scitex 2.17.13

A comprehensive Python library for scientific computing and data analysis

scitex.ai · Read the Docs · pip install scitex

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SciTeX — Modular Python Toolkit for Researchers and AI Agents

Four Freedoms for Research

0. The freedom to run your research anywhere — your machine, your terms.
1. The freedom to study how every step works — from raw data to final manuscript.
2. The freedom to redistribute your workflows, not just your papers.
3. The freedom to modify any module and share improvements with the community.

AGPL-3.0 — because research infrastructure deserves the same freedoms as the software it runs on.

🎬 Demo

40 min, zero human intervention — AI agent conducts full research pipeline:

Literature search → Data analysis → Statistics → Figures → 21-page manuscript → Peer review simulation

📦 Installation

uv pip install scitex          # Core (minimal)
uv pip install scitex[plt,stats,scholar]  # Typical research setup
uv pip install scitex[all]     # Recommended: Full installation

⚙️ Configuration

Modular environment configuration via .env.d/:

# 1. Copy examples
cp -r .env.d.examples .env.d

# 2. Edit with your credentials
$EDITOR .env.d/

# 3. Source in shell (~/.bashrc or ~/.zshrc)
source /path/to/.env.d/entry.src

Structure:

.env.d/
├── entry.src              # Single entry point
├── 00_scitex.env          # Base settings (SCITEX_DIR)
├── 00_crossref-local.env  # CrossRef database
├── 00_figrecipe.env       # Plotting config
├── 01_scholar.env         # OpenAthens, API keys
├── 01_audio.env           # TTS backends
└── ...                    # Per-module configs

→ Full configuration reference

Three Interfaces

🐍 Python API for Humans and AI Agents

@stx.session — Reproducible Experiment Tracking

import scitex as stx

@stx.session
def main(filename="demo.jpg"):
    fig, ax = stx.plt.subplots()
    ax.plot_line(t, signal)
    ax.set_xyt("Time (s)", "Amplitude", "Title")
    stx.io.save(fig, filename)
    return 0

Output:

script_out/FINISHED_SUCCESS/2025-01-08_12-30-00_AbC1/
├── demo.jpg                    # Figure with embedded metadata
├── demo.csv                    # Auto-exported plot data
├── CONFIGS/CONFIG.yaml         # Reproducible parameters
└── logs/{stdout,stderr}.log    # Execution logs

stx.io — Universal File I/O (30+ formats)

stx.io.save(df, "output.csv")
stx.io.save(fig, "output.jpg")
df = stx.io.load("output.csv")

stx.stats — Publication-Ready Statistics (23 tests)

result = stx.stats.test_ttest_ind(group1, group2, return_as="dataframe")
# Includes: p-value, effect size, CI, normality check, power

→ Full module status

🖥️ CLI Commands for Humans and AI Agents

scitex --help-recursive              # Show all commands
scitex scholar fetch "10.1038/..."   # Download paper by DOI
scitex scholar bibtex refs.bib       # Enrich BibTeX
scitex stats recommend               # Suggest statistical tests
scitex audio speak "Done"            # Text-to-speech
scitex capture snap                  # Screenshot

# List available APIs and tools
scitex list-python-apis              # List all Python APIs (210 items)
scitex mcp list-tools                # List all MCP tools (120+ tools)
scitex introspect api scitex.stats   # List APIs for specific module

→ Full CLI reference

🔧 MCP Tools — 120+ tools for AI Agents

Turn AI agents into autonomous scientific researchers.

Typical workflow: Scholar (find papers) → Stats (analyze) → Plt (visualize) → Writer (manuscript) → Capture (verify)

Category	Tools	Description
writer	28	LaTeX manuscript compilation
scholar	23	PDF download, metadata enrichment
capture	12	Screen monitoring and capture
introspect	12	Python code introspection
audio	10	Text-to-speech, audio playback
stats	10	Automated statistical testing
plt	9	Matplotlib figure creation
diagram	9	Mermaid and Graphviz diagrams
dataset	8	Scientific dataset access
social	7	Social media posting
canvas	7	Scientific figure canvas
template	6	Project scaffolding
verify	6	Reproducibility verification
dev	6	Ecosystem version management
ui	5	Notifications
linter	3	Code pattern checking

Claude Desktop (~/.config/claude/claude_desktop_config.json):

{
  "mcpServers": {
    "scitex": {
      "command": "scitex",
      "args": ["mcp", "start"],
      "env": {
        "SCITEX_ENV_SRC": "${SCITEX_ENV_SRC}"
      }
    }
  }
}

→ Full MCP tool reference

🧩 Standalone Packages

SciTeX integrates several standalone packages that can be used independently:

Package	scitex Module	Description
figrecipe	scitex.plt	Publication-ready matplotlib figures
crossref-local	scitex.scholar.crossref_scitex	Local CrossRef database (167M+ papers)
openalex-local	scitex.scholar.openalex_scitex	Local OpenAlex database (250M+ papers)
socialia	scitex.social	Social media posting (Twitter, LinkedIn)
scitex-writer	scitex.writer	LaTeX manuscript compilation
scitex-dataset	scitex.dataset	Scientific dataset access

Each package works standalone or as part of scitex:

pip install figrecipe        # Use independently
pip install scitex[plt]      # Or via scitex

📖 Documentation

• Read the Docs: Complete API reference
• Examples: Usage examples and demonstrations

🤝 Contributing

We welcome contributions! See CONTRIBUTING.md.

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AGPL-3.0