celltype-cli 0.1.0__py3-none-any.whl

celltype_cli-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: celltype-cli
+Version: 0.1.0
+Summary: CellType CLI — An autonomous agent for drug discovery research
+Author: CellType Inc.
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: anthropic>=0.40
+Requires-Dist: claude-agent-sdk>=0.1
+Requires-Dist: httpx>=0.27
+Requires-Dist: markdown>=3.5
+Requires-Dist: nbformat>=5.7
+Requires-Dist: numpy>=1.24
+Requires-Dist: openai>=1.0
+Requires-Dist: pandas>=2.0
+Requires-Dist: prompt-toolkit>=3.0
+Requires-Dist: python-dotenv>=1.0
+Requires-Dist: rich>=13.0
+Requires-Dist: scipy>=1.10
+Requires-Dist: typer>=0.12
+Provides-Extra: all
+Requires-Dist: anndata>=0.10; extra == 'all'
+Requires-Dist: biopython>=1.81; extra == 'all'
+Requires-Dist: celltypist>=1.6; extra == 'all'
+Requires-Dist: cellxgene-census>=1.0; extra == 'all'
+Requires-Dist: fair-esm>=2.0; extra == 'all'
+Requires-Dist: rdkit>=2023.03; extra == 'all'
+Requires-Dist: scanpy>=1.9; extra == 'all'
+Requires-Dist: scikit-learn>=1.3; extra == 'all'
+Requires-Dist: seaborn>=0.13; extra == 'all'
+Requires-Dist: tiledbsoma>=1.0; extra == 'all'
+Requires-Dist: torch>=2.0; extra == 'all'
+Requires-Dist: transformers>=4.40; extra == 'all'
+Provides-Extra: analysis
+Requires-Dist: scikit-learn>=1.3; extra == 'analysis'
+Requires-Dist: seaborn>=0.13; extra == 'analysis'
+Provides-Extra: api
+Requires-Dist: duckdb>=1.0; extra == 'api'
+Requires-Dist: fastapi>=0.100; extra == 'api'
+Requires-Dist: uvicorn[standard]>=0.20; extra == 'api'
+Provides-Extra: biology
+Requires-Dist: biopython>=1.81; extra == 'biology'
+Provides-Extra: chemistry
+Requires-Dist: rdkit>=2023.03; extra == 'chemistry'
+Provides-Extra: dev
+Requires-Dist: pytest-cov>=5.0; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.5; extra == 'dev'
+Provides-Extra: ml
+Requires-Dist: fair-esm>=2.0; extra == 'ml'
+Requires-Dist: torch>=2.0; extra == 'ml'
+Requires-Dist: transformers>=4.40; extra == 'ml'
+Provides-Extra: notebook
+Requires-Dist: nbconvert>=7.0; extra == 'notebook'
+Provides-Extra: singlecell
+Requires-Dist: anndata>=0.10; extra == 'singlecell'
+Requires-Dist: celltypist>=1.6; extra == 'singlecell'
+Requires-Dist: cellxgene-census>=1.0; extra == 'singlecell'
+Requires-Dist: scanpy>=1.9; extra == 'singlecell'
+Requires-Dist: tiledbsoma>=1.0; extra == 'singlecell'
+Description-Content-Type: text/markdown
+
+# celltype-cli
+
+An autonomous agent for drug discovery research. Like Claude Code, but for biology.
+
+Ask questions in natural language. celltype-cli plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions.
+
+<img src="assets/ct2.gif" alt="ct demo" width="70%">
+
+## Benchmark
+
+CellType CLI achieves **90% accuracy** on [BixBench-Verified-50](https://github.com/bixbench/bixbench), outperforming all existing agentic systems for computational biology.
+
+![BixBench Benchmark Results](assets/bixbench_benchmark.png)
+
+| System | Accuracy |
+|--------|----------|
+| **celltype-cli (Opus 4.6)** | **90.0%** |
+| Phylo BiomniLab | 88.7% |
+| Edison Analysis | 78.0% |
+| Claude Code (Opus 4.6) | 65.3% |
+| OpenAI Agents SDK (GPT 5.2) | 61.3% |
+
+## Why ct?
+
+- **190+ drug discovery tools** — Target prioritization, compound profiling, dose-response modeling, pathway enrichment, safety assessment, clinical development, and more.
+- **Claude-powered reasoning** — Built on the Claude Agent SDK. Claude plans multi-step research workflows, calls tools, self-corrects, and synthesizes findings.
+- **Managed data pipelines** — One-command download of DepMap, PRISM, L1000, and proteomics datasets with auto-discovery loaders.
+- **30+ database APIs** — PubMed, ChEMBL, UniProt, Open Targets, ClinicalTrials.gov, Reactome, PDBe, and more — no setup required.
+- **Research UX** — Interactive terminal with @mentions, session resume, trace logging, HTML reports, and notebook export.
+- **Persistent sandbox** — Stateful Python and R execution across turns (pandas, scipy, gseapy, pydeseq2, BioPython).
+- **Open source** — MIT licensed.
+
+## Installation
+
+### Quick install
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/celltype/cli/main/install.sh | bash
+```
+
+Detects Python 3.10+, installs via `pipx` or `pip`, and launches an interactive setup wizard.
+
+### Manual install
+
+```bash
+# With pipx (isolated environment, recommended)
+pipx install celltype-cli
+
+# Or with pip
+pip install celltype-cli
+
+# Or with optional scientific stacks (RDKit, scanpy, torch, etc.)
+pip install "celltype-cli[all]"
+
+# Run the setup wizard
+ct setup
+```
+
+### Authentication
+
+```bash
+# Interactive setup (recommended)
+ct setup
+
+# Or set directly
+export ANTHROPIC_API_KEY="sk-ant-..."
+
+# Non-interactive (CI/scripting)
+ct setup --api-key sk-ant-api03-...
+```
+
+## Getting Started
+
+### Basic usage
+
+```bash
+# Start interactive session
+ct
+
+# Single query
+ct "What are the top degradation targets for this compound?"
+
+# Validate setup
+ct doctor
+```
+
+### Interactive commands
+
+Inside `ct` interactive mode:
+
+- `/help` — command reference + examples
+- `/tools` — list all tools with status
+- `/agents N <query>` — run N parallel research agents
+- `/case-study <id>` — curated multi-agent case studies
+- `/sessions`, `/resume` — session lifecycle
+- `/copy`, `/export` — save/share outputs
+- `/usage` — token and cost tracking
+
+### Quick examples
+
+**Target prioritization**
+```
+$ ct "I have a CRBN molecular glue. Proteomics shows it degrades
+      IKZF1, GSPT1, and CK1α. Which target should I prioritize?"
+```
+
+**Combination strategy**
+```
+$ ct "My lead compound is immune-cold. What combination strategy should I use?"
+```
+
+**Resistance biomarkers**
+```
+$ ct "Build a resistance biomarker panel for my lead compound"
+```
+
+## Key Features
+
+### 190+ Domain Tools
+
+| Category | Examples |
+|----------|---------|
+| **Target** | Neosubstrate scoring, degron prediction, co-essentiality networks |
+| **Chemistry** | SAR analysis, fingerprint similarity, scaffold clustering |
+| **Expression** | L1000 signatures, pathway enrichment, TF activity, immune scoring |
+| **Viability** | Dose-response modeling, PRISM screening, therapeutic windows |
+| **Biomarker** | Mutation sensitivity, resistance profiling, dependency validation |
+| **Clinical** | Indication mapping, population sizing, TCGA stratification |
+| **Safety** | Anti-target flagging, multi-modal profiling, SALL4 risk |
+| **Literature** | PubMed, OpenAlex, ChEMBL search |
+| **DNA** | ORF finding, codon optimization, primer design, Golden Gate/Gibson assembly |
+| **Data APIs** | MyGene, UniProt, Reactome, PDBe, ClinicalTrials.gov, and 25+ more |
+
+### Data Management
+
+```bash
+# Download core datasets
+ct data pull depmap        # DepMap CRISPR, mutations, expression
+ct data pull prism         # PRISM cell viability
+ct data pull msigdb        # Gene sets
+ct data pull alphafold     # Protein structures (on-demand)
+
+# Or point to existing data
+ct config set data.depmap /path/to/depmap/
+ct config set data.prism /path/to/prism/
+```
+
+Without local data, ct still works using 30+ database APIs.
+
+### Reports
+
+Every query auto-saves a markdown report. Convert to branded, self-contained HTML:
+
+```bash
+ct report list              # list reports
+ct report publish           # convert latest .md to .html
+ct report show              # open in browser
+```
+
+Dark theme, responsive layout, inline CSS. No CDN, no JavaScript. Shareable via email/Slack.
+
+## Known Limitations
+
+- **Local data for some tools** — Target, viability, expression, combination, biomarker tools need local DepMap/PRISM/L1000 datasets. The planner auto-excludes unavailable tools and uses API alternatives.
+- **Optional dependencies** — RDKit (chemistry), scanpy (single-cell), torch (protein embeddings). Tools report install instructions if missing.
+- **API rate limits** — PubMed, UniProt, Open Targets may rate-limit heavy usage.
+
+## Troubleshooting
+
+| Symptom | Fix |
+|---------|-----|
+| `ct` fails at startup | `ct doctor` |
+| No API key | `ct setup` or `export ANTHROPIC_API_KEY=...` |
+| Data not found | `ct data pull <dataset>` |
+| Missing dependency | `pip install "celltype-cli[all]"` |
+| Session lost | `ct --continue` (sessions auto-save) |
+
+## Contributing
+
+```bash
+git clone https://github.com/celltype/cli.git
+cd cli
+pip install -e ".[dev]"
+ct setup
+pytest tests/
+```
+
+We welcome contributions — bug reports, feature requests, documentation improvements, and pull requests.
+
+## Enterprise & On-Premise
+
+celltype-cli is free and open source, powered by Claude out of the box.
+
+For pharma and biotech teams that need to keep data on-premise, CellType offers proprietary research agent models purpose-built to replace frontier LLMs — deployable locally behind your firewall with zero data leaving your infrastructure.
+
+**[Contact us](mailto:hello@celltype.com)** to learn more.
+
+## License
+
+MIT — see [LICENSE](LICENSE)
+
+---
+
+Built by [CellType Inc.](https://celltype.com)

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celltype_cli-0.1.0.dist-info/WHEEL

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celltype_cli-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+ct = ct.cli:entry

celltype_cli-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 CellType Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

ct/__init__.py

@@ -0,0 +1,3 @@
+"""celltype-cli: An autonomous agent for drug discovery research."""
+
+__version__ = "0.1.0"