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Andrey Fedorov aaf763c3a6 Update imaging-data-commons skill from v1.4.0 to upstream v1.8.1 
Rebased onto current main and re-synced from
ImagingDataCommons/imaging-data-commons-skill, which now holds SKILL.md under 500
lines upstream. references/core_capabilities.md is therefore removed rather than
refreshed: its content was redistributed into the topical guides that already own
each subject (sql_patterns, index_tables_guide, cli_guide, licensing_and_citation)
instead of a catch-all file, and upstream CI holds the budget so the split does not
have to be redone after each sync.

New since v1.4.0: the hosted IDC MCP server and REST API as first-class access paths
(references/mcp_guide.md, references/rest_api_guide.md), so a metadata question no
longer requires a ~77 MB idc-index install; licensing_and_citation.md; idc-index
0.12.5 / IDC data v24; scripts/check_version.py as the startup version check.

tests/imaging-data-commons/test_check_version.py covers the bundled script: offline,
standard library only, no idc-index needed. It is a copy of the upstream file, which
is written to be vendored — only two path constants and the frontmatter-version
assertion differ.

Verified: pytest tests/_meta tests/imaging-data-commons -> 29 passed, 1030 subtests;
skills-ref validate skills/imaging-data-commons -> valid; SKILL.md 495 lines.
2026-08-10 17:06:22 -04:00
..
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
Update imaging-data-commons skill from v1.4.0 to upstream v1.8.1
2026-08-10 17:06:22 -04:00
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
ncats-arax
Add bounded NCATS ARAX knowledge graph skill
2026-08-08 02:44:06 -04:00
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