
• jhudsl-robot is no longer needed!
• The resources/exclude_files.txt file allows you to remove files from the spelling and URL checks.
• Scripts are moved to ottr-reports
• There's periodic URL checker! (For courses that aren't having changes much anymore, their URLs will still be checked periodically since sometimes links move!)
• There's now a downloadable preview in case htmlpreview is not showing what you are looking for
• The checker comments are updated to make it more clear!
• The base_ottr docker image is updated so that tidyverse and R are a newer version and this is MacOS compatible locally.
• There's now a OTTR Quarto for websites: https://github.com/fhdsl/OTTR_Quarto

What's Changed

• Testing latest release and docker image by @cansavvy in #620
• Edit the git config steps by @cansavvy in #633
• Git-config updates part 2 by @cansavvy in #638
• Add new repository to sync by @malachig in #634
• make book txt -- add to config file as an option by @cansavvy in #641
• Make old manuscript files actually delete by @cansavvy in #643
• Fix wonky html for Google Analytics by @KatherineCox in #640
• Attempt #2 at making manuscript folder actually delete by @cansavvy in #644
• Add new repository to sync by @juliambowden in #650
• Update README.md w/ course by @avahoffman in #655
• when starting course, replace README by @KatherineCox in #667
• Make it so courses are re-rendered when quizzes are changed by @cansavvy in #668
• Update w analytics reminder by @avahoffman in #691
• Add a WIP callout box by @KatherineCox in #695
• Bump actions versions by @avahoffman in #707
• Pass in branch name for OTTR comments to send people by @cansavvy in #710
• Fix transfer quiz repo files by @avahoffman in #712
• Ensure Coursera quizzes are rendered by @avahoffman in #713
• Have URLs periodically checked by @cansavvy in #673
• Delete scripts and have them downloaded from ottr-reports instead by @cansavvy in #721
• Fix little bug in periodic URL checker by @cansavvy in #723
• Add new repository to sync by @williamtmillsiv in #725
• Fix broken URLs for OTTR website by @kweav in #724
• Comprehensive preview add by @cansavvy in #729
• add contributing md by @kweav in #731
• add code of conduct to starting-course.yml by @kweav in #733

GitHub Actions Changes

• Make spelling comment more clear by @cansavvy in jhudsl/ottr-reports#26
• Don't check URLs in ignore list by @tmooney in jhudsl/ottr-reports#24
• Add accent debugging to spell check by @avahoffman in jhudsl/ottr-reports#27
• Add exclude_files.txt feature by @cansavvy in jhudsl/ottr-reports#29
• Have status update ran separately so its quicker by @cansavvy in jhudsl/ottr-reports#30
• Add the time of the report by @cansavvy in jhudsl/ottr-reports#14
• Update report-maker.yml by @cansavvy in jhudsl/ottr-reports#32
• Second attempt at status update being quicker by @cansavvy in jhudsl/ottr-reports#34
• Beef up the README by @howardbaek in jhudsl/ottr-reports#35

Full Changelog: 1.9.5...2.0.0

1.9.6

Addresses a few bugs that were caught after 1.9.5 #620

1.9.5

Wiki/Documentation updates

• Minor fixes

Template/style changes:

• None

Github action changes:

• Address deprecation of set-output
• Related to set-output deprecation, bumped up versions of some github action marketplace items like checkout@v3 and [email protected]

Docker image updates:

• ottrpal has some bug fixes to address glitches around fill in the blank questions. These will be updated in the docker image shortly.

What's Changed

• Sync setup data sharing by @carriewright11 in #578
• Add an ordered example by @avahoffman in #587
• Add Cluster 101 by @avahoffman in #589
• New tab target by @avahoffman in #588
• Another Fhdsl theme update by @avahoffman in #598
• Fix link by @avahoffman in #601
• Add Using Leanpub course to sync.yml by @avahoffman in #603
• updating template authors to add Ava by @carriewright11 in #608
• adding Overleaf_Tutorial by @carriewright11 in #609
• Address deprecation of set-output by @cansavvy in #610
• actions/checkout@v2 -> actions/checkout@v3 by @cansavvy in #611
• Bump changed files to v13.1 by @cansavvy in #614

Full Changelog: 1.9...1.9.5

v1.9 Consolidated GHA and OTTR-fying beta

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

Full Changelog: 1.8.1...1.9

v1.8.1 URL check fix

Wiki/Documentation updates

• Most common errors and how to fix them are documented here: https://github.com/jhudsl/OTTR_Template/wiki/Most-common-errors-and-pitfalls

Template/style changes:

• Add template description that has the links to different course formats: leanpub, coursera, bookdown.

Github action changes:

• Fix the URL checker since the one we were using no longer supports Rmds #514
• Other minor handling updates in regards to spelling checks

Docker image updates:

• None

What's Changed

• Try to fix merge conflict by @cansavvy in #474
• Cansavvy/merge conflict by @cansavvy in #475
• Add docker image as option by @cansavvy in #479
• Add a "no quizzes" handling ability as well as some merge conflict resolutions by @cansavvy in #480
• Switch handling of spell check errors by @cansavvy in #486
• One more spell check edit by @cansavvy in #489
• Wiki images by @carriewright11 in #491
• Save url check to a file like the other checks do by @cansavvy in #490
• Update sync.yml by @avahoffman in #494
• Change AnVIL Template Name by @avahoffman in #497
• Update update-enrollment.md by @KatherineCox in #505
• Delete style_coursera.css by @cansavvy in #508
• Add report-maker.yml here. by @cansavvy in #512
• Write our own url-checking script and get away from using url-checker-actions by @cansavvy in #515
• Add course formats bullet point template by @cansavvy in #516
• Update scripts so url check is fixed by @cansavvy in #518
• Add ability to ignore a url in the url checker by @cansavvy in #520

Full Changelog: 1.8...1.8.1

Release v1.8 config_automation.yml

** Note** This update will show render-preview check as broken because of some merge conflicts that should only happen this one time. So, you can ignore the fail of render-preview and merge what you need from this pull request anyway.

ottr package has been renamed to ottrpal because ottr is recently been taken on CRAN

Wiki/Documentation updates

• Information about how to pick and choose GitHub actions: https://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots
• Leanpub publishing is now done based on iframes (like Coursera has been)

Template/style changes:

• None

Github action changes:

• config_automation.yml now allows users to more easily select which checks and renders you want for your course! Read more about this here: https://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots
• Leanpub and Coursera are detangled from each other. You can render one or the other and not have to render both.

Docker image updates:

• ottr -> ottrpal in the Docker image
• CRAN mirror setting issue has been resolved
• From now on jhudsl/course_template:main is what is ready for prime time, but jhudsl/course_template:latest is what is currently the latest development (which may or may not work properly).

What's Changed

• Make docker unfail by @cansavvy in #431
• Try out screenshot creator as a part of the new Leanpub set up by @cansavvy in #422
• Update sync.yml with OTTR_Template_Website by @cansavvy in #437
• Add the polishing changes from #435 in their own PR by @cansavvy in #442
• Update sync.yml by @arpanda in #444
• Docker CRAN mirror setting issue by @cansavvy in #446
• Staging -> Main by @cansavvy in #458
• Disentangle bookdown/coursera/leanpub rendering. by @cansavvy in #459
• Separate styler from spell check by @cansavvy in #463
• Add screenshots for updating the Wiki by @cansavvy in #462
• Update transfer render with the iframe updates by @cansavvy in #464
• Fix delete preview and update sync.yml by @cansavvy in #465
• Make default that leanpub/quiz stuff is turned off in config_automation.yml by @cansavvy in #467
• Set to specific docker image by @cansavvy in #469
• ottr -> ottrpal by @cansavvy in #472
• Add spelling errors to get screenshots by @cansavvy in #473

Full Changelog: 1.7...1.8

leanbuild -> ottr

leanbuild package has been renamed to ottr

Wiki/Documentation updates

• The starting guide and About Docker sections have been reorganized and restructured along with their corresponding automatic issues

Template/style changes:

• The example 02-chapter examples have been updated

Github action changes:

• The render-bookdown.yml has been updated because of a Docker image issue

Docker image updates:

• leanbuild -> ottr in the Docker image

What's Changed

• Set to bash intentionally by @cansavvy in #419
• Test leanpub from here by @cansavvy in #420
• Minor polishing of steps by @cansavvy in #421
• Add new repository to sync by @tmm211 in #425
• Polish Examples in Rmds by @cansavvy in #426
• Fix a thing to avoid broken Docker builds later in render-bookdown by @cansavvy in #427
• Prep for leanbuild -> ottr rename by @cansavvy in #428

New Contributors

• @tmm211 made their first contribution in #425

Full Changelog: 1.6...1.7

1.6

*for reasons I do not totally understand Render preview may still fail on existing pull requests but once the sync pull request is merged, this appears to be resolved and everything works as expected again.

Still looking into this

Wiki/Documentation updates

• jhudsl-robot is now the official user for outside of jhudsl OTTR users to grant permissions to so that GHA still work.
• Screenshots are updated
• More details have been added about Leanpub quizzes

Template/style changes:

• AnViL has a style set now!

Github action changes:

• Sync GHA has a test version now that allows us to send changes to one repo at a time
• Spell check and render-preview have some fixes to make them work more reliably.
• starting-course.yml has a work around fix for if people have their main branch protected too quickly -- it now will create a PR
• _Quizzes repos have spell check and quiz check comments

Docker image updates:

• gh (a git client ) is added

What's Changed

• updating AnVIL style-set by @KatherineCox in #373
• Fixing GHA by @cansavvy in #376
• Update sync.yml by @arpanda in #374
• Git add step adjustments by @cansavvy in #380
• Sync ocs guide by @carriewright11 in #382
• Make all github actions use jhudsl-robot by @jhudsl-robot in #387
• Figuring out better system for downloading spell check file by @cansavvy in #386
• Add guidance about jhudsl-robot by @cansavvy in #389
• Delete first in starting course GHA by @cansavvy in #390
• Don't use GITHUB_TOKEN by @cansavvy in #391
• Only make the jhudsl library issue if its a jhudsl organization by @cansavvy in #392
• Try to adjust for if its a forked PR by @cansavvy in #394
• One more adjustment for forks by @cansavvy in #396
• Testing forks 2 by @jhudsl-robot in #395
• Undo fork pull request adjustments by @cansavvy in #399
• Make test sync better and more customizeable by @cansavvy in #404
• Spell check store as a gist by @cansavvy in #405
• Return to pre-gist method of spell check by @cansavvy in #409
• Update screenshot for new repo - Set to Public by @cansavvy in #410
• Update template button screenshot by @cansavvy in #411
• See if fetch-depth: 0 fixes the shallow problem by @cansavvy in #412
• Update screenshot for git-secret.png by @cansavvy in #414
• Some tweaks to git branch handling on GHA by @cansavvy in #418

New Contributors

• @arpanda made their first contribution in #374
• @jhudsl-robot made their first contribution in #387

Full Changelog: 1.5...1.6