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>
jhudsl · Oct 4, 2022 · 19ce025 · 19ce025
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diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -1,4 +1,4 @@
-# Candace Savonen Dec 2021
+# Candace Savonen Aug 2022
 
 name: Pull Request
 
@@ -57,92 +57,38 @@ jobs:
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
       dockerfiles_changed: steps.verify-changed-files.outputs.files_changed
 
+########################## Make the error reports ##############################
   spell-check:
     name: Check spelling
     needs: yaml-check
-    runs-on: ubuntu-latest
     if: ${{needs.yaml-check.outputs.toggle_spell_check == 'yes'}}
-    container:
-      image: jhudsl/course_template:main
-
-    steps:
-      - name: Checkout files
-        uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
-
-      - name: Configure git
-        run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
-
-          branch_name='preview-${{ github.event.pull_request.number }}'
-          git fetch --all
-          git checkout $branch_name
-          git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
-        shell: bash
-
-      - name: Run spell check
-        id: spell_check_run
-        run: |
-          results=$(Rscript "scripts/spell-check.R")
-          echo "::set-output name=sp_chk_results::$results"
-
-      - name: Commit spell check errors
-        run: |
-          branch_name='preview-${{ github.event.pull_request.number }}'
-          git add --force check_reports/spell_check_results.tsv || echo "No changes to commit"
-          git commit -m 'Add spell check file' || echo "No changes to commit"
-          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
-          git push --force origin $branch_name || echo "No changes to commit"
-
-      - name: Build components of the spell check comment
-        id: build-components
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
-        run: |
-          branch_name='preview-${{ github.event.pull_request.number }}'
-          sp_error_url=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/check_reports/spell_check_results.tsv
-          echo ::set-output name=time::$(date +'%Y-%m-%d')
-          echo ::set-output name=commit_id::$GITHUB_SHA
-          echo ::set-output name=sp_error_url::$sp_error_url
+    uses: ./.github/workflows/report-maker.yml
+    with:
+      check_type: spelling
+      error_min: 3
+      gh_pat: secrets.GH_PAT
 
-      # 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: spelling errors
-
-      - name: Spelling errors!
-        if: ${{ steps.spell_check_run.outputs.sp_chk_results >= 3 }}
-        uses: peter-evans/create-or-update-comment@v1
-        with:
-          comment-id: ${{ steps.fc.outputs.comment-id }}
-          issue-number: ${{ github.event.pull_request.number }}
-          body: |
-            :warning: There are spelling errors that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/Spell-check).
-            [Download the errors here.](${{ steps.build-components.outputs.sp_error_url }})
-            _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
-          edit-mode: replace
-
-      - name: Check spell check results - fail if too many errors
-        if: ${{ steps.spell_check_run.outputs.sp_chk_results >= 3 }}
-        run: exit 1
-
-      - name: No spelling errors
-        if: ${{ steps.spell_check_run.outputs.sp_chk_results < 3 }}
-        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 spelling errors! :tada:
-            _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
-          edit-mode: replace
+  url-check:
+    name: Check URLs
+    needs: yaml-check
+    if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
+    uses: ./.github/workflows/report-maker.yml
+    with:
+      check_type: urls
+      error_min: 0
+      gh_pat: secrets.GH_PAT
+
+  quiz-check:
+    name: Check quiz formatting
+    if: ${{needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
+    needs: yaml-check
+    uses: ./.github/workflows/report-maker.yml
+    with:
+      check_type: quiz_format
+      error_min: 0
+      gh_pat: secrets.GH_PAT
 
+############################# Style the code ###################################
   style-code:
     name: Style code
     needs: yaml-check
@@ -166,181 +112,7 @@ jobs:
           git commit -m 'Style Rmds' || echo "No changes to commit"
           git push origin || echo "No changes to commit"
 
-  url-check:
-    name: Check URLs
-    needs: yaml-check
-    runs-on: ubuntu-latest
-    if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
-    container:
-      image: jhudsl/course_template:main
-
-    steps:
-    - name: checkout repo
-      uses: actions/checkout@v2
-
-    - name: Configure git
-      run: |
-        git config --local user.email "itcrtrainingnetwork@gmail.com"
-        git config --local user.name "jhudsl-robot"
-
-        branch_name='preview-${{ github.event.pull_request.number }}'
-        git fetch --all
-        git checkout $branch_name
-        git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
-      shell: bash
-
-    - name: URLs checker
-      id: url_errors
-      run: |
-        chk_results=$(Rscript scripts/url-check.R)
-        echo $chk_results
-
-        echo "::set-output name=url_results::$chk_results"
-
-    - name: Commit URL check
-      run: |
-        branch_name='preview-${{ github.event.pull_request.number }}'
-        git add --force check_reports/url_checks.tsv || echo "No changes to commit"
-        git commit -m 'Add URL check file' || echo "No changes to commit"
-        git fetch
-        git merge -s recursive --strategy-option=ours origin/${{ github.head_ref }} --allow-unrelated-histories
-        git push --force origin $branch_name || echo "No changes to commit"
-
-    - name: Build components of the spell check comment
-      id: build-components
-      env:
-        GH_PAT: ${{ secrets.GH_PAT }}
-      run: |
-        branch_name='preview-${{ github.event.pull_request.number }}'
-        url_errors=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/check_reports/url_checks.tsv
-        echo ::set-output name=time::$(date +'%Y-%m-%d')
-        echo ::set-output name=commit_id::$GITHUB_SHA
-        echo ::set-output name=url_errors::$url_errors
-
-    # 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: broken URLs
-
-    - name: URL errors!
-      if: ${{ steps.url_errors.outputs.url_results > 0 }}
-      uses: peter-evans/create-or-update-comment@v1
-      with:
-        comment-id: ${{ steps.fc.outputs.comment-id }}
-        issue-number: ${{ github.event.pull_request.number }}
-        body: |
-          :warning: There are broken URLs that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots#check-for-broken-urls).
-          [Download the errors here.](${{ steps.build-components.outputs.url_errors }})
-          _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
-        edit-mode: replace
-
-    - name: Check URL results - fail if too many errors
-      if: ${{ steps.url_errors.outputs.url_results > 0 }}
-      run: exit 1
-
-    - name: No URL errors
-      if: ${{ steps.url_errors.outputs.url_results == 0 }}
-      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 broken URLs detected! :tada:
-          _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
-        edit-mode: replace
-
-  check-quizzes:
-    name: Check Leanpub quizzes
-    needs: yaml-check
-    runs-on: ubuntu-latest
-    container:
-      image: jhudsl/course_template:main
-    if: ${{needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
-    steps:
-      - name: Checkout files
-        uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
-
-      - name: Configure git
-        run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
-
-          branch_name='preview-${{ github.event.pull_request.number }}'
-          git fetch --all
-          git checkout $branch_name
-          git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
-        shell: bash
-
-      - name: Run quiz check
-        id: quiz_check_run
-        run: |
-          Rscript -e "ottrpal::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='preview-${{ github.event.pull_request.number }}'
-          git add --force question_error_report.tsv || echo "No changes to commit"
-          git commit -m 'Add question error report file' || echo "No changes to commit"
-          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
-          git push origin $branch_name || echo "No changes to commit"
-
-      - name: Build components of the quiz check comment
-        id: build-components
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
-        run: |
-          branch_name='preview-${{ 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
-
-      - 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
-
-      - name: Check quiz check results - fail if too many errors
-        if: ${{ steps.quiz_check_run.outputs.quiz_chk_results >= 2 }}
-        run: exit 1
-
-      - 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
+############################# Render Preview ###################################
 
   render-preview:
     name: Render preview
@@ -451,6 +223,8 @@ jobs:
             _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace
 
+############################## Build Docker ####################################
+
   build-docker:
     name: Build Docker image
     needs: yaml-check

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
@@ -181,6 +181,7 @@ jobs:
           git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
           git add --force manuscript/*
           git add --force resources/*
+          git add --force docs/*
           git commit -m 'Render Leanpub' || echo "No changes to commit"
           git pull --allow-unrelated-histories --strategy-option=ours
           git push origin main || echo "No changes to push"
@@ -217,7 +218,9 @@ jobs:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
           git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          git add --force .
+          git add --force manuscript/*
+          git add --force resources/*
+          git add --force docs/*
           git commit -m 'Render Coursera quizzes' || echo "No changes to commit"
           git pull --allow-unrelated-histories --strategy-option=ours
           git push origin main || echo "No changes to push"