Timothy Kassis 991bd993ac Update optimize-for-gpu skill documentation and assets ...

- Enhanced the skill description for clarity and accuracy regarding GPU acceleration.
- Updated compatibility notes to reflect requirements for RAPIDS 26.06 and Python 3.11+.
- Revised the library selection guidance to emphasize preferred usage patterns and legacy considerations.
- Improved the optimization workflow section with detailed steps for defining contracts and checking suitability.
- Added new code transformation patterns and clarified the use of cuSpatial and cuVS.
- Updated the cuCIM reference to include installation instructions and performance characteristics.
- Replaced the existing optimize-for-gpu.png image with a new version to better illustrate the skill's capabilities.

2026-08-07 13:35:13 -07:00

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adaptyv

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

aeon

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

analytical-method-validation

Add analytical-method-validation skill

2026-07-27 16:34:28 -07:00

anndata

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

arbor

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

arboreto

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

astropy

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

autoskill

Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.

2026-07-28 10:50:49 -07:00

benchling-integration

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

bgpt-paper-search

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

bids

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

biopython

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

bioservices

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

bulk-rnaseq

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

cellxgene-census

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

cirq

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

citation-management

citation-management: correct documented commands, bump to 2.0

2026-07-31 10:59:16 -07:00

clinical-decision-support

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

clinical-reports

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

cobrapy

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

consciousness-council

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

dask

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

database-lookup

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

datamol

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

deepchem

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

deepspot-m

deepspot-m: document the ~19k-gene panel limit, drop redundant eval calls, add diagram

2026-08-07 13:09:04 -07:00

deeptools

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

depmap

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

dhdna-profiler

Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.

2026-07-28 10:50:49 -07:00

diffdock

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

dnanexus-integration

DNANexus improvements

2026-07-23 10:53:35 -07:00

docx

Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.

2026-07-28 10:50:49 -07:00

esm

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

etetoolkit

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

exa-search

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

experimental-design

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

exploratory-data-analysis

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

flowio

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

fluidsim

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

generate-image

Update image generation and citation management scripts to use 'uv pip install' for package installations. Modify skill versions for infographics and generate-image to reflect recent changes. Enhance error handling and review logic in infographic generation scripts, ensuring better feedback on quality assessments.

2026-07-31 10:26:56 -07:00

geniml

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

genomic-coordinates

Add genomic-coordinates skill

2026-07-26 15:33:36 -07:00

genomic-intelligence

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

geomaster

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

geopandas

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

get-available-resources

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

gget

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

ginkgo-cloud-lab

Update Ginkgo Cloud Lab skill

2026-06-23 19:48:32 -04:00

glycoengineering

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

gtars

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

histolab

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

hugging-science

Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.

2026-07-28 10:50:49 -07:00

hypogenic

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

hypothesis-generation

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

imaging-data-commons

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

infographics

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

iso-standards-readiness

Replace iso-13485-certification with iso-standards-readiness

2026-07-26 16:26:52 -07:00

labarchive-integration

Update LabArchives skill for current APIs

2026-07-23 11:02:05 -07:00

lamindb

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

latchbio-integration

Update DNAnexus, ETE, FlowIO, LatchBio, MarkItDown, MatchMS, Opentrons, pysam, Qiskit, and SHAP skills

2026-07-23 10:43:55 -07:00

latex-posters

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

liteparse

Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.

2026-07-28 10:50:49 -07:00

literature-review

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

markdown-mermaid-writing

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

market-research-reports

market-research-reports: fix ledger validator crash on publication_date=not-stated

2026-07-31 10:57:18 -07:00

markitdown

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

matchms

Update DNAnexus, ETE, FlowIO, LatchBio, MarkItDown, MatchMS, Opentrons, pysam, Qiskit, and SHAP skills

2026-07-23 10:43:55 -07:00

matlab

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

matplotlib

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

medchem

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

modal

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

molecular-dynamics

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

molfeat

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

networkx

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

neurokit2

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

neuropixels-analysis

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

nextflow

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

omero-integration

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

onekgpd

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

ontology-term-resolution

Add ontology-term-resolution skill

2026-07-26 14:45:44 -07:00

open-notebook

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

openpiv

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

opentrons-integration

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

optimize-for-gpu

Update optimize-for-gpu skill documentation and assets

2026-08-07 13:35:13 -07:00

pacsomatic

Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.

2026-07-28 10:50:49 -07:00

paper-lookup

Update paper-lookup to 2.0

2026-07-27 18:32:30 -07:00

paperclip

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

paperzilla

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

parallel-web

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

pathml

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

pathogen-variant-surveillance

Add pathogen-variant-surveillance skill

2026-07-27 15:40:33 -07:00

pathway-enrichment

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

pdf

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

peer-review

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

pennylane

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

phylogenetics

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

pi-agent

Update pi-agent skill to latest Pi docs

2026-07-26 15:50:24 -07:00

pkpd-modeling

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

polars

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

polars-bio

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

pptx

Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.

2026-07-28 10:50:49 -07:00

pptx-posters

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

primekg

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

protocolsio-integration

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

pufferlib

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

pydeseq2

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

pydicom

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

pyhealth

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

pylabrobot

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

pymatgen

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

pymc

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

pymoo

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

pyopenms

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

pysam

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

pytdc

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

pytorch-lightning

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

pyzotero

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

qiskit

Update DNAnexus, ETE, FlowIO, LatchBio, MarkItDown, MatchMS, Opentrons, pysam, Qiskit, and SHAP skills

2026-07-23 10:43:55 -07:00

qutip

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

rdkit

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

relsa-severity-assessment

Introduced a new skill for relsa-severity-assessment

2026-08-07 12:08:05 -07:00

research-grants

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

research-lookup

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

rowan

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

scanpy

Test every script-bearing skill, and enforce that it stays that way

2026-07-28 10:20:12 -07:00

scholar-evaluation

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

scientific-brainstorming

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

scientific-critical-thinking

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

scientific-schematics

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

scientific-slides

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

scientific-visualization

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

scientific-writing

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

scikit-bio

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

scikit-learn

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

scikit-survival

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

scvelo

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

scvi-tools

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

seaborn

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

shap

Update DNAnexus, ETE, FlowIO, LatchBio, MarkItDown, MatchMS, Opentrons, pysam, Qiskit, and SHAP skills

2026-07-23 10:43:55 -07:00

simpy

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

stable-baselines3

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

statistical-analysis

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

statistical-power

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

statsmodels

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

sympy

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

tamarind

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

tiledbvcf

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

timesfm-forecasting

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

torch-geometric

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

torchdrug

Update Torchdrug and venue-templates skills

2026-07-20 12:07:48 -07:00

transformers

Update transformers skill metadata and dependencies; remove uv.lock file

2026-06-13 07:30:28 -07:00

treatment-plans

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00

umap-learn

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

uncertainty-and-units

Add uncertainty-and-units skill under skills/uncertainty-and-units

2026-07-26 15:08:29 -07:00

usfiscaldata

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

vaex

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

venue-templates

Update Torchdrug and venue-templates skills

2026-07-20 12:07:48 -07:00

what-if-oracle

Update skill metadata formatting and improve .gitignore entries

2026-07-26 09:29:16 -07:00

xlsx

Enforce use of uv for packagment installation whenever needed

2026-07-31 10:29:07 -07:00

zarr-python

Update documentation and improve test structure for autoskill

2026-07-26 09:54:14 -07:00