Initial commit

.github/workflows/build-pdf.yml

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+name: Build proceeding PDF
+on:
+  push:
+    branches:
+      - master
+
+env:
+ PUB_NAME: ${{ github.event.repository.name }}
+jobs:
+  buildPDF:
+    runs-on: ubuntu-latest
+
+    container:
+      image: agahkarakuzu/bhproceedings@sha256:bfc1b7f3b714b12e04a6a6ef1f440e9f19997ac1bfecc2187f2476cf47c22ab3
+
+    steps:
+     - name: Checkout repository
+       uses: actions/checkout@v2
+     - name: Compile PDF
+       run: |
+        mkdir -p data
+        [ -e data/report.json ] && rm data/report.json
+        [ -e data/ghdetails.json ] && rm data/ghdetails.json
+        m2j report.md >> data/report.json
+        cat <<EOF > data/ghdetails.json
+        {"pub_name" : "${{env.PUB_NAME}}","repo":"$GITHUB_REPOSITORY"}
+        EOF
+        pandoc -s -N --template ./latex/brainhack-report-template.tex report.md -o ./latex/brainhack-${{env.PUB_NAME}}.tex
+        pandoc -s -N --template ./latex/brainhack-html-template.tex report.md -o ./latex/brainhack-${{env.PUB_NAME}}-html.tex
+        cd latex
+        pdflatex brainhack-${{env.PUB_NAME}}.tex
+        bibtex brainhack-${{env.PUB_NAME}}
+        pdflatex brainhack-${{env.PUB_NAME}}.tex
+        pdflatex brainhack-${{env.PUB_NAME}}.tex
+        pandoc brainhack-${{env.PUB_NAME}}-html.tex -f latex -t html -s -o report.html --bibliography ../report.bib
+        cp report.html ../layouts/partials/report.html
+        mkdir -p ../static/pdf
+        cp brainhack-${{env.PUB_NAME}}.pdf ../static/pdf/brainhack-${{env.PUB_NAME}}.pdf
+     - uses: actions/upload-artifact@v2
+       with:
+         name: PDF Report ${{env.PUB_NAME}}
+         path: static/pdf/brainhack-${{env.PUB_NAME}}.pdf
+     - uses: actions/upload-artifact@v2
+       with:
+         name: HTML Report ${{env.PUB_NAME}}
+         path: layouts/partials/report.html
+     - uses: actions/upload-artifact@v2
+       with:
+         name: JSON Report ${{env.PUB_NAME}}
+         path: data/report.json
+     - uses: actions/upload-artifact@v2
+       with:
+         name: JSON GitHub ${{env.PUB_NAME}}
+         path: data/ghdetails.json
+  buildHugo:
+   runs-on: ubuntu-latest
+   needs: buildPDF
+   steps:  
+     - name: Checkout repository
+       uses: actions/checkout@v2
+       with:
+        submodules: true
+        fetch-depth: 0
+     - uses: actions/download-artifact@master
+       with:
+         name: PDF Report ${{env.PUB_NAME}}
+         path: static/pdf
+     - uses: actions/download-artifact@master
+       with:
+         name: HTML Report ${{env.PUB_NAME}}
+         path: layouts/partials
+     - uses: actions/download-artifact@master
+       with:
+         name: JSON Report ${{env.PUB_NAME}}
+         path: data
+     - uses: actions/download-artifact@master
+       with:
+         name: JSON GitHub ${{env.PUB_NAME}}
+         path: data
+     - name: Commit files
+       run: |
+        rsync -r figures/ static
+        git config --local user.email "[email protected]"
+        git config --local user.name "BHBOT"
+        git add static/pdf/brainhack-${{env.PUB_NAME}}.pdf
+        git commit -m "[ADD] 🤖 Compiled PDF" -a
+        ls ./static/pdf
+     - name: Push changes
+       uses: ad-m/github-push-action@master
+       with:
+        github_token: ${{ secrets.PAT_BOT }}   
+     - name: Setup Hugo
+       uses: peaceiris/actions-hugo@v2
+       with:
+         hugo-version: '0.71.1'
+     - name: Build
+       run: hugo --minify
+       env:
+          HUGO_PARAMS_github: ${{github.workspace}}
+     - name: Deploy
+       uses: peaceiris/actions-gh-pages@v3
+       with:
+         github_token: ${{ secrets.PAT_BOT }}
+         publish_dir: ./public

.gitignore

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+public

.gitmodules

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+[submodule "themes/business-frontpage"]
+	path = themes/business-frontpage
+	url = https://github.com/cowboysmall-tools/hugo-business-frontpage-theme.git

README.md

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+<h2 align="center"> STEP 1 - Get the machinery running ⚙️ </h2>
+
+<h3 align="center"> Fork this repository </h3>
+
+<p align="center"><img src="https://github.com/channelCS/github-buttons/blob/master/2x/github_fork.png"></p>
+
+
+<h3 align="center"> Enable actions </h3>
+<h3 align="center"> ✅</h3>
+
+<p align="center">Go to the <code>Actions</code> tab in your forked repo, and click the green button that says "I understand my actions, go ahead and enable them".</p>
+
+
+<h3 align="center">  Create a GitHub access token </h3>
+<h3 align="center"> 🔑 </h3>
+
+<p align="center">Follow <a href="https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token#creating-a-token">these steps</a> and make sure that you check the <b>repo</b>, <b>admin:repo_hook</b> and <b>workflow</b> boxes while creating your access token.</p> 
+
+
+<h3 align="center"> Create an encrypted secret for your repo </h3>
+<h3 align="center"> 🕵️‍♀️ </h3>
+
+
+<p align="center"> Simply follow <a href="https://docs.github.com/en/free-pro-team@latest/actions/reference/encrypted-secrets#creating-encrypted-secrets-for-a-repository">these steps</a>.</p>
+
+<p align="center">  The name of the secret must be <code>PAT_BOT</code> and the value must be the key you obtained from the previous step. </p>
+
+
+<h3 align="center"> Push a dummy change to the <code>master</code> </h3>
+<h3 align="center"> 📤 </h3>
+
+<p align="center"> It can be anything, such as simply editing this <code>README.md</code> file you are reading at the moment. </p>
+
+
+<h3 align="center"> What now ?  </h3>
+<h3 align="center"> 👀 </h3>
+
+<p align="center">After pushing your changes to the <code>master</code> branch, visit the <b>Actions</b> tab of your repository. You should see an action named <b>Build proceeding PDF</b>, which consists of two steps <code>buildPDF</code> and <code>buildHugo</code>.</p>  
+
+<p align="center">Soon after a successful action run, your web page will be deployed. You should see <b>Environments</b> section appeared in your repository (on the right column). In the <b>Environments</b> page, click the <code>View Deployment</code> button to visit your report page! At this stage, it should be identical to the <a href="http://brainhack-proceedings.github.io/template">BrainHack proceedings template webpage</a>.</p>
+
+<p align="center">Unless you change the name of the repo you forked from <code>template</code> to something else, your page will be published at <i>your_GitHub_handle.github.io/template</i>.</p> 
+
+
+## STEP 2 - Edit your report ✍️
+
+
+* Place your figures in the [`figures`](figures) folder. 
+
+* Edit [`report.md`](report.md) file to create your own report. The template markdown will walk you through how to cite references, add figures and equations etc.
+
+* Edit [`report.bib`](report.bib) to add your bibliography in [BibTeX](http://www.bibtex.org/) format.
+
+
+| ⚠️ Warning|
+| :--- |
+|Please do not change the name or the location of [report.md](report.md) and [report.bib](report.bib). Unless you provide an absolute path for your figures, they will be looked for in the `figures` folder.|
+
+
+**Whenever you push your changes to the `master` branch** (either directly or via merging a branch), GitHub actions will be triggered to update your report. That's it! 
+
+If actions run completes successfully, 🟠 (running) will turn into ✅ (success). If your build fails, you will see ❌ instead. In that case, you can read the logs to see what went wrong.

archetypes/default.md

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+---
+title: "{{ replace .Name "-" " " | title }}"
+date: {{ .Date }}
+draft: true
+---
+

config.toml

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+baseURL = "//brainhack-proceedings.github.io/template/"
+languageCode = "en-us"
+title = "BrainHack 2020"
+publishdir = "public"
+theme = "business-frontpage"
+
+[params]
+    author = "OHBM Brainhack 2020"
+    description = "Proceeding page."
+
+    [params.navbar]
+    name = "Ignored"
+    url = "https://ohbm.github.io/hackathon2020/"
+
+   [[params.navbar.nav]]
+    name = "About"
+    url = "https://ohbm.github.io/hackathon2020/"
+
+   [[params.navbar.nav]]
+    name = "Papers"
+    url = "https://brainhack-proceedings.github.io/papers"
+
+   [[params.navbar.nav]]
+    name = "Blog"
+    url = "https://brainhack-proceedings.github.io/blog"
+
+    [[params.navbar.nav]]
+    name = "Submit"
+    url = "https://github.com/brainhack-proceedings/submit"
+
+    [params.header]
+    name = "Brainhack proceedings"
+    tagline = "Brainhack proceedings"
+
+    [params.footer]
+        copyright = "BrainHack"

data/ghdetails.json

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+{"pub_name" : "template","repo":"brainhack-proceedings/template"}

data/report.json

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+{
+  "report": {
+    "event": "OHBM Brainhack 2020",
+    "title": "Title goes here",
+    "author": [
+      {
+        "initials": "JD",
+        "surname": "Doe",
+        "firstname": "Jane",
+        "email": "[email protected]",
+        "affiliation": "aff1, aff2",
+        "corref": "aff1"
+      },
+      {
+        "initials": "JJD",
+        "surname": "Doe",
+        "firstname": "John J.",
+        "email": "[email protected]",
+        "affiliation": "aff2",
+        "url": "https://jonhdoe.website.com"
+      }
+    ],
+    "affiliations": [
+      {
+        "id": "aff1",
+        "orgname": "Research Lab 1, Organization 1",
+        "street": "street_name_goes_here",
+        "postcode": "post_code_goes_here",
+        "city": "Montreal",
+        "state": "Quebec",
+        "country": "Canada"
+      },
+      {
+        "id": "aff2",
+        "orgname": "Research Lab 2, Organization 2",
+        "street": "street_name_goes_here",
+        "postcode": "post_code_goes_here",
+        "city": "Montreal",
+        "state": "Quebec",
+        "country": "Canada"
+      }
+    ],
+    "summary": "Please write a brief summary of your project. This section will appear on the webpage.",
+    "url": "http://github.com/repo_owner/repo_name",
+    "coi": "Please add if there are competing interests. Otherwise, type None.",
+    "acknow": "The authors would like to thank the organizers and attendees of OHBM Brainhack 2020.",
+    "contrib": "JD and JJD wrote the software, JD performed tests, and JD and JJD wrote the report.",
+    "tags": [
+      "tag1",
+      "tag2",
+      "tag3"
+    ],
+    "supplemental": [
+      "Material 1",
+      "Material 2"
+    ],
+    "bibliography": "report",
+    "preview": "# Introduction\nThe bibliography (\\code{report.bib}) must respect …",
+    "basename": "report"
+  }
+}

deploy.sh

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+#!/bin/sh
+
+#DIR=$(dirname "$0")
+
+#cd $DIR/..
+
+if [[ $(git status -s) ]]
+then
+    echo "The working directory is dirty. Please commit any pending changes."
+    exit 1;
+fi
+
+echo "Deleting old publication"
+rm -rf public
+mkdir public
+git worktree prune
+rm -rf .git/worktrees/public/
+
+echo "Checking out gh-pages branch into public"
+git worktree add -B gh-pages public origin/gh-pages
+
+echo "Removing existing files"
+rm -rf public/*
+
+echo "Generating site"
+HUGO_ENV="production" hugo
+
+echo "Updating gh-pages branch"
+cd public && git add --all && git commit -m "Deploy to gh-pages"
+
+echo "pushing to publish"
+git push origin gh-pages -f