Initial commit

.Rbuildignore

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+^LICENSE\.md$
+.github
+Dockerfile
+_pkgdown.yml

.github/workflows/basic_checks.yaml

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+name: Check, build, and push image
+
+on: [push, pull_request]
+
+env:
+  cache-version: v1
+
+jobs:
+  r-build-and-check:
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:devel
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Query dependencies and update old packages
+        run: |
+          BiocManager::install(ask=FALSE)
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: /usr/local/lib/R/site-library
+          key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-
+
+      # This lets us augment with additional dependencies
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+          
+      - name: Install dependencies
+        run: |
+          BiocManager::repositories()
+          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+
+      - name: Build pkgdown
+        run: |
+           PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'
+
+      # deploy needs rsync? Seems so.
+      - name: Install deploy dependencies
+        run: |
+          apt-get update
+          apt-get -y install rsync
+
+      - name: Deploy 🚀
+        uses: JamesIves/github-pages-deploy-action@releases/v4
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages # The branch the action should deploy to.
+          FOLDER: docs # The folder the action should deploy.
+  docker-build-and-push:
+    #needs: r-build-and-check
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set Environment Variables
+        run: |
+          REPO_LOWER="$(echo "${{ github.repository }}" | tr '[:upper:]' '[:lower:]')"
+          REGISTRY=ghcr.io
+          echo "BUILD_DATE=$(date +'%Y-%m-%d %H:%M:%S')" >> $GITHUB_ENV
+          echo "GIT_SHA=$(echo ${{ github.sha }} | cut -c1-7)" >> $GITHUB_ENV
+          echo "REGISTRY=${REGISTRY}" >> $GITHUB_ENV
+          echo "IMAGE=${REGISTRY}/${REPO_LOWER}" >> $GITHUB_ENV
+          
+      - name: Show environment
+        run: |
+          env
+
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@1e95c1de343b5b0c23352d6417ee3e48d5bcd422
+        with:
+          cosign-release: 'v1.4.0'
+
+
+      # Workaround: https://github.com/docker/build-push-action/issues/461
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.IMAGE }}
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: |
+            ${{ env.IMAGE }}:latest
+            ${{ env.IMAGE }}:${{ env.GIT_SHA }}
+

.gitignore

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+inst/doc
+*~

DESCRIPTION

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+Package: BuildABiocWorkshop
+Title: Bioconductor or R Workshop Template and Github Actions
+Version: 2.0.0
+Authors@R: 
+    person(given = "Sean",
+           family = "Davis",
+           role = c("aut", "cre"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0002-8991-6458"))
+Description: This package serves as a template for using github actions to 
+    prepare a Bioconductor Workshop package for use. In particular,
+    a pkgdown website and docker image are generated based on workflow 
+    settings. 
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.0
+Depends: 
+    Biobase
+Suggests: 
+    knitr,
+    rmarkdown,
+    pkgdown
+URL: https://seandavi.github.io/BuildABiocWorkshop/
+BugReports: https://github.com/seandavi/BuildABiocWorkshop/issues/new/choose
+VignetteBuilder: knitr
+DockerImage: ghcr.io/seandavi/buildabiocworkshop:latest

Dockerfile

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+FROM bioconductor/bioconductor_docker:devel
+
+WORKDIR /home/rstudio
+
+COPY --chown=rstudio:rstudio . /home/rstudio/
+
+RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask=FALSE)"
+
+RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())"

LICENSE

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+YEAR: 2020
+COPYRIGHT HOLDER: Sean Davis

LICENSE.md

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+# MIT License
+
+Copyright (c) 2020 Sean Davis
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+

README.md

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+# BuildABiocWorkshop
+
+This package is a template for building a Bioconductor workshop. The package
+includes Github actions to:
+
+1. Set up bioconductor/bioconductor_docker:devel on Github resources
+2. Install package dependencies for your package (based on the `DESCRIPTION` file)
+3. Run `rcmdcheck::rcmdcheck`
+4. Build a pkgdown website and push it to github pages
+5. Build a docker image with the installed package and dependencies and deploy to [the Github Container Repository](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry#pulling-container-images) at the name `ghcr.io/gihub_user/repo_name`, all lowercase. 
+
+## Responsibilities
+
+Package authors are primarily responsible for:
+
+1. Creating a landing site of their choosing for their workshops (a website). This website should be listed in the `DESCRIPTION` file as the `URL`.
+2. Creating a docker image that will contain workshop materials and the installed packages necessary to run those materials. The name of the resulting docker image, including "tag" if desired, should be listed in a non-standard tag, `DockerImage:` in the `DESCRIPTION` file. 
+
+Both of those tasks can be accomplished using the Github actions included in this template package. The vignette accompanying this package describes how to accomplish both of these tasks.
+
+## Details
+
+For detailed instructions, see the `How to build a workshop` article/vignette.
+
+## Results of successful deployment
+
+- A working docker image that contains the installed package and dependencies.
+- An up-to-date `pkgdown` website at https://YOURUSERNAME.github.io/YOURREPOSITORYNAME/
+- Docker image will be tagged with `latest`, `sha-XXXXXX` where `XXXXXX` is the hash of the current `master` commit, and `master`. 
+
+## To use the resulting image:
+
+```sh
+docker run -e PASSWORD=<choose_a_password_for_rstudio> -p 8787:8787 YOURDOCKERIMAGENAME
+```
+Once running, navigate to http://localhost:8787/ and then login with `rstudio`:`yourchosenpassword`. 
+
+To try with **this** repository docker image:
+
+```sh
+docker run -e PASSWORD=abc -p 8787:8787 ghcr.io/bioconductor/buildabiocworkshop
+```
+
+*NOTE*: Running docker that uses the password in plain text like above exposes the password to others 
+in a multi-user system (like a shared workstation or compute node). In practice, consider using an environment 
+variable instead of plain text to pass along passwords and other secrets in docker command lines. 
+
+
+## Whatcha get
+
+- https://bioconductor.github.io/BuildABiocWorkshop
+- A Docker image that you can run locally, in the cloud, or (usually) even as a singularity container on HPC systems. 

_pkgdown.yml

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+url: https://seandavi.github.io/BuildABiocWorkshop
+
+template:
+  params:
+    bootswatch: flatly
+    #ganalytics: UA-99999999-9
+
+home:
+  title: "BuildABiocWorkshop"
+  type: inverse
+
+
+navbar:
+  right:
+   - icon: fa-github
+     href: https://github.com/seandavi/BuildABiocWorkshop
+
+

vignettes/.gitignore

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+*.html
+*.R

vignettes/HOWTO_BUILD_WORKSHOP.Rmd

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+---
+title: "How To Build A Workshop Package"
+subtitle: "In other words, how do I use what's here"
+author: Sean Davis^[[email protected]]
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{How to Use this Package to Build a Bioc Workshop}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+First, this package doesn't do much except add a template Github Action to
+build all the pieces necessary for a workshop.
+
+## Quickstart
+
+- [ ] Create a repo from this template and rename it (do not fork the repository).
+  - [ ] Ensure that "Read and Write Permissions" is checked under [General > Workflow permissions](https://github.com/seandavi/BuildABiocWorkshop/settings/actions). 
+- [ ] Edit `DESCRIPTION` file
+  - [ ] Change package name
+  - [ ] Change title and description
+  - [ ] Change authors
+  - [ ] Check dependencies
+  - [ ] Change DockerImage tag
+- [ ] Edit '_pkgdown.yml' (and `.github/workflows yaml file` as needed)
+- [ ] Write a normal R package that can be installed
+- [ ] Include one or more vignettes that will constitute the workshop materials
+
+## Details
+
+To accomplish this follow each of the 7 steps below. Once your edit the yaml files, Github actions will run each time you commit to github and will create for you:
+
+- the pkgdown website
+- the docker image 
+
+### 1. Clone this repo
+
+Clone this repo, fork and **rename** it,
+
+OR 
+
+(PREFERRED) create a repo from this template
+
+### 2. Edit `DESCRIPTION` file
+
+- Change the package name to something identifiable and descriptive, ideally 
+something that will be somewhat unique. 
+- Edit the title and description as per any normal R package.
+- Update authors (unless you want me to get credit for your work).
+- Workshop packages are normal R packages, so dependencies work as usual. Append libraries to the Depends/Suggests/Imports in this package DESCRIPTION File, which includes;
+
+Depends: 
+    Biobase
+Suggests: 
+    knitr,
+    rmarkdown,
+    pkgdown
+  If your packages depend on a github R repos, be sure to specify the correct repo `username/reponame`.  Installation will deal with this. 
+
+- Edit the last 3 lines of the DESCRIPTION FILE, URL, BugReports and DockerImage (described in more detail below)
+
+### 3. Set up a website (Github Pages)
+
+In your repository, click on settings or url https://github.com/*GITHUB_USERNAME*/*REPO_NAME*/settings.  Midway down the page, in the GitHub Pages section, select source 'gh-pages branch'.  If only 'master branch' is visible, select master for now, but once Github actions runs, 'gh-pages branch' will be available and is required to render the website. 
+
+In the DESCRIPTION file, update the URL: to the website url eg https://seandavi.github.io/BuildABiocWorkshop/ (but substitute your own repo, etc.)
+
+### 4. Edit _pkgdown.yml
+
+Edit the file _pkgdown.yml, updating the url:, title and href: which should be your website url, title of your workshop and github repos url respectively.  You do not need to edit this file further. You do not need to add menus or links to vignettes. GitHub Actions and pkgdown will do this when it builds the website
+
+### 5. Edit `.github/workflows yaml` as needed (likely no need)
+
+
+You do not need to create a docker image manually. Github actions will read Dockerfile located in this template, and using the yaml files will create, build and push to the Github Container Registry an image with the name (default) `ghcr.io/yourgithubuser/yourgithubreponame`, all lowercase. 
+
+
+In the DESCRIPTION file, the **DockerImage: should match your the docker image name (should be lowercase)**.
+
+
+### 6. Edit README.md, add vignettes to vignettes folder
+
+Edit the README.md. and add one or more Rmd vignettes that will constitute the workshop materials. It is normal R package that should pass `rcmdcheck::rcmdcheck()`, and be installed using regular R package install commands.  
+
+