PubMed Weekly Update Download and Parse

This skill downloads the past week's (Monday-Sunday) PubMed daily update xml.gz files from ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/, parses them with the bundled streaming scripts, and produces ONE combined Excel workbook (combined.xlsx) plus a summary JSON.

Workflow Overview

1. Python environment check: ensure uv is available (install via the bioresearcher-python-setup-uv skill if needed)
2. Date-range calculation: compute the past week's Monday-Sunday range
3. FTP listing + filtering: fetch available xml.gz updatefiles and keep those modified within the week
4. Download with retry + resume: download each filtered file (3 attempts, 2s delay, .part resume)
5. Parse + combine via scripts: parse all downloaded files and produce one Excel workbook
6. Report: verify outputs and summarize to the user

Prerequisites

• Internet connection and access to the NCBI FTP server
• uv package manager (if missing, load the bioresearcher-python-setup-uv skill and follow it EXACTLY, then return here)
• openpyxl is provided at runtime via uv run --with openpyxl