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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>
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,19 +1,23 @@ | ||
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| For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-settings). | ||
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| ### Needed settings: | ||
| For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course). | ||
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| - [ ] This course repository is set to `public`. | ||
| - [ ] [Add the `jhudsl-robot` as a collaborator to your repository.](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-settings#add-jhudsl-robot-as-a-collaborator). | ||
| - [ ] [GH_PAT has been set up as a GitHub secret](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-token) | ||
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| #### Turn on GitHub pages | ||
| - [ ] Go to `Settings` > `Pages`. Underneath `Source`, choose `main` for the branch and select the `docs` folder. Then click `Save`. | ||
| - [ ] Check `Enforce HTTPS`. | ||
| - [ ] GitHub pages is turned on | ||
| - [ ] Go to `Settings` > `Pages`. Underneath `Source`, choose `main` for the branch and select the `docs` folder. Then click `Save`. | ||
| - [ ] Check `Enforce HTTPS`. | ||
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| #### Set protections for main branch | ||
| \* Don't set these settings right away! Wait a few minutes after starting your repository. | ||
| - [ ] [Github secret `GH_PAT` has been set](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-token) | ||
| `Name`: `GH_PAT` | ||
| `value`: A personal access token [following these instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token#creating-a-token). | ||
| Underneath `Select scopes`, check both `repo` and `workflow`. | ||
| Then copy the PAT and save as the value. | ||
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| - [ ] `main` branch has been set up: | ||
| - [ ] `Require pull request reviews before merging` box is checked. | ||
| - [ ] `Require status checks to pass before merging` box is checked. | ||
| - [ ] Underneath that `Require branches to be up to date before merging` box is checked. | ||
| - [ ] Click `Save` at the bottom of the page! | ||
| - [ ] [Set branch protections settings](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#9-set-up-branch-rules) | ||
| - [ ] `main` branch has been set up: | ||
| - [ ] `Require pull request reviews before merging` box is checked. | ||
| - [ ] `Require status checks to pass before merging` box is checked. | ||
| - [ ] Underneath that `Require branches to be up to date before merging` box is checked. | ||
| - [ ] Click `Save` at the bottom of the page! |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,117 @@ | ||
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| # Candace Savonen Jan 2022 | ||
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| name: Check Leanpub Quizzes | ||
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| on: | ||
| workflow_dispatch: | ||
| ### UNCOMMENT THIS SECTION IF YOU WISH PREPARE YOUR COURSE QUIZZES FOR LEANPUB AUTOMATICALLY | ||
| # pull_request: | ||
| # branches: [ main, staging] | ||
| # paths: | ||
| # - 'quizzes/*' | ||
| ######### END OF SECTION ######### | ||
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| jobs: | ||
| check-quizzes: | ||
| runs-on: ubuntu-latest | ||
| container: | ||
| image: jhudsl/course_template | ||
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| steps: | ||
| - name: Checkout files | ||
| uses: actions/checkout@v2 | ||
| with: | ||
| fetch-depth: 0 | ||
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| - name: Configure git | ||
| run: | | ||
| git config --local user.email "itcrtrainingnetwork@gmail.com" | ||
| git config --local user.name "jhudsl-robot" | ||
| branch_name='check-${{ github.event.pull_request.number }}' | ||
| exists=$(git ls-remote https://${{ secrets.GH_PAT }}@github.com/$GITHUB_REPOSITORY $branch_name | wc -l | xargs) | ||
| if [[ $exists == 0 ]];then | ||
| echo branch doesnt exist | ||
| git checkout -b $branch_name | ||
| git push --set-upstream origin $branch_name | ||
| else | ||
| echo branch does exist | ||
| git fetch --all | ||
| git checkout $branch_name | ||
| git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} | ||
| fi | ||
| shell: bash | ||
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| - name: Run quiz check | ||
| id: quiz_check_run | ||
| run: | | ||
| Rscript -e "ottr::check_quizzes(quiz_dir = 'quizzes', write_report = TRUE, verbose = TRUE)" | ||
| results=0 | ||
| if -f "question_error_report.tsv"; then | ||
| results=$(wc -l < question_error_report.tsv >/dev/null) | ||
| fi | ||
| echo ::set-output name=quiz_chk_results::$results | ||
| - name: Commit quiz check errors | ||
| run: | | ||
| branch_name='check-${{ github.event.pull_request.number }}' | ||
| git diff --name-only origin/main -- question_error_report.tsv >/dev/null && changes=true || changes=false | ||
| echo $changes | ||
| if $changes == true; then | ||
| git diff --name-only origin/$branch_name question_error_report.tsv >/dev/null && changes=true || changes=false | ||
| echo $changes | ||
| if $changes == true; then | ||
| git add --force question_error_report.tsv | ||
| git diff-index --quiet HEAD || git commit -m 'Add question error report file' | ||
| git pull --set-upstream origin $branch_name --allow-unrelated-histories | ||
| git push origin $branch_name | ||
| fi | ||
| fi | ||
| - name: Build components of the quiz check comment | ||
| id: build-components | ||
| env: | ||
| GH_PAT: ${{ secrets.GH_PAT }} | ||
| run: | | ||
| branch_name='check-${{ github.event.pull_request.number }}' | ||
| quiz_error_url=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/question_error_report.tsv | ||
| echo ::set-output name=time::$(date +'%Y-%m-%d') | ||
| echo ::set-output name=commit_id::$GITHUB_SHA | ||
| echo ::set-output name=quiz_error_url::$quiz_error_url | ||
| # Handle the commenting | ||
| - name: Find Comment | ||
| uses: peter-evans/find-comment@v1 | ||
| id: fc | ||
| with: | ||
| issue-number: ${{ github.event.pull_request.number }} | ||
| comment-author: 'github-actions[bot]' | ||
| body-includes: quiz errors | ||
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| - name: Quiz errors! | ||
| if: ${{ steps.quiz_check_run.outputs.quiz_chk_results >= 2 }} | ||
| uses: peter-evans/create-or-update-comment@v1 | ||
| with: | ||
| comment-id: ${{ steps.fc.outputs.comment-id }} | ||
| issue-number: ${{ github.event.pull_request.number }} | ||
| body: | | ||
| :warning: There are quiz errors that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/Publishing-on-Leanpub#setting-up-quizzes). | ||
| [Download the errors here.](${{ steps.build-components.outputs.quiz_error_url }}) | ||
| _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_ | ||
| edit-mode: replace | ||
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| - name: Check quiz check results - fail if too many errors | ||
| if: ${{ steps.quiz_check_run.outputs.quiz_chk_results >= 2 }} | ||
| run: exit 1 | ||
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| - name: No quiz errors | ||
| if: ${{ steps.quiz_check_run.outputs.quiz_chk_results < 2 }} | ||
| uses: peter-evans/create-or-update-comment@v1 | ||
| with: | ||
| comment-id: ${{ steps.fc.outputs.comment-id }} | ||
| issue-number: ${{ github.event.pull_request.number }} | ||
| body: | | ||
| No quiz errors detected! :tada: | ||
| _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_ | ||
| edit-mode: replace |
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