Initial commit

.docker/Dockerfile

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+# start with official ruby docker image as base
+FROM ruby:3.1.2
+
+# set working directory within container
+WORKDIR /usr/src/app
+
+# pull in ruby (jekyll) and python (cite process) package info
+COPY Gemfile Gemfile.lock _cite/requirements.txt ./
+
+# install ruby packages
+RUN VERSION=$(grep -A 1 'BUNDLED WITH' Gemfile.lock | tail -n 1 | xargs); \
+ gem install bundler --version ${VERSION} && \
+ bundle _${VERSION}_ install
+
+# install python
+RUN apt update && apt install -y python3 python3-pip
+
+# install python packages
+RUN python3 -m pip install --no-cache-dir --upgrade --requirement requirements.txt
+
+# install python package for listening for file changes
+RUN pip install "watchdog[watchmedo]==3.0.0"
+
+# ports used by jekyll
+EXPOSE 4000
+EXPOSE 35729
+
+# run jekyll and cite process
+COPY .docker/entrypoint.sh /var
+CMD [ "/var/entrypoint.sh" ]

.docker/entrypoint.sh

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+#! /bin/bash
+
+# print folder contents for debugging
+echo "Contents:"
+echo ""
+ls
+echo ""
+
+# run cite process
+python3 _cite/cite.py
+
+# run jekyll serve in hot-reload mode
+# rerun whenever _config.yaml changes (jekyll hot-reload doesn't work with this file)
+watchmedo auto-restart \
+ --debug-force-polling \
+ --patterns="_config.yaml" \
+ --signal SIGTERM \
+ -- bundle exec jekyll serve --open-url --force_polling --livereload --trace --host=0.0.0.0 \
+ | sed "s/LiveReload address.*//g;s/0.0.0.0/localhost/g" &
+
+# rerun cite process whenever _data files change
+watchmedo shell-command \
+ --debug-force-polling \
+ --recursive \
+ --wait \
+ --command="python3 _cite/cite.py" \
+ --patterns="_data/sources*;_data/orcid*;_data/pubmed*;_data/google-scholar*" \

.docker/run.sh

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+#! /bin/bash
+
+# name of image
+IMAGE=lab-website-renderer:latest
+
+# name of running container
+CONTAINER=lab-website-renderer
+
+# choose platform flag
+PLATFORM=""
+
+# default vars
+DOCKER_RUN="docker run"
+WORKING_DIR=$(pwd)
+
+# fix windows faux linux shells/tools
+if [[ $OSTYPE == msys* ]] || [[ $OSTYPE == cygwin* ]]; then
+ DOCKER_RUN="winpty docker run"
+ WORKING_DIR=$(cmd //c cd)
+fi
+
+# build docker image
+docker build ${PLATFORM} \
+ --tag ${IMAGE} \
+ --file ./.docker/Dockerfile . && \
+
+# run built docker image
+${DOCKER_RUN} ${PLATFORM} \
+ --name ${CONTAINER} \
+ --init \
+ --rm \
+ --interactive \
+ --tty \
+ --publish 4000:4000 \
+ --publish 35729:35729 \
+ --volume "${WORKING_DIR}:/usr/src/app" \
+ ${IMAGE} "$@"

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: true
+contact_links:
+ - name: 💬 Start a discussion
+ url: https://github.com/greenelab/lab-website-template/discussions
+ about: I need help, I have a question, or other discussion.
+ - name: 📚 Docs issue
+ url: https://github.com/greenelab/lab-website-template-docs/issues
+ about: I have a question or issue related to the template documentation.

.github/ISSUE_TEMPLATE/issue.yaml

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+name: 🐞 Create an issue
+description: I think I've discovered a bug, I want to request a feature/change, or other issue.
+
+body:
+ - type: checkboxes
+ attributes:
+ label: Checks
+ options:
+ - label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first.
+ required: true
+
+ - type: input
+ id: repo
+ attributes:
+ label: Link to your website repo
+ description: "**Strongly recommended** so we can help troubleshoot your issue."
+ placeholder: ex. https://github.com/greenelab/greenelab.com
+
+ - type: input
+ id: version
+ attributes:
+ label: Version of Lab Website Template you are using
+ description: See your `CITATION.cff` file.
+ placeholder: ex. 1.0.0
+
+ - type: textarea
+ id: description
+ attributes:
+ label: Description
+ description: |
+ Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in?
+ placeholder: Description
+ validations:
+ required: true

.github/pull_request_template.md

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+STOP!!!
+
+You are about to open this pull request against THE TEMPLATE ITSELF. You probably meant to open it against your own website repo.
+
+---
+
+FOR THE TEMPLATE MAINTAINER(S)
+
+New template version checklist:
+
+- [ ] I have updated CITATION and CHANGELOG as appropriate.
+- [ ] I have updated lab-website-template-docs as appropriate.
+- [ ] I have checked the testbed as appropriate.

.github/user_pull_request_template.md

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+This website is based on the Lab Website Template.
+See its documentation for working with this site:
+
+https://greene-lab.gitbook.io/lab-website-template-docs

.github/workflows/build-preview.yaml

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+name: build-preview
+run-name: build pull request preview
+
+on:
+ # run when called from another workflow
+ workflow_call:
+
+ # run if user manually requests it
+ workflow_dispatch:
+
+# variables
+env:
+ PREVIEWS_FOLDER: preview
+
+permissions:
+ contents: write
+ pull-requests: write
+
+jobs:
+ build-preview:
+ runs-on: ubuntu-latest
+
+ steps:
+ # for debugging
+ - name: Print contexts
+ uses: crazy-max/ghaction-dump-context@v1
+
+ - name: Checkout branch contents
+ uses: actions/checkout@v3
+ with:
+ repository: ${{ github.event.pull_request.head.repo.full_name }}
+ ref: ${{ github.head_ref }}
+
+ - name: Install Ruby packages
+ if: github.event.action != 'closed'
+ uses: ruby/setup-ruby@v1
+ with:
+ ruby-version: "3.0"
+ bundler-cache: true
+
+ - name: Get Pages url
+ if: github.event.action != 'closed'
+ id: pages
+ uses: actions/configure-pages@v2
+ with:
+ enablement: false
+
+ - name: Build preview version of site
+ if: github.event.action != 'closed'
+ run: |
+ JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}/${{ env.PREVIEWS_FOLDER }}/pr-${{ github.event.number }}"
+
+ - name: Commit preview to Pages branch
+ uses: rossjrw/pr-preview-action@v1
+ with:
+ source-dir: _site
+ umbrella-dir: ${{ env.PREVIEWS_FOLDER }}

.github/workflows/build-site.yaml

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+name: build-site
+run-name: build live site
+
+on:
+ # run when called from another workflow
+ workflow_call:
+
+ # run if user manually requests it
+ workflow_dispatch:
+
+# variables
+env:
+ PREVIEWS_FOLDER: preview
+
+permissions:
+ contents: write
+
+jobs:
+ build-site:
+ runs-on: ubuntu-latest
+
+ steps:
+ # for debugging
+ - name: Print contexts
+ uses: crazy-max/ghaction-dump-context@v1
+
+ - name: Checkout branch contents
+ uses: actions/checkout@v3
+
+ - name: Install Ruby packages
+ uses: ruby/setup-ruby@v1
+ with:
+ ruby-version: "3.0"
+ bundler-cache: true
+
+ - name: Get Pages url
+ id: pages
+ uses: actions/configure-pages@v2
+ with:
+ enablement: false
+
+ - name: Build live version of site
+ run: |
+ JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}"
+
+ - name: Commit live site to Pages branch
+ uses: JamesIves/github-pages-deploy-action@v4
+ with:
+ folder: _site
+ clean-exclude: ${{ env.PREVIEWS_FOLDER }}
+ force: false

.github/workflows/first-time-setup.yaml

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+name: first-time-setup
+run-name: first time setup of repo
+
+on:
+ # run if user manually requests it
+ workflow_dispatch:
+
+permissions:
+ contents: write
+
+jobs:
+ first-time-setup:
+ runs-on: ubuntu-latest
+
+ steps:
+ # for debugging
+ - name: Print contexts
+ uses: crazy-max/ghaction-dump-context@v1
+
+ - name: Create Pages branch
+ uses: peterjgrainger/[email protected]
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ with:
+ branch: "gh-pages"
+
+ - name: Checkout Pages branch
+ uses: actions/checkout@v3
+ with:
+ ref: gh-pages
+
+ # clean slate, as if starting from orphan branch
+ - name: Clear Pages branch
+ run: rm -rf * .github .docker .gitignore
+
+ # prevent GitHub from running Jekyll a second time after build
+ - name: Make .nojekyll file
+ run: touch .nojekyll
+
+ - name: Make placeholder homepage
+ run: echo "Placeholder homepage" > index.html
+
+ - name: Commit changes to Pages branch
+ uses: stefanzweifel/git-auto-commit-action@v4
+ with:
+ branch: gh-pages
+ commit_message: "Clear branch"
+
+ - name: Checkout main branch
+ uses: actions/checkout@v3
+
+ - name: Remove files user doesn't need
+ run: |
+ rm -rf \
+ CHANGELOG.md \
+ testbed.md \
+ .github/ISSUE_TEMPLATE \
+ .github/workflows/versioning.yaml \
+ .github/pull_request_template.md \
+ 
+ - name: Rename files
+ run: |
+ mv .github/user_pull_request_template.md .github/pull_request_template.md
+
+ - name: Set vars for personalization
+ run: |
+ user="${{ github.repository_owner }}"
+ description="An engaging 1-3 sentence description of your lab."
+ echo "USER=${user}" >> $GITHUB_ENV
+ echo "DESCRIPTION=${description}" >> $GITHUB_ENV
+
+ - name: Personalize readme for user
+ run: |
+ echo "
+ # ${{ env.USER }}'s Website
+
+ Visit **[website url](#)** 🚀
+
+ _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
+ " > README.md
+
+ - name: Personalize Jekyll config for user
+ uses: actions/github-script@v6
+ with:
+ script: |
+ const { readFileSync, writeFileSync } = require("fs");
+ const file = "_config.yaml";
+ const contents = readFileSync(file)
+ .toString()
+ .replace(/(^title: ).*$/m, "$1${{ env.USER }}")
+ .replace(/(^subtitle: ).*$/m, "$1")
+ .replace(/(^description: ).*$/m, "$1${{ env.DESCRIPTION }}")
+ .replace(/(^ email: ).*$/m, "$1contact@${{ env.USER }}.com")
+ .replace(/(^ github: ).*$/m, "$1${{ env.USER }}")
+ .replace(/(^ twitter: ).*$/m, "$1${{ env.USER }}")
+ .replace(/(^ youtube: ).*$/m, "$1${{ env.USER }}");
+ writeFileSync(file, contents);
+
+ - name: Personalize homepage for user
+ uses: actions/github-script@v6
+ with:
+ script: |
+ const { readFileSync, writeFileSync } = require("fs");
+ const file = "index.md";
+ let contents = readFileSync(file).toString();
+ const find = /\# Lab Website Template[\s\S]+({% include section\.html)/;
+ const replace = `# ${{ env.USER }}'s Website\n\n${{ env.DESCRIPTION }}\n\n$1`;
+ contents = contents.replace(find, replace);
+ writeFileSync(file, contents);
+
+ - name: Commit changed files
+ uses: stefanzweifel/git-auto-commit-action@v4
+ with:
+ commit_message: "Setup repo"