v2.64.0

What's Changed

Changes since v2.63.0:

• Update version to 2.64.0 and enhance README with skill count increase (9e8b0cb)
• Add waypoint skill (204eef5)
• Update README to include Star History chart (4934681)
• chore: update security scan report [skip ci] (28f5603)
• Update lab hardware CAD skill documentation and standards (336c4f8)
• Update README to include Reddit link and enhance user engagement (43a3e61)
• Update pi-agent skill (b2a92ba)
• Update examples and skills documentation (3c8fc0f)
• Add CAD skill for lab hardware (980e4f0)
• Add new blog entries to README for AI co-scientists and workflow importance (13385c7)
• Update review model to version 3.7 across multiple scripts (5f3de01)

v2.63.0

What's Changed

Changes since v2.62.0:

• Update documentation and versioning for Agent Plugins compliance (5ad4aae)
• Remove Star History chart from README. (f2f77ff)
• feat: enhance skill security scan for forked PRs (3956e54)
• Update imaging-data-commons skill from v1.4.0 to upstream v1.8.1 (aaf763c)
• chore: update security scan report [skip ci] (7eb9c23)
• Add bounded NCATS ARAX knowledge graph skill (550b965)
• Update optimize-for-gpu skill documentation and assets (991bd99)
• deepspot-m: document the ~19k-gene panel limit, drop redundant eval calls, add diagram (9477641)
• Introduced a new skill for relsa-severity-assessment (f8c6f0e)
• Add DeepSpot-M skill (de981da)
• chore: update security scan report [skip ci] (d767725)

v2.62.0

What's Changed

Changes since v2.61.0:

• Update version to 2.62.0 in pyproject.toml and README.md, reflecting the latest release. (ad21a38)
• citation-management: correct documented commands, bump to 2.0 (3378ece)
• citation-management: fix BibTeX corruption and metadata defects (d39264b)
• market-research-reports: fix ledger validator crash on publication_date=not-stated (95d3add)
• Update generate-image.png to reflect recent changes in image generation process. (390c8b8)
• Enforce use of uv for packagment installation whenever needed (4226ca8)
• 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. (bd99c01)
• chore: update security scan report [skip ci] (4d5f1d2)

v2.61.0

What's Changed

Changes since v2.60.0:

• Update version to 2.61.0 in pyproject.toml and README.md, reflecting the latest release. (ab2f84a)
• Update skill versions to 1.4 and 1.5 across multiple skills, including infographics, latex-posters, literature-review, scientific-schematics, and scientific-slides. Enhance API key resolution logic in various scripts to improve credential handling and error messaging. Adjust image model references for clarity in infographic and schematic generation scripts. (f1b60f8)
• Add new example for Phase 2 regimen development in examples.md and enhance pharmacology skills section in skills.md. The new example outlines a comprehensive workflow from first-in-human dose to a defensible Phase 2 regimen, detailing objectives, disciplines, skills used, and a structured prompt. Additionally, the skills section now includes a dedicated entry for PK/PD modeling, emphasizing its applications in pharmacometrics. (07021b9)
• chore: update security scan report [skip ci] (f9d7053)
• 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. (0e45106)

v2.60.0

What's Changed

Changes since v2.59.0:

• Update version to 2.60.0 and increment skill count to 158 in README.md (223f5a3)
• Test every script-bearing skill, and enforce that it stays that way (4fb7e0b)
• Add paperclip skill (d33b267)
• Add pkpd-modeling skill (4c90a52)
• Update paper-lookup to 2.0 (061882b)
• Add community health files (#218) (e7ac425)
• Update README (752753b)
• Add new skill for genomic data analysis (dbe9422)
• Add bulk RNA-seq diagram to documentation (0789168)
• More diagrams for skills (ce01a27)

v2.59.0

What's Changed

Changes since v2.57.0:

• Add zarr image (11c4e1e)
• Add skill images (effadea)
• Add analytical-method-validation skill (844f4a3)
• Add pathogen-variant-surveillance skill (e608baa)
• Anchor the scripts/ gitignore pattern to the repo root (5a9c275)
• chore: update security scan report [skip ci] (81e316b)
• Update README, examples, and skills documentation to reflect the addition of new skills and version bump to 2.57.0. The README now highlights 154 skills, including the new Ontology Term Resolution and Genomic Coordinates skills, and provides updated examples for interdisciplinary workflows. The skills documentation has been expanded to include detailed descriptions of the new skills and their functionalities. (051f93f)
• Replace iso-13485-certification with iso-standards-readiness (6d22863)
• Add From the Blog section to README (f8eb840)

v2.57.0

What's Changed

Changes since v2.56.0:

• Add pytest as a dependency in pyproject.toml for improved testing support (58746dc)
• Bump version to 2.57.0 (2598479)
• Update pi-agent skill to latest Pi docs (ef1b2d8)
• Update generate-image for the OpenRouter Image API (3f530cf)
• Add genomic-coordinates skill (ce67928)
• Add uncertainty-and-units skill under skills/uncertainty-and-units (cca1e05)
• Add ontology-term-resolution skill (87b598a)

v2.56.0

What's Changed

Changes since v2.55.0:

• Update version numberl to 2.56.0 (3036316)
• Enhance skill environment management and documentation (b80fcda)
• Enhance security scanning documentation and update dependencies (cd879d8)
• Add OpenPIV skill under skills/openpiv (#216) (dde1906)
• Update documentation and improve test structure for autoskill (2f2022d)
• Add initial test suite for autoskill functionality (8cb0f52)
• Update skill metadata formatting and improve .gitignore entries (b085e11)
• Update security report and enhance subprocess environment handling (cb83780)
• Update security documentation and scanning process (489de4c)
• Remove validate_report.py script as it is no longer needed for the security scan process. This change simplifies the codebase and eliminates redundancy in validation checks, streamlining the overall workflow. (b01cff4)
• feat(docx): enhance DOCX skill and comment script functionality (a1b84fb)
• feat(citation-management): enhance metadata handling and subprocess environment (f5a0bbc)
• perf(security-scan): scan concurrently and reuse unchanged results (665663c)
• Update security scanning process and documentation (d77f819)
• feat(citation-management): document Zotero integration via pyzotero skill (38ce7e2)
• fix(imaging-data-commons): correct 'questons' typo (23f8511)
• Update default LLM model in security scan workflow to "claude-sonnet-5" (edefe50)
• Update default LLM model in SkillScanner to "anthropic/claude-sonnet-5" (37f2064)
• fix(rdkit): correct FractionCsp3 call and MolToSmarts parameter name (94151f6)
• Correct README release details (757b63b)
• fix(markdown-mermaid-writing): correct broken internal references in style guides (0f5891a)

v2.55.0

What's Changed

Changes since v2.54.0:

• Bump version to 2.55.0 (bb87fa1)
• Synchronize repository documentation (9319f43)
• Clean refreshed skill formatting (d2d8e87)
• Redesign scientific writing safeguards (3441b92)
• Redesign PPTX poster generation (866c1df)
• Update MATLAB R2026a workflows (d518a31)
• Redesign hypothesis generation workflow (f375cf7)
• Update ISO 13485 evidence workflows (5d68dbf)
• Redesign scholar evaluation safeguards (b295e73)
• Redesign treatment plan safety (818cb87)
• Redesign peer review confidentiality (8fc3325)
• Update market research evidence workflows (ebc0cce)
• Redesign clinical reports safety (cc223d5)
• Redesign clinical decision support safety (820bcb8)
• Update QuTiP skill for version 5.3 (f7b918d)
• Update GeoPandas spatial workflows (10781b2)
• Update pymatgen for current packages (0ece03a)
• Update pydicom privacy workflows (5c3389e)
• Update FluidSim numerical workflows (ee24204)
• Update exploratory data analysis workflows (cadf380)
• Update Gtars skill for current APIs (025a3a6)
• Update Geniml skill for current APIs (dd952bd)
• Correct MCP tool signatures against the live server (aa04310)
• Update PufferLib versioned workflows (f515922)
• Update HypoGeniC safety workflows (27ea7f4)
• Add genomic-intelligence skill (8f4fb7a)
• Update protocols.io integration guidance (34d4cd5)
• Update PyLabRobot safety workflows (70a0d59)
• Update NeuroKit2 skill for current APIs (ddcd380)
• Update PathML skill for current workflows (191e153)
• Update SimPy skill for current semantics (65f4698)
• Update scikit-survival for current APIs (5a62c8a)
• Update resource detection workflows (d80ca05)
• Update scientific visualization guidance (38cd204)
• Update scientific brainstorming workflows (fd9917e)
• Update PyTDC skill for current APIs (825f800)
• Update OMERO skill for current clients (90e825e)
• Update LabArchives skill for current APIs (ee5477e)
• DNANexus improvements (7191774)
• Update DNAnexus, ETE, FlowIO, LatchBio, MarkItDown, MatchMS, Opentrons, pysam, Qiskit, and SHAP skills (53c5897)
• Update skills and documentation: Change AI models from Gemini 3.1 Pro to Gemini 3.6 Flash for improved quality review across various skills, including Generate Image, Infographics, and Clinical Decision Support. Bump version numbers in SKILL.md files to reflect updates. (831d49e)

v2.54.0

What's Changed

Changes since v2.53.0:

• Bump version (e872769)
• Update Torchdrug and venue-templates skills (3b6f0e4)
• chore: update security scan report [skip ci] (a177179)
• Update README.md: Enhance star history chart with responsive design for dark and light themes, and clarify project name change to Scientific Agent Skills. (3f825ca)
• Enhance Research Lookup Skill: Update documentation and improve backend routing for manuscript evidence compilation. The skill now targets 60 verified references, producing structured research packets. Adjusted descriptions in README and SKILL.md for clarity, and removed outdated test file. (fc0b9f6)
• Delete redundant files (cd77d3f)
• Update parallel-web skill (0433033)
• chore: update security scan report [skip ci] (e12d683)
• feat(skills): onekgpd v1.2: retargets the Dnaerys Client v0.2.1 required for Python 3.11 support (aa716d0)
• feat(skills): onekgpd v1.1: retargets the Dnaerys Client v0.2.0 required for the latest KGP live database (1e2f2dc)
• chore: update security scan report [skip ci] (4d97e29)
• Update optimize-for-gpu and paper-lookup skills (26fd7a8)
• Update research-lookup and statistical-analysis skills (afa84b4)
• Enhance database lookup skill documentation and API interaction. Updated descriptions for clarity, improved retrieval contract guidelines, and added new API version checks for ClinicalTrials.gov. Adjusted AlphaFold references to reflect current file URLs and versioning. Incremented skill version to 1.2. (1e024ea)
• Update README and documentation to reflect the addition of 2 new skills, increasing the total to 148. Updated version badge to 2.53.0 and made minor adjustments for clarity in the skills documentation. (50a46b2)
• feat(skills): onekgpd (26d7086)
• chore: update security scan report [skip ci] (e083e63)
• Add Tamarind Bio platform skill (1cb3b1a)
• add missing research grants references (b82768f)