init commit

Author: xhd0728

.bundle/config

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+---
+BUNDLE_BUILD__POSIX___SPAWN: "--with-cflags=-Wno-incompatible-function-pointer-types"

.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:
+
+  # push to dev branch
+  push:
+    branches:
+      - dev
+
+# variables
+env:
+  PREVIEWS_FOLDER: preview
+
+permissions:
+  contents: write
+
+jobs:
+  build-site:
+    runs-on: ubuntu-22.04
+
+    steps:
+      # for debugging
+      - uses: crazy-max/ghaction-dump-context@v2
+
+      - name: Checkout branch contents
+        uses: actions/checkout@v4
+
+      - name: Install Ruby packages
+        uses: ruby/[email protected]
+        with:
+          ruby-version: "3.3"
+          bundler-cache: true
+
+      - name: Get Pages url
+        id: pages
+        uses: actions/configure-pages@v4
+
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
+
+      - name: Set root url
+        run: |
+          printf "\n\nurl: ${{ steps.pages.outputs.origin }}" >> _config.yaml
+
+      - name: Build live version of site
+        run: |
+          JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}"
+
+      - name: Commit live site to Pages branch
+        uses: JamesIves/[email protected]
+        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-22.04
+
+    steps:
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
+
+      - 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@v4
+        with:
+          ref: gh-pages
+
+      - name: SSH debug
+        if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
+
+      # 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: printf "Placeholder homepage" > index.html
+
+      - name: Commit changes to Pages branch
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          branch: gh-pages
+          commit_message: "Clear branch"
+
+      - name: Checkout main branch
+        uses: actions/checkout@v4
+
+      - name: Remove files user doesn't need
+        run: |
+          rm -rf \
+            CHANGELOG.md \
+            testbed.md \
+            .github/ISSUE_TEMPLATE \
+            .github/DISCUSSION_TEMPLATE \
+            .github/workflows/versioning.yaml \
+            .github/pull_request_template.md \
+
+      - name: Commit changed files
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "Setup repo"

.github/workflows/on-pages.yaml

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+name: on-pages
+run-name: on pages deploy
+
+on:
+  workflow_run:
+    workflows: [pages-build-deployment]
+    types:
+      - completed
+    branches:
+      - gh-pages
+
+  # run if user manually requests it
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  update-url:
+    # only run on user instance of template, not template itself
+    if: github.repository != 'greenelab/lab-website-template'
+    uses: ./.github/workflows/update-url.yaml
+
+  build-site:
+    needs: update-url
+    if: needs.update-url.outputs.changed == 'true'
+    uses: ./.github/workflows/build-site.yaml

.github/workflows/update-url.yaml

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+name: update-url
+run-name: update site after url change
+
+on:
+  # run when called from another workflow
+  workflow_call:
+    outputs:
+      changed:
+        value: ${{ jobs.update-url.outputs.changed }}
+
+  # run if user manually requests it
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  update-url:
+    runs-on: ubuntu-22.04
+
+    steps:
+      # for debugging
+      - uses: crazy-max/ghaction-dump-context@v2
+
+      - name: Get Pages url
+        id: pages
+        uses: actions/configure-pages@v4
+
+      - name: Checkout branch contents
+        uses: actions/checkout@v4
+
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
+
+      # update link to site in readme
+      - name: Update readme
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const { readFileSync, writeFileSync } = require("fs");
+            const file = "README.md";
+            let contents = readFileSync(file).toString();
+            const find = /\*\*\[.*\]\(.*\)\*\*/;
+            const host = "${{ steps.pages.outputs.host }}";
+            const path = "${{ steps.pages.outputs.base_path }}";
+            const url = "${{ steps.pages.outputs.base_url }}";
+            const replace = `**[${host}${path}](${url})**`;
+            if (contents.match(find))
+              contents = contents.replace(find, replace);
+            else
+              contents = `Visit ${replace} 🚀\n\n` + contents;
+            writeFileSync(file, contents);
+
+      - name: Check if readme changed
+        id: changed
+        uses: tj-actions/verify-changed-files@v18
+        with:
+          files: |
+            README.md
+
+      - name: Commit changed files
+        if: steps.changed.outputs.files_changed == 'true'
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "Update url"
+
+    outputs:
+      changed: ${{ steps.changed.outputs.files_changed }}

.gitignore

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+_site
+.sass-cache
+.jekyll-cache
+.jekyll-metadata
+vendor
+debug.log
+__pycache__
+.cache
+!cache.db
+.DS_STORE
+.env*
+package.json
+package-lock.json
+yarn.lock
+node_modules

404.md

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+---
+title: 404
+permalink: /404.html
+---
+
+## {% include icon.html icon="fa-solid fa-heart-crack" %} Page Not Found
+
+Try searching the whole site for the content you want:
+{:.center}
+
+{% include site-search.html %}

CITATION.cff

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+# citation metadata for the template itself
+
+title: "NEUIR Lab"
+version: 2.0
+date-released: 2024-09-25
+url: "https://github.com/NEUIR/neuir.github.io"
+authors:
+  - family-names: "Xin"
+    given-names: "Haidong"
+cff-version: 2.0

Gemfile

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+source "https://rubygems.org"
+
+# jekyll
+gem "jekyll", "~> 4.3"
+gem "webrick", "~> 1.7"
+gem "html-proofer", "~> 5.0"
+
+# plugins
+group :jekyll_plugins do
+  gem "jekyll-spaceship"
+  gem "jekyll-sitemap"
+  gem "jekyll-redirect-from"
+  gem "jekyll-feed"
+  gem "jekyll-last-modified-at"
+end