app.py                         Streamlit atlas — combo explorer, causal-test caveat, rankings
mcp_server/                    live-data MCP server (NASA POWER + BigQuery, not the frozen CSV)
data/
  eu_eea_pilot_panel.csv       joined country-year-combo panel (join_panel.py's output)
  validation_baseline.json     accepted "known good" snapshot for the eval-gate pipeline
  raw/                         gitignored raw pulls (ECDC, NASA POWER, ESAC-Net, EPI)
validation_runs/               timestamped JSON logs from validate_pipeline.py runs
docs/
  phase1_access_check.md       access-verification memo
  phase3_scoping.md            causal-design scoping, grounded in the real pilot data
  phase4_scoping.md            scale-up fork (WHO GLASS vs. BigQuery vs. deepen EU/EEA) + genomic cross-check
  paper.md                     full write-up: methods, bugs found and fixed, results
src/amr_climate_atlas/
  config.py                    country lists, centroids, DOIs, ECDC/NASA POWER/BigQuery constants
  fetch_ears_net.py            EARS-Net resistance rates via ECDC Atlas (fully scriptable, see below)
  fetch_esac_net.py            antibiotic-consumption confounder (static XLSX annexes, 2010-2022)
  fetch_weather_anomaly.py     daily weather per EU/EEA country centroid (NASA POWER)
  fetch_confounders.py         EPI 2024 tabular confounder from Harvard Dataverse
  join_panel.py                joins resistance + weather + EPI into the country-year panel
  stage3_identification.py     two-way FE model + mandatory permutation test + lag check, per combo
  compare_genomic_phenotypic.py genomic (BigQuery) vs. phenotypic (EARS-Net) cross-check
  validate_pipeline.py         automated eval-gate: rerun + placebo-sanity-check + baseline drift check
.github/workflows/validate.yml ready-to-run CI (fires once this repo is pushed to GitHub)

python3 -m venv .venv && source .venv/bin/activate
pip install -r requirements.txt

PYTHONPATH=src python -m amr_climate_atlas.fetch_ears_net        # ECDC EARS-Net resistance rates
PYTHONPATH=src python -m amr_climate_atlas.fetch_esac_net        # antibiotic consumption confounder
PYTHONPATH=src python -m amr_climate_atlas.fetch_weather_anomaly # NASA POWER, EU/EEA centroids
PYTHONPATH=src python -m amr_climate_atlas.fetch_confounders     # EPI 2024 from Dataverse
PYTHONPATH=src python -m amr_climate_atlas.join_panel            # join panel
PYTHONPATH=src python -m amr_climate_atlas.stage3_identification # causal model + permutation test

streamlit run app.py                                            # the live atlas