Environment Setup

Environment Setup#

This guide will walk you through setting up your environment for automated systematic literature searches.

Prerequisites Check#

Before we begin, let’s check what you need:

âś… Required

  • Python 3.7 or higher

  • Package manager (conda/pip)

  • Code editor (VS Code recommended)

  • Internet connection

đź“š Optional but Helpful

  • Git (for version control)

  • API keys (Scopus, IEEE)

  • Institutional database access

Step 1: Install Python Environment Manager#

If you already have Anaconda, Miniconda, Miniforge, or Mamba installed, you can skip to Step 2.

Option B: Anaconda (Alternative)#

Download from anaconda.com/download and follow the installation wizard.

Step 2: Install Code Editor#

Step 3: Create Virtual Environment#

Virtual environments keep your project dependencies isolated. Let’s create one for our systematic review tools.

Open Your Terminal#

Windows:

  • If you added conda to PATH: Use PowerShell, Command Prompt, or Windows Terminal

  • If not: Search for “Miniforge Prompt” in Start menu

macOS/Linux:

  • Open Terminal application

Create the Environment#

# Create a new environment named 'autosearch' with Python 3.10
conda create -n autosearch python=3.10 -y

# Activate the environment
conda activate autosearch

You should see (autosearch) appear in your terminal prompt:

(autosearch) C:\Users\YourName>

Environment Activation

You’ll need to activate this environment every time you start a new terminal session:

conda activate autosearch

Step 4: Install Review Buddy#

Review Buddy is a production-ready toolkit for systematic reviews with a simple 3-step workflow.

Clone the Repository#

# Clone from GitHub
git clone https://github.com/leonardozaggia/review_buddy.git
cd review_buddy

Or download the ZIP file from GitHub and extract it.

Install Dependencies#

# Install required packages
pip install -r requirements.txt

This installs:

  • Core dependencies (requests, lxml, beautifulsoup4, tqdm, bibtexparser)

  • Optional: scholarly (Google Scholar), langdetect (language filtering)

Configure API Keys#

# Create .env file from template
cp .env.example .env

The .env file is already added to .gitignore to keep your keys private!

Edit .env file with your API keys (at least one required):

# Recommended: Scopus (best coverage)
SCOPUS_API_KEY=your_scopus_key_here

# Recommended: PubMed (biomedical papers)
PUBMED_EMAIL=your.email@example.com

# Optional but helpful
UNPAYWALL_EMAIL=your.email@example.com
IEEE_API_KEY=your_ieee_key_here

Verify Installation#

# Run a quick test
python 01_fetch_metadata.py

You should see available sources listed. See the Review Buddy Installation Guide for detailed setup instructions.

Step 5: Database API Keys (Optional)#

Some databases require API keys for full access. Here’s how to obtain them:

Scopus API Key#

  1. Visit Elsevier Developer Portal

  2. Create an account or log in

  3. Navigate to “My API Key”

  4. Request an API key (may require institutional email)

IEEE Xplore API Key#

  1. Visit IEEE Developer Portal

  2. Create an account or log in

  3. Navigate to “My APIs”

  4. Request an API key (usually instant approval)

Storing API Keys

To store your API keys as environment variables:

Windows (PowerShell):

$env:IEEE_TOKEN = "your-ieee-api-key"
$env:SCOPUS_TOKEN = "your-scopus-api-key"

macOS/Linux:

export IEEE_TOKEN="your-ieee-api-key"
export SCOPUS_TOKEN="your-scopus-api-key"

For permanent storage, add these to your .bashrc, .zshrc, or PowerShell profile.

This step is optional, you can rely on the .env file -> see Step 4.

Step 6: Verify Your Setup#

Let’s run a quick test to ensure everything is working:

Troubleshooting#

Common Issues#

❌ “conda not recognized”

Solution:

  • Use Miniforge Prompt instead of regular terminal

  • OR reinstall with “Add to PATH” option checked

❌ “Permission denied”

Solution:

  • Run terminal as Administrator (Windows)

  • Use sudo on macOS/Linux

  • Check firewall/antivirus settings

Quick Reference Card#

# Activate environment
conda activate autosearch

# Check findpapers version
findpapers version

# View available commands
findpapers --help

# Deactivate environment (when done)
conda deactivate

What’s Next?#

🎉 Congratulations! Your environment is ready. Choose your path:

➡️ Review Buddy Tutorial - Production-ready 3-step workflow with advanced filtering

Additional Resources#

Need Help?

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