@pikaa-ai/pikaa 0.3.22 → 0.3.24

package/skills/genomic-coordinates/SKILL.md

@@ -1,189 +0,0 @@
----
-name: genomic-coordinates
-description: Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corrupt an analysis. Use whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".
-license: MIT
-compatibility: Requires Python 3.11+. Scripts use only the standard library - no third-party packages and no network access. Variant normalisation needs a reference FASTA, and uses its .fai index when one is present.
-allowed-tools: Read Write Edit Bash
-metadata:
-  version: "1.0"
-  skill-author: K-Dense Inc.
----
-
-# Genomic Coordinates
-
-## When to use
-
-Any time a coordinate crosses a boundary: between two file formats, between two
-tools, between two assemblies, or between the genome and a transcript.
-
-## The rule
-
-**A coordinate is three facts, not one: the number, the convention it is written
-in, and the assembly it was measured against.** Carry all three or the number is
-not interpretable.
-
-Coordinate errors are the quietest class of bug in genomics. An off-by-one BED
-file parses, sorts, and intersects without complaint. A GRCh37 VCF joined against
-a GRCh38 annotation returns rows. A right-shifted indel simply fails to match its
-entry in ClinVar, and the result is a variant reported as novel. Nothing raises
-an error; the answer is just wrong, and it is wrong in a direction that looks
-plausible.
-
-So: convert with the table, not from memory, and verify against the reference
-whenever a reference is available.
-
-## The two conversions
-
-```
-1-based inclusive  ->  0-based half-open :  start - 1,  end
-0-based half-open  ->  1-based inclusive :  start + 1,  end
-```
-
-The end coordinate never moves. If a conversion changed both numbers, it is wrong.
-
-## Which format is which
-
-| 0-based, half-open | 1-based, inclusive |
-| --- | --- |
-| BED, bedGraph, bigWig, narrowPeak | GFF3, GTF, VCF |
-| BAM/CRAM (binary POS) | SAM (text POS) |
-| PSL, genePred, refFlat | WIG, Picard interval_list |
-| MAF (UCSC multiple alignment) | MAF (TCGA mutation annotation) |
-| PyRanges, pybedtools | GRanges/IRanges, samtools & UCSC & Ensembl region strings |
-
-Both "MAF" formats exist, they mean different things, and they disagree. UCSC
-serves 0-based files through a 1-based browser box. `references/format-conventions.md`
-has the full table with per-format detail.
-
-```bash
-cd skills/genomic-coordinates/scripts
-
-python3 convert_coords.py --list                          # the table
-python3 convert_coords.py --from bed --to gff chr1 999 1000
-python3 convert_coords.py --from ucsc --to bed "chr7:5,530,601-5,530,625"
-python3 convert_coords.py --from granges --to pyranges --input regions.tsv
-```
-
-```
-contig  input                 output           length  status  detail
-chr7    chr7:5530601-5530625  5530600-5530625  25      ok
-```
-
-Zero-length BED features (`chromStart == chromEnd`, a legal insertion point) are
-reported as `unrepresentable` rather than converted to `end = start - 1`. Exit
-code is 1 when any interval is degenerate or invalid.
-
-## Variants are not intervals
-
-A VCF `POS` for an indel is the **anchor base** — the base *before* the event,
-itself unchanged. And the same change can be written many ways:
-`chr1:7:CAC:C`, `chr1:3:CAC:C` and `chr1:2:GCA:G` are one deletion. Joining,
-deduplicating, or looking up variants before normalising loses real matches
-silently, and it loses them preferentially in repeats, where indels concentrate.
-
-Normalise — trim to parsimony, then left-align against the reference — before any
-comparison:
-
-```bash
-python3 normalize_variant.py --fasta ref.fa chr1 7 CAC C
-python3 normalize_variant.py --fasta ref.fa --split --input cohort.vcf
-python3 normalize_variant.py --fasta ref.fa --compare chr1:7:CAC:C chr1:2:GCA:G
-```
-
-```
-input         normalized    type      pos_shift  ref_check  changed
-chr1:7:CAC:C  chr1:2:GCA:G  deletion  5          ok         yes
-```
-
-Every record's `REF` is checked against the FASTA first. A `MISMATCH` means the
-variants and the reference are different assemblies — stop and run
-`check_contigs.py` rather than adjusting coordinates. Multi-allelic records must
-be split with `--split` **before** normalising, never after.
-
-HGVS shifts indels the opposite way, 3'-most along the transcript. For a
-minus-strand gene that is the opposite genomic direction from VCF's
-left-alignment. Details and the full procedure: `references/variant-representation.md`.
-
-## Check the assembly before trusting a join
-
-```bash
-python3 check_contigs.py --identify unknown.fa.fai
-python3 check_contigs.py variants.vcf annotation.gtf --genome GRCh38.fa.fai
-```
-
-```
-file          kind    contigs  naming        assembly  detail
-ref.fa.fai    sizes   25       plain         GRCh37    24/24 primary chromosome lengths match;
-                                                       chrM is 16569 bp, i.e. GRCh37/38 (rCRS MT)
-```
-
-The script reads `.fai`, `.chrom.sizes`, VCF headers, SAM headers, FASTA, BED,
-and GTF/GFF, identifies the assembly from primary-chromosome lengths, and reports
-every reason a join between two files would go wrong: naming mismatch, length
-conflict, coordinates past a contig end, contigs present in one file only. Exit
-code 1 on any incompatibility.
-
-**GRCh37 and hg19 differ only in the mitochondrion** — 16,569 bp (rCRS) versus
-16,571 bp. Nuclear coordinates are identical, so a mixed pipeline runs fine and
-only the mtDNA results are wrong. `check_contigs.py` reports which one it found.
-Builds, naming schemes, ALT contigs, and liftover pitfalls:
-`references/reference-builds.md`.
-
-## Audit a file against its own format
-
-```bash
-python3 audit_intervals.py peaks.bed
-python3 audit_intervals.py gencode.gtf --genome hg38.chrom.sizes
-python3 audit_intervals.py cohort.vcf --genome GRCh38.fa.fai
-```
-
-Looks for the evidence that a coordinate mistake leaves behind:
-
-| Finding | What it proves |
-| --- | --- |
-| `start_below_one` in GFF/GTF | 0-based data in a 1-based file; everything is one base left |
-| `many_zero_length` in BED | 1-based single-base features written into a 0-based file |
-| `past_contig_end` | wrong assembly, or an off-by-one at the contig edge |
-| `mixed_contig_naming` | any join will silently match one subset |
-| `first_block_offset` | BED12 `blockStarts` written as absolute coordinates |
-| `not_parsimonious` | untrimmed alleles; normalise before joining |
-| `bad_alt_allele` | Ensembl/VEP `-` notation in a VCF, which has no anchor base |
-
-Exit code 1 on any fatal finding, so it works as a CI gate on a data directory.
-
-## Transcript, CDS, and protein positions
-
-`c.742` and `chr17:7,674,220` are both "position", and neither converts to the
-other by arithmetic. Transcript coordinates count spliced bases in transcription
-order — decreasing genomic coordinate on the minus strand — and `c.1` is the `A`
-of the initiator `ATG`, not the start of the transcript.
-
-The rules that get mis-remembered: there is no `c.0`; 5' UTR positions are
-negative and 3' UTR positions take a `*`; GFF phase is the bases to *remove* to
-reach the next codon, not `start % 3`; and a `c.` description is meaningless
-without a versioned transcript accession, because the same variant numbers
-differently in each transcript. `references/transcript-coordinates.md` has the
-conversion procedure and the boundary cases.
-
-Do the conversion with a tool that holds the transcript model — VEP,
-`bcftools csq`, Mutalyzer, the `hgvs` package — not by hand.
-
-## Reporting results
-
-State the assembly next to the coordinates, every time.
-`chr7:5,530,601-5,530,625` is not a location; `chr7:5,530,601-5,530,625 (GRCh38)`
-is. Say which convention a coordinate column is in, in the column header or the
-file's documentation. When a conversion produced a result, say which direction it
-went.
-
-## References
-
-- `references/format-conventions.md` — every format's convention, with per-format
-  detail, BED12 block rules, region-string syntax, and tool behaviour.
-- `references/variant-representation.md` — VCF allele conventions, the
-  normalisation algorithm, equivalence checking, multi-allelic splitting, and how
-  HGVS disagrees with VCF.
-- `references/reference-builds.md` — build signatures, GRCh37 vs hg19, ALT
-  contigs, naming schemes, and liftover failure modes.
-- `references/transcript-coordinates.md` — genomic ↔ transcript ↔ CDS ↔ protein,
-  HGVS numbering, phase, and transcript choice.

package/skills/genomic-intelligence/SKILL.md

@@ -1,243 +0,0 @@
----
-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-expression workflow. Use when the user has a gene symbol, a genomic region, or a DNA/FASTA sequence and wants any of these predictions, mentions Genomic Intelligence, genomicintelligence.ai, api.genomicintelligence.ai, or mcp.genomicintelligence.ai."
-license: MIT
-compatibility: Python 3.10+ with the `requests` library for the REST path (no dedicated SDK). Network access required. The REST `/v1` API needs a `GI_API_KEY` (a `gi_` bearer); the hosted MCP server at mcp.genomicintelligence.ai/mcp works keyless against a capped public demo quota, key optional.
-metadata:
-  version: "1.0"
-  skill-author: Genomic Intelligence
-  trigger-keywords: DNA sequence prediction, regulatory genomics, promoter prediction, splice site prediction, enhancer activity, chromatin state, gene expression prediction, sequence to expression, log TPM, gene annotation, transcript prediction, DNA language model, genomic intelligence, hosted inference, Ensembl sequence, FASTA prediction, cis-regulatory, TSS window, DeepSEA, DeepSTARR, BigBird splice, MCP genomics
-  openclaw:
-    primaryEnv: GI_API_KEY
-    envVars:
-    - name: GI_API_KEY
-      required: false
-      description: Optional gi_ bearer key for the REST /v1 API and a higher MCP quota. The hosted MCP demo runs keyless; request a key at contact@genomicintelligence.ai.
----
-
-# Genomic Intelligence — DNA Sequence Models
-
-Genomic Intelligence (GI) serves transformer DNA language models over six
-sequence-analysis tasks on managed GPUs. Give it a **gene symbol**, a **genomic
-region**, or a **DNA/FASTA sequence**; it returns structured predictions —
-promoter regions, splice sites, enhancer activity, chromatin state, expression
-(log TPM), and de-novo gene annotation. Nothing runs locally: no model weights,
-no GPU, no heavy Python stack. It is a thin client over a hosted, versioned
-inference API.
-
-**Official docs:** [docs.genomicintelligence.ai](https://docs.genomicintelligence.ai) ·
-REST contract at [api.genomicintelligence.ai/v1/openapi.json](https://api.genomicintelligence.ai/v1/openapi.json) ·
-hosted MCP server at `https://mcp.genomicintelligence.ai/mcp`
-
-## When to use this skill
-
-Use GI when the user has DNA and wants a model prediction:
-
-- **Find promoters** in a genomic region (`promoter`)
-- **Predict splice** donor/acceptor sites (`splice`)
-- **Score enhancer activity** — developmental & housekeeping (`enhancer`)
-- **Annotate chromatin state** across hundreds of tracks (`chromatin`)
-- **Predict expression** as log(TPM+1) from a sequence + cell-type context (`expression`)
-- **Annotate genes/transcripts** de novo, no reference needed (`annotation`)
-- **Find the genes in a region and predict each one's expression** (composite)
-
-Not for local alignment, variant calling, or file I/O — use a local tool
-(BioPython, bcftools) for those. GI is for **model inference from sequence**.
-
-> For research and development use, **not clinical or diagnostic decisions**.
-
-## Two ways to call GI
-
-### Hosted MCP server (best for AI agents — keyless)
-
-GI hosts an MCP server at `https://mcp.genomicintelligence.ai/mcp` (Streamable
-HTTP). When your agent host supports MCP, prefer it: it works **keyless** against
-a capped public demo quota (zero setup), and an optional `gi_` bearer key raises
-the quota. It exposes acquisition tools that return a **sequence handle**
-(`sequence_ref`) and `predict_*` tools that take that handle — so large sequences
-never bloat the context. See [MCP workflow](#mcp-workflow-handle-based) below and
-`references/mcp.md`.
-
-### REST API (universal)
-
-Plain HTTP with `requests` against `https://api.genomicintelligence.ai/v1`. The
-REST path **requires** a `GI_API_KEY` (a `gi_` bearer). Use it on any host, in
-scripts, or when you need the raw envelope. See [Core REST workflow](#core-rest-workflow).
-
-## Access and authentication
-
-1. The **hosted MCP demo is keyless** — try it with nothing set.
-2. The **REST `/v1` API needs a key**, sent as `Authorization: Bearer <key>`.
-   Request one at [contact@genomicintelligence.ai](mailto:contact@genomicintelligence.ai).
-3. **Never hardcode the key.** Read it from the `GI_API_KEY` environment variable
-   (or a `.env` via `python-dotenv`). Never commit keys.
-
-```bash
-export GI_API_KEY="gi_yourkeyhere"     # optional for MCP; required for REST
-export GI_BASE_URL="https://api.genomicintelligence.ai"   # override for staging
-```
-
-Keys are scoped to a partner tier with concurrency and per-minute caps. A `429`
-means you hit a cap — back off and retry, or ask GI to raise your tier.
-
-## The six tasks
-
-All REST tasks share one shape: `POST /v1/tasks/{task}/predict` with body
-`{sequence, sequence_name, model?, options?}`, returning a `{data, meta}`
-envelope. What differs per task:
-
-| Task | Mode | Length bound | Notes |
-|---|---|---|---|
-| `promoter` | sync | 1–500,000 bp | sliding-window promoter regions |
-| `splice` | sync | 1–500,000 bp | donor/acceptor sites (long-context BigBird) |
-| `enhancer` | sync | 1–500,000 bp | dev + housekeeping scores (DeepSTARR, *Drosophila*) |
-| `chromatin` | sync | 1–500,000 bp | hundreds of tracks (DeepSEA) |
-| `expression` | sync | **exactly 9,198 bp** | log(TPM+1); needs a cell-type `description` |
-| `annotation` | **async** | 1–500,000 bp | de-novo transcripts; submit + poll |
-
-**Omit `model` and the API uses the task's default** — that is the recommended
-call. Default model IDs are intentionally **not** documented here: defaults
-change and retired IDs fail hard, so never hardcode one. To pin a model, or to
-pick a non-human one (Drosophila, yeast, and Arabidopsis models exist for several
-tasks), discover IDs at call time with `GET /v1/tasks/{task}/models` (REST) or
-`list_models` (MCP) — and **never invent one**. Full per-task output shapes are
-in `references/tasks.md`.
-
-Two hard rules the model enforces:
-
-- **`expression` needs exactly 9,198 bp**, a window **centred on the TSS**
-  (4,599 upstream + TSS + 4,598 downstream). Any other length is rejected. Use the acquisition helpers below to
-  build it — do not truncate by hand.
-- **`expression` needs a `description`** — a cell-type / assay string (e.g.
-  `"K562 cells"`), passed as `options.description`.
-
-## Sequence acquisition
-
-You rarely start from a raw 9,198 bp string. Acquire sequence first:
-
-- **From a gene symbol** → MCP `fetch_ensembl_sequence(gene=...)`; **from
-  coordinates** → `fetch_region(region=...)`. Both fetch public Ensembl reference
-  sequence (no key). REST users can query Ensembl REST directly. (`find_genes` is
-  the annotation task, not an acquisition tool.)
-- **For `expression`** → use the TSS-centred fetch so the window is exactly
-  9,198 bp. MCP: `fetch_gene_for_expression` (handles the centring). Do not
-  build the window by hand.
-- **From a local FASTA** → MCP `store_inline_sequence`, or read the file yourself
-  for REST. (`load_local_fasta` exists only in local deployments, not on the
-  hosted server.)
-- **A demo sequence** → MCP `load_demo_sequence(name=...)` returns a ready handle
-  (great for a keyless smoke test); `name` is required.
-
-See `references/sequence-acquisition.md` for the exact Ensembl calls and the
-expression-window math.
-
-## Core REST workflow
-
-Sync tasks (promoter, splice, enhancer, chromatin, expression) are one call:
-
-```python
-import os, requests
-
-BASE = os.environ.get("GI_BASE_URL", "https://api.genomicintelligence.ai")
-HEADERS = {"Authorization": f"Bearer {os.environ['GI_API_KEY']}"}
-
-def predict(task, sequence, sequence_name, model=None, options=None):
-    body = {"sequence": sequence, "sequence_name": sequence_name}
-    if model:   body["model"] = model
-    if options: body["options"] = options
-    r = requests.post(f"{BASE}/v1/tasks/{task}/predict", headers=HEADERS, json=body)
-    r.raise_for_status()          # 400 invalid; 401 no/bad key; 413 too long; 429 rate limit
-    return r.json()               # {"data": {...}, "meta": {...}}
-
-# Promoter:
-out = predict("promoter", seq, "TP53_region")
-print(out["data"]["summary"])
-
-# Expression — exactly 9,198 bp + a cell-type description:
-out = predict("expression", tss_window_9198bp, "HBB",
-              options={"description": "K562 cells"})
-print(out["data"]["prediction"]["expression_log_tpm"])
-```
-
-### Async: annotation
-
-`annotation` is submit-then-poll. Send `Prefer: respond-async`, get a `job_id`,
-poll until terminal:
-
-```python
-import time
-
-r = requests.post(f"{BASE}/v1/tasks/annotation/predict",
-                  headers={**HEADERS, "Prefer": "respond-async"},
-                  json={"sequence": seq, "sequence_name": "TP53"})
-r.raise_for_status()              # 202 Accepted
-job_id = r.json()["data"]["job_id"]
-
-while True:
-    j = requests.get(f"{BASE}/v1/tasks/jobs/{job_id}", headers=HEADERS)
-    if j.status_code == 200:      # terminal: body is the final {data, meta}
-        break
-    j.raise_for_status()          # 202 = still running (2xx, won't raise)
-    time.sleep(5)                 # ~20 s typical for ~20 kb
-transcripts = j.json()["data"]["transcripts"]
-```
-
-## MCP workflow (handle-based)
-
-On an MCP host, acquire a handle, then predict against it — sequences stay out of
-the context:
-
-```
-# 1. Acquire a sequence handle (each returns a sequence_ref):
-load_demo_sequence(name="promoter_tp53")  # keyless smoke test; `name` is REQUIRED
-fetch_ensembl_sequence(gene="TP53")       # gene symbol or Ensembl ID -> handle
-fetch_region(region="chr11:5,225,000-5,235,000")   # coordinates -> handle
-fetch_gene_for_expression(gene="HBB")     # TSS-centred 9,198 bp handle for expression
-
-# 2. Predict against the handle:
-predict_promoter(sequence_ref=<ref>)
-predict_expression(sequence_ref=<ref>, description="K562 cells")
-predict_splice(sequence_ref=<ref>)        # + predict_enhancer / predict_chromatin
-
-# 3. Annotation on MCP is `find_genes` (there is no predict_annotation).
-#    It takes a handle, not a region, and runs async internally:
-find_genes(sequence_ref=<ref>)            # wait=True (default) returns the result
-find_genes(sequence_ref=<ref>, wait=False)  # -> job_id; poll get_job(job_id)
-
-# Discover models with list_models(task); reference context lives in the
-# gi://models, gi://docs/tasks, and gi://account MCP resources.
-```
-
-## Composite: find genes, then predict expression
-
-To answer "what genes are in this region and how are they expressed?", use the
-composite:
-
-- **MCP:** `find_genes_and_predict_expression(sequence_ref=..., description=...)`
-  — takes a **handle, not a region** (acquire one with `fetch_region` first);
-  `description` is required. Finds genes in the sequence and returns an
-  expression prediction for each.
-- **REST:** call gene discovery, then loop `expression` per gene (build each
-  TSS-centred 9,198 bp window via the acquisition helpers).
-
-## Errors
-
-| Code | Meaning | Action |
-|---|---|---|
-| 400 | Invalid request / bad sequence | Check the body; expression must be exactly 9,198 bp and carry `description` |
-| 401 | Missing/invalid key (REST) | Set `GI_API_KEY`; or use the keyless MCP demo |
-| 413 | Sequence too long | Stay within the task's length bound (≤500,000 bp) |
-| 429 | Rate / concurrency cap | Back off and retry; ask GI to raise your tier |
-| 422 | Validation failed (`validation_failed`) | The most common failure: expression not exactly 9,198 bp, or a sequence below the model's minimum length |
-| 5xx | Server error | Retry; if persistent, contact support |
-
-## Reference files
-
-- `references/tasks.md` — per-task output shapes, model registries, the async
-  annotation contract.
-- `references/api-and-auth.md` — REST endpoints, the `{data, meta}` envelope,
-  auth, base-URL override, tiers.
-- `references/mcp.md` — the hosted MCP tool list, the handle-based flow, and the
-  `gi://` resources.
-- `references/sequence-acquisition.md` — Ensembl fetch calls and the
-  expression-window (9,198 bp, TSS-centred) math.

package/skills/geomaster/README.md

@@ -1,105 +0,0 @@
-# GeoMaster Geospatial Science Skill
-
-## Overview
-
-GeoMaster is a comprehensive geospatial science skill covering:
-- **70+ sections** on geospatial science topics
-- **500+ code examples** across 7 programming languages
-- **300+ geospatial libraries** and tools
-- Remote sensing, GIS, spatial statistics, ML/AI for Earth observation
-
-## Contents
-
-### Main Documentation
-- **SKILL.md** - Main skill documentation with installation, quick start, core concepts, common operations, and workflows
-
-### Reference Documentation
-1. **core-libraries.md** - GDAL, Rasterio, Fiona, Shapely, PyProj, GeoPandas
-2. **remote-sensing.md** - Satellite missions, optical/SAR/hyperspectral analysis, image processing
-3. **gis-software.md** - QGIS/PyQGIS, ArcGIS/ArcPy, GRASS GIS, SAGA GIS integration
-4. **scientific-domains.md** - Marine, atmospheric, hydrology, agriculture, forestry applications
-5. **advanced-gis.md** - 3D GIS, spatiotemporal analysis, topology, network analysis
-6. **programming-languages.md** - R, Julia, JavaScript, C++, Java, Go geospatial tools
-7. **machine-learning.md** - Deep learning for RS, spatial ML, GNNs, XAI for geospatial
-8. **big-data.md** - Distributed processing, cloud platforms, GPU acceleration
-9. **industry-applications.md** - Urban planning, disaster management, utilities, transportation
-10. **specialized-topics.md** - Geostatistics, optimization, ethics, best practices
-11. **data-sources.md** - Satellite data catalogs, open data repositories, API access
-12. **code-examples.md** - 500+ code examples across 7 programming languages
-
-## Key Topics Covered
-
-### Remote Sensing
-- Sentinel-1/2/3, Landsat, MODIS, Planet, Maxar
-- SAR, hyperspectral, LiDAR, thermal imaging
-- Spectral indices, classification, change detection
-
-### GIS Operations
-- Vector data (points, lines, polygons)
-- Raster data processing
-- Coordinate reference systems
-- Spatial analysis and statistics
-
-### Machine Learning
-- Random Forest, SVM, CNN, U-Net
-- Spatial statistics, geostatistics
-- Graph neural networks
-- Explainable AI
-
-### Programming Languages
-- **Python** - GDAL, Rasterio, GeoPandas, TorchGeo, RSGISLib
-- **R** - sf, terra, raster, stars
-- **Julia** - ArchGDAL, GeoStats.jl
-- **JavaScript** - Turf.js, Leaflet
-- **C++** - GDAL C++ API
-- **Java** - GeoTools
-- **Go** - Simple Features Go
-
-## Installation
-
-See [SKILL.md](SKILL.md) for detailed installation instructions.
-
-### Core Python Stack
-```bash
-conda install -c conda-forge gdal rasterio fiona shapely pyproj geopandas
-```
-
-### Remote Sensing
-```bash
-uv pip install rsgislib torchgeo earthengine-api
-```
-
-## Quick Examples
-
-### Calculate NDVI from Sentinel-2
-```python
-import rasterio
-import numpy as np
-
-with rasterio.open('sentinel2.tif') as src:
-    red = src.read(4)
-    nir = src.read(8)
-    ndvi = (nir - red) / (nir + red + 1e-8)
-```
-
-### Spatial Analysis with GeoPandas
-```python
-import geopandas as gpd
-
-zones = gpd.read_file('zones.geojson')
-points = gpd.read_file('points.geojson')
-joined = gpd.sjoin(points, zones, predicate='within')
-```
-
-## License
-
-MIT License
-
-## Author
-
-K-Dense Inc.
-
-## Contributing
-
-This skill is part of the K-Dense-AI/scientific-agent-skills repository.
-For contributions, see the main repository guidelines.