@pikaa-ai/pikaa 0.3.22 → 0.3.24
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/assets/brand/orbit-logo-option4-whale.jpg +0 -0
- package/assets/brand/orbit-logo.jpg +0 -0
- package/assets/brand/orbit-logo.png +0 -0
- package/assets/brand/orbit-logo.svg +3 -0
- package/dist/cli.js +448 -181
- package/dist/index.js +22 -2
- package/package.json +1 -2
- package/skills/adaptyv/SKILL.md +0 -240
- package/skills/aeon/SKILL.md +0 -402
- package/skills/analytical-method-validation/SKILL.md +0 -299
- package/skills/anndata/SKILL.md +0 -431
- package/skills/arbor/SKILL.md +0 -152
- package/skills/arboreto/SKILL.md +0 -267
- package/skills/astropy/SKILL.md +0 -353
- package/skills/autoskill/SKILL.md +0 -233
- package/skills/benchling-integration/SKILL.md +0 -229
- package/skills/bgpt-paper-search/SKILL.md +0 -75
- package/skills/bids/SKILL.md +0 -237
- package/skills/biopython/SKILL.md +0 -472
- package/skills/bioservices/SKILL.md +0 -399
- package/skills/bulk-rnaseq/SKILL.md +0 -198
- package/skills/cellxgene-census/SKILL.md +0 -283
- package/skills/cirq/SKILL.md +0 -370
- package/skills/citation-management/SKILL.md +0 -329
- package/skills/clinical-decision-support/SKILL.md +0 -238
- package/skills/clinical-decision-support/references/README.md +0 -62
- package/skills/clinical-reports/SKILL.md +0 -248
- package/skills/clinical-reports/references/README.md +0 -34
- package/skills/cobrapy/SKILL.md +0 -496
- package/skills/consciousness-council/SKILL.md +0 -151
- package/skills/dask/SKILL.md +0 -482
- package/skills/database-lookup/SKILL.md +0 -386
- package/skills/datamol/SKILL.md +0 -200
- package/skills/deepchem/SKILL.md +0 -244
- package/skills/deepspot-m/SKILL.md +0 -175
- package/skills/deeptools/SKILL.md +0 -412
- package/skills/depmap/SKILL.md +0 -301
- package/skills/dhdna-profiler/SKILL.md +0 -184
- package/skills/diffdock/SKILL.md +0 -488
- package/skills/dnanexus-integration/SKILL.md +0 -325
- package/skills/docx/SKILL.md +0 -99
- package/skills/esm/SKILL.md +0 -334
- package/skills/etetoolkit/SKILL.md +0 -327
- package/skills/exa-search/SKILL.md +0 -102
- package/skills/executing-plans/SKILL.md +0 -14
- package/skills/experimental-design/SKILL.md +0 -234
- package/skills/exploratory-data-analysis/SKILL.md +0 -280
- package/skills/flowio/SKILL.md +0 -310
- package/skills/fluidsim/SKILL.md +0 -279
- package/skills/frontend-design/SKILL.md +0 -100
- package/skills/generate-image/SKILL.md +0 -304
- package/skills/geniml/SKILL.md +0 -310
- package/skills/genomic-coordinates/SKILL.md +0 -189
- package/skills/genomic-intelligence/SKILL.md +0 -243
- package/skills/geomaster/README.md +0 -105
- package/skills/geomaster/SKILL.md +0 -366
- package/skills/geopandas/SKILL.md +0 -250
- package/skills/get-available-resources/SKILL.md +0 -260
- package/skills/gget/SKILL.md +0 -153
- package/skills/ginkgo-cloud-lab/SKILL.md +0 -106
- package/skills/glycoengineering/SKILL.md +0 -339
- package/skills/gtars/SKILL.md +0 -282
- package/skills/guardian-rails/SKILL.md +0 -54
- package/skills/histolab/SKILL.md +0 -243
- package/skills/hugging-science/SKILL.md +0 -132
- package/skills/hypogenic/SKILL.md +0 -290
- package/skills/hypothesis-generation/SKILL.md +0 -264
- package/skills/imaging-data-commons/SKILL.md +0 -496
- package/skills/infographics/SKILL.md +0 -315
- package/skills/iso-standards-readiness/SKILL.md +0 -352
- package/skills/lab-hardware-cad/SKILL.md +0 -372
- package/skills/labarchive-integration/SKILL.md +0 -216
- package/skills/lamindb/SKILL.md +0 -408
- package/skills/latchbio-integration/SKILL.md +0 -227
- package/skills/latex-posters/SKILL.md +0 -369
- package/skills/latex-posters/references/README.md +0 -439
- package/skills/liteparse/SKILL.md +0 -295
- package/skills/literature-review/SKILL.md +0 -263
- package/skills/markdown-mermaid-writing/SKILL.md +0 -322
- package/skills/market-research-reports/SKILL.md +0 -337
- package/skills/markitdown/SKILL.md +0 -264
- package/skills/matchms/SKILL.md +0 -276
- package/skills/matlab/SKILL.md +0 -274
- package/skills/matplotlib/SKILL.md +0 -378
- package/skills/medchem/SKILL.md +0 -321
- package/skills/modal/SKILL.md +0 -468
- package/skills/molecular-dynamics/SKILL.md +0 -458
- package/skills/molfeat/SKILL.md +0 -348
- package/skills/ncats-arax/SKILL.md +0 -178
- package/skills/networkx/SKILL.md +0 -440
- package/skills/neurokit2/SKILL.md +0 -323
- package/skills/neuropixels-analysis/SKILL.md +0 -412
- package/skills/nextflow/SKILL.md +0 -195
- package/skills/omero-integration/SKILL.md +0 -222
- package/skills/onekgpd/SKILL.md +0 -371
- package/skills/ontology-term-resolution/SKILL.md +0 -147
- package/skills/open-notebook/SKILL.md +0 -297
- package/skills/openpiv/SKILL.md +0 -469
- package/skills/opentrons-integration/SKILL.md +0 -322
- package/skills/optimize-for-gpu/SKILL.md +0 -176
- package/skills/owasp-top10/SKILL.md +0 -48
- package/skills/pacsomatic/LICENSE +0 -21
- package/skills/pacsomatic/SKILL.md +0 -150
- package/skills/paper-lookup/SKILL.md +0 -263
- package/skills/paperclip/SKILL.md +0 -413
- package/skills/paperzilla/SKILL.md +0 -159
- package/skills/parallel-web/SKILL.md +0 -128
- package/skills/pathml/SKILL.md +0 -222
- package/skills/pathogen-variant-surveillance/SKILL.md +0 -208
- package/skills/pathway-enrichment/SKILL.md +0 -194
- package/skills/pdf/SKILL.md +0 -322
- package/skills/peer-review/SKILL.md +0 -288
- package/skills/penetration-testing/SKILL.md +0 -31
- package/skills/pennylane/SKILL.md +0 -240
- package/skills/phylogenetics/SKILL.md +0 -409
- package/skills/pi-agent/SKILL.md +0 -83
- package/skills/pkpd-modeling/SKILL.md +0 -381
- package/skills/polars/SKILL.md +0 -393
- package/skills/polars-bio/SKILL.md +0 -379
- package/skills/ponytail/SKILL.md +0 -31
- package/skills/ponytail-audit/SKILL.md +0 -18
- package/skills/pptx/SKILL.md +0 -246
- package/skills/pptx-posters/SKILL.md +0 -258
- package/skills/primekg/SKILL.md +0 -99
- package/skills/protocolsio-integration/SKILL.md +0 -236
- package/skills/pufferlib/SKILL.md +0 -328
- package/skills/pydeseq2/SKILL.md +0 -369
- package/skills/pydicom/SKILL.md +0 -381
- package/skills/pyhealth/SKILL.md +0 -124
- package/skills/pylabrobot/SKILL.md +0 -216
- package/skills/pymatgen/SKILL.md +0 -404
- package/skills/pymc/SKILL.md +0 -310
- package/skills/pymoo/SKILL.md +0 -276
- package/skills/pyopenms/SKILL.md +0 -179
- package/skills/pysam/SKILL.md +0 -330
- package/skills/pytdc/SKILL.md +0 -297
- package/skills/pytorch-lightning/SKILL.md +0 -191
- package/skills/pyzotero/SKILL.md +0 -137
- package/skills/qiskit/SKILL.md +0 -259
- package/skills/qutip/SKILL.md +0 -317
- package/skills/rdkit/SKILL.md +0 -94
- package/skills/relsa-severity-assessment/SKILL.md +0 -354
- package/skills/research-grants/SKILL.md +0 -296
- package/skills/research-grants/references/README.md +0 -287
- package/skills/research-lookup/README.md +0 -106
- package/skills/research-lookup/SKILL.md +0 -338
- package/skills/rowan/SKILL.md +0 -398
- package/skills/scanpy/SKILL.md +0 -303
- package/skills/scholar-evaluation/SKILL.md +0 -296
- package/skills/scientific-brainstorming/SKILL.md +0 -282
- package/skills/scientific-critical-thinking/SKILL.md +0 -180
- package/skills/scientific-schematics/SKILL.md +0 -370
- package/skills/scientific-slides/SKILL.md +0 -379
- package/skills/scientific-visualization/SKILL.md +0 -285
- package/skills/scientific-writing/SKILL.md +0 -356
- package/skills/scikit-bio/SKILL.md +0 -470
- package/skills/scikit-learn/SKILL.md +0 -324
- package/skills/scikit-survival/SKILL.md +0 -313
- package/skills/scvelo/SKILL.md +0 -328
- package/skills/scvi-tools/SKILL.md +0 -201
- package/skills/seaborn/SKILL.md +0 -254
- package/skills/security-auditor/SKILL.md +0 -37
- package/skills/shap/SKILL.md +0 -282
- package/skills/simpy/SKILL.md +0 -283
- package/skills/stable-baselines3/SKILL.md +0 -325
- package/skills/statistical-analysis/SKILL.md +0 -446
- package/skills/statistical-power/SKILL.md +0 -200
- package/skills/statsmodels/SKILL.md +0 -238
- package/skills/sympy/SKILL.md +0 -354
- package/skills/systematic-debugging/SKILL.md +0 -35
- package/skills/tamarind/SKILL.md +0 -285
- package/skills/tdd/SKILL.md +0 -26
- package/skills/tiledbvcf/SKILL.md +0 -456
- package/skills/timesfm-forecasting/SKILL.md +0 -408
- package/skills/timesfm-forecasting/examples/global-temperature/README.md +0 -178
- package/skills/torch-geometric/SKILL.md +0 -458
- package/skills/torchdrug/SKILL.md +0 -241
- package/skills/transformers/SKILL.md +0 -195
- package/skills/treatment-plans/SKILL.md +0 -174
- package/skills/treatment-plans/references/README.md +0 -19
- package/skills/umap-learn/SKILL.md +0 -488
- package/skills/uncertainty-and-units/SKILL.md +0 -384
- package/skills/usfiscaldata/SKILL.md +0 -171
- package/skills/vaex/SKILL.md +0 -204
- package/skills/venue-templates/SKILL.md +0 -269
- package/skills/verification-before-completion/SKILL.md +0 -22
- package/skills/waypoint-bio/SKILL.md +0 -273
- package/skills/what-if-oracle/SKILL.md +0 -184
- package/skills/writing-plans/SKILL.md +0 -15
- package/skills/xlsx/SKILL.md +0 -110
- package/skills/zarr-python/SKILL.md +0 -241
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---
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name: geomaster
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description: Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, cloud-native workflows (STAC, COG, Planetary Computer), and 8 programming languages (Python, R, Julia, JavaScript, C++, Java, Go, Rust) with 500+ code examples. Use for remote sensing workflows, GIS analysis, spatial ML, Earth observation data processing, terrain analysis, hydrological modeling, marine spatial analysis, atmospheric science, and any geospatial computation task.
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license: MIT License
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metadata:
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version: "1.1"
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skill-author: K-Dense Inc.
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---
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# GeoMaster
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Comprehensive geospatial science skill covering GIS, remote sensing, spatial analysis, and ML for Earth observation across 70+ topics with 500+ code examples in 8 programming languages.
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## Installation
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```bash
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# Core Python stack (conda recommended)
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conda install -c conda-forge gdal rasterio fiona shapely pyproj geopandas
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# Remote sensing & ML
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# Network & visualization
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# Point clouds
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# Databases
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conda install -c conda-forge postgis spatialite
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```
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## Quick Start
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### NDVI from Sentinel-2
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```python
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import rasterio
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import numpy as np
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with rasterio.open('sentinel2.tif') as src:
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red = src.read(4).astype(float) # B04
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nir = src.read(8).astype(float) # B08
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ndvi = (nir - red) / (nir + red + 1e-8)
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ndvi = np.nan_to_num(ndvi, nan=0)
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profile.update(count=1, dtype=rasterio.float32)
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with rasterio.open('ndvi.tif', 'w', **profile) as dst:
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dst.write(ndvi.astype(rasterio.float32), 1)
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```
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### Spatial Analysis with GeoPandas
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```python
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# Load and ensure same CRS
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'value': ['count', 'mean', 'std', 'min', 'max']
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ee.Initialize(project='your-project')
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roi = ee.Geometry.Point([-122.4, 37.7]).buffer(10000)
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.filter(ee.Filter.lt('CLOUDY_PIXEL_PERCENTAGE', 20)))
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def add_ndvi(img):
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## Core Concepts
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### Data Types
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| Vector | Shapefile, GeoJSON, GeoPackage | GeoPandas, Fiona, GDAL |
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| Raster | GeoTIFF, NetCDF, COG | Rasterio, Xarray, GDAL |
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### Coordinate Systems
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```python
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```
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- **WFS**: Web Feature Service - vector data
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- **WCS**: Web Coverage Service - raster coverage
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- **STAC**: Spatiotemporal Asset Catalog - modern metadata
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## Common Operations
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### Spectral Indices
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```python
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def calculate_indices(image_path):
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"""NDVI, EVI, SAVI, NDWI from Sentinel-2."""
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with rasterio.open(image_path) as src:
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ndvi = (B08 - B04) / (B08 + B04 + 1e-8)
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evi = 2.5 * (B08 - B04) / (B08 + 6*B04 - 7.5*B02 + 1)
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savi = ((B08 - B04) / (B08 + B04 + 0.5)) * 1.5
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ndwi = (B03 - B08) / (B03 + B08 + 1e-8)
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return {'NDVI': ndvi, 'EVI': evi, 'SAVI': savi, 'NDWI': ndwi}
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```
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### Vector Operations
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```python
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# Buffer (use projected CRS!)
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gdf_proj = gdf.to_crs(gdf.estimate_utm_crs())
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gdf['buffer_1km'] = gdf_proj.geometry.buffer(1000)
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# Spatial relationships
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intersects = gdf[gdf.geometry.intersects(other_geometry)]
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contains = gdf[gdf.geometry.contains(point_geometry)]
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# Geometric operations
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gdf['centroid'] = gdf.geometry.centroid
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gdf['simplified'] = gdf.geometry.simplify(tolerance=0.001)
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# Overlay operations
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intersection = gpd.overlay(gdf1, gdf2, how='intersection')
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union = gpd.overlay(gdf1, gdf2, how='union')
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```
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### Terrain Analysis
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```python
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def terrain_metrics(dem_path):
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"""Calculate slope, aspect, hillshade from DEM."""
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with rasterio.open(dem_path) as src:
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dem = src.read(1)
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dy, dx = np.gradient(dem)
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|
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slope = np.arctan(np.sqrt(dx**2 + dy**2)) * 180 / np.pi
|
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|
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aspect = (90 - np.arctan2(-dy, dx) * 180 / np.pi) % 360
|
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|
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|
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# Hillshade
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az_rad, alt_rad = np.radians(315), np.radians(45)
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|
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hillshade = (np.sin(alt_rad) * np.sin(np.radians(slope)) +
|
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|
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np.cos(alt_rad) * np.cos(np.radians(slope)) *
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np.cos(np.radians(aspect) - az_rad))
|
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return slope, aspect, hillshade
|
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|
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```
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|
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|
|
199
|
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### Network Analysis
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|
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|
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```python
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import osmnx as ox
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|
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import networkx as nx
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|
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|
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|
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# Download and analyze street network
|
|
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|
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G = ox.graph_from_place('San Francisco, CA', network_type='drive')
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|
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G = ox.add_edge_speeds(G).add_edge_travel_times(G)
|
|
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|
-
|
|
209
|
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# Shortest path
|
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210
|
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orig = ox.distance.nearest_nodes(G, -122.4, 37.7)
|
|
211
|
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dest = ox.distance.nearest_nodes(G, -122.3, 37.8)
|
|
212
|
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route = nx.shortest_path(G, orig, dest, weight='travel_time')
|
|
213
|
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```
|
|
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|
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|
|
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|
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## Image Classification
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|
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|
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|
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```python
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|
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from sklearn.ensemble import RandomForestClassifier
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|
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import rasterio
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|
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from rasterio.features import rasterize
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|
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|
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|
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def classify_imagery(raster_path, training_gdf, output_path):
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"""Train RF and classify imagery."""
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|
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with rasterio.open(raster_path) as src:
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|
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image = src.read()
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profile = src.profile
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|
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transform = src.transform
|
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|
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|
|
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|
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# Extract training data
|
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|
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X_train, y_train = [], []
|
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|
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for _, row in training_gdf.iterrows():
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|
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mask = rasterize([(row.geometry, 1)],
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|
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out_shape=(profile['height'], profile['width']),
|
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|
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transform=transform, fill=0, dtype=np.uint8)
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|
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pixels = image[:, mask > 0].T
|
|
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|
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X_train.extend(pixels)
|
|
237
|
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y_train.extend([row['class_id']] * len(pixels))
|
|
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|
-
|
|
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|
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# Train and predict
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|
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rf = RandomForestClassifier(n_estimators=100, max_depth=20, n_jobs=-1)
|
|
241
|
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rf.fit(X_train, y_train)
|
|
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|
-
|
|
243
|
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prediction = rf.predict(image.reshape(image.shape[0], -1).T)
|
|
244
|
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prediction = prediction.reshape(profile['height'], profile['width'])
|
|
245
|
-
|
|
246
|
-
profile.update(dtype=rasterio.uint8, count=1)
|
|
247
|
-
with rasterio.open(output_path, 'w', **profile) as dst:
|
|
248
|
-
dst.write(prediction.astype(rasterio.uint8), 1)
|
|
249
|
-
|
|
250
|
-
return rf
|
|
251
|
-
```
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|
-
|
|
253
|
-
## Modern Cloud-Native Workflows
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254
|
-
|
|
255
|
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### STAC + Planetary Computer
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|
256
|
-
|
|
257
|
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```python
|
|
258
|
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import pystac_client
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|
259
|
-
import planetary_computer
|
|
260
|
-
import odc.stac
|
|
261
|
-
|
|
262
|
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# Search Sentinel-2 via STAC
|
|
263
|
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catalog = pystac_client.Client.open(
|
|
264
|
-
"https://planetarycomputer.microsoft.com/api/stac/v1",
|
|
265
|
-
modifier=planetary_computer.sign_inplace,
|
|
266
|
-
)
|
|
267
|
-
|
|
268
|
-
search = catalog.search(
|
|
269
|
-
collections=["sentinel-2-l2a"],
|
|
270
|
-
bbox=[-122.5, 37.7, -122.3, 37.9],
|
|
271
|
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datetime="2023-01-01/2023-12-31",
|
|
272
|
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query={"eo:cloud_cover": {"lt": 20}},
|
|
273
|
-
)
|
|
274
|
-
|
|
275
|
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# Load as xarray (cloud-native!)
|
|
276
|
-
data = odc.stac.load(
|
|
277
|
-
list(search.get_items())[:5],
|
|
278
|
-
bands=["B02", "B03", "B04", "B08"],
|
|
279
|
-
crs="EPSG:32610",
|
|
280
|
-
resolution=10,
|
|
281
|
-
)
|
|
282
|
-
|
|
283
|
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# Calculate NDVI on xarray
|
|
284
|
-
ndvi = (data.B08 - data.B04) / (data.B08 + data.B04)
|
|
285
|
-
```
|
|
286
|
-
|
|
287
|
-
### Cloud-Optimized GeoTIFF (COG)
|
|
288
|
-
|
|
289
|
-
```python
|
|
290
|
-
import rasterio
|
|
291
|
-
from rasterio.session import AWSSession
|
|
292
|
-
|
|
293
|
-
# Read COG directly from cloud (partial reads)
|
|
294
|
-
session = AWSSession(aws_access_key_id=..., aws_secret_access_key=...)
|
|
295
|
-
with rasterio.open('s3://bucket/path.tif', session=session) as src:
|
|
296
|
-
# Read only window of interest
|
|
297
|
-
window = ((1000, 2000), (1000, 2000))
|
|
298
|
-
subset = src.read(1, window=window)
|
|
299
|
-
|
|
300
|
-
# Write COG
|
|
301
|
-
with rasterio.open('output.tif', 'w', **profile,
|
|
302
|
-
tiled=True, blockxsize=256, blockysize=256,
|
|
303
|
-
compress='DEFLATE', predictor=2) as dst:
|
|
304
|
-
dst.write(data)
|
|
305
|
-
|
|
306
|
-
# Validate COG
|
|
307
|
-
from rio_cogeo.cogeo import cog_validate
|
|
308
|
-
cog_validate('output.tif')
|
|
309
|
-
```
|
|
310
|
-
|
|
311
|
-
## Performance Tips
|
|
312
|
-
|
|
313
|
-
```python
|
|
314
|
-
# 1. Spatial indexing (10-100x faster queries)
|
|
315
|
-
gdf.sindex # Auto-created by GeoPandas
|
|
316
|
-
|
|
317
|
-
# 2. Chunk large rasters
|
|
318
|
-
with rasterio.open('large.tif') as src:
|
|
319
|
-
for i, window in src.block_windows(1):
|
|
320
|
-
block = src.read(1, window=window)
|
|
321
|
-
|
|
322
|
-
# 3. Dask for big data
|
|
323
|
-
import dask.array as da
|
|
324
|
-
dask_array = da.from_rasterio('large.tif', chunks=(1, 1024, 1024))
|
|
325
|
-
|
|
326
|
-
# 4. Use Arrow for I/O
|
|
327
|
-
gdf.to_file('output.gpkg', use_arrow=True)
|
|
328
|
-
|
|
329
|
-
# 5. GDAL caching
|
|
330
|
-
from osgeo import gdal
|
|
331
|
-
gdal.SetCacheMax(2**30) # 1GB cache
|
|
332
|
-
|
|
333
|
-
# 6. Parallel processing
|
|
334
|
-
rf = RandomForestClassifier(n_jobs=-1) # All cores
|
|
335
|
-
```
|
|
336
|
-
|
|
337
|
-
## Best Practices
|
|
338
|
-
|
|
339
|
-
1. **Always check CRS** before spatial operations
|
|
340
|
-
2. **Use projected CRS** for area/distance calculations
|
|
341
|
-
3. **Validate geometries**: `gdf = gdf[gdf.is_valid]`
|
|
342
|
-
4. **Handle missing data**: `gdf['geometry'] = gdf['geometry'].fillna(None)`
|
|
343
|
-
5. **Use efficient formats**: GeoPackage > Shapefile, Parquet for large data
|
|
344
|
-
6. **Apply cloud masking** to optical imagery
|
|
345
|
-
7. **Preserve lineage** for reproducible research
|
|
346
|
-
8. **Use appropriate resolution** for your analysis scale
|
|
347
|
-
|
|
348
|
-
## Detailed Documentation
|
|
349
|
-
|
|
350
|
-
- **[Coordinate Systems](references/coordinate-systems.md)** - CRS fundamentals, UTM, transformations
|
|
351
|
-
- **[Core Libraries](references/core-libraries.md)** - GDAL, Rasterio, GeoPandas, Shapely
|
|
352
|
-
- **[Remote Sensing](references/remote-sensing.md)** - Satellite missions, spectral indices, SAR
|
|
353
|
-
- **[Machine Learning](references/machine-learning.md)** - Deep learning, CNNs, GNNs for RS
|
|
354
|
-
- **[GIS Software](references/gis-software.md)** - QGIS, ArcGIS, GRASS integration
|
|
355
|
-
- **[Scientific Domains](references/scientific-domains.md)** - Marine, hydrology, agriculture, forestry
|
|
356
|
-
- **[Advanced GIS](references/advanced-gis.md)** - 3D GIS, spatiotemporal, topology
|
|
357
|
-
- **[Big Data](references/big-data.md)** - Distributed processing, GPU acceleration
|
|
358
|
-
- **[Industry Applications](references/industry-applications.md)** - Urban planning, disaster management
|
|
359
|
-
- **[Programming Languages](references/programming-languages.md)** - Python, R, Julia, JS, C++, Java, Go, Rust
|
|
360
|
-
- **[Data Sources](references/data-sources.md)** - Satellite catalogs, APIs
|
|
361
|
-
- **[Troubleshooting](references/troubleshooting.md)** - Common issues, debugging, error reference
|
|
362
|
-
- **[Code Examples](references/code-examples.md)** - 500+ examples
|
|
363
|
-
|
|
364
|
-
---
|
|
365
|
-
|
|
366
|
-
**GeoMaster covers everything from basic GIS operations to advanced remote sensing and machine learning.**
|
|
@@ -1,250 +0,0 @@
|
|
|
1
|
-
---
|
|
2
|
-
name: geopandas
|
|
3
|
-
description: Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.
|
|
4
|
-
license: MIT
|
|
5
|
-
compatibility: Requires Python 3.10+ and uv. Bundled CLIs are local-only; runtime analysis requires the pinned GeoPandas stack below.
|
|
6
|
-
allowed-tools: Read Write Bash Glob Grep
|
|
7
|
-
metadata:
|
|
8
|
-
version: "1.1"
|
|
9
|
-
skill-author: K-Dense Inc.
|
|
10
|
-
last-reviewed: "2026-07-23"
|
|
11
|
-
---
|
|
12
|
-
|
|
13
|
-
# GeoPandas
|
|
14
|
-
|
|
15
|
-
Use GeoPandas for planar vector data represented as pandas-like `GeoSeries` and
|
|
16
|
-
`GeoDataFrame` objects. This skill targets stable **GeoPandas 1.1.4** (released
|
|
17
|
-
2026-06-26), not the unreleased 1.2 documentation.
|
|
18
|
-
|
|
19
|
-
## Reproducible environment
|
|
20
|
-
|
|
21
|
-
GeoPandas 1.1.4 requires Python 3.10+; its tagged source requires NumPy >=1.24,
|
|
22
|
-
pandas >=2.0, Shapely >=2.0, pyproj >=3.5, pyogrio >=0.7.2, and `packaging`.
|
|
23
|
-
This exact Python 3.12 snapshot was smoke-tested on 2026-07-23:
|
|
24
|
-
|
|
25
|
-
```bash
|
|
26
|
-
uv venv --python 3.12
|
|
27
|
-
uv pip install \
|
|
28
|
-
"geopandas==1.1.4" \
|
|
29
|
-
"numpy==2.5.1" \
|
|
30
|
-
"pandas==3.0.5" \
|
|
31
|
-
"shapely==2.1.2" \
|
|
32
|
-
"pyproj==3.7.2" \
|
|
33
|
-
"pyogrio==0.13.0" \
|
|
34
|
-
"pyarrow==25.0.0" \
|
|
35
|
-
"packaging==26.2"
|
|
36
|
-
```
|
|
37
|
-
|
|
38
|
-
Keep optional plotting and PostGIS packages pinned in the project lock as well.
|
|
39
|
-
Do not mix binary geospatial packages from incompatible package channels.
|
|
40
|
-
|
|
41
|
-
## Safety and privacy contract
|
|
42
|
-
|
|
43
|
-
- Treat exact coordinates, addresses, parcel boundaries, trajectories, and
|
|
44
|
-
small-area joins as sensitive. Default reports to counts, categories, coarse
|
|
45
|
-
extents, and redacted identifiers. Generalize before publication.
|
|
46
|
-
- Never automatically load a URL, cloud URI, GDAL `/vsi*` path, archive, or
|
|
47
|
-
geocode an address. Obtain explicit approval, validate provenance and hashes,
|
|
48
|
-
then stage an unpacked local file in an isolated workspace.
|
|
49
|
-
- GDAL/OGR drivers, GEOS, PROJ, pyogrio, Shapely, pyproj, and their wheels are a
|
|
50
|
-
native-code trust boundary. Prefer official wheels/conda-forge, record native
|
|
51
|
-
versions, restrict drivers, and process untrusted data in a sandbox.
|
|
52
|
-
- Do not open macro-enabled office files or nested archives through permissive
|
|
53
|
-
GDAL drivers. The bundled CLIs use an extension allowlist and reject archives.
|
|
54
|
-
- Read only named database secrets such as `GEOPANDAS_POSTGIS_PASSWORD`; use a
|
|
55
|
-
secret manager or scoped environment variable. Never embed a password in a
|
|
56
|
-
URL or source, print an engine/URL, or dump the environment.
|
|
57
|
-
- Every derived artifact needs source hashes/versions, CRS, operation parameters,
|
|
58
|
-
predicate, join cardinality, precision/repair choices, and row-count checks.
|
|
59
|
-
|
|
60
|
-
## Correctness gates
|
|
61
|
-
|
|
62
|
-
Apply these gates before trusting a result:
|
|
63
|
-
|
|
64
|
-
1. **Identity and provenance** — identify the source layer, stable feature key,
|
|
65
|
-
duplicate IDs, row count, geometry column, parser/driver, and content hash.
|
|
66
|
-
2. **Geometry state** — count null, empty, invalid, mixed, Z/M, and collapsed
|
|
67
|
-
geometries separately. `None` is missing; an empty Shapely geometry is real.
|
|
68
|
-
3. **CRS semantics** — require CRS metadata. `set_crs()` assigns metadata;
|
|
69
|
-
`to_crs()` transforms coordinates. Never guess a CRS from coordinate ranges.
|
|
70
|
-
4. **Units and operation** — GeoPandas is planar. Geographic coordinates are
|
|
71
|
-
angular; do not use them directly for buffer, distance, area, nearest joins,
|
|
72
|
-
precision grids, or tolerances. Choose a fit-for-purpose local/equal-area CRS
|
|
73
|
-
or a geodesic method.
|
|
74
|
-
5. **Transform quality** — inspect axis order, area of use, datum pipeline,
|
|
75
|
-
expected accuracy, ballpark status, and missing grids. Keep PROJ network
|
|
76
|
-
disabled unless the user explicitly approves grid retrieval.
|
|
77
|
-
6. **Topology and precision** — validate before and after repair/overlay. Pick a
|
|
78
|
-
precision grid from source accuracy and CRS units; arbitrary snapping can
|
|
79
|
-
collapse features or create bias.
|
|
80
|
-
7. **Cardinality** — state expected one-to-one, one-to-many, or many-to-many
|
|
81
|
-
behavior before `merge`, `sjoin`, or `sjoin_nearest`; audit unmatched and
|
|
82
|
-
multiplied rows afterward.
|
|
83
|
-
8. **Output contract** — use a new output path, preserve a stable feature ID,
|
|
84
|
-
document schema/CRS/encoding, reopen the artifact, and compare counts/types.
|
|
85
|
-
|
|
86
|
-
## CRS and antimeridian rules
|
|
87
|
-
|
|
88
|
-
GeoPandas stores CRS as `pyproj.CRS`. Coordinate arrays use traditional GIS
|
|
89
|
-
`(x, y)` order, while authority definitions can advertise latitude-first axes.
|
|
90
|
-
Use `Transformer(..., always_xy=True)` for explicit coordinate-array pipelines,
|
|
91
|
-
and record that choice.
|
|
92
|
-
|
|
93
|
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`to_crs()` transforms vertices and assumes each segment is straight in the
|
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94
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source CRS; it does not transform geodesic arcs. Geometries crossing ±180° or a
|
|
95
|
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projection boundary can be badly wrapped. Detect crossings, split/unwrap and
|
|
96
|
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densify in a documented geographic representation, transform parts, then
|
|
97
|
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validate. Do not use Web Mercator as a general measurement CRS.
|
|
98
|
-
|
|
99
|
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```python
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|
100
|
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crs = gdf.crs # a pyproj.CRS when present
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101
|
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if crs is None or crs.is_geographic:
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raise ValueError("Choose a justified projected CRS before planar measurement")
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103
|
-
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104
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unit_names = [axis.unit_name for axis in crs.axis_info]
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105
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areas = gdf.geometry.area # square CRS units, not automatically square metres
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```
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107
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|
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108
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See [CRS management](references/crs-management.md).
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109
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110
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## Core API decisions
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111
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112
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### Data structures
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113
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-
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114
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- A `GeoDataFrame` can hold multiple geometry columns, each with CRS metadata,
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115
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but only `active_geometry_name` drives frame-level spatial operations.
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116
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- Binary `GeoSeries` methods are row-wise and align by index by default. Use
|
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117
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`align=False` only when positional pairing is explicitly intended and lengths
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118
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and order were verified.
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119
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- Duplicate column names and duplicate feature IDs are ambiguous; reject or
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120
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resolve them before joins and exports.
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121
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-
|
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122
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-
See [data structures](references/data-structures.md).
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123
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-
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124
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### Geometry validity, precision, and union
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125
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-
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126
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Use `is_valid` and redacted `is_valid_reason()` categories before
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127
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`make_valid(method="linework"|"structure", keep_collapsed=...)`. Repair can
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128
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change geometry type or dimension; retain the original and compare counts,
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129
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area, types, empties, and collapsed parts.
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130
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-
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131
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`set_precision(grid_size, mode=...)` uses **CRS units** and may remove duplicate
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132
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vertices or collapse features. `union_all(method="unary", grid_size=...)` is the
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133
|
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robust default. Use `coverage` only after `is_valid_coverage()` proves
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134
|
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non-overlap and edge matching; use `disjoint_subset` with Shapely >=2.1 when its
|
|
135
|
-
partitioning assumption is useful.
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|
136
|
-
|
|
137
|
-
See [geometric operations](references/geometric-operations.md).
|
|
138
|
-
|
|
139
|
-
### Joins, overlay, clip, and dissolve
|
|
140
|
-
|
|
141
|
-
- `sjoin` predicates are directional: `left.within(right)` is not
|
|
142
|
-
`left.contains(right)`. `intersects` includes boundary contact; `contains`
|
|
143
|
-
excludes boundary-only points, while `covers` includes boundary points.
|
|
144
|
-
- `predicate="dwithin"` requires `distance`; scalar or per-left-row distances
|
|
145
|
-
are in CRS units. `sjoin_nearest` returns all equidistant nearest matches and
|
|
146
|
-
does **not** implement a `k=` parameter.
|
|
147
|
-
- `overlay(..., make_valid=True)` repairs invalid input but can change types;
|
|
148
|
-
`keep_geom_type=None` drops other types with a warning. Precision mismatch can
|
|
149
|
-
create slivers; quantify them rather than silently deleting them.
|
|
150
|
-
- `clip` dissolves the mask. Rectangle clipping is fast but possibly dirty and
|
|
151
|
-
may omit a line collapsed to a point; validate its output.
|
|
152
|
-
- `dissolve` combines `groupby.agg` with `union_all`; choose explicit attribute
|
|
153
|
-
aggregations and audit null group keys.
|
|
154
|
-
|
|
155
|
-
See [spatial analysis](references/spatial-analysis.md).
|
|
156
|
-
|
|
157
|
-
### I/O, Arrow, and PostGIS
|
|
158
|
-
|
|
159
|
-
GeoPandas 1.x defaults to pyogrio. Driver availability and semantics come from
|
|
160
|
-
the installed GDAL, not GeoPandas alone. Prefer local GeoPackage for general
|
|
161
|
-
interchange and WKB GeoParquet for columnar interoperability.
|
|
162
|
-
|
|
163
|
-
GeoParquet defaults to stable schema 1.0.0. Native GeoArrow encodings and bbox
|
|
164
|
-
covering require schema 1.1.0 and remain less interoperable. A missing GeoParquet
|
|
165
|
-
`crs` key means `OGC:CRS84`; explicit `crs: null` means unknown—do not conflate
|
|
166
|
-
them. Reopen and validate every export.
|
|
167
|
-
|
|
168
|
-
Use parameterized SQL and a SQLAlchemy `Engine`/`Connection` for PostGIS.
|
|
169
|
-
`if_exists="replace"` is destructive; default to `"fail"` and use a transaction.
|
|
170
|
-
|
|
171
|
-
See [data I/O](references/data-io.md).
|
|
172
|
-
|
|
173
|
-
## Migration checklist
|
|
174
|
-
|
|
175
|
-
For code moving from GeoPandas 0.14 or earlier:
|
|
176
|
-
|
|
177
|
-
- GeoPandas 1.0 supports Shapely >=2 only; PyGEOS, Shapely <2, and the rtree
|
|
178
|
-
spatial-index backend were removed.
|
|
179
|
-
- pyogrio replaced Fiona as the installed/default I/O engine. Set `engine=`
|
|
180
|
-
explicitly and test schema, empty, datetime, encoding, and append behavior.
|
|
181
|
-
- Replace `sjoin(op=...)` with `predicate=`, `sindex.query_bulk()` with
|
|
182
|
-
`sindex.query()`, `unary_union` with `union_all()`, and
|
|
183
|
-
`GeometryArray.data` with `to_numpy()`/`np.asarray`.
|
|
184
|
-
- Replace `read_file(include_fields=...|ignore_fields=...)` with `columns=`.
|
|
185
|
-
Use `schema_version=`, not the removed GeoParquet `version=` compatibility.
|
|
186
|
-
- Do not use removed `geopandas.datasets`, internal `geopandas.io.*` entry
|
|
187
|
-
points, plot `axes`/`colormap`, or set-operation operators.
|
|
188
|
-
- `explode()` now defaults `index_parts=False`; a named Series passed to
|
|
189
|
-
`set_geometry()` supplies the new active-column name; a named right index can
|
|
190
|
-
replace `index_right` in `sjoin` output.
|
|
191
|
-
- Do not assign `.crs` to override metadata or rely on deprecated
|
|
192
|
-
`set_geometry(drop=...)`; use explicit `set_crs()` and rename/drop steps.
|
|
193
|
-
- GeoPandas 1.1 requires Python >=3.10, pandas >=2.0, NumPy >=1.24, and pyproj
|
|
194
|
-
>=3.5. Version 1.1.2 fixed SQL injection through a PostGIS geometry-column
|
|
195
|
-
name; the pinned 1.1.4 includes that fix.
|
|
196
|
-
|
|
197
|
-
### Plotting and exploration
|
|
198
|
-
|
|
199
|
-
Maps are analytical outputs: label units, classification method, missing data,
|
|
200
|
-
normalization denominator, and date. `explore()` can expose every attribute in
|
|
201
|
-
tooltips/popups and contact tile/CDN servers; generalize first and use
|
|
202
|
-
`tiles=None`, `tooltip=False`, and `popup=False` for a local draft.
|
|
203
|
-
|
|
204
|
-
See [visualization](references/visualization.md).
|
|
205
|
-
|
|
206
|
-
## Bundled local CLIs
|
|
207
|
-
|
|
208
|
-
All helpers are deterministic, reject network/archive paths, bound input bytes
|
|
209
|
-
and feature counts, keep imports lazy so `--help` is dependency-free, and emit
|
|
210
|
-
JSON without coordinates or record identifiers.
|
|
211
|
-
|
|
212
|
-
| CLI | Purpose |
|
|
213
|
-
|---|---|
|
|
214
|
-
| `scripts/vector_inventory.py` | Redacted local vector/GeoParquet technical inventory |
|
|
215
|
-
| `scripts/crs_reprojection_plan.py` | CRS units, axes, candidate transform and antimeridian plan |
|
|
216
|
-
| `scripts/geometry_validity_report.py` | Dry-run validity audit; optional repair to a new GeoPackage |
|
|
217
|
-
| `scripts/spatial_join_audit.py` | Predicate semantics, duplicate IDs and join cardinality |
|
|
218
|
-
| `scripts/export_plan.py` | Non-executing vector/GeoParquet export contract |
|
|
219
|
-
| `scripts/sensitive_coordinates_checklist.py` | Privacy/generalization release gate |
|
|
220
|
-
|
|
221
|
-
```bash
|
|
222
|
-
python skills/geopandas/scripts/vector_inventory.py --help
|
|
223
|
-
python skills/geopandas/scripts/crs_reprojection_plan.py \
|
|
224
|
-
--source-crs EPSG:4326 --target-crs EPSG:32631
|
|
225
|
-
python skills/geopandas/scripts/geometry_validity_report.py data.gpkg
|
|
226
|
-
python skills/geopandas/scripts/spatial_join_audit.py points.gpkg zones.gpkg \
|
|
227
|
-
--predicate within --left-id point_id --right-id zone_id
|
|
228
|
-
python skills/geopandas/scripts/export_plan.py data.gpkg result.parquet \
|
|
229
|
-
--format geoparquet --schema-version 1.0.0 \
|
|
230
|
-
--stable-id-column feature_id --id-unique-verified
|
|
231
|
-
python skills/geopandas/scripts/sensitive_coordinates_checklist.py \
|
|
232
|
-
--public-output --precise-points --contains-addresses
|
|
233
|
-
```
|
|
234
|
-
|
|
235
|
-
## Reference index
|
|
236
|
-
|
|
237
|
-
- [Data structures](references/data-structures.md)
|
|
238
|
-
- [CRS management](references/crs-management.md)
|
|
239
|
-
- [Geometric operations](references/geometric-operations.md)
|
|
240
|
-
- [Spatial analysis](references/spatial-analysis.md)
|
|
241
|
-
- [Data I/O](references/data-io.md)
|
|
242
|
-
- [Visualization](references/visualization.md)
|
|
243
|
-
|
|
244
|
-
## Sources (verified 2026-07-23)
|
|
245
|
-
|
|
246
|
-
- [GeoPandas 1.1.4 on PyPI](https://pypi.org/project/geopandas/1.1.4/) — released 2026-06-26.
|
|
247
|
-
- [GeoPandas 1.1.4 release](https://github.com/geopandas/geopandas/releases/tag/v1.1.4) — bug-fix release.
|
|
248
|
-
- [GeoPandas 1.1.4 tagged dependencies](https://github.com/geopandas/geopandas/blob/v1.1.4/pyproject.toml).
|
|
249
|
-
- [Stable GeoPandas documentation](https://geopandas.org/en/stable/).
|
|
250
|
-
- [GeoPandas 1.0 migration release](https://github.com/geopandas/geopandas/releases/tag/v1.0.0).
|