`.
-
-- [ ] Every image has alternative text added to it.
-
-- [ ] The beginning of each Rmd contains this chunk so the images are saved in the correct spot:
-
-`````
-```{r, include = FALSE}
-ottrpal::set_knitr_image_path()
-```
-`````
diff --git a/inst/extdata/OTTR_Template-main/.github/automatic-issues/set-repo-settings.md b/inst/extdata/OTTR_Template-main/.github/automatic-issues/set-repo-settings.md
deleted file mode 100644
index da404bf..0000000
--- a/inst/extdata/OTTR_Template-main/.github/automatic-issues/set-repo-settings.md
+++ /dev/null
@@ -1,22 +0,0 @@
-
-For more information on these settings see instructions in [Starting a new OTTR course](https://www.ottrproject.org/getting_started.html#starting-a-new-ottr-course).
-
-- [ ] This course repository is set to `public`.
-- [ ] [Github secret `GH_PAT` has been set](https://www.ottrproject.org/getting_started.html#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.
-
-- [ ] 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`.
-
-- [ ] [Set branch protections settings](https://www.ottrproject.org/getting_started.html#8_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!
-
-- [ ] [Customize GitHub actions](https://www.ottrproject.org/customize-robots.html) for what you will need in this course.
diff --git a/inst/extdata/OTTR_Template-main/.github/automatic-issues/templates-to-edit.md b/inst/extdata/OTTR_Template-main/.github/automatic-issues/templates-to-edit.md
deleted file mode 100644
index 76ec6e9..0000000
--- a/inst/extdata/OTTR_Template-main/.github/automatic-issues/templates-to-edit.md
+++ /dev/null
@@ -1,34 +0,0 @@
-
-[Follow the instructions here in ottrproject.org](https://www.ottrproject.org/writing_content_courses.html) for details on how to start editing your OTTR course
-
-The following files need to be edited to get this new course started!
-
-### Files that need edited upon creating a new course.
-
-- [ ] `README.md` - Fill in all the `{ }`.
-- [ ] `index.Rmd` - `title:` should be updated.
-- [ ] `01-intro.Rmd` - replace the information there with information pertinent to this new course.
-- [ ] `02-chapter_of_course.Rmd` - This Rmd has examples of how to set things up, if you don't need it as a reference, it can be deleted.
-
-### Files that need to be edited upon adding each new chapter (including upon creating a new course):
-
-- [ ] `_bookdown.yml` - The list of Rmd files that need to be rendered needs to be updated. See [instructions](https://www.ottrproject.org/course_publishing.html#publishing-with-bookdown).
-- [ ] `book.bib` - any citations need to be added. See [instructions](https://www.ottrproject.org/more_features.html#citing-sources).
-
-### Picking a style
-
-See more [about customizing style on this page in the guide](https://www.ottrproject.org/customize-style.html).
-By default this course template will use the jhudsl data science lab style. However, you can customize and switch this to another style set.
-
-#### Using a style set
-
-[Read more about the style sets here](https://www.ottrproject.org/customize-style.html#Using_a_style_set).
-
-- [ ] On a new branch, copy the `style-sets/
All materials in this course are licensed under a Creative Commons Attribution 4.0 International License unless noted otherwise. diff --git a/inst/extdata/OTTR_Template-main/.github/switch_sync_repo.R b/inst/extdata/OTTR_Template-main/.github/switch_sync_repo.R deleted file mode 100644 index 7975abf..0000000 --- a/inst/extdata/OTTR_Template-main/.github/switch_sync_repo.R +++ /dev/null @@ -1,39 +0,0 @@ -#!/usr/bin/env Rscript - -# This script switches the repo entry for the yaml file to whatever is specified -# Written by Candace Savonen Jan 2022 - -if (!("optparse" %in% installed.packages())){ - install.packages("optparse") -} - -library(optparse) - -option_list <- list( - optparse::make_option( - c("--repo"), - type = "character", - default = "jhudsl/OTTR_Template_Test", - help = "GitHub repository name, e.g. jhudsl/OTTR_Template_Test", - ) -) - -# Read the arguments passed -opt_parser <- optparse::OptionParser(option_list = option_list) -opt <- optparse::parse_args(opt_parser) - -# Find .git root directory -root_dir <- rprojroot::find_root(rprojroot::has_dir(".git")) - -# Get test sync yaml path -sync_file_path <- file.path(root_dir, ".github", "test-sync.yml") - -yaml_contents <- yaml::yaml.load_file(sync_file_path) - -# Only keep first grouping -yaml_contents$group <- yaml_contents$group[[1]] - -# Switch out repo -yaml_contents$group$repos <- opt$repo - -yaml::write_yaml(yaml_contents, sync_file_path) diff --git a/inst/extdata/OTTR_Template-main/.github/sync.yml b/inst/extdata/OTTR_Template-main/.github/sync.yml deleted file mode 100644 index af86770..0000000 --- a/inst/extdata/OTTR_Template-main/.github/sync.yml +++ /dev/null @@ -1,162 +0,0 @@ -# Candace Savonen Aug 2021 -# For info on how to update this file see: https://github.com/marketplace/actions/repo-file-sync-action#%EF%B8%8F-sync-configuration - -group: - - files: - - source: .github/workflows/ - dest: .github/workflows/ - deleteOrphaned: true - exclude: | - send-updates.yml - test-send-updates.yml - starting-course.yml - release-notes.yml - docker-test.yml - docker-build.yml - - source: scripts/ - dest: scripts/ - deleteOrphaned: true - - source: .github/ISSUE_TEMPLATE/course-problem-report.md - dest: .github/ISSUE_TEMPLATE/course-problem-report.md - - source: .github/ISSUE_TEMPLATE/course-content-add.md - dest: .github/ISSUE_TEMPLATE/course-content-add.md - - source: .github/ISSUE_TEMPLATE/url-error.md - dest: .github/ISSUE_TEMPLATE/url-error.md - - source: style-sets - dest: style-sets - - source: assets/box_images/ - dest: assets/box_images/ - - source: resources/exclude_files.txt - dest: resources/exclude_files.txt - # Repositories to receive changes - repos: | - jhudsl/Documentation_and_Usability - jhudsl/Informatics_Research_Leadership - jhudsl/Data_Management_for_Cancer_Research - jhudsl/Computing_for_Cancer_Informatics - jhudsl/Adv_Reproducibility_in_Cancer_Informatics - jhudsl/Reproducibility_in_Cancer_Informatics - jhudsl/Dissemination_and_Engagement - fhdsl/Cancer_Clinical_Informatics - jhudsl/Machine_Learning_for_Cancer_Informatics - jhudsl/Cancer_Informatics_Data_Visualization - jhudsl/Cancer_Genome_Informatics - fhdsl/Cancer_Imaging_Informatics - datatrail-jhu/DataTrail_Template - abyzovlab/CNVpytor-course - tmm211/dsp-terra-mooc-test2 - fhdsl/Choosing_Genomics_Tools - fhdsl/NIH_Data_Sharing - fhdsl/FH_Cluster_Guide - fhdsl/Using_Leanpub - fhdsl/Ethical_Data_Handling_for_Cancer_Research - fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles - fhdsl/Design_of_Data_Analysis - fhdsl/Tools_for_Reproducible_Workflows_in_R - fhdsl/Introduction_to_reproducible_research - mccoy-lab/hgv_modules - griffithlab/pVACtools_Intro_Course - griffithlab/CIVIC_SVI_Course - PracticalGenomics/cogaps-on-sciserver - fhdsl/AI_for_software - fhdsl/AI_for_Decision_Makers - griffithlab/Immuno_Workflow_Course - fhdsl/S1_Intro_to_R - fhdsl/S1_Intro_to_Command_Line - fhdsl/S1_Intro_to_Git_GitHub - fhdsl/WDL_Workflows_Guide - fhdsl/S2-Collaborative-Git-GitHub - fhdsl/GitHub_Automation_for_Scientists - williamtmillsiv/introduction_to_bioinformatics -###ADD NEW REPO HERE following the format above# - -### These are custom groups for syncing -- not all files needs to be synced - - files: - - source: config_automation.yml - dest: config_automation.yml - - source: .github/workflows/pull-request.yml - dest: .github/workflows/pull-request.yml - repos: | - jhudsl/OTTR_Template_Website - - - files: - - source: config_automation.yml - dest: config_automation.yml - - source: .github/workflows/delete-preview.yml - dest: .github/workflows/delete-preview.yml - - source: .github/workflows/send-updates.yml - dest: .github/workflows/send-updates.yml - - source: .github/workflows/test-send-updates.yml - dest: .github/workflows/test-send-updates.yml - - source: scripts/make_screenshots.R - dest: scripts/make_screenshots.R - - source: scripts/switch_sync_repo.R - dest: scripts/switch_sync_repo.R - repos: | - jhudsl/OTTR_Quizzes - - - files: - - source: .github/workflows/ - dest: .github/workflows/ - exclude: | - starting-course.yml - release-notes.yml - - source: .github/switch_sync_repo.R - dest: .github/switch_sync_repo.R - - source: .github/ISSUE_TEMPLATE/course-problem-report.md - dest: .github/ISSUE_TEMPLATE/course-problem-report.md - - source: .github/ISSUE_TEMPLATE/course-content-add.md - dest: .github/ISSUE_TEMPLATE/course-content-add.md - - source: code_of_conduct.md - dest: code_of_conduct.md - - source: assets/box_images/ - dest: assets/box_images/ - - source: assets/style.css - dest: assets/style.css - - source: assets/toc_close.css - dest: assets/toc_close.css - - source: scripts/ - dest: scripts/ - deleteOrphaned: true - - source: style-sets/fhdasl/ - dest: style-sets/fhdasl/ - repos: | - jhudsl/AnVIL_Template - - - files: - - source: config_automation.yml - dest: config_automation.yml - - source: .github/workflows/ - dest: .github/workflows/ - deleteOrphaned: true - - source: .github/switch_sync_repo.R - dest: .github/switch_sync_repo.R - - source: .github/automatic-issues/ - dest: .github/automatic-issues/ - - source: assets/box_images/ - dest: assets/box_images/ - - source: assets/style.css - dest: assets/style.css - - source: assets/toc_close.css - dest: assets/toc_close.css - - source: scripts/ - dest: scripts/ - deleteOrphaned: true - repos: | - C-MOOR/C-MOOR_Template - - - files: - - source: config_automation.yml - dest: config_automation.yml - - source: .github/workflows/ - dest: .github/workflows/ - deleteOrphaned: true - - source: .github/switch_sync_repo.R - dest: .github/switch_sync_repo.R - - source: assets/box_images/ - dest: assets/box_images/ - - source: scripts/ - dest: scripts/ - deleteOrphaned: true - repos: | - opencasestudies/OCS_Guide diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/check-url.yml b/inst/extdata/OTTR_Template-main/.github/workflows/check-url.yml deleted file mode 100644 index a437049..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/check-url.yml +++ /dev/null @@ -1,107 +0,0 @@ -name: Periodic URL Check - -on: - workflow_dispatch: - schedule: - - cron: '0 0 1 * *' - -jobs: - set-up: - name: Load user automation choices - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v3 - with: - fetch-depth: 0 - - # Use the yaml-env-action action. - - name: Load environment from YAML - uses: doughepi/yaml-env-action@v1.0.0 - with: - files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence. - outputs: - toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}" - - url-check: - name: Check URLs - needs: set-up - if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}} - runs-on: ubuntu-latest - container: - image: jhudsl/base_ottr:main - - steps: - - name: Checkout - uses: actions/checkout@v3 - with: - fetch-depth: 0 - - # Delete the branch if this has been run before - - name: Delete branch locally and remotely - run: git push origin --delete preview-spell-error || echo "No branch to delete" - - # Make the branch fresh - - name: Make the branch fresh - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - echo branch doesnt exist - git checkout -b preview-spell-error || echo branch exists - git push --set-upstream origin preview-spell-error || echo echo branch exists remotely - shell: bash - - - name: Run the check - uses: jhudsl/ottr-reports@main - id: check_results - continue-on-error: true - with: - check_type: urls - error_min: 1 - - - name: Declare file path and time - id: check-report - run: | - error_num=$(cat check_reports/url_checks.tsv | wc -l) - error_num="$((error_num-1))" - echo "error_num=$error_num" >> $GITHUB_OUTPUT - echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/check_reports/url_checks.tsv" >> $GITHUB_OUTPUT - shell: bash - - - name: Stop if failure - if: steps.check_results.outcome == 'failure' - run: exit 1 - - - name: Print out error variables - run: | - echo ${{ steps.check-report.outputs.error_url }} - echo ${{ steps.check-report.outputs.error_num }} - - - name: Find issues - id: find-issue - env: - GH_PAT: ${{ secrets.GH_PAT }} - run: | - echo "$GITHUB_REPOSITORY" - curl -o find_issue.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/find_issue.R - issue_exists=$(Rscript --vanilla find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT) - echo URL issue exists: $issue_exists - echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT - - - name: If too many URL errors, then make an issue - if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence == 0}} - uses: JasonEtco/create-an-issue@v2 - with: - filename: .github/ISSUE_TEMPLATE/url-error.md - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - FILE_URL: ${{ steps.check-report.outputs.error_url }} - ERROR_NUM: ${{ steps.check-report.outputs.error_num }} - - - name: If no URL errors than delete the branch we made - if: ${{ steps.check-report.outputs.error_num < 1 }} - run: | - git config --system --add safe.directory "$GITHUB_WORKSPACE" - git push origin --delete preview-spell-error || echo "No branch to delete" diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/delete-preview.yml b/inst/extdata/OTTR_Template-main/.github/workflows/delete-preview.yml deleted file mode 100644 index faa83cc..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/delete-preview.yml +++ /dev/null @@ -1,27 +0,0 @@ -# Candace Savonen Apr 2021 - -name: Delete Preview - -on: - pull_request: - types: [closed] - -jobs: - delete-preview: - runs-on: ubuntu-latest - steps: - - # This is because if a PR is closed before a render finishes it won't find it. - - name: Sleep for 5 minutes - run: sleep 300s - shell: bash - - # Check out current repository - - name: checkout - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - # Delete the branch! - - name: Delete branch locally and remotely - run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete" diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/docker-build.yml b/inst/extdata/OTTR_Template-main/.github/workflows/docker-build.yml deleted file mode 100644 index 51a8302..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/docker-build.yml +++ /dev/null @@ -1,79 +0,0 @@ -# Candace Savonen Apr 2021 - -name: Build Docker - -on: - workflow_dispatch: - inputs: - dockerhubpush: - description: 'Push to Dockerhub?' - required: true - default: 'false' - tag: - description: 'What tag to use?' - required: true - default: 'none' -jobs: - build-docker: - name: Build Docker image - runs-on: ubuntu-latest - - steps: - - name: checkout repo - uses: actions/checkout@v4 - - - name: Login as github actions bot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - - name: Don't re-test if this is a sync branch - run: | - echo This was tested on OTTR_Template no need to re-run - - # Set up Docker build - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v1 - - # Setup layer cache - - name: Cache Docker layers - uses: actions/cache@v2 - with: - path: /tmp/.buildx-cache - key: ${{ runner.os }}-buildx-${{ github.sha }} - restore-keys: | - ${{ runner.os }}-buildx- - - # Set up Docker build - - name: Set up Docker Build - if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }} - uses: docker/setup-buildx-action@v1 - - - name: Get token - run: echo ${{ secrets.GH_PAT }} > docker/git_token.txt - - # Build docker image - - name: Build Docker image - uses: docker/build-push-action@v2 - with: - push: false - load: true - context: docker - file: docker/Dockerfile - tags: jhudsl/base_ottr - - # Login to Dockerhub - - name: Login to DockerHub - if: ${{ github.event.inputs.dockerhubpush != 'false' }} - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - # Push the Docker image if set to true from a manual trigger - - name: Push Docker image if manual trigger set to true - if: ${{ github.event.inputs.dockerhubpush != 'false' }} - run: | - docker tag jhudsl/base_ottr:latest jhudsl/base_ottr:$github.event.inputs.tag - docker push jhudsl/base_ottr:$github.event.inputs.tag diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/docker-test.yml b/inst/extdata/OTTR_Template-main/.github/workflows/docker-test.yml deleted file mode 100644 index 5775f41..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/docker-test.yml +++ /dev/null @@ -1,91 +0,0 @@ - -# Candace Savonen Apr 2022 - -name: Build Docker Image - -on: - workflow_dispatch: - inputs: - directory: - required: true - type: string - tag: - required: true - type: string - dockerhubpush: - description: 'Push to Dockerhub?' - required: false - default: 'false' - type: string - secrets: - GH_PAT: - required: true - DOCKERHUB_USERNAME: - required: false - DOCKERHUB_TOKEN: - required: false - -jobs: - - build-docker: - name: Build Docker image - runs-on: ubuntu-latest - - steps: - - name: checkout repo - uses: actions/checkout@v4 - - - name: Verify Dockerfiles changed? - uses: tj-actions/verify-changed-files@v17 - id: verify-changed-files - with: - files: | - ${{ inputs.directory }}/Dockerfile - ${{ inputs.directory }}/github_package_list.tsv - - - name: Login as github actions bot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - # Set up Docker build - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v1 - - # Setup layer cache - - name: Cache Docker layers - uses: actions/cache@v2 - with: - path: /tmp/.buildx-cache - key: ${{ runner.os }}-buildx-${{ github.sha }} - restore-keys: | - ${{ runner.os }}-buildx- - - - name: Set up Docker Build - uses: docker/setup-buildx-action@v1 - - - name: Get token - run: echo ${{ secrets.GH_PAT }} > ${{ inputs.directory }}/git_token.txt - - - name: Build Docker image - uses: docker/build-push-action@v2 - with: - push: false - load: true - context: ${{ inputs.directory }} - file: ${{ inputs.directory }}/Dockerfile - tags: ${{ inputs.tag }} - - # Login to Dockerhub - - name: Login to DockerHub - if: ${{ inputs.dockerhubpush != 'false' }} - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - # Push the Docker image if set to true from a manual trigger - - name: Push Docker image if manual trigger set to true - if: ${{ inputs.dockerhubpush != 'false' }} - run: docker push ${{ inputs.tag }} diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/pull_request.yml b/inst/extdata/OTTR_Template-main/.github/workflows/pull_request.yml deleted file mode 100644 index d81d780..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/pull_request.yml +++ /dev/null @@ -1,230 +0,0 @@ -# Candace Savonen 2021 -# Updated Jan 2023 - -name: Pull Request - -on: - pull_request: - branches: [ main, staging ] - -jobs: - - yaml-check: - name: Load user automation choices - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v4 - with: - fetch-depth: 0 - token: ${{ secrets.GH_PAT }} - - # Use the yaml-env-action action. - - name: Load environment from YAML - uses: doughepi/yaml-env-action@v1.0.0 - with: - files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence. - - # Delete the branch if this has been run before - - name: Delete branch locally and remotely - run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete" - - # Make the branch fresh - - name: Make the branch fresh - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - branch_name='preview-${{ github.event.pull_request.number }}' - echo branch doesnt exist - git checkout -b $branch_name || echo branch exists - git push --set-upstream origin $branch_name || echo echo branch exists remotely - shell: bash - - - outputs: - toggle_spell_check: "${{ env.SPELL_CHECK }}" - toggle_style_code: "${{ env.STYLE_CODE }}" - toggle_url_check: "${{ env.URL_CHECKER }}" - toggle_quiz_check: "${{ env.CHECK_QUIZZES }}" - toggle_render_preview: "${{ env.RENDER_PREVIEW }}" - rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}" - -########################## Make the error reports ############################## - spell-check: - name: Check spelling - needs: yaml-check - if: ${{needs.yaml-check.outputs.toggle_spell_check == 'yes'}} - uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main - with: - check_type: spelling - error_min: 3 - gh_pat: secrets.GH_PAT - branch_name: ${GITHUB_HEAD_REF} - - url-check: - name: Check URLs - needs: yaml-check - if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}} - uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main - with: - check_type: urls - error_min: 0 - gh_pat: secrets.GH_PAT - branch_name: ${GITHUB_HEAD_REF} - - quiz-check: - name: Check quiz formatting - if: ${{needs.yaml-check.outputs.toggle_quiz_check == 'yes'}} - needs: yaml-check - uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main - with: - check_type: quiz_format - error_min: 0 - gh_pat: secrets.GH_PAT - branch_name: ${GITHUB_HEAD_REF} - -############################# Style the code ################################### - style-code: - name: Style code - needs: yaml-check - runs-on: ubuntu-latest - if: ${{needs.yaml-check.outputs.toggle_style_code == 'yes'}} - container: - image: jhudsl/base_ottr:main - - steps: - - name: Checkout files - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - - name: Run styler - run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()" - - - name: Commit styled files - run: | - git config --system --add safe.directory "$GITHUB_WORKSPACE" - git add \*.Rmd - git commit -m 'Style Rmds' || echo "No changes to commit" - git push origin || echo "No changes to commit" - -############################# Render Preview ################################### - - render-preview: - name: Render preview - needs: yaml-check - runs-on: ubuntu-latest - container: - image: ${{needs.yaml-check.outputs.rendering_docker_image}} - if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}} - - steps: - - name: Checkout files - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - # Set up git checkout - - name: Set up git checkout - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - branch_name='preview-${{ 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 - - # Run bookdown rendering - - name: Run bookdown render - id: bookdown - run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')" - - # Run TOC-less version - # Rendered content for Leanpub and Coursera is very similar. - # This job creates a shared scaffold for both. - - name: Run TOC-less version of render - id: tocless - run: Rscript -e "ottrpal::render_without_toc()" - - # This checks on the steps before it and makes sure that they completed. - # If the renders didn't complete we don't want to commit the file changes - - name: Check on render steps - if: steps.bookdown.outcome != 'success' || steps.tocless.outcome != 'success' - run: | - echo Bookdown status ${{steps.bookdown.outcome}} - echo Toc-less status ${{steps.tocless.outcome}} - exit 1 - - - name: Website preview for download - run: zip website-preview.zip docs/* -r - - # Commit the rendered bookdown files - - name: Commit rendered bookdown files to preview branch - id: commit - run: | - branch_name='preview-${{ github.event.pull_request.number }}' - git diff origin/main -- docs >/dev/null && changes=true || changes=false - echo "changes=$changes" >> $GITHUB_OUTPUT - git add . --force - git commit -m 'Render preview' || echo "No changes to commit" - git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours - git push --force || echo "No changes to commit" - shell: bash - - - name: Find Comment - uses: peter-evans/find-comment@v2 - id: fc - with: - issue-number: ${{ github.event.pull_request.number }} - comment-author: 'github-actions[bot]' - body-includes: latest commit - - - name: Build components of the comment - id: build-components - run: | - course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-") - bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html") - tocless_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/no_toc/index.html") - docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/docs/$course_name.docx") - zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip") - echo "zip_link=$zip_link" >> $GITHUB_OUTPUT - echo "bookdown_link=$bookdown_link" >> $GITHUB_OUTPUT - echo "tocless_link=$tocless_link" >> $GITHUB_OUTPUT - echo "docx_link=$docx_link" >> $GITHUB_OUTPUT - echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT - echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT - echo ${{steps.commit.outputs.changes}} - - - name: Create or update comment - if: steps.commit.outputs.changes == 'true' - uses: peter-evans/create-or-update-comment@v2 - with: - comment-id: ${{ steps.fc.outputs.comment-id }} - issue-number: ${{ github.event.pull_request.number }} - body: | - Re-rendered previews from the latest commit: - - :eyes: Quick [preview of course website here](${{ steps.build-components.outputs.bookdown_link }}) \* - - :microscope: Comprehensive [download of the course website here](${{ steps.build-components.outputs.zip_link }}) - - Download the [.docx file](${{ steps.build-components.outputs.docx_link }}) - - \* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea. - - _Updated at ${{ steps.build-components.outputs.time }} with changes from the latest commit ${{ steps.build-components.outputs.commit_id }}_ - edit-mode: replace - - - name: Comment if no changes - if: steps.commit.outputs.changes == 'false' - uses: peter-evans/create-or-update-comment@v2 - with: - comment-id: ${{ steps.fc.outputs.comment-id }} - issue-number: ${{ github.event.pull_request.number }} - body: | - The latest commit did not produce rendering changes. - - _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_ - edit-mode: replace diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/release-notes.yml b/inst/extdata/OTTR_Template-main/.github/workflows/release-notes.yml deleted file mode 100644 index d76e0e2..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/release-notes.yml +++ /dev/null @@ -1,35 +0,0 @@ -# Candace Savonen Sept 2021 - -name: Release note PR comment - -on: - pull_request: - branches: [ main, staging ] - types: [ opened ] - -jobs: - pr-comment: - runs-on: ubuntu-latest - steps: - - - uses: mshick/add-pr-comment@v1 - if: ${{ github.head_ref == 'repo-sync/OTTR_Template/default' }} - with: - message: | - **Please carefully review these changes and decide which are useful for your course.** - See the release notes: https://github.com/jhudsl/OTTR_Template/releases - - - If you don't want the changes from a particular file, you can always [revert that particular commit](https://git-scm.com/docs/git-revert) before merging the sync PR. - If you will not want any updates on this file in the future, you may want to remove a file from being synced in your repo [by reconfiguring the sync file](https://github.com/jhudsl/OTTR_Template/blob/main/.github/sync.yml). - - - If you want only some changes, but they are not on a whole file basis, you could check out the branch and make manual edits. To checkout the branch, navigate to your own repository you should be able to run: - ``` - git checkout repo-sync/OTTR_Template/default - ``` - - If you don't want any of the changes you can close the PR entirely. - - You may want to unenroll your repository from the sync GitHub actions by [filing a PR](https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) on `OTTR_Template` - to delete [your repo name from this file](https://github.com/jhudsl/OTTR_Template/blob/main/.github/sync.yml) if this will continue to be the case. - - repo-token-user-login: 'github-actions[bot]' # The user.login for temporary GitHub tokens - allow-repeats: false # This is the default diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/render-all.yml b/inst/extdata/OTTR_Template-main/.github/workflows/render-all.yml deleted file mode 100644 index 12643d8..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/render-all.yml +++ /dev/null @@ -1,248 +0,0 @@ - -# Candace Savonen Apr 2021 - -name: Render all output courses - -on: - workflow_dispatch: - push: - branches: [ main, staging ] - paths: - - '**.Rmd' - - assets/* - - quizzes/* - -jobs: - - yaml-check: - name: Load user automation choices - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v4 - - # Use the yaml-env-action action. - - name: Load environment from YAML - uses: doughepi/yaml-env-action@v1.0.0 - with: - files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence. - outputs: - toggle_bookdown: "${{ env.RENDER_BOOKDOWN }}" - toggle_coursera: "${{ env.RENDER_COURSERA }}" - toggle_leanpub: "${{ env.RENDER_LEANPUB }}" - make_book_txt: "${{ env.MAKE_BOOK_TXT }}" - rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}" - toggle_quiz_check: "${{ env.CHECK_QUIZZES }}" - - render-bookdown: - name: Render bookdown - needs: yaml-check - runs-on: ubuntu-latest - container: - image: ${{needs.yaml-check.outputs.rendering_docker_image}} - if: ${{needs.yaml-check.outputs.toggle_bookdown == 'yes'}} - - steps: - - name: checkout - uses: actions/checkout@v4 - with: - fetch-depth: 0 - token: ${{ secrets.GH_PAT }} - - - name: Login as github actions bot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - # We want a fresh run of the renders each time - - name: Delete old docs/* - run: rm -rf docs/* - - # Run bookdown rendering - - name: Run bookdown render - id: bookdown - run: | - Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all'); - file.copy(from = 'assets', to = 'docs/assets', overwrite = TRUE)" - - # This checks on the steps before it and makes sure that they completed. - # If the renders didn't complete we don't want to commit the file changes - - name: Check on render step - if: steps.bookdown.outcome != 'success' - run: | - echo Bookdown status ${{steps.bookdown.outcome}} - exit 1 - - # Commit the rendered bookdown files - - name: Commit rendered bookdown files - env: - GH_PAT: ${{ secrets.GH_PAT }} - run: | - git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY} - git fetch origin - git add --force docs/* - git commit -m 'Render bookdown' || echo "No changes to commit" - git pull --allow-unrelated-histories --strategy-option=ours - git push -u origin main || echo "No changes to push" - - render-tocless: - name: Render TOC-less version for Leanpub or Coursera - needs: [yaml-check] - runs-on: ubuntu-latest - container: - image: ${{needs.yaml-check.outputs.rendering_docker_image}} - if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes' || needs.yaml-check.outputs.toggle_leanpub == 'yes'}} - - steps: - - name: checkout - uses: actions/checkout@v4 - with: - fetch-depth: 0 - token: ${{ secrets.GH_PAT }} - - - name: Login as github-actions bot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - # Rendered content for Leanpub and Coursera is very similar. - # This job creates a shared scaffold for both. - - name: Run TOC-less version of render - id: tocless - run: Rscript -e "ottrpal::render_without_toc()" - - # Commit the TOC-less version files - - name: Commit tocless bookdown files - env: - GH_PAT: ${{ secrets.GH_PAT }} - run: | - git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY} - git fetch origin - git add --force docs/no_toc* - git commit -m 'Render toc-less' || echo "No changes to commit" - git pull --allow-unrelated-histories --strategy-option=ours - git push -u origin main || echo "No changes to push" - - render-leanpub: - name: Finish Leanpub prep - needs: [yaml-check, render-tocless] - runs-on: ubuntu-latest - container: - image: jhudsl/ottrpal:main - if: ${{needs.yaml-check.outputs.toggle_leanpub == 'yes'}} - - steps: - - name: checkout - uses: actions/checkout@v4 - with: - fetch-depth: 0 - token: ${{ secrets.GH_PAT }} - - - name: Login as github actions bot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - # Create screenshots - - name: Run the screenshot creation - run: | - # Remove old folder - rm -rf resources/chapt_screen_images - - # Make new screenshots - curl -o make_screenshots.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/make_screenshots.R - chapt_urls=$(Rscript --vanilla make_screenshots.R \ - --git_pat ${{ secrets.GH_PAT }} \ - --repo $GITHUB_REPOSITORY \ - --output_dir resources/chapt_screen_images) - - # We want a fresh run of the renders each time - - name: Delete manuscript/ - env: - GH_PAT: ${{ secrets.GH_PAT }} - run: | - rm -rf manuscript/ - git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY} - git fetch origin - git add . - git commit -m 'Delete manuscript folder' || echo "No changes to commit" - git pull --allow-unrelated-histories --strategy-option=ours - git push -u origin main || echo "No changes to push" - - - name: Run ottrpal::bookdown_to_embed_leanpub - if: needs.yaml-check.outputs.toggle_quiz_check == 'no' - run: | - Rscript -e "ottrpal::bookdown_to_embed_leanpub( - render = FALSE, \ - chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \ - make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'), \ - quiz_dir = NULL)" - - - name: Run ottrpal::bookdown_to_embed_leanpub - if: needs.yaml-check.outputs.toggle_quiz_check == 'yes' - run: | - Rscript -e "ottrpal::bookdown_to_embed_leanpub( - render = FALSE, \ - chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \ - make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'))" - - # Commit the rendered Leanpub files - - name: Commit rendered Leanpub files - env: - GH_PAT: ${{ secrets.GH_PAT }} - run: | - mkdir -p manuscript - 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 --force --set-upstream origin main || echo "No changes to push" - - render-coursera: - name: Finish Coursera prep - needs: [yaml-check, render-tocless] - runs-on: ubuntu-latest - container: - image: ${{needs.yaml-check.outputs.rendering_docker_image}} - if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes'}} - - steps: - - name: checkout - uses: actions/checkout@v4 - with: - fetch-depth: 0 - token: ${{ secrets.GH_PAT }} - - - name: Login as github action - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - # Run Coursera version - - name: Convert Leanpub quizzes to Coursera - if: needs.yaml-check.outputs.toggle_leanpub == 'yes' && needs.yaml-check.outputs.toggle_quiz_check == 'yes' - id: coursera - run: Rscript -e "ottrpal::convert_coursera_quizzes()" - - # Commit the rendered bookdown files - # Only commit coursera quizzes if the directory is present - - name: Commit rendered Coursera files - env: - GH_PAT: ${{ secrets.GH_PAT }} - run: | - git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY} - git fetch origin - if [ -d 'coursera_quizzes' ]; then - git add --force coursera_quizzes/* - fi - 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 -u origin main || echo "No changes to push" diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/send-updates.yml b/inst/extdata/OTTR_Template-main/.github/workflows/send-updates.yml deleted file mode 100644 index f636dc0..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/send-updates.yml +++ /dev/null @@ -1,45 +0,0 @@ -# Candace Savonen Aug 2021 - -name: Sync Files - -on: - release: - types: - - published - workflow_dispatch: - inputs: - prtag: - description: 'Tag to use?' - required: true - default: 'null' - -jobs: - sync: - runs-on: ubuntu-latest - steps: - - name: Checkout Repository - uses: actions/checkout@v4 - - - name: Login as github actions bot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - - name: Get the version - id: get_tag - run: | - if [ github.event.inputs.prtag == 'null' ] - then - echo "version=$(echo $GITHUB_REF | cut -d / -f 3)" >> $GITHUB_OUTPUT - fi - if [ github.event.inputs.prtag != 'null' ] - then - echo "version=${{ github.event.inputs.prtag }}" >> $GITHUB_OUTPUT - fi - - - name: Run Mechanics File Sync - uses: BetaHuhn/repo-file-sync-action@v1.17.21 - with: - GH_PAT: ${{ secrets.GH_PAT }} - COMMIT_BODY: release-${{ steps.get_tag.outputs.version }} diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/starting-course.yml b/inst/extdata/OTTR_Template-main/.github/workflows/starting-course.yml deleted file mode 100644 index dc87be4..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/starting-course.yml +++ /dev/null @@ -1,142 +0,0 @@ -# Code adapted from https://github.com/JetBrains/intellij-platform-plugin-template/blob/deb171483598ee8a5d7621154db880e87b4db4ef/.github/workflows/template-cleanup.yml -# by Candace Savonen for this repository. - -name: Starting a new course - -on: - push: - branches: [ main, staging ] - workflow_dispatch: - -jobs: - # Run cleaning process only if workflow is triggered by not being in the Bookdown template anymore - template-cleanup: - name: Template Cleanup - runs-on: ubuntu-latest - if: github.event.repository.name != 'OTTR_Template' - steps: - - name: checkout repo - uses: actions/checkout@v4 - - - name: Login as jhudsl-robot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.email "itcrtrainingnetwork@gmail.com" - git config --global user.name "jhudsl-robot" - -##### Delete Template-specific files that aren't needed for new courses - - # Cleanup Template-specific bits - - name: Cleanup - run: | - # Cleanup - mv .github/course_README_template.md README.md - rm -rf \ - .github/workflows/report-maker.yml \ - .github/workflows/send-updates.yml \ - .github/workflows/test-send-updates.yml \ - .github/sync.yml \ - .github/test-sync.yml \ - .github/workflows/starting-course.yml \ - .github/ISSUE_TEMPLATE/course-template-problem-report.md \ - .github/ISSUE_TEMPLATE/course-template-feature-request.md \ - .github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md \ - resources/code_output \ - resources/screenshots \ - resources/course_screenshots \ - resources/gs_slides \ - resources/image_to_slide_key.tsv \ - resources/images/02-chapter_of_course_files \ - resources/images/03-test_cases_files \ - resources/images/04-figures_files \ - resources/chapt_screen_images \ - Course_Name.rds \ - code_of_conduct.md \ - CONTRIBUTING.md \ - docs/*.html \ - docs/*.md \ - manuscript/* - - - # Commit modified files - - name: Commit deleted files - id: commit_it - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.email "itcrtrainingnetwork@gmail.com" - git config --global user.name "jhudsl-robot" - git add . - git commit -m "Template cleanup" - pushed_it=true - git push || pushed_it=false - echo "pushed_it=$pushed_it" >> $GITHUB_OUTPUT - - # If main is already protected, then file a PR - - name: Create PR with deleted files - if: steps.commit_it.outputs.pushed_it == 'false' - uses: peter-evans/create-pull-request@v3 - id: pr - with: - commit-message: Delete unnecessary files - signoff: false - branch: auto_copy_rendered_files - delete-branch: true - title: 'Automatic course set up' - body: | - ### Description: - This PR was initiated by the github actions. It helps set up this repository to be ready to write your course. - It deletes some remnant files you don't need for your course but were used when this was a template. - labels: | - automated - reviewers: $GITHUB_ACTOR - token: ${{secrets.GH_PAT}} - -##### Filing issues! - - # Issue for what repository settings need to be set - - name: New Course - Set Repository Settings - uses: peter-evans/create-issue-from-file@v4 - with: - title: New Course - Set Repository Settings - content-filepath: .github/automatic-issues/set-repo-settings.md - labels: automated training issue - - # Issue for what needs to be edited - - name: New Course - Templates to Edit - uses: peter-evans/create-issue-from-file@v4 - with: - title: New Course - Templates to Edit - content-filepath: .github/automatic-issues/templates-to-edit.md - labels: automated training issue - - # Issue for how to enroll repo for updates - - name: New Course - Template Update Enrollment - uses: peter-evans/create-issue-from-file@v4 - with: - title: New Course - Template Update Enrollment - content-filepath: .github/automatic-issues/update-enrollment.md - labels: automated training issue - - # Issue for adding a method of feedback - - name: Reminder - Add a method of user feedback - uses: peter-evans/create-issue-from-file@v4 - with: - title: Reminder - Add user feedback method - content-filepath: .github/automatic-issues/add-feedback-method.md - labels: automated training issue - - - name: Get organization name - id: get_org_name - run: | - org_name=$(dirname ${{github.repository}}) - echo "org_name=$org_name" >> $GITHUB_OUTPUT - echo $org_name - - # Issue for adding the course to the jhudsl library - - name: Reminder - Add to jhudsl library - if: ${{ steps.get_org_name.outputs.org_name == 'jhudsl' }} - uses: peter-evans/create-issue-from-file@v4 - with: - title: Reminder - Add to jhudsl library - content-filepath: .github/automatic-issues/add-to-library.md - labels: automated training issue diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/test-send-updates.yml b/inst/extdata/OTTR_Template-main/.github/workflows/test-send-updates.yml deleted file mode 100644 index 61e6b71..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/test-send-updates.yml +++ /dev/null @@ -1,40 +0,0 @@ -# Candace Savonen Aug 2021 - -name: Test Sync Files - -on: - workflow_dispatch: - inputs: - repo: - description: 'What repo to test on e.g. jhudsl/OTTR_Template_Test' - required: true - default: 'jhudsl/OTTR_Template_Test' - -jobs: - test-sync: - runs-on: ubuntu-latest - container: - image: jhudsl/base_ottr:main - - steps: - - name: Checkout Repository - uses: actions/checkout@master - - - name: Login as github actions bot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - - name: Set up test-sync.yml - run: | - cp .github/sync.yml .github/test-sync.yml - # Switch out repo argument - Rscript --vanilla .github/switch_sync_repo.R --repo ${{ github.event.inputs.repo }} - - - name: Run Mechanics File Sync - uses: BetaHuhn/repo-file-sync-action@v1.17.21 - with: - GH_PAT: ${{ secrets.GH_PAT }} - COMMIT_BODY: "test-run" - CONFIG_PATH: .github/test-sync.yml diff --git a/inst/extdata/OTTR_Template-main/.github/workflows/transfer-rendered-files.yml b/inst/extdata/OTTR_Template-main/.github/workflows/transfer-rendered-files.yml deleted file mode 100644 index dae4141..0000000 --- a/inst/extdata/OTTR_Template-main/.github/workflows/transfer-rendered-files.yml +++ /dev/null @@ -1,117 +0,0 @@ -# This code was adapted from code written by Josh Shapiro -# for the Childhood Cancer Data Lab, an initiative of Alexs Lemonade Stand Foundation. -# https://github.com/AlexsLemonade/exercise-notebook-answers - -# Adapted for this jhudsl repository by Candace Savonen Apr 2021 - -name: Copy over from main template to _Quizzes repo - -on: - workflow_dispatch: - workflow_run: - workflows: [ "Render all output courses" ] - branches: [ main, staging ] - types: - - completed - -jobs: - - yaml-check: - name: Load user automation choices - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v4 - - # Use the yaml-env-action action. - - name: Load environment from YAML - uses: doughepi/yaml-env-action@v1.0.0 - with: - files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence. - outputs: - toggle_coursera: "${{ env.RENDER_COURSERA }}" - toggle_leanpub: "${{ env.RENDER_LEANPUB }}" - - - file-quizzes-pr: - name: File _Quizzes Transfer PR - runs-on: ubuntu-latest - container: - image: jhudsl/ottrpal:main - needs: [yaml-check] - if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes' || needs.yaml-check.outputs.toggle_leanpub == 'yes'}} - - steps: - - name: Checkout from Bookdown Repo - uses: actions/checkout@v4 - with: - path: bookdown - token: ${{ secrets.GH_PAT }} - - - name: Run git repo check - id: git_repo_check - env: - GH_PAT: ${{ secrets.GH_PAT }} - run: | - # What's the Quizzes repository's name? - QUIZ_REPO=$(echo ${GITHUB_REPOSITORY} | sed "s/_Bookdown/ /g" | sed "s/_Template/ /g" | awk '{print $1"_Quizzes"}') - echo $QUIZ_REPO - - # Run repo check script - curl -o git_repo_check.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/git_repo_check.R - results=$(Rscript --vanilla git_repo_check.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT") - echo $QUIZ_REPO exists: $results - - echo "git_results=$results" >> $GITHUB_OUTPUT - echo "leanpub_repo=$QUIZ_REPO" >> $GITHUB_OUTPUT - - - name: Checkout code from Leanpub repo - if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }} - uses: actions/checkout@v4 - with: - path: quizzes - repository: ${{ steps.git_repo_check.outputs.leanpub_repo }} - token: ${{ secrets.GH_PAT }} - - - name: Get files from Bookdown repo - if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }} - shell: bash - env: - GH_PAT: ${{ secrets.GH_PAT }} - run: | - # Copy over images folder (from bookdown to quizzes repo) - mkdir -p quizzes/resources/chapt_screen_images - cp bookdown/resources/chapt_screen_images/* quizzes/resources/chapt_screen_images - - # Copy over _bookdown.yml (from bookdown to quizzes repo) - cp bookdown/_bookdown.yml quizzes/_bookdown.yml - - - name: Create PR with resources files - if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }} - uses: peter-evans/create-pull-request@v3 - id: cpr - with: - path: quizzes # Must create the PR in the Quizzes Repo - token: ${{ secrets.GH_PAT }} - commit-message: Copy files from Bookdown repository - signoff: false - branch: auto_copy_rendered_files - delete-branch: true - title: 'GHA: Automated transfer of ottrpal-needed files from Bookdown repository' - body: | - ### Description: - This PR was initiated by transfer-rendered.yml in the Bookdown repository. - It copies over the ottrpal-needed folder (for the `bookdown_to_embed_leanpub(render = FALSE)` function - to run properly. - - resources/chapt_screen_images/* - - _bookdown.yml - labels: | - automated - reviewers: $GITHUB_ACTOR - - # Write out PR info - - name: Check outputs - if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }} - run: | - echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}" - echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}" diff --git a/inst/extdata/OTTR_Template-main/.gitignore b/inst/extdata/OTTR_Template-main/.gitignore deleted file mode 100644 index 3da8ec4..0000000 --- a/inst/extdata/OTTR_Template-main/.gitignore +++ /dev/null @@ -1,11 +0,0 @@ -# ignore nonsense files -.DS_Store -.Rhistory -.local -.rstudio -.bash_history -.RData -.httr-oauth -docker/git_token.txt -.Rproj.user -docs/* diff --git a/inst/extdata/OTTR_Template-main/01-intro.Rmd b/inst/extdata/OTTR_Template-main/01-intro.Rmd deleted file mode 100644 index 886eb52..0000000 --- a/inst/extdata/OTTR_Template-main/01-intro.Rmd +++ /dev/null @@ -1,23 +0,0 @@ - -```{r, include = FALSE} -ottrpal::set_knitr_image_path() -``` - -# Introduction - - -## Motivation - - -## Target Audience - -The course is intended for ... - -## Curriculum - -The course covers... - - -```{r} -devtools::session_info() -``` diff --git a/inst/extdata/OTTR_Template-main/02-chapter_of_course.Rmd b/inst/extdata/OTTR_Template-main/02-chapter_of_course.Rmd deleted file mode 100644 index d35bbe3..0000000 --- a/inst/extdata/OTTR_Template-main/02-chapter_of_course.Rmd +++ /dev/null @@ -1,261 +0,0 @@ - -# A new chapter - -If you haven't yet read the getting started Wiki pages; [start there](https://www.ottrproject.org/getting_started.html). - -To see the rendered version of this chapter and the rest of the template, see here: https://jhudatascience.org/OTTR_Template/. - -Every chapter needs to start out with this chunk of code: - - -```{r, include = FALSE} -ottrpal::set_knitr_image_path() -``` - -## Learning Objectives - -Every chapter also needs Learning objectives that will look like this: - -This chapter will cover: - -- {You can use https://tips.uark.edu/using-blooms-taxonomy/ to define some learning objectives here} -- {Another learning objective} - -## Libraries - -For this chapter, we'll need the following packages attached: - -*Remember to add [any additional packages you need to your course's own docker image](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image). - -```{r} -library(magrittr) -``` - -## Topic of Section - -You can write all your text in sections like this, using `##` to indicate a new header. you can use additional pound symbols to create lower levels of headers. - -See [here](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf) for additional general information about how you can format text within R Markdown files. In addition, see [here](https://pandoc.org/MANUAL.html#pandocs-markdown) for more in depth and advanced options. - -### Subtopic - -Here's a subheading (using three pound symbols) and some text in this subsection! - -## Code examples - -You can demonstrate code like this: - -```{r} -output_dir <- file.path("resources", "code_output") -if (!dir.exists(output_dir)) { - dir.create(output_dir) -} -``` - -And make plots too: - -```{r} -hist_plot <- hist(iris$Sepal.Length) -``` - -You can also save these plots to file: - -```{r} -png(file.path(output_dir, "test_plot.png")) -hist_plot -dev.off() -``` - -## Image example - -How to include a Google slide. It's simplest to use the `ottrpal` package: - - -```{r, fig.align='center', out.width="100%", echo = FALSE, fig.alt= "Major point!! example image"} -ottrpal::include_slide("https://docs.google.com/presentation/d/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ/edit#slide=id.gcc4fbee202_0_141") -``` - -But if you have the slide or some other image locally downloaded you can also use HTML like this: - -
-
-## Video examples
-You may also want to embed videos in your course. If alternatively, you just want to include a link you can do so like this:
-
-Check out this [link to a video](https://www.youtube.com/embed/VOCYL-FNbr0) using markdown syntax.
-
-### Using `knitr`
-
-To embed videos in your course, you can use `knitr::include_url()` like this:
-Note that you should use `echo=FALSE` in the code chunk because we don't want the code part of this to show up. If you are unfamiliar with [how R Markdown code chunks work, read this](https://rmarkdown.rstudio.com/lesson-3.html).
-
-
-```{r, echo=FALSE}
-knitr::include_url("https://www.youtube.com/embed/VOCYL-FNbr0")
-```
-
-### Using HTML
-
-
-
-### Using `knitr`
-
-```{r, fig.align="center", echo=FALSE, out.width="100%"}
-knitr::include_url("https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview")
-```
-
-### Using HTML
-
-
-
-## Website Examples
-
-Yet again you can use a link to a website like so:
-
-[A Website](https://yihui.org)
-
-You might want to have users open a website in a new tab by default, especially if they need to reference both the course and a resource at once.
-
-[A Website](https://yihui.org){target="_blank"}
-
-Or, you can embed some websites.
-
-### Using `knitr`
-
-This works:
-
-```{r, fig.align="center", echo=FALSE}
-knitr::include_url("https://yihui.org")
-```
-
-
-### Using HTML
-
-
-
-
-If you'd like the URL to show up in a new tab you can do this:
-
-```
-LinkedIn
-```
-
-## Citation examples
-
-We can put citations at the end of a sentence like this [@rmarkdown2021].
-Or multiple citations [@rmarkdown2021, @Xie2018].
-
-but they need a ; separator [@rmarkdown2021; @Xie2018].
-
-In text, we can put citations like this @rmarkdown2021.
-
-## Stylized boxes
-
-Occasionally, you might find it useful to emphasize a particular piece of information. To help you do so, we have provided css code and images (no need for you to worry about that!) to create the following stylized boxes.
-
-You can use these boxes in your course with either of two options: using HTML code or Pandoc syntax.
-
-### Using `rmarkdown` container syntax
-
-The `rmarkdown` package allows for a different syntax to be converted to the HTML that you just saw and also allows for conversion to LaTeX. See the [Bookdown](https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html) documentation for more information [@Xie2020]. Note that Bookdown uses Pandoc.
-
-
-```
-::: {.notice}
-Note using rmarkdown syntax.
-
-:::
-```
-
-::: {.notice}
-Note using rmarkdown syntax.
-
-:::
-
-As an example you might do something like this:
-
-::: {.notice}
-Please click on the subsection headers in the left hand
-navigation bar (e.g., 2.1, 4.3) a second time to expand the
-table of contents and enable the `scroll_highlight` feature
-([see more](introduction.html#scroll-highlight))
-:::
-
-
-### Using HTML
-
-To add a warning box like the following use:
-
-```
-
-Followed by the text you want inside
-
-```
-
-This will create the following:
-
-
-
-Followed by the text you want inside
-
-
-
-Here is a `` box:
-
-
-
-Note text
-
-
-
-Here is a `` box:
-
-
-
-GitHub text
-
-
-
-
-Here is a `` box:
-
-
-
-dictionary text
-
-
-
-
-Here is a `` box:
-
-
-
-reflection text
-
-
-
-
-Here is a `` box:
-
-
-
-## Print out session info
-
-You should print out session info when you have code for [reproducibility purposes](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/managing-package-versions.html).
-
-```{r}
-devtools::session_info()
-```
-
-[many links]: https://github.com/jhudsl/OTTR_Template
diff --git a/inst/extdata/OTTR_Template-main/About.Rmd b/inst/extdata/OTTR_Template-main/About.Rmd
deleted file mode 100644
index b1c1d7f..0000000
--- a/inst/extdata/OTTR_Template-main/About.Rmd
+++ /dev/null
@@ -1,65 +0,0 @@
-
-# About the Authors {-}
-
-These credits are based on our [course contributors table guidelines](https://www.ottrproject.org/more_features.html#giving-credits-to-contributors).
-
-
-
-
-|Credits|Names|
-|-------|-----|
-|**Pedagogy**||
-|Lead Content Instructor(s)|[FirstName LastName]|
-|Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved| Delivered the course in some way - video or audio|
-|Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved | If any other authors besides lead instructor|
-|Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involved| Wrote less than a chapter|
-|Content Editor(s)/Reviewer(s) | Checked your content|
-|Content Director(s) | Helped guide the content direction|
-|Content Consultants (include chapter name/link in parentheses or word "General") - make new line if more than one chapter involved | Gave high level advice on content|
-|Acknowledgments| Gave small assistance to content but not to the level of consulting |
-|**Production**||
-|Content Publisher(s)| Helped with publishing platform|
-|Content Publishing Reviewer(s)| Reviewed overall content and aesthetics on publishing platform|
-|**Technical**||
-|Course Publishing Engineer(s)| Helped with the code for the technical aspects related to the specific course generation|
-|Template Publishing Engineers|[Candace Savonen], [Carrie Wright], [Ava Hoffman]|
-|Publishing Maintenance Engineer|[Candace Savonen]|
-|Technical Publishing Stylists|[Carrie Wright], [Ava Hoffman], [Candace Savonen]|
-|Package Developers ([ottrpal]) [Candace Savonen], [John Muschelli], [Carrie Wright]|
-|**Art and Design**||
-|Illustrator(s)| Created graphics for the course|
-|Figure Artist(s)| Created figures/plots for course|
-|Videographer(s)| Filmed videos|
-|Videography Editor(s)| Edited film|
-|Audiographer(s)| Recorded audio|
-|Audiography Editor(s)| Edited audio recordings|
-|**Funding**||
-|Funder(s)| Institution/individual who funded course including grant number|
-|Funding Staff| Staff members who help with funding|
-
-
-
-```{r, echo = FALSE}
-devtools::session_info()
-```
-
-
-
-[FirstName LastName]: link to personal website
-[John Muschelli]: https://johnmuschelli.com/
-[Candace Savonen]: https://www.cansavvy.com/
-[Carrie Wright]: https://carriewright11.github.io/
-[Ava Hoffman]: https://www.avahoffman.com/
-
-
-
-[ottrpal]: https://github.com/jhudsl/ottrpal
-
-
diff --git a/inst/extdata/OTTR_Template-main/CONTRIBUTING.md b/inst/extdata/OTTR_Template-main/CONTRIBUTING.md
deleted file mode 100644
index c011e0b..0000000
--- a/inst/extdata/OTTR_Template-main/CONTRIBUTING.md
+++ /dev/null
@@ -1,118 +0,0 @@
-# Want to contribute to OTTR?
-
-## Code of Conduct
-
-The [Contributor Covenant Code of Conduct can be found here](https://github.com/jhudsl/OTTR_Template/blob/main/code_of_conduct.md)
-
-## What are the different OTTR repositories/resources?
-
-Open-source Tools for Training Resources (OTTR) are a set of GitHub repositories designed to offer efficiency and flexibility in creating and maintaining training resources for courses and informatics tools. Below different repositories and resources that part of the OTTR universe are listed with brief explanations of what they do. The repositories and resources are split between "Functionality" and "Documentation" where the "Functionality" section focuses on the repositories or code that make OTTR functional; and the "Documentation" section focuses on the resources that explain how to use and maintain OTTR.
-
-### Functionality
-#### OTTR_Template
-
-The [OTTR_Template repository](https://github.com/jhudsl/OTTR_Template) is a template used to create OTTR courses, specifically when you're writing one course, but publishing it in three places: (bookdown/website), Leanpub, and Coursera. If used with [a pull request model](https://www.ottrproject.org/writing_content_courses.html#about-ottr-and-pull-requests), courses built with the template will be checked for spelling errors and periodically for broken URLs, and can be previewed and automatically rendered after updates.
-
-#### OTTR_Quizzes
-
-The [OTTR_Quizzes repository](https://github.com/jhudsl/OTTR_Quizzes) can be used when you want your course quizzes to remain private rather being housed in a public, open source repository. Use of this repository is in conjunction with the main OTTR_Template. All edits and additions to non-quiz content should take place
-
-#### OTTR_Template_Website
-
-The [OTTR_Template_Website repository](https://github.com/jhudsl/OTTR_Template_Website) is a template used to create OTTR websites. Like the main OTTR_Template, if used with [a pull request model](https://www.ottrproject.org/writing_content_courses.html#about-ottr-and-pull-requests), websites built with the template will be checked for spelling errors and periodically for broken URLs, and can be previewed and automatically rendered after updates. Unlike the main OTTR_Template, it only produces a website as output.
-
-#### ottr-reports
-
-The [ottr-reports repository](https://github.com/jhudsl/ottr-reports) houses the functionality for reporting the results of the GitHub Action checks on spelling, URLs, and quiz formatting.
-
-#### ottrpal
-
-The [ottrpal repository](https://github.com/jhudsl/ottrpal) provides the functionality to convert an OTTR course to files ready for use in Leanpub and Coursera
-
-#### cow
-
-The [cow repository](https://github.com/jhudsl/cow) isn't officially an OTTR repository, but is a GitHub API wrapper in R which has additional functions to help wrangle GitHub published courses like OTTR courses.
-
-### Documentation
-
-#### ottrproject.org
-
-The [ottrproject.org repository](https://github.com/jhudsl/ottrproject.org) renders the [OTTR documentation website](https://www.ottrproject.org/). The repository is generated from the [OTTR_Template_Website template](https://github.com/jhudsl/OTTR_Template_Website).
-
-#### OTTR paper
-
-There's an [OTTR paper](https://pubmed.ncbi.nlm.nih.gov/37207236/) published in the Journal of Statistics and Data Science Education by C. Savonen, C. Wright, A. Hoffman, et al. in 2023. [For information on citing the manuscript, see here](https://www.ottrproject.org/index.html#how-to-cite-ottr)
-
-#### Cheatsheets
-
-TBA
-
-#### Videos
-
-TBA
-
-## How should you suggest changes or alert us about problems?
-
-There are various ways in which you can request or suggest changes to OTTR. Below we discuss ways in which you can make suggestions or requests, but leave the implementation to others or implement the suggestions yourselves.
-
-### You want to make suggestions, but leave the implementation to someone else
-
-If you want to alert us about an issue or make suggestions, you can open a GitHub Issue or submit a response in our [OTTR Feedback Google Form](https://forms.gle/jGQnd5oemHWyuUq28).
-
-If you aren't sure what repository the suggestion pertains to -- or if the suggestion pertains to multiple repositories file it to the [`OTTR_Template` repo](https://github.com/jhudsl/OTTR_Template/issues/new/choose).
-
-#### GitHub Issues
-
-Open an issue describing the bug or feature request for the relevant repository using the following links.
-
-| Repository | Issues Link |
-|:---------------------:|:---------------------------------------------------------------------------:|
-| OTTR_Template | [Open an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose) |
-| OTTR_Quizzes | [Open an issue here](https://github.com/jhudsl/OTTR_Quizzes/issues/new/choose) |
-| OTTR_Template_Website | [Open an issue here](https://github.com/jhudsl/OTTR_Template_Website/issues/new/choose)|
-| ottr-reports | [Open an issue here](https://github.com/jhudsl/ottr-reports/issues/new/choose) |
-| ottrpal | [Open an issue here](https://github.com/jhudsl/ottrpal/issues/new/choose) |
-| cow | [Open an issue here](https://github.com/jhudsl/cow/issues/new/choose) |
-| ottrproject.org | [Open an issue here](https://github.com/jhudsl/ottrpal/issues/new/choose) |
-
-##### Description of choices for issue type (if given)
-
-Most of the links above will directly open an issue for you to fill out a description of the problem or request, but several of the repositories provide choices (and related description templates) for the type of issue you want to open. Those choices could include the following:
-
-* **Feature Request** or **Course Template Feature Request**: Use this issue if you want to make a suggestion for an addition.
-* **Problem Report** or **Course Template Problem Report**: Use this issue if you want to report a problem or possible improvement.
-* **New Content Idea**: This is a template meant for opening an issue in an OTTR course, so that someone can suggest an additional topic or idea for that specific course. It can be used for general suggestions for content.
-* **Course Problem Report**: This is a template meant for opening an issue in an OTTR course, so that someone can point out a problem or suggest an improvement for that specific course. It shouldn't be used for opening an issue in one of these repos.
-
-##### Assign an OTTR maintainer
-
-Assign an OTTR maintainer (`@cansavvy` or `@carriewright11` or `@avahoffman`) to the issue. If you aren't sure who the issue pertains to, assign `@cansavvy` and she'll make sure it gets to the right person.
-
-#### Google Form
-
-This [OTTR Feedback Google Form](https://docs.google.com/forms/d/e/1FAIpQLSfcc_h1MPfCOWyQup4Z76lzlBGz8cAkDQmBiqfxqOZ4_4lCkQ/viewform) can be used to ask questions about any problems you encounter or submit feedback such as ideas or requests for improvements.
-
-### You want to make suggestions, and implement them yourself!
-
-If you want to implement an improvement or fix a problem, open a branch, make the changes to the code there, and then open a pull request. [See this chapter "Using Version Control with GitHub"](https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics/using-version-control-with-github.html) from our Advanced Reproducibility course for more information on this pull request model if needed.
-
-#### Request Review
-
-Make sure to request review of your pull request from an OTTR maintainer (`@cansavvy` or `@carriewright11` or `@avahoffman`).
-
-## What if you want to make several courses with similar branding using OTTR?
-
-If you plan to use the OTTR template several times for related courses within an organization and want each to have a shared branding or functionality variation, you may want to make your own template from the OTTR_Template, incorporating the stylistic changes in your spinoff template before making specific courses from the spinoff template.
-
-OTTR_Template --> Spinoff_Template (Make stylistic changes, mark as a template repository) --> Course Repository
-
-Examples that have done this include:
-
-| Spinoff template | Link |
-|:------------------:|:-------------------------------------------------------------------------:|
-| AnVIL Template | [GitHub Source Code](https://github.com/jhudsl/AnVIL_Template) |
-| DataTrail Template | [GitHub Source Code](https://github.com/datatrail-jhu/DataTrail_Template) |
-|Quarto website| [GitHub Source Code](https://github.com/fhdsl/OTTR_Quarto)|
-|Metric collection dashboard template| [GitHub Source Code](https://github.com/fhdsl/metricminer-dashboard)|
-
-If you are interested in this and have questions, reach out to the OTTR maintainers by filing a GitHub issue and assigning `@cansavvy`, `@carriewright11`, and `@avahoffman`.
diff --git a/inst/extdata/OTTR_Template-main/Course_Name.rds b/inst/extdata/OTTR_Template-main/Course_Name.rds
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diff --git a/inst/extdata/OTTR_Template-main/GA_Script.html b/inst/extdata/OTTR_Template-main/GA_Script.html
deleted file mode 100644
index 96568c1..0000000
--- a/inst/extdata/OTTR_Template-main/GA_Script.html
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-
diff --git a/inst/extdata/OTTR_Template-main/LICENSE.md b/inst/extdata/OTTR_Template-main/LICENSE.md
deleted file mode 100644
index da6ab6c..0000000
--- a/inst/extdata/OTTR_Template-main/LICENSE.md
+++ /dev/null
@@ -1,396 +0,0 @@
-Attribution 4.0 International
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diff --git a/inst/extdata/OTTR_Template-main/OTTR_Template.Rproj b/inst/extdata/OTTR_Template-main/OTTR_Template.Rproj
deleted file mode 100644
index 628359e..0000000
--- a/inst/extdata/OTTR_Template-main/OTTR_Template.Rproj
+++ /dev/null
@@ -1,17 +0,0 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: knitr
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-
-BuildType: Website
diff --git a/inst/extdata/OTTR_Template-main/README.md b/inst/extdata/OTTR_Template-main/README.md
deleted file mode 100644
index 8c59ad3..0000000
--- a/inst/extdata/OTTR_Template-main/README.md
+++ /dev/null
@@ -1,32 +0,0 @@
-## OTTR for Courses!
-
-Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada:
-
-The purpose of this course template and guide is to make course publishing maintenance across multiple different platforms _less painful_.
-
-_This template and guide helps you_:
-
-- Edit and write a course in [RMarkdown files](https://rmarkdown.rstudio.com/) and have it published to multiple different platforms:
- - [Leanpub](https://leanpub.com/bookstore?type=course)
- - [Bookdown](https://bookdown.org/)
- - [Coursera](https://www.coursera.org/)
-- Have [Github action robots](https://www.ottrproject.org/customize-robots.html) do your repetitive tasks like spell check and re-rendering.
-- Use [automagic conversion](https://github.com/jhudsl/ottrpal) to ease the lift of prepping the material for different platforms' formats.
-- Use [our Docker image](https://hub.docker.com/repository/docker/jhudsl/base_ottr) for consistency across authors as well as to help you [avoid dependency hell](https://en.wikipedia.org/wiki/Dependency_hell).
-
-[See the OTTR pre-print here!](https://arxiv.org/abs/2203.07083)
-
-
-
-## Courses that have been made using this template:
-- [Documentation and Usability](https://jhudatascience.org/Documentation_and_Usability/)
-- [Leadership for Cancer Informatics Research](https://jhudatascience.org/Informatics_Research_Leadership/)
-- [Reproducibility in Cancer Informatics](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/)
-- [Advanced Reproducibility in Cancer Informatics](https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics/)
-
-## To Get Started
-- Go to the [ottrproject.org](https://www.ottrproject.org/).
-- Check out the [rendered version of the template](https://jhudatascience.org/OTTR_Template/).
-- Check out our [course on using Leanpub](https://hutchdatascience.org/Using_Leanpub/index.html) for help publishing on this platform.
-- Please take a look at the [code of conduct](./code_of_conduct.md).
-- If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please [file an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose)! Your feedback is very much appreciated.
diff --git a/inst/extdata/OTTR_Template-main/References.Rmd b/inst/extdata/OTTR_Template-main/References.Rmd
deleted file mode 100644
index 98d65dc..0000000
--- a/inst/extdata/OTTR_Template-main/References.Rmd
+++ /dev/null
@@ -1,2 +0,0 @@
-
-# References
diff --git a/inst/extdata/OTTR_Template-main/_bookdown.yml b/inst/extdata/OTTR_Template-main/_bookdown.yml
deleted file mode 100644
index b163ca5..0000000
--- a/inst/extdata/OTTR_Template-main/_bookdown.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-book_filename: "Course_Name"
-chapter_name: "Chapter "
-repo: https://github.com/jhudsl/OTTR_Template/
-rmd_files: ["index.Rmd",
- "01-intro.Rmd",
- "02-chapter_of_course.Rmd",
- "About.Rmd",
- "References.Rmd"]
-new_session: yes
-delete_merged_file: true
-language:
- ui:
- chapter_name: "Chapter"
-output_dir: "docs"
diff --git a/inst/extdata/OTTR_Template-main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-2-1.png b/inst/extdata/OTTR_Template-main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-2-1.png
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diff --git a/inst/extdata/OTTR_Template-main/_output.yml b/inst/extdata/OTTR_Template-main/_output.yml
deleted file mode 100644
index 509a629..0000000
--- a/inst/extdata/OTTR_Template-main/_output.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-bookdown::gitbook:
- css: assets/style.css
- includes:
- before_body: assets/big-image.html
- after_body: [assets/footer.html, assets/open-new-tab.html]
- highlight: tango
- config:
- toc:
- collapse: section
- before: |
- 
- after: |
-
-
-
-
\ No newline at end of file
diff --git a/inst/extdata/OTTR_Template-main/assets/hideOutput.js b/inst/extdata/OTTR_Template-main/assets/hideOutput.js
deleted file mode 100644
index 245d55f..0000000
--- a/inst/extdata/OTTR_Template-main/assets/hideOutput.js
+++ /dev/null
@@ -1,57 +0,0 @@
-/*$(document).ready(function() {
-
-
- // Copy Button
- $chunks = $('pre.sourceCode > code.sourceCode');
- $chunks.each(function(i, val) {
- $(this).prepend("").click(function() {
- var $temp = $("
-
-Work in Progress text
-
-
-
-
-## Dropdown summaries
-
-You can hide additional information in a dropdown menu
-Here's more words that are hidden. -
- after: |
- This content was published with bookdown using
- -The Johns Hopkins Data Science Lab
-Style adapted from: rstudio4edu-book (CC-BY 2.0)
diff --git a/inst/extdata/OTTR_Template-main/assets/big-image.html b/inst/extdata/OTTR_Template-main/assets/big-image.html deleted file mode 100644 index 1df3779..0000000 --- a/inst/extdata/OTTR_Template-main/assets/big-image.html +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - -
- 
-
diff --git a/inst/extdata/OTTR_Template-main/assets/box_images/dictionary.png b/inst/extdata/OTTR_Template-main/assets/box_images/dictionary.png
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