sciagent-skill-creator
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Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, PostGIS), CRS handling, geometric ops (buffer, simplify, centroid, affine), spatial analysis (joins, overlays, dissolve, clipping, distance), visualization
Claude Code
$ npx -y skills add jaechang-hits/SciAgent-Skills --skill geopandas-geospatial --agent claude-code
Codex
$ npx skills add jaechang-hits/SciAgent-Skills --skill geopandas-geospatial -a codex -y
Cursor
$ npx skills add jaechang-hits/SciAgent-Skills --skill geopandas-geospatial -a cursor -y
Gemini CLI
$ npx skills add jaechang-hits/SciAgent-Skills --skill geopandas-geospatial -a gemini-cli -y
GitHub Copilot
$ npx skills add jaechang-hits/SciAgent-Skills --skill geopandas-geospatial -a github-copilot -y
OpenCode
$ npx skills add jaechang-hits/SciAgent-Skills --skill geopandas-geospatial -a opencode -y
Windsurf
$ npx skills add jaechang-hits/SciAgent-Skills --skill geopandas-geospatial -a windsurf -y
name: geopandas-geospatial description: >- Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, PostGIS), CRS handling, geometric ops (buffer, simplify, centroid, affine), spatial analysis (joins, overlays, dissolve, clipping, distance), visualization (choropleth, interactive maps, basemaps). Use for spatial joins, overlays, CRS transforms, area/distance, maps. license: BSD-3-Clause
GeoPandas extends pandas with spatial operations on geometric types, combining pandas DataFrames with Shapely geometries and Fiona for file I/O. It enables reading, writing, manipulating, and visualizing geospatial vector data (points, lines, polygons) with a familiar pandas-like API.
pip install geopandas matplotlib # Optional: # pip install folium — interactive maps # pip install mapclassify — classification schemes for choropleth # pip install contextily — basemaps # pip install pyarrow — faster I/O (2-4x speedup) # pip install psycopg2 geoalchemy2 — PostGIS support
import geopandas as gpd
# Read spatial data
gdf = gpd.read_file("data.geojson")
print(f"Shape: {gdf.shape}, CRS: {gdf.crs}")
print(f"Geometry types: {gdf.geometry.geom_type.unique()}")
# Reproject, compute area, save
gdf_proj = gdf.to_crs("EPSG:3857")
gdf_proj['area_m2'] = gdf_proj.geometry.area
gdf_proj.to_file("output.gpkg")
# Quick map
gdf.plot(column='population', legend=True, figsize=(10, 8))import geopandas as gpd
# Read various formats
gdf = gpd.read_file("data.shp") # Shapefile
gdf = gpd.read_file("data.geojson") # GeoJSON
gdf = gpd.read_file("data.gpkg") # GeoPackage
gdf = gpd.read_file("data.gpkg", layer="roads") # Specific layer
# Filtered reading (load only needed data)
gdf = gpd.read_file("data.gpkg", bbox=(xmin, ymin, xmax, ymax))
gdf = gpd.read_file("data.gpkg", columns=["name", "geometry"])
gdf = gpd.read_file("data.gpkg", where="population > 10000")
# Arrow acceleration (2-4x faster)
gdf = gpd.read_file("data.gpkg", use_arrow=True)
# Parquet/Feather (columnar, fast, preserves CRS)
gdf = gpd.read_parquet("data.parquet")
gdf.to_parquet("output.parquet")
# PostGIS database
from sqlalchemy import create_engine
engine = create_engine("postgresql://user:pass@host/db")
gdf = gpd.read_postgis("SELECT * FROM parcels", con=engine, geom_col='geom')
gdf.to_postgis("output_table", con=engine)
# Write
gdf.to_file("output.gpkg") # GeoPackage (recommended)
gdf.to_file("output.shp") # Shapefile
gdf.to_file("output.geojson", driver="GeoJSON")# Check current CRS
print(gdf.crs) # e.g., EPSG:4326
print(gdf.crs.is_geographic) # True for lat/lon
print(gdf.crs.is_projected) # True for meters
# Reproject (transforms coordinates)
gdf_proj = gdf.to_crs("EPSG:3857") # Web Mercator
gdf_proj = gdf.to_crs(epsg=32633) # UTM zone 33N
# Set CRS (only when metadata missing, does NOT transform coordinates)
gdf = gdf.set_crs("EPSG:4326")
# Estimate appropriate UTM zone
utm_crs = gdf.estimate_utm_crs()
gdf_utm = gdf.to_crs(utm_crs)**Common EPSG codes**:
| Code | Name | Use | |------|------|-----| | 4326 | WGS 84 | GPS coordinates, web data | | 3857 | Web Mercator | Web mapping (Google/OSM tiles) | | 326xx | UTM zones (N) | Area/distance calculations | | 5070 | Albers Equal Area (US) | Area-preserving US maps |
# Buffer (expand/erode geometry by distance) buffered = gdf.geometry.buffer(100) # 100 units (meters if projected) eroded = gdf.geometry.buffer(-50) # Negative = erosion # Simplify (reduce complexity) simplified = gdf.geometry.simplify(tolerance=10, preserve_topology=True) # Centroid, convex hull, envelope centroids = gdf.geometry.centroid hulls = gdf.geometry.convex_hull bounds = gdf.geometry.envelope # Union all geometries unified = gdf.geometry.union_all() # Affine transformations rotated = gdf.geometry.rotate(angle=45, origin='center') scaled = gdf.geometry.scale(xfact=2.0, yfact=2.0) translated = gdf.geometry.translate(xoff=100, yoff=50) # Geometric properties areas = gdf.geometry.area # Use projected CRS for accuracy lengths = gdf.geometry.length # Perimeter for polygons is_valid = gdf.geometry.is_valid # Validate geometry total = gdf.geometry.total_bounds # [minx, miny, maxx, maxy]
# Spatial join (combine datasets by spatial relationship)
joined = gpd.sjoin(points_gdf, polygons_gdf, predicate='intersects')
joined = gpd.sjoin(gdf1, gdf2, predicate='within')
joined = gpd.sjoin(gdf1, gdf2, predicate='contains', how='left')
# Nearest neighbor join
nearest = gpd.sjoin_nearest(gdf1, gdf2, max_distance=1000, distance_col='dist')
# Overlay operations (set-theoretic)
intersection = gpd.overlay(gdf1, gdf2, how='intersection')
union = gpd.overlay(gdf1, gdf2, how='union')
difference = gpd.overlay(gdf1, gdf2, how='difference')
sym_diff = gpd.overlay(gdf1, gdf2, how='symmetric_difference')
# Dissolve (aggregate by attribute)
dissolved = gdf.dissolve(by='region', aggfunc='sum')
dissolved = gdf.dissolve(by='region', aggfunc={'population'Turn your AI coding agent into a life sciences expert — 199 bioinformatics skills for Claude Code covering RNA-seq, single-cell analysis, genomics, proteomics, drug discovery, and more. Boosted BixBench from 65% to 92%. Open source.
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