scitex 2.4.2__tar.gz → 2.5.0__tar.gz

scitex-2.5.0/PKG-INFO

@@ -0,0 +1,761 @@
+Metadata-Version: 2.4
+Name: scitex
+Version: 2.5.0
+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: MIT
+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 :: MIT License
+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: 2025-11-19 16:19:32
+!-- 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
+
+<!-- badges -->
+[![PyPI version](https://badge.fury.io/py/scitex.svg)](https://badge.fury.io/py/scitex)
+[![Python Versions](https://img.shields.io/pypi/pyversions/scitex.svg)](https://pypi.org/project/scitex/)
+[![License](https://img.shields.io/github/license/ywatanabe1989/SciTeX-Code)](https://github.com/ywatanabe1989/SciTeX-Code/blob/main/LICENSE)
+[![Tests](https://github.com/ywatanabe1989/SciTeX-Code/actions/workflows/ci.yml/badge.svg)](https://github.com/ywatanabe1989/SciTeX-Code/actions)
+[![Coverage](https://codecov.io/gh/ywatanabe1989/SciTeX-Code/branch/main/graph/badge.svg)](https://codecov.io/gh/ywatanabe1989/SciTeX-Code)
+[![Stats Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/ywatanabe1989/GIST_ID/raw/scitex-stats-coverage.json)](https://github.com/ywatanabe1989/SciTeX-Code/actions/workflows/stats-coverage.yml)
+[![Logging Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/ywatanabe1989/GIST_ID/raw/scitex-logging-coverage.json)](https://github.com/ywatanabe1989/SciTeX-Code/actions/workflows/logging-coverage.yml)
+[![Documentation](https://readthedocs.org/projects/scitex/badge/?version=latest)](https://scitex.readthedocs.io/en/latest/?badge=latest)
+[![Code Style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+
+## 📦 Installation
+
+``` bash
+pip install scitex # ~600 MB, Core + utilities
+pip install scitex[dl,ml,jupyter,neuro,web,gui,scholar,writer,dev] # ~2-5 GB, Complete toolkit
+```
+
+### Alial
+
+``` 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)
+```
+
+**Optional Groups**:
+
+| Group       | Packages                                                | Size Impact |
+|-------------|---------------------------------------------------------|-------------|
+| **dl**      | PyTorch, transformers                                   | +2-4 GB     |
+| **ml**      | scikit-image, catboost, optuna, OpenAI, Anthropic, Groq | ~200 MB     |
+| **jupyter** | JupyterLab, papermill                                   | ~100 MB     |
+| **neuro**   | MNE, obspy (EEG/MEG analysis)                           | ~200 MB     |
+| **web**     | FastAPI, Flask, Streamlit                               | ~50 MB      |
+| **gui**     | Flask, DearPyGui, PyQt6 (multi-backend figure editors)  | ~100 MB     |
+| **scholar** | Selenium, PDF tools, paper management                   | ~150 MB     |
+| **writer**  | LaTeX compilation tools                                 | ~10 MB      |
+| **dev**     | Testing, linting (dev only)                             | ~100 MB     |
+
+## 🚀 Quick Start
+
+
+### The SciTeX Advantage: **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()
+```
+
+#### Without SciTeX ([188 Lines of Code](./examples/demo_session_plt_io_pure_python.py))
+<details>
+<summary>Click to see the pure Python equivalent requiring 3.3× more code</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>
+
+### What You Get With `@stx.session`
+
+Both implementations produce **identical outputs**, but SciTeX eliminates 131 lines of boilerplate:
+```bash
+demo_session_plt_io_out/
+├── demo.csv              # Auto-extracted plot data
+├── demo.jpg              # With embedded metadata
+└── FINISHED_SUCCESS/
+    └── 2025Y-11M-18D-09h12m03s_HmH5-main/
+        ├── CONFIGS/
+        │   ├── CONFIG.pkl    # Python object
+        │   └── CONFIG.yaml   # Human-readable
+        └── logs/
+            ├── stderr.log
+            └── stdout.log
+```
+
+**What SciTeX Automates:**
+- ✅ Session ID generation and tracking
+- ✅ Output directory management (`RUNNING/` → `FINISHED_SUCCESS/`)
+- ✅ Argument parsing with auto-generated help
+- ✅ Logging to files and console
+- ✅ Config serialization (YAML + pickle)
+- ✅ CSV export from matplotlib plots
+- ✅ Metadata embedding in images
+- ✅ Symlink management for centralized outputs
+- ✅ Error handling and directory cleanup
+- ✅ Global variable injection (CONFIG, plt, COLORS, logger, rng_manager)
+
+**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
+
+### Try It Yourself
+```bash
+pip install scitex
+python ./examples/demo_session_plt_io.py
+```
+
+## 📦 Module Overview
+
+SciTeX is organized into focused modules for different aspects of scientific computing:
+
+### 🔧 Core Utilities
+| Module                                          | Description                                                         |
+|-------------------------------------------------|---------------------------------------------------------------------|
+| [`scitex.gen`](./src/scitex/gen#readme)         | Project setup, session management, and experiment tracking          |
+| [`scitex.io`](./src/scitex/io#readme)           | Universal I/O for 30+ formats (CSV, JSON, HDF5, Zarr, pickle, etc.) |
+| [`scitex.path`](./src/scitex/path#readme)       | Path manipulation and project structure utilities                   |
+| [`scitex.logging`](./src/scitex/logging#readme) | Structured logging with color support and context                   |
+
+### 📊 Data Science & Statistics
+| Module                                      | Description                                                              |
+|---------------------------------------------|--------------------------------------------------------------------------|
+| [`scitex.stats`](./src/scitex/stats#readme) | 16 statistical tests, effect sizes, power analysis, multiple corrections |
+| [`scitex.plt`](./src/scitex/plt#readme)     | Enhanced matplotlib with auto-export and scientific captions             |
+| [`scitex.pd`](./src/scitex/pd#readme)       | Pandas extensions for research workflows                                 |
+
+### 🧠 AI & Machine Learning
+| Module                                      | Description                                             |
+|---------------------------------------------|---------------------------------------------------------|
+| [`scitex.ai`](./src/scitex/ai#readme)       | GenAI (7 providers), classification, training utilities |
+| [`scitex.torch`](./src/scitex/torch#readme) | PyTorch training loops, metrics, and utilities          |
+| [`scitex.nn`](./src/scitex/nn#readme)       | Custom neural network layers                            |
+
+### 🌊 Signal Processing
+| Module                                  | Description                                                   |
+|-----------------------------------------|---------------------------------------------------------------|
+| [`scitex.dsp`](./src/scitex/dsp#readme) | Filtering, spectral analysis, wavelets, PAC, ripple detection |
+
+### 📚 Literature Management
+| Module                                          | Description                                                     |
+|-------------------------------------------------|-----------------------------------------------------------------|
+| [`scitex.scholar`](./src/scitex/scholar#readme) | Paper search, PDF download, BibTeX enrichment with IF/citations |
+
+### 🌐 Web & Browser
+| Module                                          | Description                                                |
+|-------------------------------------------------|------------------------------------------------------------|
+| [`scitex.browser`](./src/scitex/browser#readme) | Playwright automation with debugging, PDF handling, popups |
+
+### 🗄️ Data Management
+| Module                                | Description                         |
+|---------------------------------------|-------------------------------------|
+| [`scitex.db`](./src/scitex/db#readme) | SQLite3 and PostgreSQL abstractions |
+
+### 🛠️ Utilities
+| Module                                                | Description                                         |
+|-------------------------------------------------------|-----------------------------------------------------|
+| [`scitex.decorators`](./src/scitex/decorators#readme) | Function decorators for caching, timing, validation |
+| [`scitex.rng`](./src/scitex/rng#readme)               | Reproducible random number generation               |
+| [`scitex.resource`](./src/scitex/resource#readme)     | System resource monitoring (CPU, memory, GPU)       |
+| [`scitex.dict`](./src/scitex/dict#readme)             | Dictionary manipulation and nested access           |
+| [`scitex.str`](./src/scitex/str#readme)               | String utilities for scientific text processing     |
+
+## 📖 Documentation
+
+### 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
+
+## 🤝 Contributing
+
+We welcome contributions! Please see our [Contributing Guide](CONTRIBUTING.md) for details.
+
+
+## 📄 License
+
+This project is licensed under the MIT License.
+
+## 📧 Contact
+
+Yusuke Watanabe (ywatanabe@scitex.ai)
+
+<!-- EOF -->