scitex 2.13.0__py3-none-any.whl → 2.15.1__py3-none-any.whl

scitex/scholar/docs/to_claude/guidelines/python/scitex/02-file-template.md

@@ -1,132 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-08-31 17:42:35
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-02-file-template.md
-!-- --- -->
-
-## Script Template
-
-SCITEX PYTHON SCRIPT MUST STRICTLY FOLLOW THIS STANDARD FORMAT:
-
-```python
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-05-31 07:15:35 (ywatanabe)"
-# File: ./relative/path/from/project/script.py
-# ----------------------------------------
-import os
-__FILE__ = (
-    "./relative/path/from/project/script.py"
-)
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-Functionalities:
-  - Does XYZ
-  - Does XYZ
-  - Does XYZ
-  - Saves XYZ
-
-Dependencies:
-  - scripts:
-    - /path/to/script1
-    - /path/to/script2
-  - packages:
-    - package1, package2, ...
-
-Input:
-  - /path/to/input/file.xxx
-  - /path/to/input/file.xxx
-
-Output:
-  - /path/to/input/file.xxx
-  - /path/to/input/file.xxx
-
-(Remove me: Please fill docstrings above, while keeping the bulette point style, and remove this instruction line)
-"""
-
-"""Imports"""
-import argparse
-import scitex as stx
-
-"""Warnings"""
-# stx.pd.ignore_SettingWithCopyWarning()
-# warnings.simplefilter("ignore", UserWarning)
-# with warnings.catch_warnings():
-#     warnings.simplefilter("ignore", UserWarning)
-
-"""Parameters"""
-# from stx.io import load_configs
-# CONFIG = load_configs()
-
-"""Functions & Classes"""
-def main(args):
-    return 0
-
-
-def parse_args() -> argparse.Namespace:
-    """Parse command line arguments."""
-    parser = argparse.ArgumentParser(description="")
-    # parser.add_argument(
-    #     "--var",
-    #     "-v",
-    #     type=int,
-    #     choices=None,
-    #     default=1,
-    #     help="(default: %(default)s)",
-    # )
-    # parser.add_argument(
-    #     "--flag",
-    #     "-f",
-    #     action="store_true",
-    #     default=False,
-    #     help="(default: %%(default)s)",
-    # )
-    args = parser.parse_args()
-    return args
-
-
-def run_main() -> None:
-    """Initialize scitex framework, run main function, and cleanup."""
-    global CONFIG, CC, sys, plt
-
-    import sys
-    import matplotlib.pyplot as plt
-
-    args = parse_args()
-
-    CONFIG, sys.stdout, sys.stderr, plt, CC = stx.session.start(
-        sys,
-        plt,
-        args=args,
-        file=__FILE__,
-        verbose=False,
-        agg=True,
-    )
-
-    exit_status = main(args)
-
-    stx.session.close(
-        CONFIG,
-        verbose=False,
-        notify=False,
-        message="",
-        exit_status=exit_status,
-    )
-
-
-if __name__ == "__main__":
-    run_main()
-
-# EOF
-```
-
-**⚠️ DO NOT MODIFY THE `run_main()` FUNCTION**  
-This handles stdout/stderr direction, logging, configuration, and more
-
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/scitex/03-configuration.md

@@ -1,53 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-06-14 06:40:55
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT-SCITEX-03-configuration.md
-!-- --- -->
-
-## Configuration Examples
-
-### PATH.yaml
-
-```yaml
-# Time-stamp: "2025-01-18 00:00:34 (ywatanabe)"
-# File: ./config/PATH.yaml
-
-PATH:
-  ECoG:
-    f"./data/patient_{patient_id}/{date}/ecog_signal.npy"
-```
-
-### COLORS.yaml
-
-```yaml
-# Time-stamp: "2025-01-18 00:00:34 (ywatanabe)"
-# File: ./config/COLORS.yaml
-
-COLORS:
-  SEIZURE_TYPE:
-    "1": "red"
-    "2": "orange"
-    "3": "pink"
-    "4": "gray"
-```
-
-Accessing configurations:
-
-```python
-import scitex as stx
-CONFIG = stx.io.load_configs()
-
-# Access config values
-print(CONFIG.COLORS.SEIZURE_TYPE)  # {"1": "red", "2": "orange", "3": "pink", "4": "gray"}
-
-# Resolve f-strings
-patient_id = "001"
-date = "2025_0101"
-print(eval(CONFIG.PATH.ECoG))  # "./data/patient_001/2025_0101/ecog_signal.npy"
-```
-
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/scitex/04-coding-style.md

@@ -1,126 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-29 20:33:05
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-04-scitex-coding-style.md
-!-- --- -->
-
-## Python Coding Style
-
-## Path management
-- ALL PATH MUST BE WRITTEN IN RELATIVE PATH
-- ALL RELATIVE PATHS MUST START FROM DOT: (e.g., `./target`, `../target`, `../../target`)
-- Relative from:
-    - **For SAVING, starts from the script path instead of cwd**
-    - **For other cases, starts from the current working directory**
-- Scripts MUST BE RUNfrom project root
-- Centralize path definitions in `./config/PATH.yaml`
-
-For scitex package development:
-- Use underscore prefix for imports (e.g., `import numpy as _np`)
-- Use relative imports (e.g., `from ..io._load import load`)
-
-### Naming Conventions
-
-| Type | Convention | Example |
-|------|------------|---------|
-| Variable names | snake_case | `data_frame`, `patient_id` |
-| Load paths | `lpath(s)` | `lpath = './data/input.csv'` |
-| Save paths | `spath(s)` | `spath = './data/output.csv'` |
-| Directory names | Noun form | `mnist-creation/`, `data-analysis/` |
-| Script files | Verb first (for actions) | `classify_mnist.py`, `preprocess_data.py` |
-| Class files | CapitalCase | `ClassName.py` |
-| Constants | UPPERCASE | `MAX_ITERATIONS = 100` |
-
-### Type Hints
-
-```python
-from typing import Union, Tuple, List, Dict, Any, Optional, Callable
-from collections.abc import Iterable
-
-# Define custom type aliases
-ArrayLike = Union[List, Tuple, np.ndarray, pd.Series, pd.DataFrame, xr.DataArray, torch.Tensor]
-
-def process_data(data: ArrayLike, factor: float = 1.0) -> np.ndarray:
-    """Process the input data."""
-    return np.array(data) * factor
-```
-
-### Docstring Format (NumPy Style)
-
-```python
-def func(arg1: int, arg2: str) -> bool:
-    """Summary line.
-
-    Extended description of function.
-
-    Example
-    ----------
-    >>> xx, yy = 1, "test"
-    >>> out = func(xx, yy)
-    >>> print(out)
-    True
-
-    Parameters
-    ----------
-    arg1 : int
-        Description of arg1
-    arg2 : str
-        Description of arg2
-
-    Returns
-    -------
-    bool
-        Description of return value
-    """
-    return True
-```
-
-For simple functions, one-line docstrings are acceptable:
-
-```python
-def add(a: int, b: int) -> int:
-    """Add two numbers and return the result."""
-    return a + b
-```
-
-### Function Organization
-
-Organize functions hierarchically:
-
-```python
-# 1. Main entry point
-# ---------------------------------------- 
-def main():
-    """Main function that coordinates the workflow."""
-    data = load_data()
-    processed = process_data(data)
-    save_results(processed)
-
-
-# 2. Core functions
-# ---------------------------------------- 
-def load_data():
-    """Load and prepare input data."""
-    pass
-
-def process_data(data):
-    """Process the data."""
-    pass
-
-def save_results(results):
-    """Save processing results."""
-    pass
-
-
-# 3. Helper functions
-# ---------------------------------------- 
-def validate_inputs(data):
-    """Validate input data."""
-    pass
-```
-
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/scitex/05-testing-guide.md

@@ -1,56 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-29 20:33:09
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-05-scitex-testing-guide.md
-!-- --- -->
-
-## Testing Guidelines
-
-- Use pytest (not unittest)
-- Create small, focused test functions
-- One test function per test file
-- Define test classes in dedicated scripts
-
-### Test File Structure
-
-```python
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-05-03 00:49:28 (ywatanabe)"
-# File: ./tests/scitex/plt/test_function.py
-
-import pytest
-import numpy as np
-
-def test_function():
-    """Test specific functionality."""
-    from stx.module.path import function
-    
-    # Setup test data
-    input_data = np.array([1, 2, 3])
-    
-    # Call function
-    result = function(input_data)
-    
-    # Assert expected results
-    assert isinstance(result, np.ndarray)
-    assert result.shape == (3,)
-    assert np.array_equal(result, np.array([2, 4, 6]))
-
-if __name__ == "__main__":
-    import os
-    pytest.main([os.path.abspath(__file__)])
-```
-
-### Running Tests
-
-Use the script in the project root:
-
-```bash
-./run_tests.sh
-```
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/scitex/06-examples-guide.md

@@ -1,42 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-08-31 17:55:12
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-06-examples-guide.md
-!-- --- -->
-
-# Example Guidelines
-
-## MUST USE `SCITEX`
-All example files MUST use `scitex` and follow the `scitex` framework
-Understand all the `scitex` guidelines in this directory
-
-## `./examples` directory
-- Output directory creation is automatically handled by:
-  - `stx.session.start`
-  - `stx.session.close`
-  - `stx.io.save`
-- `./examples` directory must contain key features to demonstrate the project
-
-## MUST RUN AND PRODUCE EXPLANATORY RESULTS
-- Implementing examples is not sufficient
-- ALWAYS RUN IMPLEMENTED EXAMPLES AND PRODUCE EXPLANATORY RESULTS
-  - Embrace figures for visual understanding
-  - Logs are automatically created by the scitex framework is also valuable
-  - The less comment in the script, the better.
-  - If comments need, it should be handled in `src` or `scripts`, possibly with verbose option.
-
-## Start from small
-1. Ensure each example works correctly one by one
-   Before working on multiple example files, complete a specific example
-   For example, if an issue found across multiple files, first, try to fix it on a file and run it to check the troubleshooting works.
-2. Increment this step gradually until all examples are prepared correctly.
-
-
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-```
-
-CLAUDE UNDERSTOOD: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT-SCITEX-06-examples-guide.md
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/scitex/11-gen-module.md

@@ -1,15 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-08-31 17:55:12
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-11-gen-module.md
-!-- --- -->
-
-## `stx.gen`
-
-- `stx.gen` is a module for general utilities
-
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/scitex/11-session-module.md

@@ -1,24 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-08-31 17:55:11
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-11-session-module.md
-!-- --- -->
-
-## `stx.session`
-
-- `stx.session` is a module for general utilities
-
-### Environment Management
-```python
-# Initialize environment (logging, paths, matplotlib, random seed)
-stx.session.start(...)
-
-# Clean up environment
-stx.session.close(...)
-```
-
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/scitex/12-io-module.md

@@ -1,112 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-06-14 06:43:09
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT-SCITEX-12-io-module.md
-!-- --- -->
-
-## `stx.io`
-
-- `stx.io` is a module for saving/loading data
-
-### Input/Output Operations
-**!!! IMPORTANT !!!**
-**DO NOT MKDIR IN PYTHON SCRITPS. `stx.io.save` MKDIR AUTOMATICALLY**
-**PATH MUST BE ALWAYS RELATIVE FROM THE SCRIPT ITSELF**
-
-### `stx.io.load_configs`
-```python
-# Load all YAML files from ./config as a combined, dot-accessible dictionary
-CONFIG = stx.io.load_configs()
-
-# Access configuration values
-print(CONFIG.PATH.DATA)  # Access path defined in PATH.yaml
-
-# Resolve f-strings in config
-patient_id = "001"
-data_path = eval(CONFIG.PATH.PATIENT_DATA)  # f"./data/patient_{patient_id}/data.csv"
-```
-
-#### `stx.io.load`
-```python
-# Load data with automatic format detection based on extension
-data = stx.io.load('./data/results.csv')  # CSV file, using pandas
-config = stx.io.load('./config/params.yaml')  # YAML file
-array = stx.io.load('./data/features.npy')  # NumPy array
-```
-
-Supported File Extensions for `stx.io.load` are:
-
-| Category | Extensions |
-|----------|------------|
-| **Numeric Data** | `.npy`, `.npz`, `.mat`, `.h5`, `.hdf5` |
-| **Tabular Data** | `.csv`, `.xlsx`, `.xls`, `.tsv` |
-| **Text & Config** | `.json`, `.yaml`, `.yml`, `.xml`, `.txt` |
-| **Python Objects** | `.pkl`, `.pickle`, `.joblib` |
-| **Media** | `.jpg`, `.png`, `.gif`, `.tiff`, `.pdf`, `.mp3`, `.wav` |
-| **Documents** | `.docx`, `.pdf` |
-| **Special** | `.db`, `.sqlite3`, `.edf` (EEG data) |
-
-#### `stx.io.save`
-
-Basic Usage:
-
-``` python
-# /path/to/script.py
-obj = ...
-
-# Saves to `/path/to/script_out/aab.ext`
-stx.io.save(obj, "./aab.ext", symlink_from_cwd=False)
-
-# Saves to `/path/to/script_out/aab.ext` and create symlink to `$(pwd)/aab.ext`
-stx.io.save(obj, "./aab.ext", symlink_from_cwd=True) 
-
-# Saves to `/path/to/script_out/aab/bbb.ext`
-stx.io.save(obj, "./aab/bbb.ext", symlink_from_cwd=False) 
-
-# Saves to `/path/to/script_out/aab/bbb.ext` and create symlink to `$(pwd)/aab/bbb.ext`
-stx.io.save(obj, "./aab/bbb.ext", symlink_from_cwd=True) 
-```
-
-Supported File Extensions for `stx.io.save` are:
-
-| Category | Extensions |
-|----------|------------|
-| **Numeric Data** | `.npy`, `.npz`, `.mat`, `.h5`, `.hdf5` |
-| **Tabular Data** | `.csv`, `.xlsx`, `.tsv` |
-| **Text & Config** | `.json`, `.yaml`, `.yml`, `.txt` |
-| **Python Objects** | `.pkl`, `.pickle`, `.joblib` |
-| **Media** | `.jpg`, `.png`, `.gif`, `.tiff`, `.mp4`, `.html` |
-| **Visualizations** | `.png`, `.jpg`, `.svg`, `.pdf`, `.html` |
-
-
-Rules:
-- `stx.io.save` saves data in a unified manner with respecting extension
-- `stx.io.save` ensures the target directory exits
-  - It calls `os.makedir("/path/to/target/directory", exists_ok=True)` internally
-  - ENSURE NOT TO CREATE ANY DIRECTORY BY YOURSELF
-- `stx.io.save` creates symlink
-  - ALWAYS explicitly specify `symlink_from_cwd=True` or `symlink_from_cwd=False`
-- Relative path MUST start from dot (e.g., `./path/to/target` or `../../path/to/target`
-- By combining `stx.plt.subplots`, **PLOTTED DATA IS TRACKED AND SAVED AS CSV AS WELL AS THE IMAGE THEMSELVES**
-  - Use `.jpg` for images to reduce size
-
-#### Reversibility of `stx.io.save` and `stx.io.load`
-
-Objects saved with `stx.io.save()` can be loaded with `stx.io.load()` while maintaining their original structure:
-
-```python
-# Save any Python object in a extension-aware manner
-data = {"name": "example", "values": np.array([1, 2, 3])}
-stx.io.save(data, './data/example.pkl', symlink_from_cwd=True)
-
-# Load it back with identical structure
-loaded_data = stx.io.load('./data/example.pkl')
-
-# data and loaded_data are identical
-```
-
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/scitex/13-plt-module.md

@@ -1,101 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-06-14 06:43:44
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT-SCITEX-13-plt-module.md
-!-- --- -->
-
-## `stx.plt`
-
-- `stx.plt` is a module for enhancing matplotlib for scientific purposes
-
-### `stx.plt.subplots`
-- `stx.plt.subplots` is a wrapper for `matplotlib.pyplot.plt.subplots`
-- However, it is not perfectly compatible
-- When problem found, create a bug-report to:
-  `~/proj/scitex_repo/project_management/bug-report-<title>.md`
-
-Features of `stx.plt.subplots`:
-- Track plotted data
-- `stx.io.save(fig, "./path/to/image.jpg", symlink_from_cwd=True)` creates
-  - 1. `./path/to/image.jpg` (as described in the `stx.io.save` block)
-  - 2. `./path/to/image.csv` <- Plotted data. IMPORTANT FOR CODE UNDERSTANDING AND REPRODUCIBILITY
-  - 3. Symlinks to both the jpg and csv files
-
-###### Basic Usage
-```python
-# Create trackable plots
-fig, axes = stx.plt.subplots(ncols=2)   # Returns wrapper objects that track plotting data
-
-# Set axis properties with combined method
-ax.set_xyt('X-axis', 'Y-axis', 'Title')  # ALWAYS use scitex wrappers instead of matplotlib methods
-```
-#### Creating Plots
-
-```python
-# Create a figure with tracked axes
-fig, axes = stx.plt.subplots(ncols=2, figsize=(10, 5))
-
-# Plot data
-axes[0].plot(x, y, label='Data')
-axes[1].scatter(x, z, label='Scatter')
-
-# Set labels and title using scitex wrapper method (PREFERRED WAY)
-axes[0].set_xyt('X-axis', 'Y-axis', 'Data Plot')
-axes[1].set_xyt('X-axis', 'Y-axis', 'Scatter Plot')
-
-# Add legend
-for ax in axes:
-    ax.legend()
-```
-
-#### Exporting Plot Data
-
-```python
-# Automatically export to CSV when saving figure
-stx.io.save(fig, './data/figures/plot.png', symlink_from_cwd=True)
-# Creates:
-# - /path/to/script_out/data/figures/plot.png
-# - /path/to/script_out/data/figures/plot.csv
-# - ./data/figures/plot.png -> /path/to/script_out/data/figures/plot.png
-# - ./data/figures/plot.csv -> /path/to/script_out/data/figures/plot.csv
-```
-
-## Example: Plot with CSV Export
-
-```python
-import numpy as np
-import scitex
-
-# Create data
-x = np.linspace(0, 10, 100)
-y1 = np.sin(x)
-y2 = np.cos(x)
-
-# Create figure with scitex
-fig, axes = stx.plt.subplots(ncols=2, figsize=(10, 5))
-
-# Plot data
-axes[0].plot(x, y1, label='sin(x)')
-axes[1].plot(x, y2, label='cos(x)')
-
-# Use scitex wrapper methods for labels and titles
-axes[0].set_xyt('x', 'y', 'Sine Function')
-axes[1].set_xyt('x', 'y', 'Cosine Function')
-
-# Add legends
-for ax in axes:
-    ax.legend()
-
-# Save figure - CSV automatically exported with the same basename
-stx.io.save(fig, './data/figures/trig_functions.png', symlink_from_cwd=True)
-```
-
-This creates:
-- `./data/figures/trig_functions.png` (the figure)
-- `./data/figures/trig_functions.csv` (the data in CSV format)
-
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-
-<!-- EOF -->