Get staging up to date #570
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This reverts commit f95a790. forgot I was on main#
This reverts commit fbc1c3e. forgot I was on main
…_Bookdown into main pulling new changes
…_Bookdown into main getting remote changes
…_Bookdown into main merging in remote changes
…_Bookdown into main getting remote changes
…_Bookdown into main getting remote changes
…_Bookdown into main getting remote changes
…_Bookdown into main getting remote changes - conflicted with out-of-date style files
…_Bookdown into main getting remote changes
…_Bookdown into main getting remote changes
…_Bookdown into main getting remote changes
* delete report.maker.yml * Add report-maker.yml here
Remove AnVIL repos from sync
remove GDSCN style-set
because they are managed in ottr-docker
* 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
* 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 * Delete report-maker.yml from this repo
* 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>
* switch to base_ottr * Ad to config_automation.yml * Replace all instances of "jhudsl/course_template" -> "jhudsl/base_ottr"
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No spelling errors! 🎉 |
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Re-rendered previews from the latest commit:
Updated at 2022-10-06 with changes from be6dd41 |
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No broken urls! 🎉 |
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Yes. This all looks appropriate and the checks have passed. |
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Purpose/implementation Section
What changes are being implemented in this Pull Request?
I've been slacking and not really using the staging branch as intended. This is a pull request to try to get that up to date so maybe I do this properly again.