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* Revert "updating templates_to_edit image" This reverts commit f95a790. forgot I was on main# * Revert "updating issue pics" This reverts commit fbc1c3e. forgot I was on main * Add report-maker.yml here. (#512) * delete report.maker.yml * Add report-maker.yml here * Need to add + 1 because the column names don't count * change strategy for declaring error_min * Try to fix syntax around inputs.error_min * Try this * Update report-maker.yml * substract 1 * Forgot to delete old attempt * Try to fix chk_results declarations * Get rid of straggling quote * Print out error number * Fix reports * Set version * specify git_path * Fix file path * Try copying over? * ls workspace * Nope that didn't work * Set version * Change version * Check all the urls * Don't need to specify git_path * force pass true * exclude docs and manuscript folder * exclude files * try to add Rmd * Write our own url-checking script and get away from using url-checker-actions (#515) * Add url-checker to docker image * Add url-check.R adds! * Revert "Add url-checker to docker image " This reverts commit fe5c7ed. * Update report-maker.yml * Add course formats bullet point template (#516) * Add course formats bullet points to template * Also add ottrpal to dictionary.txt * Render bookdown * Update scripts so url check is fixed (#518) * Update scripts * try to fix url checker * Add a broken url as a test * rearrange steps * get rid of -1 * get rid of extra stuff * Fix results Thing * Fix file path * .csv -> .tsv * Revert "Add a broken url as a test" This reverts commit 973453f. * Add files via upload * Add ability to ignore a url in the url checker (#520) * Try to ignore some urls * If there's not a file, then download it * Fix some things * Test deleting the files * Revert "Test deleting the files" This reverts commit b8707f0. * Delete report-maker.yml * Fix false URL finds * Fix false URL finds (#521) * Update ignore-urls.txt * Update url-check.R * Try to fix url identifier * More polishing to url-check.R * Polishing polishing * A few more regex refinings * Update sync.yml (#522) * Polishing url-check.R (#523) * Fix false URL finds * Try to fix url identifier * More polishing to url-check.R * Polishing polishing * A few more regex refinings * Update to stop url at } * Fix } * Boxes (#524) * Revert "updating templates_to_edit image" This reverts commit f95a790. forgot I was on main# * Revert "updating issue pics" This reverts commit fbc1c3e. forgot I was on main * adding ITN style code for boxes * adding images and general style code for boxes * showing examples of style boxes * Render bookdown * Boxes (#525) * Revert "updating templates_to_edit image" This reverts commit f95a790. forgot I was on main# * Revert "updating issue pics" This reverts commit fbc1c3e. forgot I was on main * adding ITN style code for boxes * adding images and general style code for boxes * showing examples of style boxes * moving images from assets to subdir called box_images to allow for easy sync of these images * forgot about dictionary image * updating paths for style.css file for general template use * updating paths for itn style doc * adding asset box image dir to sync * add boxes to GDSCN css code * adding boxes to AnVIL css code * adding boxes to DataTrail css * Render bookdown * make AnVIL_Template group in sync.yml * Revert "make AnVIL_Template group in sync.yml" This reverts commit 4490781. * make an AnVIL_Template group in sync.yml (#527) * Boxes (#529) * Revert "updating templates_to_edit image" This reverts commit f95a790. forgot I was on main# * Revert "updating issue pics" This reverts commit fbc1c3e. forgot I was on main * adding ITN style code for boxes * adding images and general style code for boxes * showing examples of style boxes * moving images from assets to subdir called box_images to allow for easy sync of these images * forgot about dictionary image * updating paths for style.css file for general template use * updating paths for itn style doc * adding asset box image dir to sync * add boxes to GDSCN css code * adding boxes to AnVIL css code * adding boxes to DataTrail css * adding initial version of reflection box * adding reflection box to other style sets * Update sync.yml (#526) * Update sync.yml * Edit Credits section * Render bookdown * Render bookdown * Update sync.yml (#530) * Update sync list for AnVIL_Template (#538) Subscribing to `style.css` so we can get updates like those nice new style boxes! * Branches sometimes overwrite each other - trying to fix (#537) * Try to update the git push * Add broken urls and spelling errors * This appears to work better * Revert "Add broken urls and spelling errors" This reverts commit b4b49e6. * clean and consolidate styling for callout boxes (#541) * clean and consolidate styling for callout boxes * remove old style boxes entirely * Render bookdown * Update transfer-rendered-files.yml - specify docker image (#542) * Try to update the git push * Add broken urls and spelling errors * This appears to work better * Update transfer-rendered-files.yml * Revert "Add broken urls and spelling errors" This reverts commit b4b49e6. * Update to ottrpal:latest to test * temporarily turn on leanpub * forgot the jhudsl/ part * Don't specify latest * Fix spec * Switch to main * restore default options * fixing rendering of rest of ch 2 * adding more inform about header sytax and syntax in general, as well as more about stylized boxes. * adding back the borders to the boxes that got removed * trying to add back doc file * trying to add back doc file * trying to add back doc files * trying to add back doc files for docs/coursera * trying to add back doc files for docs/no_toc * trying to add back doc files for docs/404.html * trying to add back doc files for docs/ * trying to add back doc files for Course_Name.rds * trying to add back doc files for book.bib * updating spelling * adding more structure for subheadings and more information * adding more documentation and updating pdf example * updating readme to include rendered version * adding rendered link * Render bookdown * Add styler to render all workflow * Revert "Add styler to render all workflow" This reverts commit e24bf2d. * Update ignore-urls.txt * Add git config to address no commit * Add ugly code to test * Add explicit git checkout * Add branch name for origin * Try this * Fix branch declaration * Fix that * Try REF_NAME * head_ref * Style Rmds * Add styler to render all workflow (#546) * Update README.md * Add ottr-fy.R script * Update README.md * Update README.md * Add latest ottr-fy.R script * Update with bookdown option * Bump create-issue-from-file action (#552) * Delete style-sets/AnVIL directory (#553) * Render bookdown * Remove AnVIL repos from sync * Update sync.yml (#554) * Create super bare bones theme for fhdasl stuff * Remove fhdasl_style from path * Add things to dictionary * remove GDSCN style-set * Render bookdown * Render bookdown * Get rid of archive of spelling results * Add docker-test here * Delete the docker files here because they are managed in ottr-docker * Get 404s properly (#564) * Get 404s * Restore to failed/success so downstream works * Need some more logic * Minor fix * SHouldn't have https://jhudatascience.org/{Course_Name} anymore anyway * Add pull-request.yml to use report-maker.yml here (#513) * Update Staging branch with what's in main (#438) * Return to pre-gist method of spell check (#409) * Return to pre-gist method of spell check * Get rid of gist stuff on delete-preview too * Temporarily add spelling errors to test * Commit before testing * Switch to use -z * Fix git diff step * Just look at the local main since it should be up to date * make it simple * Get rid of double bracket * No brackets? * Revert "Temporarily add spelling errors to test" This reverts commit 9e9a932. * Update screenshot for new repo (#410) * Update template button screenshot (#411) * Update screenshot for new repo * Update template button too * See if `fetch-depth: 0` fixes the shallow problem (#412) * Update screenshot for new repo * Update template button too * fetch it all * Switch to devtools::session_info() * Render bookdown * Update screenshot for git-secret.png (#414) * Update screenshot for git-secret.png * Crop off irrelevant git secrets * syntax updates * Needed a semicolon * Fix branch handling * Update spell check set up * Update main * add brackets * set shell intentionally * fix if statements * Create PR if it can't push directly * Make sure it merges * Alter branch test * quote the 0? * switch to -z * Delete extra then * This should work * Change to preview- again whoops * Add a push step * Update starting course * set upstream * Set to bash intentionally (#419) * set to bash * Update * no workflow dispatch * Test leanpub from here (#420) * Test leanpub from here * Update comments * Add check quizzes too * Couple edits * Shut them off for now * Update comments * Render leanpub * Minor polishing of steps (#421) * Test leanpub from here * Update comments * Add check quizzes too * Couple edits * Shut them off for now * Update comments * Note which places needed to be uncommented * Just making the step clearer * Add a git fetch * Add quizzes to spell check * Update README.md * Render leanpub * Add new repository to sync * Polish Examples in Rmds (#426) * Echo false in examples * Updating wiki * Render bookdown * Render bookdown (#427) * Prep for ottr rename (#428) * Render bookdown * Make docker unfail (#431) * Make docker not fail * Add Dockerfile example * Get rid of extra line * Skip build for this test * comment out push part too for this test * undo test Dockerfile * Render bookdown * Try out screenshot creator as a part of the new Leanpub set up (#422) * Try out screenshot creator * Fix spacing * Get rid of typo * fix argument spec * Fix git pat handling * Add copy over assets step * Try this * Try installing just the packages we need * Add install of remotes * Try using devtools instead * try set environ * Try to install R first * Add prereqs * Try rocker r-base * Put installations in script * Try different strategy * Switch to tidyverse * Make directory in bash * I guess I'm making this its own docker image * This isn't working but I want it in case I come back to it * Switch to wkhtmltopdf * Lets' try it * Trying leanbuild steps on their own dockerfile * Test build of leanbuild docker image * Try out webshot r package * fix file path to script * Oh. Actually fix it * Try installing webshot::install_phantomjs * Try installing phantomjs on its own first * Set this up * Build from jhudsl/course_template * Switch back to main dockerfile * assets problem * It works! * Revert "assets problem" This reverts commit 2aada9b. * Add markdown maker basics * Push this version before I delete things * Clean up * Delete the pdfs * Reconfig with latest ottr package changes * Turn on render again * Add PR instead * Move copying step * Add an :: that was missing * Fix arguments for getting pages url * misplaced quotes * Add make_book_txt = TRUE * It's working! Undo the commenting part * Set base to main * Revert "It's working! Undo the commenting part" This reverts commit 92e5081. * rm manuscript folder * Just commit to main * Delete old manuscript files * Copy over assets * Render bookdown * Remove manuscript if it is there * Set group and user id to get rid of permissions probs * Forgot \ 's * Render bookdown * Make it force push * only force manuscript dir * Render Leanpub * Render Leanpub * Render Leanpub * Add to transfer PRs * Delete manuscript folder * Add to sync.yml * Render Leanpub * Remove _Template bit * Add coursera bit and _Quizzes * Clean out manuscript folder when starting new course * Make transfers go to the right folder * add / * Update sync.yml with OTTR_Template_Website (#437) Co-authored-by: jhudsl-robot <itcrtrainingnetwork@gmail.com> Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: jhudsl-robot <97678365+jhudsl-robot@users.noreply.github.com> Co-authored-by: Tiffany Miller <tiffanym@broadinstitute.org> Co-authored-by: jhudsl-robot <itcrtrainingnetwork@gmail.com> * Delete packages.bib * Minor edits to index.Rmd * Delete extraneous files * Consolidate and config a pull request GHA (#448) * Create config_automation.yml * Update style-and-sp-check.yml * Update the filename 😑 * Checking dependency * Update style-and-sp-check.yml * Testing that file is carried over * Add toggle to second check * Change config to test * Test removal of some extra text * Change config to test (again) * Update config_automation.yml * What does the output look like with more checks added? * Fix spacing * Forgot "steps:" * BIG YAML * Get rid of other ones * Fix names * Add needs * Try adding docker to it * Fix syntax * Gotta check it out first * Extra "if" lying around * Set logically differently * Testing change * Add Ava's suggestions! Co-authored-by: AM Hoffman <avamariehoffman@gmail.com> * Consolidate and config a rendering GHA (#449) * Create config_automation.yml * Update style-and-sp-check.yml * Update the filename 😑 * Checking dependency * Update style-and-sp-check.yml * Testing that file is carried over * Add toggle to second check * Change config to test * Test removal of some extra text * Change config to test (again) * Update config_automation.yml * What does the output look like with more checks added? * Fix spacing * Forgot "steps:" * BIG YAML * Get rid of other ones * Fix names * Add needs * Try adding docker to it * Make a render-all yaml * Fix syntax * Gotta check it out first * Extra "if" lying around * Set logically differently * Echo no branch to delete if there is none to delete * Update sync.yml * fix syntax * Fix name of render-all * Add names Co-authored-by: AM Hoffman <avamariehoffman@gmail.com> * Update pull-request.yml to use report-maker.yml * Need to add + 1 because the column names don't count * Turn on quiz check for testing * Add comment * Try out different syntax for + 1 * Add errors to test * Add a quiz error * Add url error * Make quiz error * Add question error * Add URL * Switch version of url-checker * Add url-checker to docker image * Add url-check.R adds! * Update report-maker.yml * fix script * Get rid of fake errors * Revert "Add question error" This reverts commit dc411cb. * Fix quiz * Add a correct answer * Stop checking quizzes * Try out new github action * Fix indents * Try this out? * Fix comments * git force --add * Updates * Get rid of secrets: * Try ottr-reports set up * Get rid of secrets. * Test secrets.GH_PAT * Ignore checks for testing purposes * Try secrets.GH_PAT again * Try supplying secret through environment * Switch order of steps * Try somewhere else * use ls- R again * Try again * Re-run without script directory perl thing * Try $GITHUB_WORKSPACE * Maybe we need to check out files in report_maker * Use basename * Try to fix syntax * Name output variable in earlier step * Declare report name * Add error URL * Fix error url * Drop quotes and {} * echo it maybe * add more explicit variable declaration * Drop brackets * no quotes * Try to fix quotes * Try quotes * Try `contains()` * Commit reports to the branch * Try to supply token * add secrets designation * Use V3 checkout * switch gh_pat designation * login as jhudsl-robot * Move the steps: * No login * Specify GH_PAT * Try this instead * Try environment thing * Revert "Try environment thing" This reverts commit ac469b8. * Don't set inputs.gh_pat * set git config * Try to fix error 11 * Fix an inputs.gh_pat * specify ref * Adjust the logic * git add adjust * Add errors to check that this is working * Try again * Calculate error number by hand * Declare number of errors * Try this instead * Forgot a $ * Try to fix number thing * Still trying to fix error count * print out error numbers * Add spelling errors * Try to set up the error_num another way * Print out error numbers * Remove errors and see if this works * Fix branch merge option Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: jhudsl-robot <97678365+jhudsl-robot@users.noreply.github.com> Co-authored-by: Tiffany Miller <tiffanym@broadinstitute.org> Co-authored-by: jhudsl-robot <itcrtrainingnetwork@gmail.com> Co-authored-by: AM Hoffman <avamariehoffman@gmail.com> * Call report-maker.yml from here (#565) * Call report-maker.yml from here * Delete report-maker.yml from this repo * Update links in automatic issues (#567) * Update links in automatic issue set-repo-settings * remove duplicate GH_PAT * update more links * Update links in update-enrollment.md * update templates-to-edit * Update all refs to Wiki with new stuff * Update link in .github/automatic-issues/templates-to-edit.md * Update another link in .github/automatic-issues/set-repo-settings.md * another link * another link Co-authored-by: Candace Savonen <cansav09@gmail.com> * Render bookdown * switch the name and refs of course_template to base_ottr (#569) * switch to base_ottr * Ad to config_automation.yml * Replace all instances of "jhudsl/course_template" -> "jhudsl/base_ottr" * Render bookdown * Update sync.yml Co-authored-by: Carrie Wright <cwrigh60@jhu.edu> Co-authored-by: jhudsl-robot <itcrtrainingnetwork@gmail.com> Co-authored-by: Carrie Wright <23014755+carriewright11@users.noreply.github.com> Co-authored-by: Katherine Cox <katherinecox@jhu.edu> Co-authored-by: avahoffman <avamariehoffman@gmail.com> Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: jhudsl-robot <97678365+jhudsl-robot@users.noreply.github.com> Co-authored-by: Tiffany Miller <tiffanym@broadinstitute.org>
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