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

scitex/scholar/docs/to_claude/guidelines/python/scitex/14-dsp-module.md

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-<!-- ---
-!-- Timestamp: 2025-06-14 06:44:09
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT-SCITEX-14-dsp-module.md
-!-- --- -->
-
-## `stx.dsp`
-
-- `stx.dsp` is a module for digital signal processing
-
-### `stx.dsp` Module (Digital Signal Processing)
-
-#### Signal Processing Functions
-
-```python
-# Filtering
-filtered = stx.dsp.filt.bandpass(signal, fs=1000, f_range=[8, 12])
-filtered = stx.dsp.filt.lowpass(signal, fs=1000, f_cutoff=30)
-
-# Transforms
-envelope = stx.dsp.hilbert(signal, get='envelope')
-phase = stx.dsp.hilbert(signal, get='phase')
-wavelet_output = stx.dsp.wavelet(signal, fs=1000)
-
-# Analysis
-freqs, psd = stx.dsp.psd(signal, fs=1000)
-mi = stx.dsp.pac(signal, fs=1000, f_phase=[2, 6], f_amp=[30, 90])
-```
-
-## Example: Signal Processing
-
-```python
-import numpy as np
-import scitex
-
-# Generate test signal (10 Hz sine wave with 1000 Hz sampling rate)
-fs = 1000  # Sampling frequency in Hz
-t = np.arange(0, 1, 1/fs)  # 1 second of data
-signal = np.sin(2 * np.pi * 10 * t)  # 10 Hz sine wave
-
-# Apply bandpass filter
-filtered_signal = stx.dsp.filt.bandpass(signal, fs=fs, f_range=[8, 12])
-
-# Calculate power spectral density
-freqs, psd = stx.dsp.psd(filtered_signal, fs=fs)
-
-# Extract signal envelope
-envelope = stx.dsp.hilbert(filtered_signal, get='envelope')
-
-# Plot results
-fig, axes = stx.plt.subplots(nrows=3, ncols=1, figsize=(10, 8))
-
-# Plot signals
-axes[0].plot(t[:500], signal[:500], label='Original')
-axes[0].plot(t[:500], filtered_signal[:500], label='Filtered (8-12 Hz)')
-axes[0].set_xyt('Time (s)', 'Amplitude', 'Time Domain')
-axes[0].legend()
-
-# Plot PSD
-axes[1].plot(freqs, psd)
-axes[1].set_xyt('Frequency (Hz)', 'Power/Frequency (dB/Hz)', 'Frequency Domain')
-axes[1].set_xlim(0, 50)  # Display up to 50 Hz
-
-# Plot envelope
-axes[2].plot(t[:500], filtered_signal[:500], label='Filtered')
-axes[2].plot(t[:500], envelope[:500], label='Envelope')
-axes[2].set_xyt('Time (s)', 'Amplitude', 'Signal Envelope')
-axes[2].legend()
-
-# Save figure with automatic CSV export
-stx.io.save(fig, './data/figures/signal_analysis.png', symlink_from_cwd=True)
-```
-
-## 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/15-pd-module.md

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-<!-- ---
-!-- Timestamp: 2025-06-14 06:44:21
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT-SCITEX-15-pd-module.md
-!-- --- -->
-
-### `stx.pd` Module (Pandas Utilities)
-
-```python
-# Round numeric values
-rounded_df = stx.pd.round(df, factor=3)
-
-# Enhanced DataFrame slicing
-filtered = stx.pd.slice(df, {'column1': 'value', 'column2': [1, 2, 3]})
-
-# Coordinate conversion
-xyz_data = stx.pd.to_xyz(df)
-```
-
-## 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/16-stats-module.md

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-<!-- ---
-!-- Timestamp: 2025-06-14 06:44:32
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT-SCITEX-16-stats-module.md
-!-- --- -->
-
-## `stx.stats`
-
-- `stx.stats` is a module for statistical tests
-
-```python
-# Format p-values with stars
-stars = stc.stats.p2stars(0.001)  # '***'
-
-# Apply multiple comparison correction
-corrected = stc.stats.fdr_correction(results_df)
-
-# Correlation tests
-r, p = stc.stats.tests.corr_test(x, y, method='pearson')
-```
-
-## Statistical Reporting
-
-Report statistical results with:
-- p-value
-- Significance stars
-- Sample size
-- Effect size
-- Test name
-- Statistic value
-- Null hypothesis
-
-```python
-# Example results dictionary
-results = {
-    "p_value": pval,
-    "stars": stc.stats.p2stars(pval),  # Format: 0.02 -> "*", 0.009 -> "**"
-    "n1": n1,
-    "n2": n2,
-    "dof": dof,
-    "effsize": effect_size,
-    "test_name": test_name_text,
-    "statistic": statistic_value,
-    "H0": null_hypothesis_text,
-}
-```
-
-### Using p2stars
-
-```python
->>> stc.stats.p2stars(0.0005)
-'***'
->>> stc.stats.p2stars("0.03")
-'*'
->>> stc.stats.p2stars("1e-4")
-'***'
->>> df = pd.DataFrame({'p_value': [0.001, "0.03", 0.1, "NA"]})
->>> stc.stats.p2stars(df)
-   p_value
-0  0.001 ***
-1  0.030   *
-2  0.100
-3     NA  NA
-```
-
-### Multiple Comparisons Correction
-
-Always use FDR correction for multiple comparisons:
-
-```python
-# Apply FDR correction to DataFrame with p_value column
-corrected_results = stc.stats.fdr_correction(results_df)
-```
-
-## 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/17-other-modules.md

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-<!-- ---
-!-- Timestamp: 2025-08-31 13:35:51
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-17-other-modules.md
-!-- --- -->
-
-### Utility Functions
-```python
-# Convert p-values to significance stars (e.g., *)
-stx.stats.p2stars(p_value)
-
-# Apply FDR correction for multiple comparisons
-stx.stats.fdr_correction(results_df)
-
-# Round numeric values in dataframe
-stx.pd.round(df, factor=3)
-```
-
-## 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/17-str-module.md

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-<!-- ---
-!-- Timestamp: 2025-08-31 13:38:08
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-17-str-module.md
-!-- --- -->
-
-### str module
-
-## Print colored header
-This print colored text output with specified border. Since this creates message + 4 lines, please used this for only important headers.
-```python
-stx.str.printc("message here", c='blue', char="-", n=40)
-#
-# ----------------------------------------
-# message here
-# ----------------------------------------
-#
-```
-
-## 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/18-directory-structure-for-scientific-work.md

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-<!-- ---
-!-- Timestamp: 2025-05-30 08:21:56
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT-SCITEX-18-directory-structure-for-scientific-work.md
-!-- --- -->
-
-## Directory Structure of Scientific Project
-
-```
-<project root>
-│
-├── config/                 # Configuration files
-│   └── *.yaml              # YAML config files (PATH.yaml, etc.)
-│
-├── data/                   # Centralized data storage
-│   └── <dir_name>/         # Organized by category
-│        └── file.ext → ../../scripts/<script>_out/file.ext  # Symlinks to script outputs
-│
-└── scripts/                # Script files and outputs
-    └── <category>/
-        ├── script.py       # Python script
-        └── script_out/     # Output directory for this script
-            ├── file.ext    # Output files
-            └── logs/       # Logging directory for each run (managed by `stx.session.start` and `stx.session.close`)
-                ├── RUNNING
-                ├── FINISHED_SUCCESS
-                └── FINISHED_FAILURE
-└── examples/
-└── tests/
-└── .dev/
-```
-
-
-**IMPORTANT**: 
-- DO NOT CREATE DIRECTORIES IN PROJECT ROOT  
-- Create child directories under predefined directories instead
-
-## Temporal Working Space: `./.dev`
-- For your temporally work, use `./.dev`
-  - Organize playground with categoris: 
-    `./.dev/category-name-1/...`
-    `./.dev/category-name-2/...`
-
-## 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/19-directory-structure-for-pip-package.md

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-<!-- ---
-!-- Timestamp: 2025-08-31 17:57:04
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-19-directory-structure-for-pip-package.md
-!-- --- -->
-
-
-## Directory Structure for Python PIP Packages
-
-### Modern Python Package Structure (PEP 517/518)
-
-```
-<project-root>/
-├── src/                      # Source code directory
-│   └── <package_name>/       # Your actual package
-│       ├── __init__.py
-│       ├── module1.py
-│       ├── module2.py
-│       └── subpackage/
-│           └── __init__.py
-├── tests/                    # Test files (mirrors src/ structure)
-│   ├── conftest.py          # pytest configuration
-│   ├── sync_tests_with_source.sh  # Auto-sync test structure with src/
-│   └── <package_name>/      # Mirrors src/<package_name>/
-│       ├── test_module1.py
-│       ├── test_module2.py
-│       └── subpackage/
-│           └── test_submodule.py
-├── examples/                 # Example scripts (can mirror src/ for complex packages)
-│   ├── 01_filename.py
-│   ├── 02_filename.py
-│   └── data/                 # Example inputs (gitignored)
-│   └── outputs/              # Example outputs (gitignored)
-├── docs/                     # Documentation
-├── .dev/                     # Temporary work (gitignored)
-│   ├── experiments/
-│   └── scratch/
-├── pyproject.toml
-├── README.md
-├── LICENSE
-├── .gitignore
-├── MANIFEST.in
-└── requirements.txt
-```
-
-### Test Directory Mirroring
-
-The `tests/` directory **MUST mirror the structure of `src/`** for consistency:
-
-```bash
-# Example mirroring:
-src/
-└── gpac/
-    ├── __init__.py
-    ├── _PAC.py
-    ├── _Filters/
-    │   ├── __init__.py
-    │   ├── _BaseFilter.py
-    │   └── _BandpassFilter.py
-    └── utils/
-        └── helpers.py
-
-tests/
-├── sync_tests_with_source.sh   # Auto-sync script
-└── gpac/
-    ├── test__PAC.py           # Note: test_ prefix
-    ├── _Filters/
-    │   ├── test__BaseFilter.py
-    │   └── test__BandpassFilter.py
-    └── utils/
-        └── test_helpers.py
-```
-
-### Auto-sync Script: `sync_tests_with_source.sh`
-
-This script automatically:
-1. Creates test directory structure mirroring `src/`
-2. Creates test files for all source modules
-3. Preserves existing test code when updating
-4. Adds source code as comments for reference
-5. Moves stale test files to `.old-<timestamp>/` directories
-
-Key features:
-- Run with `-m` or `--move` to move stale test files
-- Preserves your test code when syncing
-- Adds pytest runner boilerplate
-- Includes source code as comments at the end of each test file
-
-### Examples Directory Structure
-
-For complex packages, examples can also mirror the source structure:
-
-```bash
-examples/
-├── sync_examples_with_source.sh  # Auto-sync script for examples
-├── example_quickstart.py         # General examples
-├── example_advanced.py
-├── <package_name>/              # Module-specific examples (optional)
-│   ├── example_module1.py
-│   └── subpackage/
-│       └── example_submodule.py
-└── outputs/                     # All outputs go here (gitignored)
-    └── <auto-generated>/        # Created by stx.io.save()
-```
-
-### Auto-sync Script: `sync_examples_with_source.sh`
-
-This script helps create example placeholders for key modules:
-1. Creates example directory structure for important modules only
-2. Generates example templates with scitex conventions
-3. Preserves existing example code when updating
-4. Moves stale example files to `.old-<timestamp>/` directories
-
-Key features:
-- Run with `-m` or `--move` to move stale example files
-- Only creates examples for key modules (not every source file)
-- Templates include stx.io conventions
-- Example naming: `_ModuleName.py` → `example_ModuleName.py`
-
-### Key Points
-
-1. **Use `pyproject.toml` ONLY** - Don't create `setup.py` unless absolutely necessary
-2. **Source in `src/`** - Prevents accidental imports during development
-3. **Tests MUST mirror `src/`** - Use `sync_tests_with_source.sh` to maintain
-4. **Examples use scitex conventions**:
-   ```python
-   import scitex as stx
-   
-   # Save outputs to examples/outputs/<script_name>/
-   sdir = stx.io.get_dirpath(__file__, "outputs")
-   stx.io.save(fig, sdir / "results.png")
-   ```
-5. **Test file naming**: `test_<source_filename>.py` (with test_ prefix)
-
-### Minimal pyproject.toml Template
-
-```toml
-[build-system]
-requires = ["setuptools>=61.0", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "your-package"
-version = "0.1.0"
-authors = [{name="Your Name", email="email@example.com"}]
-description = "Package description"
-readme = "README.md"
-license = {text = "MIT"}
-requires-python = ">=3.8"
-dependencies = [
-    "numpy>=1.19.0",
-    "scitex>=1.0.0",
-]
-
-[project.urls]
-Homepage = "https://github.com/username/repo"
-Repository = "https://github.com/username/repo"
-
-[tool.setuptools]
-package-dir = {"" = "src"}
-packages = ["your_package"]
-
-[tool.pytest.ini_options]
-testpaths = ["tests"]
-pythonpath = ["src"]
-```
-
-### Temporal Working Space: `.dev/`
-- For temporary experiments and development work
-- Organize with categories:
-  ```
-  .dev/
-  ├── experiments/        # Testing new features
-  ├── benchmarks/         # Performance testing
-  ├── prototypes/         # Quick prototypes
-  └── scratch/           # Temporary files
-  ```
-- Add `.dev/` to `.gitignore`
-
-### Important Rules
-1. **NEVER create files/directories in project root** - Use predefined directories
-2. **NEVER create setup.py** - Use pyproject.toml only
-3. **ALWAYS use src/ layout** - Better testing and import isolation
-4. **ALWAYS follow scitex conventions** in examples
-5. **ALWAYS mirror src/ structure in tests/** - Use sync_tests_with_source.sh
-6. **ALWAYS use test_ prefix** for test files (e.g., `test_module.py`)
-
-### Example Directory After Following Guidelines
-```
-my-package/
-├── src/
-│   └── my_package/
-│       ├── __init__.py
-│       ├── core.py
-│       ├── utils.py
-│       └── models/
-│           ├── __init__.py
-│           └── base.py
-├── tests/
-│   ├── conftest.py
-│   ├── sync_tests_with_source.sh
-│   └── my_package/
-│       ├── test_core.py
-│       ├── test_utils.py
-│       └── models/
-│           └── test_base.py
-├── examples/
-│   ├── sync_examples_with_source.sh
-│   ├── example_basic_usage.py
-│   ├── my_package/          # Optional: module-specific examples
-│   │   └── models/
-│   │       └── example_custom_model.py
-│   └── outputs/             # Created by stx.io.save()
-│       └── example_basic_usage/
-│           └── results.png
-├── pyproject.toml
-├── README.md
-├── LICENSE
-└── .gitignore
-```
-
-### Benefits of This Structure
-
-1. **Easy navigation** - Test location mirrors source location
-2. **Automatic maintenance** - sync_tests_with_source.sh keeps structure updated
-3. **Clear organization** - Examples can be general or module-specific
-4. **Modern packaging** - pyproject.toml handles everything
-5. **scitex integration** - Consistent output handling across examples
-
-## 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/99-example-project.md

@@ -1,19 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-29 20:33:45
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/SCITEX-99-scitex-example-project.md
-!-- --- -->
-
-## SCITEX-based Project Examples
- - For Scientific Project
-   - Use `./scripts` instead of `./src`
-   - See `./docs/to_claude/examples/example-scitex-project`
- - For Python Pip Package Project
-   - Use `./src` instead of `./scripts`
-   - See `./docs/to_claude/examples/`
-
-## 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/zen_of_python.md

@@ -1,82 +0,0 @@
-# The Zen of Python
-
-by Tim Peters
-
-Beautiful is better than ugly.
-Explicit is better than implicit.
-Simple is better than complex.
-Complex is better than complicated.
-Flat is better than nested.
-Sparse is better than dense.
-Readability counts.
-Special cases aren't special enough to break the rules.
-Although practicality beats purity.
-Errors should never pass silently.
-Unless explicitly silenced.
-In the face of ambiguity, refuse the temptation to guess.
-There should be one-- and preferably only one --obvious way to do it.
-Although that way may not be obvious at first unless you're Dutch.
-Now is better than never.
-Although never is often better than *right* now.
-If the implementation is hard to explain, it's a bad idea.
-If the implementation is easy to explain, it may be a good idea.
-Namespaces are one honking great idea -- let's do more of those!
-
-## Key Principles Explained
-
-### Beautiful is better than ugly
-Write code that is aesthetically pleasing and well-structured.
-
-### Explicit is better than implicit
-Make your intentions clear in your code. Don't rely on implicit behavior.
-
-### Simple is better than complex
-Choose simple solutions over complex ones when possible.
-
-### Complex is better than complicated
-If complexity is necessary, keep it manageable and understandable.
-
-### Flat is better than nested
-Avoid deep nesting of code structures. Flat structures are easier to read.
-
-### Sparse is better than dense
-Don't try to pack too much into a single line or expression.
-
-### Readability counts
-Code is read more often than it's written. Optimize for readability.
-
-### Special cases aren't special enough to break the rules
-Maintain consistency even when dealing with edge cases.
-
-### Although practicality beats purity
-Sometimes practical solutions are better than theoretically pure ones.
-
-### Errors should never pass silently
-Handle errors explicitly and visibly.
-
-### Unless explicitly silenced
-If you intentionally ignore an error, make it clear that it's intentional.
-
-### In the face of ambiguity, refuse the temptation to guess
-When unclear, ask for clarification rather than making assumptions.
-
-### There should be one-- and preferably only one --obvious way to do it
-Python aims for having one clear way to accomplish tasks.
-
-### Although that way may not be obvious at first unless you're Dutch
-A nod to Python's creator, Guido van Rossum, who is Dutch.
-
-### Now is better than never
-Don't procrastinate on necessary improvements.
-
-### Although never is often better than *right* now
-But don't rush into poorly thought-out solutions.
-
-### If the implementation is hard to explain, it's a bad idea
-Complex implementations that can't be explained simply are likely flawed.
-
-### If the implementation is easy to explain, it may be a good idea
-Simple, explainable solutions are often the best.
-
-### Namespaces are one honking great idea -- let's do more of those!
-Use namespaces to organize code and avoid naming conflicts.

scitex/scholar/docs/to_claude/guidelines/science/IMPORTANT-general.md

@@ -1,16 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-20 05:23:52
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.claude/to_claude/guidelines/IMPORTANT_guidelines_Scientific_Rules.md
-!-- --- -->
-
-## Figure Rules
-- Axes must have labels with units, ticks (n_ticks=3-5), and tick labels
-- Ranges must not be misleading:
-  - Bar graphs must start from 0
-  - Variables within range [0, 1] should be displayed in [0, 1] range
-- Figures are among the most important elements in science
-  - Ensure all generated figures are scientifically valid
-  - Consider aesthetic aspects as well although YOU MUST AVOID TO CONTROL IMPRESSIONS
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/science/IMPORTANT-scientific-attitude.md

@@ -1,25 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-06-07 07:12:28
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.claude/to_claude/guidelines/science/IMPORTANT-scientific-attitude.md
-!-- --- -->
-
-
-## Evidence Requirements
-- Run current codebase scripts and logs, not past versions
-- Code is dynamic - regression inevitable
-- All claims must be supported by files as evidence
-- Do not believe what is written but what and how code runs
-
-## Critical Analysis
-- Think critically and work logically
-- Analyze contradictory evidence systematically
-- Apply self-criticism: is claim reasonable? what trade-offs exist? are we too optimistic?
-- Maintain scientific rigor while advancing project
-
-## Scientific Standards
-- Be honest - seek truth and solid findings
-- Ensure reproducibility by the current code
-- Maintain rigor in all analysis
-
-<!-- EOF -->