Setup and Troubleshooting

Reference for installing dependencies and diagnosing common failures.

Installation

cd skills/documentation/research/pubmed-search
uv venv
source .venv/bin/activate
uv pip install -r requirements.txt

Alternative: standard venv

cd skills/documentation/research/pubmed-search
python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

Verify

python3 scripts/pubmed_search.py --help

Activating the environment

Every shell session requires activating the venv before running the script:

source skills/documentation/research/pubmed-search/.venv/bin/activate

Optional: API Key Configuration

The script works without an API key using the free PubMed E-utilities API. For higher rate limits, obtain a free key at ncbi.nlm.nih.gov/account and set these environment variables (or add to a .env file in the skill root):

export PUBMED_API_KEY="your-api-key-here"
export PUBMED_EMAIL="your-email@example.com"

Rate limits:

  • Without API key: 3 requests per second
  • With API key: up to 10 requests per second

Troubleshooting

HTTP 429 / rate limit

PubMed rate-limits unauthenticated requests. If you receive a 429:

  1. Wait 30 seconds and retry once.
  2. If still failing, set PUBMED_API_KEY (see above).
  3. Alternatively, configure the PubTator MCP server (see SKILL.md When Not to Use).
  4. Do not retry in a loop — it extends the cooldown.

Empty result set on a valid query

If the search URL is correct but returns zero PMIDs, verify the query manually:

curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CRISPR&retmax=5&retmode=xml"

If the response contains <Count>0</Count>, the query genuinely returns no results. Broaden your search terms.

PDF download returns “not open access”

Only articles with a PubMed Central (PMC) ID and an open-access licence can be downloaded automatically. For other articles, the script returns a direct PubMed URL where you can check access options.

requests import error

If the script fails with ModuleNotFoundError: No module named 'requests', the venv is not activated or dependencies are not installed:

source .venv/bin/activate
pip install -r requirements.txt

Wrong Python version

The script requires Python 3.10+. Check with:

python3 --version

If below 3.8, use mise or pyenv to install a compatible version.

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