scitex 2.10.3__py3-none-any.whl → 2.13.0__py3-none-any.whl

scitex-2.13.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: scitex
+Version: 2.13.0
+Summary: A comprehensive Python library for scientific computing and data analysis
+Project-URL: Homepage, https://github.com/ywatanabe1989/scitex-code
+Project-URL: Documentation, https://scitex.readthedocs.io
+Project-URL: Repository, https://github.com/ywatanabe1989/scitex-code
+Project-URL: Bug Tracker, https://github.com/ywatanabe1989/scitex-code/issues
+Author-email: Yusuke Watanabe <ywatanabe@scitex.ai>
+License: AGPL-3.0
+License-File: LICENSE
+Keywords: data-analysis,machine-learning,neural-networks,research,scientific-computing,signal-processing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU Affero General Public License v3
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
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+Description-Content-Type: text/markdown
+
+<!-- ---
+!-- Timestamp: 2026-01-08 11:41:42
+!-- Author: ywatanabe
+!-- File: /home/ywatanabe/proj/scitex-code/README.md
+!-- --- -->
+
+# SciTeX
+
+A Python framework for scientific research that makes the entire research pipeline more standardized, structured, and reproducible by automating repetitive processes.
+
+Part of the fully open-source SciTeX project: https://scitex.ai
+
+## 📊 Status
+
+<!-- badges -->
+<div align="center">
+  <table>
+    <tr>
+      <td align="center"><strong>Package</strong></td>
+      <td>
+        <a href="https://badge.fury.io/py/scitex"><img src="https://badge.fury.io/py/scitex.svg" alt="PyPI version"></a>
+        <a href="https://pypi.org/project/scitex/"><img src="https://img.shields.io/pypi/pyversions/scitex.svg" alt="Python Versions"></a>
+        <a href="https://github.com/ywatanabe1989/SciTeX-Code/blob/main/LICENSE"><img src="https://img.shields.io/github/license/ywatanabe1989/SciTeX-Code" alt="License"></a>
+      </td>
+    </tr>
+    <tr>
+      <td align="center"><strong>Install</strong></td>
+      <td>
+        <img src="https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/core.json&label=core" alt="Core Install Time">
+        <img src="https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/all.json&label=all" alt="All Install Time">
+        <img src="https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/heavy.json&label=heavy" alt="Heavy Install Time">
+        <img src="https://img.shields.io/badge/uv-recommended-blue" alt="uv recommended">
+      </td>
+    </tr>
+  </table>
+</div>
+
+<details>
+<summary><strong>Module Status - Tests & Installation</strong></summary>
+
+### Core Modules
+
+| Module | Description | Install (Time) | Tests |
+|--------|-------------|----------------|-------|
+| [`io`](./src/scitex/io#readme) | Universal I/O (30+ formats) | `scitex[io]` ![io](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/io.json) | [![io](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-io.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-io.yml) |
+| [`path`](./src/scitex/path#readme) | Path utilities | `scitex[path]` ![path](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/path.json) | [![path](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-path.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-path.yml) |
+| [`str`](./src/scitex/str#readme) | String processing | `scitex[str]` ![str](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/str.json) | [![str](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-str.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-str.yml) |
+| [`dict`](./src/scitex/dict#readme) | Dictionary utilities | core ![dict](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/dict.json) | [![dict](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-dict.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-dict.yml) |
+| [`types`](./src/scitex/types#readme) | Type checking | core ![types](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/types.json) | [![types](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-types.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-types.yml) |
+| [`config`](./src/scitex/config#readme) | Configuration management | `scitex[config]` ![config](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/config.json) | [![config](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-config.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-config.yml) |
+| [`utils`](./src/scitex/utils#readme) | General utilities | `scitex[utils]` ![utils](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/utils.json) | [![utils](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-utils.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-utils.yml) |
+| [`decorators`](./src/scitex/decorators#readme) | Function decorators | `scitex[decorators]` ![decorators](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/decorators.json) | [![decorators](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-decorators.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-decorators.yml) |
+| [`logging`](./src/scitex/logging#readme) | Structured logging | `scitex[logging]` ![logging](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/logging.json) | [![logging](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-logging.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-logging.yml) |
+| [`gen`](./src/scitex/gen#readme) | Project setup | `scitex[gen]` ![gen](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/gen.json) | [![gen](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-gen.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-gen.yml) |
+
+### Data Science & Statistics
+
+| Module | Description | Install (Time) | Tests |
+|--------|-------------|----------------|-------|
+| [`stats`](./src/scitex/stats#readme) | Statistical tests & analysis | `scitex[stats]` ![stats](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/stats.json) | [![stats](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-stats.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-stats.yml) |
+| [`pd`](./src/scitex/pd#readme) | Pandas extensions | `scitex[pd]` ![pd](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/pd.json) | [![pd](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-pd.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-pd.yml) |
+| [`linalg`](./src/scitex/linalg#readme) | Linear algebra | `scitex[linalg]` ![linalg](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/linalg.json) | [![linalg](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-linalg.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-linalg.yml) |
+| [`plt`](./src/scitex/plt#readme) | Enhanced matplotlib | `scitex[plt]` ![plt](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/plt.json) | [![plt](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-plt.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-plt.yml) |
+| [`dsp`](./src/scitex/dsp#readme) | Signal processing | `scitex[dsp]` ![dsp](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/dsp.json) | [![dsp](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-dsp.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-dsp.yml) |
+
+### AI & Machine Learning
+
+| Module | Description | Install (Time) | Tests |
+|--------|-------------|----------------|-------|
+| [`ai`](./src/scitex/ai#readme) | GenAI (7 providers) | `scitex[ai]` ![ai](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/ai.json) | [![ai](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-ai.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-ai.yml) |
+| [`nn`](./src/scitex/nn#readme) | Neural network layers | `scitex[nn]` ![nn](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/nn.json) | [![nn](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-nn.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-nn.yml) |
+| [`torch`](./src/scitex/torch#readme) | PyTorch utilities | `scitex[torch]` ![torch](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/torch.json) | [![torch](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-torch.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-torch.yml) |
+
+### System & Tools
+
+| Module | Description | Install (Time) | Tests |
+|--------|-------------|----------------|-------|
+| [`cli`](./src/scitex/cli#readme) | Command-line tools | `scitex[cli]` ![cli](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/cli.json) | [![cli](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-cli.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-cli.yml) |
+| [`sh`](./src/scitex/sh#readme) | Shell utilities | `scitex[sh]` ![sh](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/sh.json) | [![sh](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-sh.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-sh.yml) |
+| [`git`](./src/scitex/git#readme) | Git operations | `scitex[git]` ![git](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/git.json) | [![git](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-git.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-git.yml) |
+| [`session`](./src/scitex/session#readme) | Session management | `scitex[session]` ![session](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/session.json) | [![session](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-session.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-session.yml) |
+| [`resource`](./src/scitex/resource#readme) | System monitoring | `scitex[resource]` ![resource](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/resource.json) | [![resource](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-resource.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-resource.yml) |
+| [`db`](./src/scitex/db#readme) | Database abstractions | `scitex[db]` ![db](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/db.json) | [![db](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-db.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-db.yml) |
+
+### Research & Publishing
+
+| Module | Description | Install (Time) | Tests |
+|--------|-------------|----------------|-------|
+| [`writer`](./src/scitex/writer#readme) | Document generation | `scitex[writer]` ![writer](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/writer.json) | [![writer](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-writer.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-writer.yml) |
+| [`tex`](./src/scitex/tex#readme) | LaTeX processing | `scitex[tex]` ![tex](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/tex.json) | [![tex](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-tex.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-tex.yml) |
+| [`msword`](./src/scitex/msword#readme) | MS Word conversion | `scitex[msword]` ![msword](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/msword.json) | [![msword](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-msword.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-msword.yml) |
+| [`scholar`](./src/scitex/scholar#readme) | Literature management | `scitex[scholar]` ![scholar](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/scholar.json) | [![scholar](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-scholar.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-scholar.yml) |
+| [`diagram`](./src/scitex/diagram#readme) | Diagram generation | `scitex[diagram]` ![diagram](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/diagram.json) | [![diagram](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-diagram.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-diagram.yml) |
+
+### Web & Automation
+
+| Module | Description | Install (Time) | Tests |
+|--------|-------------|----------------|-------|
+| [`web`](./src/scitex/web#readme) | Web scraping | `scitex[web]` ![web](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/web.json) | [![web](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-web.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-web.yml) |
+| [`browser`](./src/scitex/browser#readme) | Browser automation | `scitex[browser]` ![browser](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/browser.json) | [![browser](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-browser.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-browser.yml) |
+
+### Other Modules
+
+| Module | Description | Install (Time) | Tests |
+|--------|-------------|----------------|-------|
+| [`audio`](./src/scitex/audio#readme) | Audio processing | `scitex[audio]` ![audio](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/audio.json) | [![audio](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-audio.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-audio.yml) |
+| [`capture`](./src/scitex/capture#readme) | Screen capture | `scitex[capture]` ![capture](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/capture.json) | [![capture](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-capture.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-capture.yml) |
+| [`repro`](./src/scitex/repro#readme) | Reproducibility | `scitex[repro]` ![repro](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/repro.json) | [![repro](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-repro.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-repro.yml) |
+| [`benchmark`](./src/scitex/benchmark#readme) | Performance testing | `scitex[benchmark]` ![benchmark](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/benchmark.json) | [![benchmark](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-benchmark.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-benchmark.yml) |
+| [`security`](./src/scitex/security#readme) | Security utilities | `scitex[security]` ![security](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/security.json) | [![security](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-security.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-security.yml) |
+| [`dt`](./src/scitex/dt#readme) | Datetime utilities | `scitex[dt]` ![dt](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/dt.json) | [![dt](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-dt.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-dt.yml) |
+| [`dev`](./src/scitex/dev#readme) | Development tools | `scitex[dev]` ![dev](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/dev.json) | [![dev](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-dev.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-dev.yml) |
+| [`schema`](./src/scitex/schema#readme) | Data schemas | `scitex[schema]` ![schema](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/schema.json) | [![schema](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-schema.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-schema.yml) |
+| [`bridge`](./src/scitex/bridge#readme) | Module integration | `scitex[bridge]` ![bridge](https://img.shields.io/endpoint?url=https://ywatanabe1989.github.io/scitex-code/badges/bridge.json) | [![bridge](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-bridge.yml/badge.svg)](https://github.com/ywatanabe1989/scitex-code/actions/workflows/test-bridge.yml) |
+
+</details>
+
+## 📦 Installation
+
+``` bash
+uv pip install scitex[all]     # Recommended: Full installation with all modules
+uv pip install scitex          # Core only (numpy, pandas, PyYAML, tqdm)
+uv pip install scitex[heavy]   # Include heavy deps (torch, mne, optuna, etc.)
+```
+
+> **Note**: Heavy dependencies (torch, mne, optuna, catboost, jax, tensorflow, umap-learn)
+> are optional and NOT included by default. Install with `scitex[heavy]` if needed.
+> Modules gracefully handle missing dependencies with `*_AVAILABLE` flags.
+
+<details>
+<summary><strong>Arial Font Setup for Figures</strong></summary>
+
+``` bash
+# Ubuntu
+sudo apt update
+sudo apt-get install ttf-mscorefonts-installer
+sudo DEBIAN_FRONTEND=noninteractive \
+    apt install -y ttf-mscorefonts-installer
+sudo mkdir -p /usr/share/fonts/truetype/custom
+sudo cp /mnt/c/Windows/Fonts/arial*.ttf /usr/share/fonts/truetype/custom/
+sudo fc-cache -fv
+rm ~/.cache/matplotlib -rf
+
+# WSL
+mkdir -p ~/.local/share/fonts/windows
+cp /mnt/c/Windows/Fonts/arial*.ttf ~/.local/share/fonts/windows/
+fc-cache -fv ~/.local/share/fonts/windows
+rm ~/.cache/matplotlib -rf
+```
+
+``` python
+# Check
+import matplotlib
+print(matplotlib.rcParams['font.family'])
+
+import matplotlib.font_manager as fm
+fonts = fm.findSystemFonts()
+print("Arial found:", any("Arial" in f or "arial" in f for f in fonts))
+[a for a in fonts if "Arial" in a or "arial" in a][:5]
+
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+
+mpl.rcParams["font.family"] = "Arial"
+mpl.rcParams["font.sans-serif"] = ["Arial"]  # 念のため
+
+fig, ax = plt.subplots(figsize=(3, 2))
+ax.text(0.5, 0.5, "Arial Test", fontsize=32, ha="center", va="center")
+ax.set_axis_off()
+
+fig.savefig("arial_test.png", dpi=300)
+plt.close(fig)
+```
+
+</details>
+
+## Why SciTeX?
+
+SciTeX automates research analysis code.
+
+<!-- **What SciTeX Automates:**
+ !-- - ✅ Symlink management for centralized outputs
+ !-- - ✅ Error handling and directory cleanup
+ !-- - ✅ Global variable injection (CONFIG, plt, COLORS, logger, rng)
+ !-- 
+ !-- **Research Benefits:**
+ !-- - 📊 **Figures + data always together** - CSV auto-exported from every plot
+ !-- - 🔄 **Perfect reproducibility** - Every run tracked with unique session ID
+ !-- - 🌍 **Universal format** - CSV data readable anywhere
+ !-- - 📝 **Zero manual work** - Metadata embedded automatically
+ !-- - 🎯 **3.3× less code** - Focus on research, not infrastructure -->
+
+
+<details>
+<summary><strong><code>@scitex.session</code></strong> — Reproducible Experiment Tracking + Auto-CLI</summary>
+
+Standardized outputs with automatic logging. Scripts and outputs closely linked for full traceability.
+
+**Auto-CLI Generation**: Function arguments automatically become argparse options:
+
+```python
+# /path/to/script.py
+import scitex as stx
+
+@stx.session
+def main(
+    # arg1,                     # Required: -a ARG1, --arg1 ARG1
+    # kwarg1="value1",          # Optional: -k KWARG1, --kwarg1 KWARG1 (default: value1)
+    CONFIG=stx.INJECTED,        # Auto-injected from $(pwd)/config/*.yaml files
+    plt=stx.INJECTED,           # Pre-configured matplotlib
+    COLORS=stx.INJECTED,        # Color palette
+    rng=stx.INJECTED,           # Seeded random generator
+    logger=stx.INJECTED,        # Session logger
+):
+    """This docstring becomes --help description."""
+    
+    stx.io.save(results, "results.csv", symlink_to="./data/")
+    # SUCC: Saved to: /path/to/script_out/tmp.txt (4.0 B)
+    # SUCC: Symlinked: /path/to/script_out/tmp.txt ->
+    # SUCC:            ./data/tmp.txt
+    
+    return 0
+```
+
+```bash
+$ python script.py --help
+usage: script.py [-a ARG1] [-k KWARG1]
+  -a ARG1, --arg1 ARG1     (required)
+  -k KWARG1, --kwarg1 KWARG1  (default: value1)
+
+$ python script.py -a myvalue
+# Runs with arg1="myvalue", kwarg1="value1"
+```
+
+**Output Structure**:
+```bash
+/path/to/script.py
+/path/to/script_out/
+├── FINISHED_SUCCESS/
+│    └── 2025-01-08_12-30-00_AbC1/ # Session ID allocated
+│        ├── results.csv
+│        ├── CONFIGS/
+│        │   ├── CONFIG.pkl    # Python object
+│        │   └── CONFIG.yaml   # Human-readable
+│        └── logs/
+│            ├── stderr.log    # Standard Errors
+│            └── stdout.log    # Standard Outputs
+├── FINISHED_FAILED/
+│    └── ...
+└── RUNNING/
+     └── ...
+```
+
+</details>
+
+<details>
+<summary><strong><code>scitex.plt</code></strong> — Auto-Export Figures with Data</summary>
+
+Figures and data always together. CSV auto-exported from every plot.
+
+```python
+import scitex as stx
+
+fig, ax = stx.plt.subplots()
+ax.plot_line(x, y)  # Data tracked automatically
+stx.io.save(fig, "plot.png")
+# Creates: plot.png + plot.csv
+```
+
+</details>
+
+<details>
+<summary><strong><code>scitex.io</code></strong> — Universal File I/O (30+ formats)</summary>
+
+One API for all formats: CSV, JSON, YAML, pickle, NumPy, HDF5, Zarr, PyTorch, images, PDFs, EEG formats.
+
+```python
+import scitex as stx
+
+# Unified API Call for +30 formats
+stx.io.save(df, "output.csv")
+stx.io.save(arr, "output.npy")
+stx.io.save(fig, "output.jpg")
+
+# Round Trip Loading
+df = stx.io.load("output.csv")
+arr = stx.io.load("output.npy")
+```
+
+</details>
+
+<details>
+<summary><strong><code>scitex.stats</code></strong> — Publication-Ready Statistics (23 tests)</summary>
+
+Automatic assumption checking, effect sizes, multiple comparison corrections, 9 export formats.
+
+```python
+import scitex as stx
+
+result = stx.stats.test_ttest_ind(
+    group1, group2,
+    return_as="dataframe"  # or "latex", "markdown", "excel"
+)
+# Includes: p-value, effect size, CI, normality check, power analysis
+```
+
+</details>
+
+<details>
+<summary><strong><code>scitex.scholar</code></strong> — Literature Management & BibTeX Enrichment</summary>
+
+BibTeX enrichment with abstracts for LLM context, DOI resolution, PDF download, Impact Factor.
+
+```bash
+scitex scholar bibtex papers.bib --project myresearch --num-workers 8
+```
+
+```bibtex
+# Before: Minimal BibTeX
+@article{Smith2024,
+  title = {Neural Networks},
+  author = {Smith, John},
+  doi = {10.1038/s41586-024-00001-1}
+}
+
+# After: Enriched with abstract for LLM context
+@article{Smith2024,
+  title = {Neural Networks for Brain Signal Analysis},
+  author = {Smith, John and Lee, Alice},
+  doi = {10.1038/s41586-024-00001-1},
+  journal = {Nature},
+  year = {2024},
+  abstract = {We present a novel deep learning approach...},  # Rich context for LLMs
+  impact_factor = {64.8}
+}
+```
+
+</details>
+
+<details>
+<summary><strong><code>scitex.writer</code></strong> — LaTeX Manuscript Management</summary>
+
+Python interface for LaTeX manuscripts with git-based version control.
+
+```python
+from scitex.writer import Writer
+
+writer = Writer("my_paper")
+intro = writer.manuscript.contents.introduction
+
+lines = intro.read()
+intro.write(lines + ["New paragraph..."])
+intro.commit("Update introduction")
+
+result = writer.compile_manuscript()
+```
+
+</details>
+
+<details>
+<summary><strong><code>scitex.ai</code></strong> — Unified AI/ML Interface (7 providers)</summary>
+
+Single API for OpenAI, Anthropic, Google, Perplexity, DeepSeek, Groq, local models.
+
+```python
+from scitex.ai.genai import GenAI
+
+ai = GenAI(provider="openai")
+response = ai("Explain this data pattern")
+
+# Switch providers instantly
+ai = GenAI(provider="anthropic", model="claude-3-opus-20240229")
+```
+
+</details>
+
+## 🖥️ CLI Commands
+
+SciTeX provides a comprehensive command-line interface:
+
+<details>
+<summary><strong>CLI Commands</strong></summary>
+
+```bash
+# SciTeX Cloud (https://scitex.ai)
+scitex cloud login                    # Login to SciTeX Cloud
+scitex cloud clone user/project       # Clone from cloud
+scitex cloud create my-project        # Create new repository
+scitex cloud enrich -i refs.bib -o enriched.bib  # BibTeX enrichment API
+
+# Configuration
+scitex config list                    # Show all configured paths
+scitex config init                    # Initialize directories
+
+# Research Tools
+scitex scholar bibtex papers.bib      # Process BibTeX, download PDFs
+scitex scholar single --doi "10.1038/nature12373"
+
+# TIP: Get BibTeX from Scholar QA (https://scholarqa.allen.ai/chat/)
+#      Ask questions → Export All Citations → Save as .bib file
+scitex stats recommend --data data.csv
+
+# Media
+scitex audio speak "Hello world"
+scitex capture snap --output screenshot.jpg
+
+# Document Processing
+scitex tex compile manuscript.tex
+scitex writer compile my_paper
+
+# Utilities
+scitex resource usage                 # System resource monitoring
+scitex security check --save          # Security audit
+scitex web get-urls https://example.com
+scitex completion                     # Enable tab completion
+```
+
+</details>
+
+## 🔌 MCP Servers
+
+<details>
+<summary><strong>Model Context Protocol (MCP) servers for AI agent integration</strong></summary>
+
+SciTeX provides Model Context Protocol (MCP) servers for AI agent integration:
+
+| Server | Description |
+|--------|-------------|
+| `scitex-audio` | Text-to-speech for agent feedback |
+| `scitex-capture` | Screen monitoring and capture |
+| `scitex-plt` | Matplotlib figure creation |
+| `scitex-stats` | Automated statistical testing |
+| `scitex-scholar` | PDF download and metadata enrichment |
+| `scitex-diagram` | Mermaid and flowchart creation |
+| `scitex-template` | Project scaffolding |
+| `scitex-canvas` | Scientific figure canvas |
+
+**Claude Desktop Configuration** (`~/.config/claude/claude_desktop_config.json`):
+
+```json
+{
+  "mcpServers": {
+    "scitex-audio": {
+      "command": "scitex-audio"
+    },
+    "scitex-capture": {
+      "command": "scitex-capture"
+    },
+    "scitex-scholar": {
+      "command": "scitex-scholar"
+    }
+  }
+}
+```
+
+</details>
+
+## 🚀 Quick Start
+
+
+### Research Analysis with **70% Less Code**
+
+Compare these two implementations that produce **identical research outputs**:
+
+#### With SciTeX ([57 Lines of Code]((./examples/demo_session_plt_io.py)))
+
+```python
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-11-18 09:34:36 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-code/examples/demo_session_plt_io.py
+
+
+"""Minimal Demonstration for scitex.{session,io,plt}"""
+
+import numpy as np
+import scitex as stx
+
+
+def demo(filename, verbose=False):
+    """Show metadata without QR code (just embedded)."""
+
+    # matplotlib.pyplot wrapper.
+    fig, ax = stx.plt.subplots()
+
+    t = np.linspace(0, 2, 1000)
+    signal = np.sin(2 * np.pi * 5 * t) * np.exp(-t / 2)
+
+    ax.plot_line(t, signal)  # Original plot for automatic CSV export
+    ax.set_xyt(
+        "Time (s)",
+        "Amplitude",
+        "Clean Figure (metadata embedded, no QR overlay)",
+    )
+
+    # Saving: stx.io.save(obj, rel_path, **kwargs)
+    stx.io.save(
+        fig,
+        filename,
+        metadata={"exp": "s01", "subj": "S001"},  # with meatadata embedding
+        symlink_to="./data",  # Symlink for centralized outputs
+        verbose=verbose,  # Automatic terminal logging (no manual print())
+    )
+    fig.close()
+
+    # Loading: stx.io.load(path)
+    ldir = __file__.replace(".py", "_out")
+    img, meta = stx.io.load(
+        f"{ldir}/{filename}",
+        verbose=verbose,
+    )
+
+
+@stx.session
+def main(filename="demo.jpg", verbose=True):
+    """Run demo for scitex.{session,plt,io}."""
+
+    demo(filename, verbose=verbose)
+
+    return 0
+
+
+if __name__ == "__main__":
+    main()
+```
+
+
+<details>
+<summary><strong>Equivalent Script without SciTeX ([188 Lines of Code](./examples/demo_session_plt_io_pure_python.py)), requiring 3.3× more code</strong></summary>
+
+```python
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-11-18 09:34:51 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-code/examples/demo_session_plt_io_pure_python.py
+
+
+"""Minimal Demonstration - Pure Python Version"""
+
+import argparse
+import json
+import logging
+import os
+import shutil
+import sys
+from datetime import datetime
+from pathlib import Path
+import random
+import string
+
+import matplotlib.pyplot as plt
+import numpy as np
+from PIL import Image
+from PIL.PngImagePlugin import PngInfo
+
+
+def generate_session_id():
+    """Generate unique session ID."""
+    timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
+    random_suffix = ''.join(random.choices(string.ascii_uppercase + string.digits, k=4))
+    return f"{timestamp}_{random_suffix}"
+
+
+def setup_logging(log_dir):
+    """Set up logging infrastructure."""
+    log_dir.mkdir(parents=True, exist_ok=True)
+    logger = logging.getLogger(__name__)
+    logger.setLevel(logging.INFO)
+    
+    stdout_handler = logging.FileHandler(log_dir / "stdout.log")
+    stderr_handler = logging.FileHandler(log_dir / "stderr.log")
+    console_handler = logging.StreamHandler(sys.stdout)
+    
+    formatter = logging.Formatter('%(levelname)s: %(message)s')
+    stdout_handler.setFormatter(formatter)
+    stderr_handler.setFormatter(formatter)
+    console_handler.setFormatter(formatter)
+    
+    logger.addHandler(stdout_handler)
+    logger.addHandler(stderr_handler)
+    logger.addHandler(console_handler)
+    
+    return logger
+
+
+def save_plot_data_to_csv(fig, output_path):
+    """Extract and save plot data."""
+    csv_path = output_path.with_suffix('.csv')
+    data_lines = ["ax_00_plot_line_0_line_x,ax_00_plot_line_0_line_y"]
+    
+    for ax in fig.get_axes():
+        for line in ax.get_lines():
+            x_data = line.get_xdata()
+            y_data = line.get_ydata()
+            for x, y in zip(x_data, y_data):
+                data_lines.append(f"{x},{y}")
+    
+    csv_path.write_text('\n'.join(data_lines))
+    return csv_path, csv_path.stat().st_size / 1024
+
+
+def embed_metadata_in_image(image_path, metadata):
+    """Embed metadata into image file."""
+    img = Image.open(image_path)
+    
+    if image_path.suffix.lower() in ['.png']:
+        pnginfo = PngInfo()
+        for key, value in metadata.items():
+            pnginfo.add_text(key, str(value))
+        img.save(image_path, pnginfo=pnginfo)
+    elif image_path.suffix.lower() in ['.jpg', '.jpeg']:
+        json_path = image_path.with_suffix(image_path.suffix + '.meta.json')
+        json_path.write_text(json.dumps(metadata, indent=2))
+        img.save(image_path, quality=95)
+
+
+def save_figure(fig, output_path, metadata=None, symlink_to=None, logger=None):
+    """Save figure with metadata and symlink."""
+    output_path = Path(output_path)
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    
+    if metadata is None:
+        metadata = {}
+    metadata['url'] = 'https://scitex.ai'
+    
+    if logger:
+        logger.info(f"📝 Saving figure with metadata to: {output_path}")
+        logger.info(f"  • Embedded metadata: {metadata}")
+    
+    csv_path, csv_size = save_plot_data_to_csv(fig, output_path)
+    if logger:
+        logger.info(f"✅ Saved to: {csv_path} ({csv_size:.1f} KiB)")
+    
+    fig.savefig(output_path, dpi=150, bbox_inches='tight')
+    embed_metadata_in_image(output_path, metadata)
+    
+    if symlink_to:
+        symlink_dir = Path(symlink_to)
+        symlink_dir.mkdir(parents=True, exist_ok=True)
+        symlink_path = symlink_dir / output_path.name
+        if symlink_path.exists() or symlink_path.is_symlink():
+            symlink_path.unlink()
+        symlink_path.symlink_to(output_path.resolve())
+
+
+    def demo(output_dir, filename, verbose=False, logger=None):
+    """Generate, plot, and save signal."""
+    fig, ax = plt.subplots(figsize=(8, 6))
+    
+    t = np.linspace(0, 2, 1000)
+    signal = np.sin(2 * np.pi * 5 * t) * np.exp(-t / 2)
+    
+    ax.plot(t, signal)
+    ax.set_xlabel("Time (s)")
+    ax.set_ylabel("Amplitude")
+    ax.set_title("Damped Oscillation")
+    ax.grid(True, alpha=0.3)
+    
+    output_path = output_dir / filename
+    save_figure(fig, output_path, metadata={"exp": "s01", "subj": "S001"},
+                symlink_to=output_dir.parent / "data", logger=logger)
+    plt.close(fig)
+    
+    return 0
+
+
+def main():
+    """Run demo - Pure Python Version."""
+    parser = argparse.ArgumentParser(description="Run demo - Pure Python Version")
+    parser.add_argument('-f', '--filename', default='demo.jpg')
+    parser.add_argument('-v', '--verbose', type=bool, default=True)
+    args = parser.parse_args()
+    
+    session_id = generate_session_id()
+    script_path = Path(__file__).resolve()
+    output_base = script_path.parent / (script_path.stem + "_out")
+    running_dir = output_base / "RUNNING" / session_id
+    logs_dir = running_dir / "logs"
+    config_dir = running_dir / "CONFIGS"
+    
+    logger = setup_logging(logs_dir)
+    
+    print("=" * 40)
+    print(f"Pure Python Demo")
+    print(f"{session_id} (PID: {os.getpid()})")
+    print(f"\n{script_path}")
+    print(f"\nArguments:")
+    print(f"    filename: {args.filename}")
+    print(f"    verbose: {args.verbose}")
+    print("=" * 40)
+    
+    config_dir.mkdir(parents=True, exist_ok=True)
+    config_data = {
+        'ID': session_id,
+        'FILE': str(script_path),
+        'SDIR_OUT': str(output_base),
+        'SDIR_RUN': str(running_dir),
+        'PID': os.getpid(),
+        'ARGS': vars(args)
+    }
+    (config_dir / "CONFIG.json").write_text(json.dumps(config_data, indent=2))
+    
+    try:
+        result = demo(output_base, args.filename, args.verbose, logger)
+        success_dir = output_base / "FINISHED_SUCCESS" / session_id
+        success_dir.parent.mkdir(parents=True, exist_ok=True)
+        shutil.move(str(running_dir), str(success_dir))
+        logger.info(f"\n✅ Script completed: {success_dir}")
+        return result
+    except Exception as e:
+        error_dir = output_base / "FINISHED_ERROR" / session_id
+        error_dir.parent.mkdir(parents=True, exist_ok=True)
+        shutil.move(str(running_dir), str(error_dir))
+        logger.error(f"\n❌ Error: {e}", exc_info=True)
+        raise
+
+
+if __name__ == "__main__":
+    sys.exit(main())
+```
+
+</details>
+
+
+## 📖 Documentation
+
+<details>
+<summary><strong>Resources</strong></summary>
+
+### Online Documentation
+- **[Read the Docs](https://scitex.readthedocs.io/)**: Complete API reference and guides
+- **[Interactive Examples](https://scitex.readthedocs.io/en/latest/examples/index.html)**: Browse all tutorial notebooks
+- **[Quick Start Guide](https://scitex.readthedocs.io/en/latest/getting_started.html)**: Get up and running quickly
+
+### Local Resources
+- **[Master Tutorial Index](./examples/00_SCITEX_MASTER_INDEX.ipynb)**: Comprehensive guide to all features
+- **[Examples Directory](./examples/)**: 25+ Jupyter notebooks covering all modules
+- **[Module List](./docs/scitex_modules.csv)**: Complete list of all functions
+- **(Experimental) [MCP Servers Documentation](./mcp_servers/README.md)**
+
+### Key Tutorials
+1. **[I/O Operations](./examples/01_scitex_io.ipynb)**: Essential file handling (start here!)
+2. **[Plotting](./examples/14_scitex_plt.ipynb)**: Publication-ready visualizations
+3. **[Statistics](./examples/11_scitex_stats.ipynb)**: Research-grade statistical analysis
+4. **[Scholar](./examples/16_scitex_scholar.ipynb)**: Literature management with impact factors
+5. **[AI/ML](./examples/16_scitex_ai.ipynb)**: Complete machine learning toolkit
+
+</details>
+
+## 🤝 Contributing
+
+We welcome contributions! Please see our [Contributing Guide](CONTRIBUTING.md) for details.
+
+
+## 📄 License
+
+AGPL-3.0.
+
+## 📧 Contact
+
+Yusuke Watanabe (ywatanabe@scitex.ai)
+
+<!-- EOF -->