- Bumped version in plugin.json and pyproject.toml to 2.66.0.
- Updated skill metadata versions across multiple skills, reflecting improvements and new features.
- Added citation guidelines to various skill documentation to ensure proper referencing of the "Scientific Agent Skills" paper.
- Added a new badge linking to the arXiv paper.
- Updated the citation section to include the full citation for the paper "Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents."
- Clarified the importance of citing the paper alongside individual skills used in research.
- Bumped version number in plugin.json and pyproject.toml to 2.65.0.
- Updated README to indicate an increase in the number of available skills from 161 to 163.
The "API Reference" bullets in references/callbacks.md and
references/vectorized_envs.md pointed at
`/en/master/common/callbacks.html` and `/en/master/common/vec_env.html`,
which both return 404. Upstream Stable-Baselines3 documents the
`stable_baselines3.common.callbacks` and `stable_baselines3.common.vec_env`
modules on the same pages as their narrative guides, not under `common/`.
Repoint both links at the module anchors on the guide pages:
- guide/callbacks.html#module-stable_baselines3.common.callbacks
- guide/vec_envs.html#module-stable_baselines3.common.vec_env
Both targets and both anchors were verified against the live docs and the
upstream genindex. The "Official ... Guide" bullet directly above each one
already used the correct `guide/` path, so the two `common/` URLs were
inconsistent within their own files.
Bump metadata.version to "1.2".
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
- Changed the webinar announcement to a link for the recorded session of "Getting Started with K-Dense BYOK."
- Updated the description to reflect the content covered in the recording, ensuring users can access the walkthrough at their convenience.
- Added details about an upcoming live webinar titled "Getting Started with K-Dense BYOK," including date, time, and registration link.
- This addition aims to provide users with a hands-on walkthrough of the K-Dense BYOK setup and features.
- Revised language to indicate that diagrams are optional for skills and not required for changes.
- Removed outdated commands related to diagram generation from the main instructions.
- Emphasized the importance of regenerating diagrams when skill workflows change to maintain accuracy.
- Added new blog entries on using Multica for scientific research, introducing the waypoint-bio and lab-hardware-cad agent skills, and discussing the agentic data scientist and Karpathy ML engineer.
- Updated the README to reflect the expanded resources and insights available for users in the scientific community.
- Bumped version number in plugin.json and pyproject.toml to 2.64.0.
- Updated README to reflect an increase in the number of available skills from 161 to 163.
- Added a new section for Star History with an embedded chart to visualize the repository's star growth over time.
- This addition enhances the README by providing insights into the project's popularity and community engagement.
- Bumped version to 1.2 and updated last-reviewed date in SKILL.md.
- Enhanced standards.json with updated notes and additional dimensions for clarity.
- Expanded build123d-patterns.md to include detailed geometry checks and their semantics.
- Improved fabrication-limits.md with laser cutting guidelines and corner radius considerations.
- Updated validation.md to clarify checks for declared interfaces and geometry.
- Added new geometry checks functionality in scripts to validate model geometry against built solids.
- Adjusted check.py to include geometry evaluation commands for better verification processes.
- Added a Reddit badge and link to the README for broader community engagement.
- Updated the "Stay up to date" section to include Reddit alongside existing social media links for new skills and updates.
- Added a new example for virtual spatial transcriptomics from archival H&E slides, detailing objectives, disciplines, skills used, and workflow steps.
- Introduced the NCATS ARAX skill for querying biomedical knowledge-graph relationships, including detailed usage instructions and capabilities.
- Updated the examples list to reflect the new addition and ensure comprehensive coverage of relevant topics.
- Included a new section on AI co-scientists with a link to a live Q&A session addressing practical concerns for researchers.
- Added multiple entries discussing the significance of workflow in scientific research, emphasizing verification and reproducibility in AI applications.
- Updated the README to enhance the resourcefulness of the documentation for users exploring AI in scientific contexts.
- Changed the review model from "google/gemini-3.6-flash" to "google/gemini-3.7-flash" in the following scripts:
- generate_infographic_ai.py
- generate_schematic_ai.py (in latex-posters, literature-review, scientific-schematics, and scientific-slides)
- generate_slide_image_ai.py
- Updated documentation to reflect the new review model version in iterative_refinement.md.
- Enhanced AGENTS.md and CONTRIBUTING.md to clarify the structure and requirements for the Agent Plugins package, including the need for `plugin.json` to be schema-valid and version-synced with `pyproject.toml`.
- Updated README.md to reflect the new version 2.63.0 and added details about the repository being a portable Agent Plugins package.
- Added tests in test_repo_contract.py to ensure compliance with the Agent Plugins manifest schema and discoverability of skills.
This update ensures better adherence to the Agent Plugins standard and improves the overall documentation for contributors.
- Added handling for missing SKILL_SCANNER_LLM_API_KEY in forked pull requests.
- Implemented a sticky comment to inform users when the scan is skipped due to the absence of the API key.
- Updated workflow documentation to clarify the behavior of the scanner in forked contexts.
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.
Add a standard-library ARAX client for typed one-hop and endpoint-pinned two-hop Translator queries, selected-provider federation, entity normalization, and provenance-preserving artifacts. Include offline fixtures and tests, isolated test metadata, and README discovery.
- 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.
- State that predict_genes only accepts symbols in the released tokens.csv
panel (model.gene_names) and raises KeyError otherwise; temper the
transcriptome-coverage claims to match.
- Use from_pretrained's device argument; the model already returns in eval
mode and predict_genes runs under no_grad, so drop the redundant
model.eval()/no_grad lines (also clears MDBLOCK_PYTHON_EVAL_EXEC scan FPs).
- Rebuild the tile batch inside the multi-source loop, matching the advice
beneath the example.
- Pin the install to deepspotm==1.0.0.
- Add the required docs/images/deepspot-m.png workflow diagram.
Adds skills/deepspot-m for transcriptome-wide virtual spatial transcriptomics from H&E histology tiles, plus references for the API and whole slide runs. Updates the README counts and docs/skills.md.
SKILL.md's one copy-pasteable Phase 3 command used --remove-duplicates, which
argparse rejects; the real flag is --deduplicate. A sweep of every documented
invocation against the actual --help output found eleven more flags that do not
exist: validate_citations.py --auto-fix, --strict, --output,
--check-required-fields, --check-authors, --check-duplicates, --check-syntax;
format_bibtex.py --validate, --report, --style; doi_to_bibtex.py --clipboard;
and search_google_scholar.py --open-access-only. Several sat in worked examples
an agent would run verbatim.
citation_validation.md documented an "auto-fix" mode of validate_citations.py
that never existed -- the script only reports. Those sections now point at
format_bibtex.py, which is what rewrites.
Other corrections:
- --report wrote a JSON document to report.txt.
- three of five declared dependencies were never imported.
- Phase 2.5 was marked MANDATORY but needed web access that allowed-tools did
not grant; WebSearch and WebFetch are now declared.
- no compatibility field, despite needing a Python version, a package, and
network access.
- the schematics section told a citation skill to produce diagrams by default,
and named generate_schematic.py while generate_schematic_ai.py sat beside it
unexplained. Reduced to a pointer at scientific-schematics.
- venue reference counts are labelled as rules of thumb rather than submission
requirements, which is what they are.
Documents search_openalex.py and the shared _common.py, and regenerates the
workflow diagram, which no longer matched what the skill does.
Version 1.8 -> 2.0: format_bibtex.py no longer overwrites its input by default.
The field parser in format_bibtex.py and validate_citations.py matched
`\{([^}]*)\}`, which stops at the first closing brace. Any title with a
protected term -- `{Highly accurate prediction with {AlphaFold}}` -- was
truncated mid-value, and rewriting it produced a .bib with unbalanced braces
that no BibTeX engine reads. extract_metadata.py emits that protection
deliberately, so the documented Phase 2 -> Phase 3 pipeline corrupted its own
output, and format_bibtex.py defaulted to overwriting the input in place.
Replace both parsers with a brace-depth scanner in scripts/_common.py, which
also owns entry rendering, page normalisation, and one citation-key scheme
shared by every producer -- entries from Crossref, PubMed, OpenAlex, and
Scholar now collide when they are the same paper, which is what makes
deduplication work at all. Writing is opt-in: without --output or --in-place
the result goes to stdout and the input is untouched.
Also fixed:
- pages: `replace('-', '--')` turned `583--589` into `583----589`; PubMed's
abbreviated `1123-30` now expands to `1123--1130` rather than staying a
range that resolves to nothing.
- publisher was read from Crossref and dropped by the writer, so every @book
and @techreport failed the required-field check.
- an arXiv preprint with a DataCite DOI was typed @article with no journal --
guaranteed to fail validation. It is @misc unless journal_ref names a venue.
- --url and PMCID were classified by identify_type but had no handler, so a
publisher URL without a DOI in its path errored out. URLs now resolve via
the citation_doi meta tag; PMCIDs via the NCBI ID converter.
- citation keys were unsanitised in search_pubmed.py: `Müller2021pmid123`
and `O'Brien2021pmid124` are not valid BibTeX keys.
- DOIs were interpolated into API URLs unquoted.
- verify_doi used HEAD on doi.org, which follows to the publisher; several
answer HEAD with 403 behind a bot check, so good DOIs looked unresolvable.
Ask Crossref, then DataCite, and treat transport failures as unknown.
- valid_entries subtracted the error count from the entry count and reported
`Valid entries: -2` for a one-entry file.
- structured abstracts kept only their first section; titles lost inline
markup and carried PubMed's trailing full stop.
- two `note` fields could be emitted in one entry.
- --auto-fix was advertised in --help as "not implemented yet" and did nothing.
- venue_standards was assigned inside validate_file, so a fresh validator did
not have it.
Add search_openalex.py: ~250M works, keyless REST API, cursor pagination,
abstracts rebuilt from the inverted index. The skill's own "single source
bias" pitfall previously had only two sources to offer, one of them scraped.
Drop the bundled schematic generators (1,148 lines) in favour of the
scientific-schematics skill, and update the shared-copy contract accordingly.
Reference-list length is editorial judgement, so a venue shortfall is now a
warning; only an explicit --min-count is enforced as an error.
Dependencies drop from eight packages to two: bibtexparser, biopython,
crossref-commons, pylatexenc, and selenium were declared but never imported,
and the parsing layer is now standard library.
The sentinel "not-stated" is exactly 10 characters, so it satisfied the
len(publication) == 10 ISO-date guard and reached
date.fromisoformat("not-stated"), raising an uncaught ValueError instead of
the documented warning. SKILL.md instructs recording "not-stated" when the
publication date is unavailable, so this crashed on valid ledgers.
Check the sentinel before the retrieval/publication comparison, and add
regression tests for both the not-stated warning and the still-enforced
retrieval-precedes-publication error.
Fixes#219
