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‎.docker/Dockerfile‎

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

‎.docker/entrypoint.sh‎

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

‎.docker/run.sh‎

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

‎.github/DISCUSSION_TEMPLATE/general.yaml‎

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body:
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- type: checkboxes
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attributes:
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label: Checks
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options:
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- 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.
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required: true
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- type: input
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id: repo
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attributes:
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label: Link to your website repo
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description: "In almost all cases, **we cannot help you if you don't provide this**."
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placeholder: ex. https://github.com/greenelab/greenelab.com
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validations:
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required: true
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- type: input
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id: version
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attributes:
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label: Version of Lab Website Template you are using
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description: See your `CITATION.cff` file.
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placeholder: ex. 1.0.0
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validations:
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required: true
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- type: textarea
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id: description
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attributes:
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label: Description
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description: |
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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?
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placeholder: Description
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validations:
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required: true

‎.github/DISCUSSION_TEMPLATE/q-a.yaml‎

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body:
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- type: checkboxes
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attributes:
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label: Checks
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options:
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- 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.
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required: true
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- type: input
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id: repo
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attributes:
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label: Link to your website repo
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description: "In almost all cases, **we cannot help you if you don't provide this**."
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placeholder: ex. https://github.com/greenelab/greenelab.com
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validations:
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required: true
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- type: input
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id: version
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attributes:
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label: Version of Lab Website Template you are using
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description: See your `CITATION.cff` file.
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placeholder: ex. 1.0.0
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validations:
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required: true
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- type: textarea
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id: description
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attributes:
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label: Description
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description: |
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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?
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placeholder: Description
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validations:
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required: true

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: true
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contact_links:
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- name: 💬 Start a discussion
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url: https://github.com/greenelab/lab-website-template/discussions
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about: I need help, I have a question, or other discussion.
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- name: 📚 Docs issue
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url: https://github.com/greenelab/lab-website-template-docs/issues
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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
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description: I think I've discovered a bug, I want to request a feature/change, or other issue.
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body:
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- type: checkboxes
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attributes:
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label: Checks
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options:
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- 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.
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required: true
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- type: input
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id: repo
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attributes:
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label: Link to your website repo
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description: "In almost all cases, **we cannot help you if you don't provide this**."
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placeholder: ex. https://github.com/greenelab/greenelab.com
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validations:
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required: true
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- type: input
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id: version
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attributes:
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label: Version of Lab Website Template you are using
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description: See your `CITATION.cff` file.
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placeholder: ex. 1.0.0
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validations:
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required: true
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- type: textarea
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id: description
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attributes:
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label: Description
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description: |
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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?
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placeholder: Description
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validations:
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required: true

‎.github/pull_request_template.md‎

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STOP!!!
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You are about to open this pull request against THE TEMPLATE ITSELF. You probably meant to open it against your own website repo.
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---
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FOR THE TEMPLATE MAINTAINER(S)
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New template version checklist:
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- [ ] I have updated CITATION and CHANGELOG as appropriate.
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- [ ] I have updated lab-website-template-docs as appropriate.
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- [ ] 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.
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See its documentation for working with this site:
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https://greene-lab.gitbook.io/lab-website-template-docs

‎.github/workflows/build-preview.yaml‎

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name: build-preview
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run-name: build pull request preview
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on:
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# run when called from another workflow
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workflow_call:
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# run if user manually requests it
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workflow_dispatch:
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# variables
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env:
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PREVIEWS_FOLDER: preview
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permissions:
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contents: write
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pull-requests: write
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jobs:
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build-preview:
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runs-on: ubuntu-latest
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steps:
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- name: Debug dump
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if: runner.debug == '1'
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uses: crazy-max/ghaction-dump-context@v2
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- name: Checkout branch contents
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if: github.event.action != 'closed'
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uses: actions/checkout@v4
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with:
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repository: ${{ github.event.pull_request.head.repo.full_name }}
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ref: ${{ github.head_ref }}
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- name: Install Ruby packages
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if: github.event.action != 'closed'
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: "3.1"
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bundler-cache: true
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- name: Get Pages url
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if: github.event.action != 'closed'
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id: pages
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uses: actions/configure-pages@v4
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- name: SSH debug
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if: runner.debug == '1'
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uses: mxschmitt/action-tmate@v3
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- name: Build preview version of site
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if: github.event.action != 'closed'
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run: |
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JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}/${{ env.PREVIEWS_FOLDER }}/pr-${{ github.event.number }}"
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- name: Commit preview to Pages branch
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if: github.event.action != 'closed'
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uses: rossjrw/pr-preview-action@v1.4.7
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with:
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source-dir: _site
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umbrella-dir: ${{ env.PREVIEWS_FOLDER }}
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- name: Checkout Pages branch
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uses: actions/checkout@v4
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with:
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ref: gh-pages
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- name: Clean up preview folders
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uses: actions/github-script@v7
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with:
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script: |
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const { rm } = require("fs").promises;
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const { PREVIEWS_FOLDER } = process.env;
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const { owner, repo } = context.repo;
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const prs = (await github.rest.pulls.list({ owner, repo, state: "closed" })).data;
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for (const { number } of prs)
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await rm(`${PREVIEWS_FOLDER}/pr-${number}`, { recursive: true, force: true });
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- name: Commit changed files
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uses: stefanzweifel/git-auto-commit-action@v5
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with:
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branch: gh-pages
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commit_message: "Clean up previews"

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