Adapt mechanism for citiation count (#3177)
## Summary This PR introduces an automated mechanism to update the citation count for authors' publications. - Inspired by @BernardoCama’s suggestion in #3150. - Resolves #3150. ## Key Changes - Adds an action to update publication citation counts. - Note: This action creates a commit on the main branch. - To trigger further GitHub Actions workflows from this commit, a Personal Access Token (PAT) must be used (the default GitHub Actions token cannot trigger subsequent workflows). - Adds and manages citation data in `_data/citations.yml`. - Adds and adapts `bin/update_scholar_citations.py` to handle citation updates. ## Usage Examples ### Timeout <img width="758" height="415" alt="image" src="https://github.com/user-attachments/assets/0a330d35-b386-4670-8668-62701f2dc68b" /> ### Success <img width="1684" height="857" alt="image" src="https://github.com/user-attachments/assets/44aa0558-e02a-4f00-b8cb-9e0ce16dd53c" />
This commit is contained in:
Dominik Fuchß
GitHub
parent
c38d33b5f8
commit
1f349ffda2
101
.github/workflows/update-citations.yml
vendored
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101
.github/workflows/update-citations.yml
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@ -0,0 +1,101 @@
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name: Update Google Scholar Citations
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on:
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schedule:
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- cron: "0 0 * * 1" # Monday
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- cron: "0 0 * * 3" # Wednesday
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- cron: "0 0 * * 5" # Friday
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workflow_dispatch:
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jobs:
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update-citations:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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# See CUSTOMIZE.md for details on how to set up PAT for triggering subsequent workflows
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# with:
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# token: ${{ secrets.PAT }}
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.13"
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- name: Install dependencies
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run: |
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echo "🔧 Installing dependencies..."
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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- name: Save current citations.yml hash
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id: before
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run: |
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echo "📦 Checking existing citations.yml hash..."
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if [ -f _data/citations.yml ]; then
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sha_before=$(sha256sum _data/citations.yml | awk '{print $1}')
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echo "sha_before=$sha_before" >> $GITHUB_OUTPUT
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echo "📝 SHA before: $sha_before"
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else
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echo "sha_before=none" >> $GITHUB_OUTPUT
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echo "📝 No existing citations.yml file found."
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fi
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- name: Run citation update script
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id: run_citation_update
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shell: bash
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run: |
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set +e
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echo "🚀 Running citation update script (single attempt)..."
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start_time=$(date)
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timeout 90 python bin/update_scholar_citations.py
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status=$?
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end_time=$(date)
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if [ $status -eq 0 ]; then
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echo "✅ Citation update succeeded (started at $start_time, ended at $end_time)."
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echo "✅ Citation update succeeded." >> $GITHUB_STEP_SUMMARY
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else
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echo "❌ Citation update script failed with exit code $status (started at $start_time, ended at $end_time)."
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echo "❌ Citation update script failed with exit code $status." >> $GITHUB_STEP_SUMMARY
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fi
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set -e
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- name: Save new citations.yml hash
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id: after
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run: |
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echo "🔍 Checking updated citations.yml hash..."
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if [ -f _data/citations.yml ]; then
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sha_after=$(sha256sum _data/citations.yml | awk '{print $1}')
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echo "sha_after=$sha_after" >> $GITHUB_OUTPUT
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echo "📝 SHA after: $sha_after"
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else
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echo "sha_after=none" >> $GITHUB_OUTPUT
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echo "📝 citations.yml was not created or is missing."
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fi
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- name: Report citations.yml change in summary
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run: |
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echo "📋 Comparing citation file hashes..."
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if [ "${{ steps.before.outputs.sha_before }}" != "${{ steps.after.outputs.sha_after }}" ]; then
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echo "✅ _data/citations.yml was updated."
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echo "✅ _data/citations.yml was updated." >> $GITHUB_STEP_SUMMARY
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else
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echo "ℹ️ _data/citations.yml was not changed."
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echo "ℹ️ _data/citations.yml was not changed." >> $GITHUB_STEP_SUMMARY
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fi
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- name: Configure Git
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run: |
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git config --local user.email "actions@github.com"
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git config --local user.name "GitHub Actions"
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echo "🔧 Git configured."
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- name: Commit and push if changed
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run: |
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git add _data/citations.yml
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git diff --staged --quiet || (
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echo "📤 Committing and pushing changes..."
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git commit -m "Update Google Scholar citations"
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git push
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)
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3
.gitignore
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3
.gitignore
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@ -10,4 +10,5 @@ Gemfile.lock
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assets/libs/
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node_modules/
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vendor
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.idea
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.idea
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.venv
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@ -10,3 +10,5 @@ _posts/2015-10-20-math.md
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_sass/font-awesome/*.scss
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_sass/tabler-icons/*.scss
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_scripts/*
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# Ignore citation YAML file generated by script
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_data/citations.yml
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44
CUSTOMIZE.md
44
CUSTOMIZE.md
@ -345,3 +345,47 @@ In this folder you need to store your file in the same format as you would in `_
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- `2025-08-27-file2.md` will be posted exactly on 27-August-2025
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- `File3.md` will not be posted at all
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- `2026-02-31-file4.md` is supposed to be posted on 31-February-2026, but there is no 31st in February hence this file will never be posted either
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## Setting up a Personal Access Token (PAT) for Google Scholar Citation Updates
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> [!TIP]
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> After setting up al-folio you may want to run `python3 bin/update_citations.py` to fill the `_data/citations.yml` file with your Google Scholar citation counts.
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This project includes an automated workflow to update the citation counts for your publications using Google Scholar.
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The workflow commits changes to `_data/citations.yml` directly to the `main` branch.
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By default, the `GITHUB_TOKEN` will be used to commit the changes.
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However, this token does not have permission to trigger subsequent workflows, such as the site rebuild workflow.
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In order to deploy the changes from `main`, you can manually trigger the `deploy` workflow.
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> [!TIP]
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> To ensure that these commits can trigger further GitHub Actions workflows (such as site rebuilds), you can use a Personal Access Token (PAT) instead of the default GitHub Actions token.
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> If you have set up a PAT, citation updates will trigger further workflows (such as site rebuilds) after committing changes. In order to run the action with a PAT, you need to uncomment the following lines from the workflow file (`update-citations.yml`):
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>
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> ```yaml
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> with:
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> token: ${{ secrets.PAT }}
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> ```
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### Why is a PAT required?
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GitHub restricts the default `GITHUB_TOKEN` from triggering other workflows when a commit is made from within a workflow. Using a PAT overcomes this limitation and allows for full automation.
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### How to set up the PAT
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1. **Create a Personal Access Token**
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- Go to [GitHub Settings > Developer settings > Personal access tokens](https://github.com/settings/tokens).
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- Click "Generate new token" (classic or fine-grained).
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- Grant at least the following permissions:
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- `repo` (for classic tokens if repo is private), `public_repo` (for classic tokens if repo is public) or `contents: read/write` (for fine-grained tokens)
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- Save the token somewhere safe.
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2. **Add the PAT as a repository secret**
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- Go to your repository on GitHub.
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- Navigate to `Settings` > `Secrets and variables` > `Actions` > `New repository secret`.
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- Name the secret `PAT` (must match the name used in the workflow).
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- Paste your PAT and save.
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3. **Workflow usage**
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The workflow `.github/workflows/update-citations.yml` uses this PAT to commit updates to `_data/citations.yml`.
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4179
_data/citations.yml
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4179
_data/citations.yml
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File diff suppressed because it is too large
Load Diff
@ -317,9 +317,27 @@
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aria-label="Google Scholar link"
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role="button"
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>
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{% assign citation_count = 0 %}
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{% assign scholar_id_key = site.scholar_userid | append: ':' | append: entry.google_scholar_id %}
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{% assign publication_key = entry.google_scholar_id %}
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{% if site.data.citations.papers[scholar_id_key] %}
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{% assign citation_count = site.data.citations.papers[scholar_id_key].citations %}
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{% elsif site.data.citations.papers[publication_key] %}
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{% assign citation_count = site.data.citations.papers[publication_key].citations %}
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{% else %}
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{% for paper in site.data.citations.papers %}
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{% assign paper_key = paper[0] %}
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{% if paper_key contains entry.google_scholar_id %}
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{% assign citation_count = paper[1].citations %}
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{% break %}
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{% endif %}
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{% endfor %}
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{% endif %}
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<img
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src="https://img.shields.io/badge/scholar-{% google_scholar_citations site.data.socials.scholar_userid entry.google_scholar_id %}-4285F4?logo=googlescholar&labelColor=beige"
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alt="{% google_scholar_citations site.data.socials.scholar_userid entry.google_scholar_id %} Google Scholar citations"
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src="https://img.shields.io/badge/scholar-{{ citation_count }}-4285F4?logo=googlescholar&labelColor=beige"
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alt="{{ citation_count }} Google Scholar citations"
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>
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</a>
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{% endif %}
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132
bin/update_scholar_citations.py
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132
bin/update_scholar_citations.py
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#!/usr/bin/env python
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import os
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import sys
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import yaml
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from datetime import datetime
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from scholarly import scholarly
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def load_scholar_user_id() -> str:
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"""Load the Google Scholar user ID from the configuration file."""
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config_file = "_data/socials.yml"
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if not os.path.exists(config_file):
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print(
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f"Configuration file {config_file} not found. Please ensure the file exists and contains your Google Scholar user ID."
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)
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sys.exit(1)
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try:
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with open(config_file, "r") as f:
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config = yaml.safe_load(f)
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scholar_user_id = config.get("scholar_userid")
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if not scholar_user_id:
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print(
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"No 'scholar_userid' found in the configuration file. Please add 'scholar_userid' to _data/socials.yml."
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)
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sys.exit(1)
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return scholar_user_id
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except yaml.YAMLError as e:
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print(
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f"Error parsing YAML file {config_file}: {e}. Please check the file for correct YAML syntax."
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)
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sys.exit(1)
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SCHOLAR_USER_ID: str = load_scholar_user_id()
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OUTPUT_FILE: str = "_data/citations.yml"
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def get_scholar_citations() -> None:
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"""Fetch and update Google Scholar citation data."""
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print(f"Fetching citations for Google Scholar ID: {SCHOLAR_USER_ID}")
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today = datetime.now().strftime("%Y-%m-%d")
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# Check if the output file was already updated today
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if os.path.exists(OUTPUT_FILE):
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try:
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with open(OUTPUT_FILE, "r") as f:
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existing_data = yaml.safe_load(f)
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if (
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existing_data
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and "metadata" in existing_data
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and "last_updated" in existing_data["metadata"]
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):
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print(f"Last updated on: {existing_data['metadata']['last_updated']}")
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if existing_data["metadata"]["last_updated"] == today:
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print("Citations data is already up-to-date. Skipping fetch.")
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return
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except Exception as e:
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print(
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f"Warning: Could not read existing citation data from {OUTPUT_FILE}: {e}. The file may be missing or corrupted."
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)
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citation_data = {"metadata": {"last_updated": today}, "papers": {}}
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scholarly.set_timeout(15)
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scholarly.set_retries(3)
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try:
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author = scholarly.search_author_id(SCHOLAR_USER_ID)
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author_data = scholarly.fill(author)
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except Exception as e:
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print(
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f"Error fetching author data from Google Scholar for user ID '{SCHOLAR_USER_ID}': {e}. Please check your internet connection and Scholar user ID."
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)
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sys.exit(1)
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if not author_data:
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print(
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f"Could not fetch author data for user ID '{SCHOLAR_USER_ID}'. Please verify the Scholar user ID and try again."
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)
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sys.exit(1)
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if "publications" not in author_data:
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print(f"No publications found in author data for user ID '{SCHOLAR_USER_ID}'.")
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sys.exit(1)
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for pub in author_data["publications"]:
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try:
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pub_id = pub.get("pub_id") or pub.get("author_pub_id")
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if not pub_id:
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print(
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f"Warning: No ID found for publication: {pub.get('bib', {}).get('title', 'Unknown')}. This publication will be skipped."
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)
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continue
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title = pub.get("bib", {}).get("title", "Unknown Title")
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year = pub.get("bib", {}).get("pub_year", "Unknown Year")
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citations = pub.get("num_citations", 0)
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print(f"Found: {title} ({year}) - Citations: {citations}")
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citation_data["papers"][pub_id] = {
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"title": title,
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"year": year,
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"citations": citations,
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}
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except Exception as e:
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print(
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f"Error processing publication '{pub.get('bib', {}).get('title', 'Unknown')}': {e}. This publication will be skipped."
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)
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# Compare new data with existing data
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if existing_data and existing_data.get("papers") == citation_data["papers"]:
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print("No changes in citation data. Skipping file update.")
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return
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try:
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with open(OUTPUT_FILE, "w") as f:
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yaml.dump(citation_data, f, width=1000, sort_keys=True)
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print(f"Citation data saved to {OUTPUT_FILE}")
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except Exception as e:
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print(
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f"Error writing citation data to {OUTPUT_FILE}: {e}. Please check file permissions and disk space."
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)
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sys.exit(1)
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if __name__ == "__main__":
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try:
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get_scholar_citations()
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except Exception as e:
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print(f"Unexpected error: {e}")
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sys.exit(1)
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@ -1 +1,3 @@
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nbconvert
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pyyaml
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scholarly
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