Initial commit

.github/ISSUE_TEMPLATE/all-other-issues.md

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+---
+name: All other issues
+about: All issues that are not for requesting read access
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+

.github/ISSUE_TEMPLATE/request-read-access-to-use-template-for-a-workshop.md

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+---
+name: Request read access to use template for a workshop
+about: Use this issue template to request read access to the repository so you can
+  use it as a template.
+title: "[Request read access] "
+labels: request
+assignees: ''
+
+---
+
+<!-- Hi there, please fill out this issue template so we can understand your use case!-->
+
+#### Your information
+
+<!-- Add some basic information about yourself like your name and institution. If a GitHub user other than the one you are filing this issue from needs read access, tell us here. -->
+
+#### Workshop format, location, and dates
+
+<!-- Tell us about your workshop. Is in virtual or in-person? If it's in-person, where will you be holding the workshop? When will the workshop run? -->

.github/workflows/copy-completed-notebooks.yml

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+name: Copy completed HTML notebooks to training website repository
+# Copy completed HTML notebooks from the training-modules repo to this repo
+# This action will open a pull request containing completed HTML notebooks
+
+# This is a manually triggered workflow that takes two inputs:
+#  # The name of the workshop being taught
+#  # The training-modules repo tag to copy notebooks from
+on:
+  workflow_dispatch:
+    inputs:
+      training-module:
+        type: choice
+        description: Use the dropdown menu to select which training workshop module this website is being created for.
+        options:
+          - "Introduction to R and Tidyverse"
+          - "Introduction to single-cell RNA-seq"
+          - "Advanced single-cell RNA-seq"
+          - "Bulk RNA-seq"
+        required: true
+      training-modules-tag:
+        type: string
+        description: The `training-modules` repo tag to copy completed notebooks from, e.g. 2023-june
+        default: "master"
+        required: true
+
+jobs:
+  file-completed-notebooks-pr:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout training-modules repository
+        uses: actions/checkout@v3
+        with:
+          repository: AlexsLemonade/training-modules
+          ref: ${{ github.event.inputs.training-modules-tag }}
+          path: training-modules
+
+      - name: Checkout this repository
+        uses: actions/checkout@v3
+        with:
+          path: website
+
+      - name: Configure git
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "GitHub Actions"
+
+      - name: Copy HTML completed notebooks from training-modules
+        shell: bash
+        run: |
+          # The completed notebooks to copy will depend on which workshop module this is.
+          # For each module, the directory of notebooks to copy are:
+          #  Intro R: intro_to_R_tidyverse/
+          #  Intro scRNA-seq: intro_to_R_tidyverse/ and scRNA-seq/
+          #  Advanced scRNA-seq: advanced-scRNA-seq/
+          #  bulk RNA-seq: RNA-seq/
+
+          # Path to copy notebooks to
+          target_path=website/completed-notebooks
+
+          # Create array of directories from which notebooks should be copied
+          case "${{ github.event.inputs.training-module }}" in
+
+            "Introduction to R and Tidyverse")
+              modules=("intro-to-R-tidyverse")
+              ;;
+
+            "Introduction to single-cell RNA-seq")
+              modules=("intro-to-R-tidyverse" "scRNA-seq")
+              ;;
+
+            "Advanced single-cell RNA-seq")
+              modules=("scRNA-seq-advanced")
+              ;;
+
+            "Bulk RNA-seq")
+              modules=("intro-to-R-tidyverse", "RNA-seq")
+              ;;
+          esac
+
+          # Copy all completed notebooks from the given directories
+          for module in ${modules[@]}; do
+            mkdir -p ${target_path}/${module}
+            cp training-modules/${module}/[0-9]*.html ${target_path}/${module}
+          done
+
+      - name: Create PR with rendered notebooks
+        uses: peter-evans/create-pull-request@v5
+        id: cpr
+        with:
+          path: website # must be a RELATIVE path to _this_ repo
+          commit-message: Copy completed notebooks from training-modules@${{ github.event.inputs.training-modules-tag }}
+          signoff: false
+          branch: auto_copy_completed_notebooks
+          delete-branch: true
+          title: 'GHA: Automated transfer of completed notebooks'
+          body: |
+            ### Description:
+            This PR was auto-generated from github actions
+              - Copy completed notebooks for the "${{ github.event.inputs.training-module }}" module from the `training-modules` repository, tag `${{ github.event.inputs.training-modules-tag }}`
+          labels: |
+            automated
+          reviewers: $GITHUB_ACTOR
+
+
+      # Write out PR info
+      - name: Check outputs
+        run: |
+          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"

.github/workflows/file-setup-issues.yml

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+name: Manually trigger issue creation for standard set up
+
+# This is a manually triggered workflow
+# https://docs.github.com/en/actions/reference/events-that-trigger-workflows#workflow_dispatch
+# https://docs.github.com/en/actions/managing-workflow-runs/manually-running-a-workflow#running-a-workflow-on-github
+on:
+  workflow_dispatch:
+
+jobs:
+  # This runs a single job that creates issues from files
+  createIssuesFromFile:
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+
+      # Check out
+      - uses: actions/checkout@v3
+
+      # Issue for turning on GitHub pages
+      - name: Create GitHub Pages issue
+        uses: peter-evans/[email protected]
+        with:
+          title: Turn on GitHub Pages
+          content-filepath: ./setup-issue-templates/gh-pages.md
+          labels: automated training issue
+
+      # Issue for turning on branch protection
+      - name: Create branch protection issue
+        uses: peter-evans/[email protected]
+        with:
+          title: Set up branch protection - pull requests required
+          content-filepath: ./setup-issue-templates/branch-protection.md
+          labels: automated training issue
+
+      # Issue updating `_config.yaml`
+      - name: Create issue for _config.yaml
+        uses: peter-evans/[email protected]
+        with:
+          title: Update _config.yaml to use values relevant to this workshop
+          content-filepath: ./setup-issue-templates/update-config.md
+          labels: automated training issue
+
+      # Issue for adding PDF versions of slides
+      - name: Create issue for slides
+        uses: peter-evans/[email protected]
+        with:
+          title: Add PDF versions of slides to `slides`
+          content-filepath: ./setup-issue-templates/pdf-slides.md
+          labels: automated training issue, slides
+
+      # Issue for creating a draft version of schedule
+      - name: Create draft schedule issue
+        uses: peter-evans/[email protected]
+        with:
+          title: Draft version of schedule
+          content-filepath: ./setup-issue-templates/draft-schedule.md
+          labels: automated training issue, schedule
+
+      # Issue for creating a training-specific release of training-modules
+      - name: Create issue for training-specific release
+        uses: peter-evans/[email protected]
+        with:
+          title: Create release of training-modules to associate with this workshop
+          content-filepath: ./setup-issue-templates/workshop-release.md
+          labels: automated training issue
+
+      # Issue for copying completed notebooks from training-modules
+      - name: Create issue for copying completed notebooks
+        uses: peter-evans/[email protected]
+        with:
+          title: Copy completed notebooks to training website
+          content-filepath: ./setup-issue-templates/copy-completed-notebooks.md
+          labels: automated training issue, blocked
+
+      # Issue for customizing participant-information.md
+      - name: Create issue for updating participant-information.md
+        uses: peter-evans/[email protected]
+        with:
+          title: Update in-person logistics in `participant-information.md`
+          content-filepath: ./setup-issue-templates/update-participant-information.md
+          labels: automated training issue
+
+      # Issue for creating a final version of schedule
+      - name: Create final schedule issue
+        uses: peter-evans/[email protected]
+        with:
+          title: Final version of schedule
+          content-filepath: ./setup-issue-templates/final-schedule.md
+          labels: automated training issue, schedule, blocked
+
+      # Issue for updating README
+      - name: Create issue for updating README
+        uses: peter-evans/[email protected]
+        with:
+          title: Update README to be user-facing (remove instructions)
+          content-filepath: ./setup-issue-templates/user-facing-readme.md
+          labels: automated training issue

.github/workflows/spell-check.yml

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+
+name: Spell check Markdown files
+
+# Controls when the action will run.
+# Pull requests to main only.
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  # This workflow contains a single job called "spell check"
+  spell-check:
+    runs-on: ubuntu-latest
+    container:
+      image: rocker/tidyverse:4.2.3
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install packages
+        run: Rscript --vanilla -e "install.packages(c('spelling'), repos = c(CRAN = '$CRAN'))"
+
+      - name: Run spell check
+        id: spell_check_run
+        run: |
+          results=$(Rscript --vanilla "scripts/spell-check.R")
+          echo "sp_chk_results=$results" >> $GITHUB_OUTPUT
+          cat spell_check_errors.tsv
+
+      - name: Archive spelling errors
+        uses: actions/upload-artifact@v3
+        if: ${{ steps.spell_check_run.outputs.sp_chk_results > 0 }}
+        with:
+          name: spell-check-results
+          path: spell_check_errors.tsv
+
+      # If there are too many spelling errors, this will stop the workflow
+      - name: Check spell check results - fail if too many errors
+        if: ${{ steps.spell_check_run.outputs.sp_chk_results > 0 }}
+        run: exit 1

.gitignore

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+# jekyll built site
+_site
+.DS_Store
+Gemfile.lock
+
+.ruby-version

CONTENTS.md

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+This file provides an overview of contents in this repository.
+
+- Please see the `LICENSE.md` file for the terms of use of this repository's materials.
+- Please see the `README.md` file for instructions on using and contributing to this repository.
+
+## Workshop files
+
+These files/directories are directly shown in the rendered website.
+
+- `workshop`
+  - This directory contains all pages that appear in the website header
+- `software-setup`
+  - This directory contains all website pages that detail software installation, setup, and procedures
+- `additional-resources`
+  - This directory contains all other website pages
+- `images`
+  - This directory contains images used in this repository's `README.md` file as well as Data Lab logo and favicon files used for the website
+- `completed-notebooks`
+  - Empty by default, this directory can be populated with completed training notebooks to link to from the schedule in `workshop/SCHEDULE.md`
+- `slides`
+  - Empty by default, this directory can be populated with slide PDFs to link to from the schedule in `workshop/SCHEDULE.md`
+- `code-of-conduct.md`
+  - The Data Lab's Code of Conduct, as displayed on the workshop website
+
+## Setup files
+
+These files/directories are used to prepare contents for a given training website.
+
+- `scripts`
+  - This directory contains a helper script for automated spell checking
+- `components`
+  - This directory contains a dictionary of words to ignore during spell check
+- `.github/workflows`
+  - This directory contains GitHub Actions Workflows used during repository setup and development
+- `setup-issue-templates`
+  - Contains templates for automatic issues filed by the manually-triggered action `.github/workflows/file-setup-issues.yml`
+
+## Jekyll files
+
+These files/directories are used by [`jekyll`](https://jekyllrb.com/) to create and render the website.
+
+- `Gemfile` and `Gemfile.lock`
+- `_config.yml`
+- `_includes`
+
+## Additional files
+
+- `ccdl-training-waiver.pdf`
+  - PDF copy of the Data Lab training waiver that participants must sign
+- `supplemental-notebooks`
+  - This directory is empty but can be used to add supplemental notebooks to distribute to participants
+

Gemfile

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+source "https://rubygems.org"
+
+gem "github-pages", group: :jekyll_plugins
+gem "webrick"