scientific-skills/geopandas/SKILL.md
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.
npx skillsauth add K-Dense-AI/claude-scientific-skills geopandasInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
3 of 9 scanners reported clean
Some scanners were skipped, did not run, or reported a non-clean status. Review each row below.
GeoPandas extends pandas to enable spatial operations on geometric types. It combines the capabilities of pandas and shapely for geospatial data analysis.
uv pip install geopandas
# For interactive maps
uv pip install folium
# For classification schemes in mapping
uv pip install mapclassify
# For faster I/O operations (2-4x speedup)
uv pip install pyarrow
# For PostGIS database support
uv pip install psycopg2
uv pip install geoalchemy2
# For basemaps
uv pip install contextily
# For cartographic projections
uv pip install cartopy
import geopandas as gpd
# Read spatial data
gdf = gpd.read_file("data.geojson")
# Basic exploration
print(gdf.head())
print(gdf.crs)
print(gdf.geometry.geom_type)
# Simple plot
gdf.plot()
# Reproject to different CRS
gdf_projected = gdf.to_crs("EPSG:3857")
# Calculate area (use projected CRS for accuracy)
gdf_projected['area'] = gdf_projected.geometry.area
# Save to file
gdf.to_file("output.gpkg")
See data-structures.md for details.
GeoPandas reads/writes multiple formats: Shapefile, GeoJSON, GeoPackage, PostGIS, Parquet.
# Read with filtering
gdf = gpd.read_file("data.gpkg", bbox=(xmin, ymin, xmax, ymax))
# Write with Arrow acceleration
gdf.to_file("output.gpkg", use_arrow=True)
See data-io.md for comprehensive I/O operations.
Always check and manage CRS for accurate spatial operations:
# Check CRS
print(gdf.crs)
# Reproject (transforms coordinates)
gdf_projected = gdf.to_crs("EPSG:3857")
# Set CRS (only when metadata missing)
gdf = gdf.set_crs("EPSG:4326")
See crs-management.md for CRS operations.
Buffer, simplify, centroid, convex hull, affine transformations:
# Buffer by 10 units
buffered = gdf.geometry.buffer(10)
# Simplify with tolerance
simplified = gdf.geometry.simplify(tolerance=5, preserve_topology=True)
# Get centroids
centroids = gdf.geometry.centroid
See geometric-operations.md for all operations.
Spatial joins, overlay operations, dissolve:
# Spatial join (intersects)
joined = gpd.sjoin(gdf1, gdf2, predicate='intersects')
# Nearest neighbor join
nearest = gpd.sjoin_nearest(gdf1, gdf2, max_distance=1000)
# Overlay intersection
intersection = gpd.overlay(gdf1, gdf2, how='intersection')
# Dissolve by attribute
dissolved = gdf.dissolve(by='region', aggfunc='sum')
See spatial-analysis.md for analysis operations.
Create static and interactive maps:
# Choropleth map
gdf.plot(column='population', cmap='YlOrRd', legend=True)
# Interactive map
gdf.explore(column='population', legend=True).save('map.html')
# Multi-layer map
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
gdf1.plot(ax=ax, color='blue')
gdf2.plot(ax=ax, color='red')
See visualization.md for mapping techniques.
# 1. Load data
gdf = gpd.read_file("data.shp")
# 2. Check and transform CRS
print(gdf.crs)
gdf = gdf.to_crs("EPSG:3857")
# 3. Perform analysis
gdf['area'] = gdf.geometry.area
buffered = gdf.copy()
buffered['geometry'] = gdf.geometry.buffer(100)
# 4. Export results
gdf.to_file("results.gpkg", layer='original')
buffered.to_file("results.gpkg", layer='buffered')
# Join points to polygons
points_in_polygons = gpd.sjoin(points_gdf, polygons_gdf, predicate='within')
# Aggregate by polygon
aggregated = points_in_polygons.groupby('index_right').agg({
'value': 'sum',
'count': 'size'
})
# Merge back to polygons
result = polygons_gdf.merge(aggregated, left_index=True, right_index=True)
# Read from different sources
roads = gpd.read_file("roads.shp")
buildings = gpd.read_file("buildings.geojson")
parcels = gpd.read_postgis("SELECT * FROM parcels", con=engine, geom_col='geom')
# Ensure matching CRS
buildings = buildings.to_crs(roads.crs)
parcels = parcels.to_crs(roads.crs)
# Perform spatial operations
buildings_near_roads = buildings[buildings.geometry.distance(roads.union_all()) < 50]
bbox, mask, or where parameters to load only needed datause_arrow=True for 2-4x faster reading/writing.simplify() to reduce complexity when precision isn't critical.is_valid before operations.copy() when modifying geometry columns to avoid side effectstools
--- name: genomic-intelligence description: Predict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights. Six tasks over a REST API and a hosted MCP server (keyless public demo): promoter regions, splice donor/acceptor sites, enhancer activity, chromatin state, sequence-to-expression (log TPM), and de-novo gene annotation, plus a composite find-genes-then-predict-expressi
tools
Use Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and the CLI.
tools
Detect host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a clearly resource-sensitive local workload. Produces a redacted JSON snapshot and conservative planning helpers without stress tests or assuming visible host hardware is usable.
tools
Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.