13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill geopandas --agent claude-code
Codex
$ npx skills add K-Dense-AI/scientific-agent-skills --skill geopandas -a codex -y
Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill geopandas -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill geopandas -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill geopandas -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill geopandas -a opencode -y
Windsurf
$ npx skills add K-Dense-AI/scientific-agent-skills --skill geopandas -a windsurf -y
name: geopandas description: Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O. license: MIT compatibility: Requires Python 3.12+ and uv for the tested stack. Bundled CLIs are local-only; runtime analysis requires the pinned GeoPandas stack below. allowed-tools: Read Write Bash Glob Grep metadata: version: "1.4" skill-author: K-Dense Inc. last-reviewed: "2026-10-01"
Use GeoPandas for planar vector data represented as pandas-like `GeoSeries` and `GeoDataFrame` objects. This skill targets stable **GeoPandas 1.2.0** (released 2026-09-28). The stable website currently carries a development build label; release-specific behavior below was checked against the v1.2.0 source and wheel.
GeoPandas 1.2.0 requires Python 3.11+, NumPy >=2, pandas >=2.2, Shapely >=2.1, pyproj >=3.7, pyogrio >=0.8, and `packaging`. The current pyproj wheel below requires Python 3.12+. This exact Python 3.12 snapshot was smoke-tested on 2026-10-01:
uv venv --python 3.12 uv pip install \ "geopandas==1.2.0" \ "numpy==2.5.3" \ "pandas==3.0.6" \ "shapely==2.1.2" \ "pyproj==3.8.0" \ "pyogrio==0.13.0" \ "pyarrow==25.0.1" \ "packaging==26.3"
Keep optional plotting and PostGIS packages pinned in the project lock as well. Do not mix binary geospatial packages from incompatible package channels.
1. Inspect a vetted local layer with `vector_inventory.py`; retain source hashes. 2. Use `crs_reprojection_plan.py` to inspect candidate transformations. It plans only: execute an appropriate `to_crs()`/pyproj transformation separately. 3. Audit geometry with `geometry_validity_report.py`; compare simulated repair changes before requesting its optional new GeoPackage output. 4. Run the intended analysis with explicit predicates, CRS units, precision, and aggregation rules. `spatial_join_audit.py` measures join cardinality; it does not export joined features or perform a dissolve. 5. Use `export_plan.py` to inspect the proposed contract, then write and reopen the actual output separately. A successful plan has not written a file. 6. Review disclosure and generalization before sharing derived geodata/maps, using `sensitive_coordinates_checklist.py` when sensitive locations occur.
Examples below use synthetic or placeholder local inputs. File/database examples need the named dataset or service; PostGIS and tile-provider calls were reviewed against upstream contracts but were not exercised against a live service.
small-area joins as sensitive. Default reports to counts, categories, coarse extents, and redacted identifiers. Generalize before publication.
geocode an address. Obtain explicit approval, validate provenance and hashes, then stage an unpacked local file in an isolated workspace.
native-code trust boundary. Prefer official wheels/conda-forge, record native versions, restrict drivers, and process untrusted data in a sandbox.
GDAL drivers. The bundled CLIs use an extension allowlist and reject archives.
secret manager or scoped environment variable. Never embed a password in a URL or source, print an engine/URL, or dump the environment.
predicate, join cardinality, precision/repair choices, and row-count checks.
Apply these gates before trusting a result:
1. **Identity and provenance** โ identify the source layer, stable feature key, duplicate IDs, row count, geometry column, parser/driver, and content hash. 2. **Geometry state** โ count null, empty, invalid, mixed, Z/M, and collapsed geometries separately. `None` is missing; an empty Shapely geometry is real. 3. **CRS semantics** โ require CRS metadata. `set_crs()` assigns metadata; `to_crs()` transforms coordinates. Never guess a CRS from coordinate ranges. 4. **Units and operation** โ GeoPandas is planar. Geographic coordinates are angular; do not use them directly for buffer, distance, area, nearest joins, precision grids, or tolerances. Choose a fit-for-purpose local/equal-area CRS or a geodesic method. 5. **Transform quality** โ inspect axis order, area of use, datum pipeline, expected accuracy, ballpark status, and missing grids. Keep PROJ network disabled unless the user explicitly approves grid retrieval. 6. **Topology and precision** โ validate before and after repair/overlay. Pick a precision grid from source accuracy and CRS units; arbitrary snapping can collapse features or create bias. 7. **Cardinality** โ state expected one-to-one, one-to-many, or many-to-many behavior before `merge`, `sjoin`, or `sjoin_nearest`; audit unmatched and multiplied rows afterward. 8. **Output contract** โ use a new output path, preserve a stable feature ID, document schema/CRS/encoding, reopen the artifact, and compare counts/types.
GeoPandas stores CRS as `pyproj.CRS`. Coordinate arrays use traditional GIS `(x, y)` order, while authority definitions can advertise latitude-first axes. Use `Transformer(..., always_xy=True)` for explicit coordinate-array pipelines, and record that choice.
`to_crs()` transforms vertices and assumes each segment is straight in the source CRS; it does not transform geodesic arcs. Geometries crossing ยฑ180ยฐ or a projection boundary can be badly wrapped. Detect crossings, split/unwrap and densify in a documented geographic representation, transfor
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