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Commits on May 18, 2026

• Fix subclustering parser for DeepSeek V4 and other reasoning models (#21)

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Commits on May 11, 2026

• Add CASSIA CLI example project generator

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• Add reference subtype benchmark expansion

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• Add reference-assisted subtype workflows

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• Add CASSIA CLI agent workflows

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Commits on Apr 14, 2026

• Fix custom URL provider API key resolution in call_llm, bump to 1.3.8

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Commits on Apr 8, 2026

• Defensive null check on LLM responses, bump to 1.3.7

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• Fix UnicodeEncodeError in progress_tracker under R/reticulate, bump to 1.3.6

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• Hotfix: disable China auto-proxy in Python/R packages, bump to v1.3.5

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Commits on Apr 3, 2026

• Fix subclustering uncertainty workflow and bump to v1.3.4

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Commits on Mar 23, 2026

• Add n_genes to pipeline, tissue/species to subclustering; bump to v1.3.3

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• Update model names across READMEs, docs, and tutorials to latest versions

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• v1.3.1: Remove Test/ from repo, sync R package, update version and APIs

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• Major bug fixes and updates across Python, R, JS, and test suite

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Commits on Feb 7, 2026

• Fix: Preserve cluster IDs in sub-clustering agent output

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Commits on Feb 2, 2026

• Fix model_settings.py path resolution and add Test 23 quota reset

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• Switch free API to lifetime 2-cluster limit and update model settings

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• Merge branch 'dev_free_api'

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• Add free API access for R/Python package users without API keys

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Commits on Dec 15, 2025

• Improve Python version detection and API key validation

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• Add Python 3.8 support and Docker install tests

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Commits on Dec 13, 2025

• Update R package for Bioconductor, improve web app, and cleanup tests

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• Bump version to 0.3.18 and simplify web app UI

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• Update scoring, merging, and report generation modules

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• Update generate_reports.py

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Commits on Dec 12, 2025

• Update ApiKeyInput component in CASSIA web app

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• Fix subclustering output handling

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• Refactor subclustering and update uncertainty quantification

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• Sync Python updates to R package and bump version

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• Update package metadata and subclustering fixes

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• Improve annotation boost defaults and auto-detection

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• Add key_markers and explanation columns to subclustering output

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• Add per-agent default model and temperature configuration

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• Auto-default reasoning for GPT-5 models and comprehensive documentation update

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• Add auto-detection for conversations JSON and update documentation

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