@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/geopandas/references/data-structures.md

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+# GeoPandas Data Structures
+
+## GeoSeries
+
+A GeoSeries is a vector where each entry is a set of shapes corresponding to one observation (similar to a pandas Series but with geometric data).
+
+```python
+import geopandas as gpd
+from shapely.geometry import Point, Polygon
+
+# Create a GeoSeries from geometries
+points = gpd.GeoSeries([Point(1, 1), Point(2, 2), Point(3, 3)])
+
+# Access geometric properties
+points.area
+points.length
+points.bounds
+```
+
+## GeoDataFrame
+
+A GeoDataFrame is a tabular data structure that contains a GeoSeries (similar to a pandas DataFrame but with geographic data).
+
+```python
+# Create from dictionary
+gdf = gpd.GeoDataFrame({
+    'name': ['Point A', 'Point B'],
+    'value': [100, 200],
+    'geometry': [Point(1, 1), Point(2, 2)]
+})
+
+# Create from pandas DataFrame with coordinates
+import pandas as pd
+df = pd.DataFrame({'x': [1, 2, 3], 'y': [1, 2, 3], 'name': ['A', 'B', 'C']})
+gdf = gpd.GeoDataFrame(df, geometry=gpd.points_from_xy(df.x, df.y))
+```
+
+## Key Properties
+
+- **geometry**: The active geometry column (can have multiple geometry columns)
+- **crs**: Coordinate reference system
+- **bounds**: Bounding box of all geometries
+- **total_bounds**: Overall bounding box
+
+## Setting Active Geometry
+
+When a GeoDataFrame has multiple geometry columns:
+
+```python
+# Set active geometry column
+gdf = gdf.set_geometry('other_geom_column')
+
+# Check active geometry column
+gdf.geometry.name
+```
+
+## Indexing and Selection
+
+Use standard pandas indexing with spatial data:
+
+```python
+# Select by label
+gdf.loc[0]
+
+# Boolean indexing
+large_areas = gdf[gdf.area > 100]
+
+# Select columns
+gdf[['name', 'geometry']]
+```

package/bin/skills/geopandas/references/geometric-operations.md

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+# Geometric Operations
+
+GeoPandas provides extensive geometric manipulation through Shapely integration.
+
+## Constructive Operations
+
+Create new geometries from existing ones:
+
+### Buffer
+
+Create geometries representing all points within a distance:
+
+```python
+# Buffer by fixed distance
+buffered = gdf.geometry.buffer(10)
+
+# Negative buffer (erosion)
+eroded = gdf.geometry.buffer(-5)
+
+# Buffer with resolution parameter
+smooth_buffer = gdf.geometry.buffer(10, resolution=16)
+```
+
+### Boundary
+
+Get lower-dimensional boundary:
+
+```python
+# Polygon -> LineString, LineString -> MultiPoint
+boundaries = gdf.geometry.boundary
+```
+
+### Centroid
+
+Get center point of each geometry:
+
+```python
+centroids = gdf.geometry.centroid
+```
+
+### Convex Hull
+
+Smallest convex polygon containing all points:
+
+```python
+hulls = gdf.geometry.convex_hull
+```
+
+### Concave Hull
+
+Smallest concave polygon containing all points:
+
+```python
+# ratio parameter controls concavity (0 = convex hull, 1 = most concave)
+concave_hulls = gdf.geometry.concave_hull(ratio=0.5)
+```
+
+### Envelope
+
+Smallest axis-aligned rectangle:
+
+```python
+envelopes = gdf.geometry.envelope
+```
+
+### Simplify
+
+Reduce geometric complexity:
+
+```python
+# Douglas-Peucker algorithm with tolerance
+simplified = gdf.geometry.simplify(tolerance=10)
+
+# Preserve topology (prevents self-intersections)
+simplified = gdf.geometry.simplify(tolerance=10, preserve_topology=True)
+```
+
+### Segmentize
+
+Add vertices to line segments:
+
+```python
+# Add vertices with maximum segment length
+segmented = gdf.geometry.segmentize(max_segment_length=5)
+```
+
+### Union All
+
+Combine all geometries into single geometry:
+
+```python
+# Union all features
+unified = gdf.geometry.union_all()
+```
+
+## Affine Transformations
+
+Mathematical transformations of coordinates:
+
+### Rotate
+
+```python
+# Rotate around origin (0, 0) by angle in degrees
+rotated = gdf.geometry.rotate(angle=45, origin='center')
+
+# Rotate around custom point
+rotated = gdf.geometry.rotate(angle=45, origin=(100, 100))
+```
+
+### Scale
+
+```python
+# Scale uniformly
+scaled = gdf.geometry.scale(xfact=2.0, yfact=2.0)
+
+# Scale with origin
+scaled = gdf.geometry.scale(xfact=2.0, yfact=2.0, origin='center')
+```
+
+### Translate
+
+```python
+# Shift coordinates
+translated = gdf.geometry.translate(xoff=100, yoff=50)
+```
+
+### Skew
+
+```python
+# Shear transformation
+skewed = gdf.geometry.skew(xs=15, ys=0, origin='center')
+```
+
+### Custom Affine Transform
+
+```python
+from shapely import affinity
+
+# Apply 6-parameter affine transformation matrix
+# [a, b, d, e, xoff, yoff]
+transformed = gdf.geometry.affine_transform([1, 0, 0, 1, 100, 50])
+```
+
+## Geometric Properties
+
+Access geometric properties (returns pandas Series):
+
+```python
+# Area
+areas = gdf.geometry.area
+
+# Length/perimeter
+lengths = gdf.geometry.length
+
+# Bounding box coordinates
+bounds = gdf.geometry.bounds  # Returns DataFrame with minx, miny, maxx, maxy
+
+# Total bounds for entire GeoSeries
+total_bounds = gdf.geometry.total_bounds  # Returns array [minx, miny, maxx, maxy]
+
+# Check geometry types
+geom_types = gdf.geometry.geom_type
+
+# Check if valid
+is_valid = gdf.geometry.is_valid
+
+# Check if empty
+is_empty = gdf.geometry.is_empty
+```
+
+## Geometric Relationships
+
+Binary predicates testing relationships:
+
+```python
+# Within
+gdf1.geometry.within(gdf2.geometry)
+
+# Contains
+gdf1.geometry.contains(gdf2.geometry)
+
+# Intersects
+gdf1.geometry.intersects(gdf2.geometry)
+
+# Touches
+gdf1.geometry.touches(gdf2.geometry)
+
+# Crosses
+gdf1.geometry.crosses(gdf2.geometry)
+
+# Overlaps
+gdf1.geometry.overlaps(gdf2.geometry)
+
+# Covers
+gdf1.geometry.covers(gdf2.geometry)
+
+# Covered by
+gdf1.geometry.covered_by(gdf2.geometry)
+```
+
+## Point Extraction
+
+Extract specific points from geometries:
+
+```python
+# Representative point (guaranteed to be within geometry)
+rep_points = gdf.geometry.representative_point()
+
+# Interpolate point along line at distance
+points = line_gdf.geometry.interpolate(distance=10)
+
+# Interpolate point at normalized distance (0 to 1)
+midpoints = line_gdf.geometry.interpolate(distance=0.5, normalized=True)
+```
+
+## Delaunay Triangulation
+
+```python
+# Create triangulation
+triangles = gdf.geometry.delaunay_triangles()
+```

package/bin/skills/geopandas/references/spatial-analysis.md

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+# Spatial Analysis
+
+## Attribute Joins
+
+Combine datasets based on common variables using standard pandas merge:
+
+```python
+# Merge on common column
+result = gdf.merge(df, on='common_column')
+
+# Left join
+result = gdf.merge(df, on='common_column', how='left')
+
+# Important: Call merge on GeoDataFrame to preserve geometry
+# This works: gdf.merge(df, ...)
+# This doesn't: df.merge(gdf, ...) # Returns DataFrame, not GeoDataFrame
+```
+
+## Spatial Joins
+
+Combine datasets based on spatial relationships.
+
+### Binary Predicate Joins (sjoin)
+
+Join based on geometric predicates:
+
+```python
+# Intersects (default)
+joined = gpd.sjoin(gdf1, gdf2, how='inner', predicate='intersects')
+
+# Available predicates
+joined = gpd.sjoin(gdf1, gdf2, predicate='contains')
+joined = gpd.sjoin(gdf1, gdf2, predicate='within')
+joined = gpd.sjoin(gdf1, gdf2, predicate='touches')
+joined = gpd.sjoin(gdf1, gdf2, predicate='crosses')
+joined = gpd.sjoin(gdf1, gdf2, predicate='overlaps')
+
+# Join types
+joined = gpd.sjoin(gdf1, gdf2, how='left')   # Keep all from left
+joined = gpd.sjoin(gdf1, gdf2, how='right')  # Keep all from right
+joined = gpd.sjoin(gdf1, gdf2, how='inner')  # Intersection only
+```
+
+The `how` parameter determines which geometries are retained:
+- **left**: Retains left GeoDataFrame's index and geometry
+- **right**: Retains right GeoDataFrame's index and geometry
+- **inner**: Uses intersection of indices, keeps left geometry
+
+### Nearest Joins (sjoin_nearest)
+
+Join to nearest features:
+
+```python
+# Find nearest neighbor
+nearest = gpd.sjoin_nearest(gdf1, gdf2)
+
+# Add distance column
+nearest = gpd.sjoin_nearest(gdf1, gdf2, distance_col='distance')
+
+# Limit search radius (significantly improves performance)
+nearest = gpd.sjoin_nearest(gdf1, gdf2, max_distance=1000)
+
+# Find k nearest neighbors
+nearest = gpd.sjoin_nearest(gdf1, gdf2, k=5)
+```
+
+## Overlay Operations
+
+Set-theoretic operations combining geometries from two GeoDataFrames:
+
+```python
+# Intersection - keep areas where both overlap
+intersection = gpd.overlay(gdf1, gdf2, how='intersection')
+
+# Union - combine all areas
+union = gpd.overlay(gdf1, gdf2, how='union')
+
+# Difference - areas in first not in second
+difference = gpd.overlay(gdf1, gdf2, how='difference')
+
+# Symmetric difference - areas in either but not both
+sym_diff = gpd.overlay(gdf1, gdf2, how='symmetric_difference')
+
+# Identity - intersection + difference
+identity = gpd.overlay(gdf1, gdf2, how='identity')
+```
+
+Result includes attributes from both input GeoDataFrames.
+
+## Dissolve (Aggregation)
+
+Aggregate geometries based on attribute values:
+
+```python
+# Dissolve by attribute
+dissolved = gdf.dissolve(by='region')
+
+# Dissolve with aggregation functions
+dissolved = gdf.dissolve(by='region', aggfunc='sum')
+dissolved = gdf.dissolve(by='region', aggfunc={'population': 'sum', 'area': 'mean'})
+
+# Dissolve all into single geometry
+dissolved = gdf.dissolve()
+
+# Preserve internal boundaries
+dissolved = gdf.dissolve(by='region', as_index=False)
+```
+
+## Clipping
+
+Clip geometries to boundary of another geometry:
+
+```python
+# Clip to polygon boundary
+clipped = gpd.clip(gdf, boundary_polygon)
+
+# Clip to another GeoDataFrame
+clipped = gpd.clip(gdf, boundary_gdf)
+```
+
+## Appending
+
+Combine multiple GeoDataFrames:
+
+```python
+import pandas as pd
+
+# Concatenate GeoDataFrames (CRS must match)
+combined = pd.concat([gdf1, gdf2], ignore_index=True)
+
+# With keys for identification
+combined = pd.concat([gdf1, gdf2], keys=['source1', 'source2'])
+```
+
+## Spatial Indexing
+
+Improve performance for spatial operations:
+
+```python
+# GeoPandas uses spatial index automatically for most operations
+# Access the spatial index directly
+sindex = gdf.sindex
+
+# Query geometries intersecting a bounding box
+possible_matches_index = list(sindex.intersection((xmin, ymin, xmax, ymax)))
+possible_matches = gdf.iloc[possible_matches_index]
+
+# Query geometries intersecting a polygon
+possible_matches_index = list(sindex.query(polygon_geometry))
+possible_matches = gdf.iloc[possible_matches_index]
+```
+
+Spatial indexing significantly speeds up:
+- Spatial joins
+- Overlay operations
+- Queries with geometric predicates
+
+## Distance Calculations
+
+```python
+# Distance between geometries
+distances = gdf1.geometry.distance(gdf2.geometry)
+
+# Distance to single geometry
+distances = gdf.geometry.distance(single_point)
+
+# Minimum distance to any feature
+min_dist = gdf.geometry.distance(point).min()
+```
+
+## Area and Length Calculations
+
+For accurate measurements, ensure proper CRS:
+
+```python
+# Reproject to appropriate projected CRS for area/length calculations
+gdf_projected = gdf.to_crs(epsg=3857)  # Or appropriate UTM zone
+
+# Calculate area (in CRS units, typically square meters)
+areas = gdf_projected.geometry.area
+
+# Calculate length/perimeter (in CRS units)
+lengths = gdf_projected.geometry.length
+```

package/bin/skills/geopandas/references/visualization.md

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+# Mapping and Visualization
+
+GeoPandas provides plotting through matplotlib integration.
+
+## Basic Plotting
+
+```python
+# Simple plot
+gdf.plot()
+
+# Customize figure size
+gdf.plot(figsize=(10, 10))
+
+# Set colors
+gdf.plot(color='blue', edgecolor='black')
+
+# Control line width
+gdf.plot(edgecolor='black', linewidth=0.5)
+```
+
+## Choropleth Maps
+
+Color features based on data values:
+
+```python
+# Basic choropleth
+gdf.plot(column='population', legend=True)
+
+# Specify colormap
+gdf.plot(column='population', cmap='OrRd', legend=True)
+
+# Other colormaps: 'viridis', 'plasma', 'inferno', 'YlOrRd', 'Blues', 'Greens'
+```
+
+### Classification Schemes
+
+Requires: `uv pip install mapclassify`
+
+```python
+# Quantiles
+gdf.plot(column='population', scheme='quantiles', k=5, legend=True)
+
+# Equal interval
+gdf.plot(column='population', scheme='equal_interval', k=5, legend=True)
+
+# Natural breaks (Fisher-Jenks)
+gdf.plot(column='population', scheme='fisher_jenks', k=5, legend=True)
+
+# Other schemes: 'box_plot', 'headtail_breaks', 'max_breaks', 'std_mean'
+
+# Pass parameters to classification
+gdf.plot(column='population', scheme='quantiles', k=7,
+         classification_kwds={'pct': [10, 20, 30, 40, 50, 60, 70, 80, 90]})
+```
+
+### Legend Customization
+
+```python
+# Position legend outside plot
+gdf.plot(column='population', legend=True,
+         legend_kwds={'loc': 'upper left', 'bbox_to_anchor': (1, 1)})
+
+# Horizontal legend
+gdf.plot(column='population', legend=True,
+         legend_kwds={'orientation': 'horizontal'})
+
+# Custom legend label
+gdf.plot(column='population', legend=True,
+         legend_kwds={'label': 'Population Count'})
+
+# Use separate axes for colorbar
+import matplotlib.pyplot as plt
+fig, ax = plt.subplots(1, 1, figsize=(10, 6))
+divider = make_axes_locatable(ax)
+cax = divider.append_axes("right", size="5%", pad=0.1)
+gdf.plot(column='population', ax=ax, legend=True, cax=cax)
+```
+
+## Handling Missing Data
+
+```python
+# Style missing values
+gdf.plot(column='population',
+         missing_kwds={'color': 'lightgrey', 'edgecolor': 'red', 'hatch': '///',
+                      'label': 'Missing data'})
+```
+
+## Multi-Layer Maps
+
+Combine multiple GeoDataFrames:
+
+```python
+import matplotlib.pyplot as plt
+
+# Create base plot
+fig, ax = plt.subplots(figsize=(10, 10))
+
+# Add layers
+gdf1.plot(ax=ax, color='lightblue', edgecolor='black')
+gdf2.plot(ax=ax, color='red', markersize=5)
+gdf3.plot(ax=ax, color='green', alpha=0.5)
+
+plt.show()
+
+# Control layer order with zorder (higher = on top)
+gdf1.plot(ax=ax, zorder=1)
+gdf2.plot(ax=ax, zorder=2)
+```
+
+## Styling Options
+
+```python
+# Transparency
+gdf.plot(alpha=0.5)
+
+# Marker style for points
+points.plot(marker='o', markersize=50)
+points.plot(marker='^', markersize=100, color='red')
+
+# Line styles
+lines.plot(linestyle='--', linewidth=2)
+lines.plot(linestyle=':', color='blue')
+
+# Categorical coloring
+gdf.plot(column='category', categorical=True, legend=True)
+
+# Vary marker size by column
+gdf.plot(markersize=gdf['value']/1000)
+```
+
+## Map Enhancements
+
+```python
+import matplotlib.pyplot as plt
+
+fig, ax = plt.subplots(figsize=(12, 8))
+gdf.plot(ax=ax, column='population', legend=True)
+
+# Add title
+ax.set_title('Population by Region', fontsize=16)
+
+# Add axis labels
+ax.set_xlabel('Longitude')
+ax.set_ylabel('Latitude')
+
+# Remove axes
+ax.set_axis_off()
+
+# Add north arrow and scale bar (requires separate packages)
+# See geopandas-plot or contextily for these features
+
+plt.tight_layout()
+plt.show()
+```
+
+## Interactive Maps
+
+Requires: `uv pip install folium`
+
+```python
+# Create interactive map
+m = gdf.explore(column='population', cmap='YlOrRd', legend=True)
+m.save('map.html')
+
+# Customize base map
+m = gdf.explore(tiles='OpenStreetMap', legend=True)
+m = gdf.explore(tiles='CartoDB positron', legend=True)
+
+# Add tooltip
+m = gdf.explore(column='population', tooltip=['name', 'population'], legend=True)
+
+# Style options
+m = gdf.explore(color='red', style_kwds={'fillOpacity': 0.5, 'weight': 2})
+
+# Multiple layers
+m = gdf1.explore(color='blue', name='Layer 1')
+gdf2.explore(m=m, color='red', name='Layer 2')
+folium.LayerControl().add_to(m)
+```
+
+## Integration with Other Plot Types
+
+GeoPandas supports pandas plot types:
+
+```python
+# Histogram of attribute
+gdf['population'].plot.hist(bins=20)
+
+# Scatter plot
+gdf.plot.scatter(x='income', y='population')
+
+# Box plot
+gdf.boxplot(column='population', by='region')
+```
+
+## Basemaps with Contextily
+
+Requires: `uv pip install contextily`
+
+```python
+import contextily as ctx
+
+# Reproject to Web Mercator for basemap compatibility
+gdf_webmercator = gdf.to_crs(epsg=3857)
+
+fig, ax = plt.subplots(figsize=(10, 10))
+gdf_webmercator.plot(ax=ax, alpha=0.5, edgecolor='k')
+
+# Add basemap
+ctx.add_basemap(ax, source=ctx.providers.OpenStreetMap.Mapnik)
+# Other sources: ctx.providers.CartoDB.Positron, ctx.providers.Stamen.Terrain
+
+plt.show()
+```
+
+## Cartographic Projections with CartoPy
+
+Requires: `uv pip install cartopy`
+
+```python
+import cartopy.crs as ccrs
+
+# Create map with specific projection
+fig, ax = plt.subplots(subplot_kw={'projection': ccrs.Robinson()}, figsize=(15, 10))
+
+gdf.plot(ax=ax, transform=ccrs.PlateCarree(), column='population', legend=True)
+
+ax.coastlines()
+ax.gridlines(draw_labels=True)
+
+plt.show()
+```
+
+## Saving Figures
+
+```python
+# Save to file
+ax = gdf.plot()
+fig = ax.get_figure()
+fig.savefig('map.png', dpi=300, bbox_inches='tight')
+fig.savefig('map.pdf')
+fig.savefig('map.svg')
+```