scitex 2.14.0__py3-none-any.whl → 2.15.1__py3-none-any.whl

scitex-2.14.0.dist-info/METADATA

@@ -1,1238 +0,0 @@
-Metadata-Version: 2.4
-Name: scitex
-Version: 2.14.0
-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 :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-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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-
-<!-- ---
-!-- Timestamp: 2026-01-09 13:47:53
-!-- 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.
-
-<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 |
-
-### All-in-One Server (Recommended)
-
-Use `scitex-mcp-server` to load all MCP modules with a single server:
-
-**Claude Desktop Configuration** (`~/.config/claude/claude_desktop_config.json`):
-
-```json
-{
-  "mcpServers": {
-    "scitex": {
-      "command": "scitex-mcp-server"
-    }
-  }
-}
-```
-
-Tools are prefixed by module (e.g., `audio_speak`, `capture_screenshot`, `scholar_enrich_bibtex`).
-
-### Individual Servers
-
-For selective module loading, configure servers individually:
-
-```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.
-
-
-
----
-
-<p align="center">
-  <a href="https://scitex.ai" target="_blank"><img src="docs/scitex-icon-navy-inverted.png" alt="SciTeX" width="40"/></a>
-  <br>
-  AGPL-3.0 · ywatanabe@scitex.ai
-</p>
-
-<!-- EOF -->