pax_global_header 0000666 0000000 0000000 00000000064 15140133332 0014505 g ustar 00root root 0000000 0000000 52 comment=f5ec92bd24677905521b689c765e9fa49adbe056
Sigima-1.1.1/ 0000775 0000000 0000000 00000000000 15140133332 0012716 5 ustar 00root root 0000000 0000000 Sigima-1.1.1/.coveragerc 0000664 0000000 0000000 00000001232 15140133332 0015035 0 ustar 00root root 0000000 0000000 [run]
#--- Ignore this warning because the process isolation feature of DataLab
#--- causes coverage to report 0% coverage when no computation is performed
#--- in the isolated process during the session.
disable_warnings = no-data-collected
parallel = True
concurrency = multiprocessing,thread
omit =
*/sigima/tests/*
*/sigima/client/stub.py
*/guidata/*
*/plotpy/*
*/qwt/*
#--- Workaround for certain builds of python-opencv package:
./config-3.9.py
./config-3.py
./config.py
#---
[report]
exclude_also =
def __repr__
if __name__ == .__main__.:
if TYPE_CHECKING:
if DEBUG[\s]*:
if self.__debug[\s]*:
Sigima-1.1.1/.env.template 0000664 0000000 0000000 00000000014 15140133332 0015314 0 ustar 00root root 0000000 0000000 PYTHONPATH=. Sigima-1.1.1/.github/ 0000775 0000000 0000000 00000000000 15140133332 0014256 5 ustar 00root root 0000000 0000000 Sigima-1.1.1/.github/ISSUE_TEMPLATE/ 0000775 0000000 0000000 00000000000 15140133332 0016441 5 ustar 00root root 0000000 0000000 Sigima-1.1.1/.github/ISSUE_TEMPLATE/bug_report.md 0000664 0000000 0000000 00000001261 15140133332 0021133 0 ustar 00root root 0000000 0000000 ---
name: Bug report
about: Create a report to help us improve
title: ''
labels: bug
assignees: ''
---
**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
Steps to reproduce the behavior:
1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error
**Expected behavior**
A clear and concise description of what you expected to happen.
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Installation information**
Describe how you installed Sigima (e.g., via pip, conda, or from source) and provide the version of Sigima you are using.
**Additional context**
Add any other context about the problem here.
Sigima-1.1.1/.github/ISSUE_TEMPLATE/doc_request.md 0000664 0000000 0000000 00000001141 15140133332 0021275 0 ustar 00root root 0000000 0000000 ---
name: Documentation request
about: Ask for documentation about a specific topic
title: ''
labels: documentation
assignees: ''
---
**Is your documentation request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
**Describe the topic you would like to be covered**
A clear and concise description of what you want to be documented.
**Describe the nature of the documentation you would like to see**
Tutorial, reference, etc.
**Additional context**
Add any other context or screenshots about the feature request here.
Sigima-1.1.1/.github/ISSUE_TEMPLATE/feature_request.md 0000664 0000000 0000000 00000001134 15140133332 0022165 0 ustar 00root root 0000000 0000000 ---
name: Feature request
about: Suggest an idea for this project
title: ''
labels: enhancement
assignees: ''
---
**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
**Describe the solution you'd like**
A clear and concise description of what you want to happen.
**Describe alternatives you've considered**
A clear and concise description of any alternative solutions or features you've considered.
**Additional context**
Add any other context or screenshots about the feature request here.
Sigima-1.1.1/.github/ISSUE_TEMPLATE/tutorial_request.md 0000664 0000000 0000000 00000001457 15140133332 0022405 0 ustar 00root root 0000000 0000000 ---
name: Tutorial request
about: Ask for a tutorial on a specific topic
title: ''
labels: documentation
assignees: ''
---
**Describe the context and technical field of the tutorial you would like to see**
A clear and concise description of your technical field, and of the specific application.
**Describe the topic you would like to be covered**
A clear and concise description of what you want to be documented.
**Describe the features you would like to see in the tutorial**
A clear and concise description of the features you would like to see in the tutorial.
**Additional context**
Add any other context or screenshots about the feature request here.
_Please attach an example data set, if possible.
And please confirm that you are willing to share this data set under the terms of DataLab's license._
Sigima-1.1.1/.github/copilot-instructions.md 0000664 0000000 0000000 00000042207 15140133332 0021020 0 ustar 00root root 0000000 0000000 # Sigima AI Coding Agent Instructions
This document provides essential guidance for AI coding agents working on the Sigima codebase—the computation engine powering DataLab's signal and image processing.
## Project Overview
**Sigima** is a **headless Python library** providing scientific computation functions for 1D signals and 2D images. It is **GUI-independent** (no Qt/PlotPyStack) and designed for testability, modularity, and remote execution.
### Core Architecture: Three-Layer Model
Sigima separates concerns into three distinct layers:
1. **`sigima.objects`**: Data model (`SignalObj`, `ImageObj` wrapping NumPy arrays)
2. **`sigima.proc`**: High-level computation functions operating on objects
3. **`sigima.tools`**: Low-level NumPy algorithms (used by `proc` and external projects)
```python
# Example: Processing a signal object (high-level)
from sigima import SignalObj
import sigima.proc.signal as sips
obj = SignalObj.create(x, y)
result = sips.normalize(obj, sigima.params.NormalizeParam.create(method="minmax"))
# Example: Using low-level tools directly (NumPy arrays)
from sigima.tools.signal import filtering
filtered_y = filtering.apply_moving_average(y, n=5)
```
**Key Design Principle**: `sigima.tools` fills gaps in NumPy/SciPy/scikit-image, not a general-purpose replacement. DataLab uses many `tools` functions independently of the object model.
### Technology Stack
- **Python**: 3.9+ (`from __future__ import annotations`)
- **Core**: NumPy (≥1.22), SciPy (≥1.10.1), scikit-image (≥0.19.2), pandas (≥1.4)
- **GUI Parameters**: guidata (≥3.13) for `DataSet` parameter classes
- **Optional**: opencv-python-headless (≥4.8.1.78)
- **Testing**: pytest with `--gui` flag for visual validation
- **Linting**: Ruff (preferred), Pylint
- **Docs**: Sphinx with French translations (sphinx-intl)
### Workspace Structure
```
Sigima/
├── sigima/
│ ├── objects/ # Data model (SignalObj, ImageObj, ROI)
│ │ ├── signal/ # SignalObj implementation
│ │ ├── image/ # ImageObj implementation
│ │ └── scalar/ # GeometryResult, TableResult
│ ├── proc/ # High-level computation functions
│ │ ├── base.py # Common processing (ROI, arithmetic)
│ │ ├── signal/ # Signal processing (filtering, FFT, fitting, etc.)
│ │ ├── image/ # Image processing (edges, morphology, detection)
│ │ └── decorator.py # @computation_function decorator
│ ├── tools/ # Low-level NumPy algorithms
│ │ ├── signal/ # Signal algorithms (peak detection, stability, etc.)
│ │ └── image/ # Image algorithms (detection, geometry, etc.)
│ ├── io/ # I/O for signals/images (CSV, formats)
│ ├── params.py # Centralized parameter import (re-exports from proc/)
│ ├── client/ # SimpleRemoteProxy for DataLab control
│ └── tests/ # pytest test suite
├── scripts/
│ └── run_with_env.py # Environment loader (.env support)
├── .env # PYTHONPATH=.;../guidata;../plotpy
└── pyproject.toml
```
**Related Projects** (sibling directories):
- `../DataLab/` - GUI application using Sigima
- `../PlotPy/` - Plotting library (used in tests with `--gui`)
- `../guidata/` - Parameter/configuration framework
## Development Workflows
### Running Commands
**ALWAYS use `scripts/run_with_env.py`** to load `.env` before running Python commands:
```powershell
# ✅ CORRECT
python scripts/run_with_env.py python -m pytest
# ❌ WRONG - Misses local guidata/plotpy
python -m pytest
```
### Testing
```powershell
# Run all tests (fast, no GUI)
python scripts/run_with_env.py python -m pytest --ff
# Run GUI-assisted validation tests (visual checks)
python scripts/run_with_env.py python -m pytest --gui
# Run specific test module
python scripts/run_with_env.py python -m pytest sigima/tests/signal/processing_unit_test.py
# Coverage
python scripts/run_with_env.py python -m coverage run -m pytest sigima
python -m coverage html
```
**Test Organization**:
- `tests/common/`: ROI, validation, worker, title formatting
- `tests/signal/`: Signal processing tests
- `tests/image/`: Image processing tests
- `tests/io/`: I/O format tests
**Pytest Configuration** (`conftest.py`):
- `env.execenv.unattended = True` (no GUI by default)
- `set_validation_mode(ValidationMode.STRICT)` for tests
- Custom flag: `--gui` enables visual validation
### Linting and Formatting
```powershell
# Ruff (preferred)
python scripts/run_with_env.py python -m ruff format
python scripts/run_with_env.py python -m ruff check --fix
# Pylint
python scripts/run_with_env.py python -m pylint sigima \
--disable=duplicate-code,fixme,too-many-arguments, \
too-many-branches,too-many-instance-attributes
```
### Translations
```powershell
# Scan and update .po files
python scripts/run_with_env.py python -m guidata.utils.translations scan \
--name sigima --directory . --copyright-holder "DataLab Platform Developers" \
--languages fr
# Compile .mo files
python scripts/run_with_env.py python -m guidata.utils.translations compile \
--name sigima --directory .
```
## Core Patterns
### 1. Computation Functions with `@computation_function` Decorator
**All `sigima.proc` functions** use this decorator to enable dual calling conventions:
```python
from sigima.proc.decorator import computation_function
import sigima.params
@computation_function()
def my_processing(src: SignalObj, p: MyParam) -> SignalObj:
"""Process signal with my algorithm.
Args:
src: Input signal
p: Processing parameters
Returns:
Processed signal
"""
dst = src.copy()
# ... processing logic using p.param1, p.param2 ...
return dst
```
**Dual calling style enabled by decorator**:
```python
# Style 1: DataSet parameter object (DataLab GUI style)
param = sigima.params.MyParam.create(param1=10, param2="value")
result = my_processing(src, param)
# Style 2: Expanded keyword arguments (script-friendly)
result = my_processing(src, param1=10, param2="value")
```
**Key Rules**:
- Parameter class MUST be a `guidata.dataset.DataSet` subclass
- Always re-export parameter classes in `sigima.params` module
- Export computation functions in `__all__` of their module AND in `sigima/proc/{signal|image}/__init__.py`
### 2. Object Model: `SignalObj` and `ImageObj`
**Core attributes**:
```python
# SignalObj
signal.x # X coordinates (1D NumPy array, float64)
signal.y # Y data (1D NumPy array, float64)
signal.dx, signal.dy # Optional uncertainties
signal.xydata # Property returning (x, y) tuple
signal.set_xydata(x, y, dx=None, dy=None)
# ImageObj
image.data # 2D NumPy array (various dtypes)
image.x0, image.y0, image.dx, image.dy # Pixel coordinates
image.metadata # Dict for labels, units, etc.
# Common to both
obj.roi # List of ROI objects (SegmentROI, RectangularROI, etc.)
obj.get_data(roi_index=None) # Extract data with optional ROI mask
obj.copy() # Deep copy with metadata
```
**Data type enforcement**:
- `SignalObj`: Automatically converts integer X/Y arrays to `float64` for computational precision
- `ImageObj`: Preserves original dtype (uint8, uint16, float32, etc.) for image operations
### 3. Parameter Classes: `guidata.dataset.DataSet`
**All computation parameters** inherit from `guidata.dataset.DataSet`:
```python
import guidata.dataset as gds
class MyParam(gds.DataSet):
"""My processing parameters."""
param1 = gds.IntItem("Parameter 1", default=10, min=1, max=100)
param2 = gds.ChoiceItem("Method", ["method1", "method2"], default="method1")
@staticmethod
def create(param1: int = 10, param2: str = "method1") -> MyParam:
"""Factory method for easy instantiation."""
return MyParam(param1=param1, param2=param2)
```
**Conventions**:
- Always provide `create()` static method for script-friendly instantiation
- Export in `sigima.params` for centralized import
- Use descriptive docstrings (shown in DataLab GUI)
### 4. Title Formatting System
**Computation results need titles**. Sigima provides a configurable system:
```python
from sigima.proc.title_formatting import TitleFormatter, FormatResultTitle
class MyParam(gds.DataSet):
# ... parameter definitions ...
def generate_title(self) -> str:
"""Generate human-readable title for this computation."""
return f"my_processing(p1={self.param1}, p2={self.param2})"
# In computation function
@computation_function()
def my_processing(src: SignalObj, p: MyParam) -> SignalObj:
dst = src.copy()
# ... processing ...
FormatResultTitle.apply(dst, src, p) # Automatically formats title
return dst
```
**Title formatting modes**:
- **Parameter mode**: Default, uses `param.generate_title()` → `"normalize[minmax]"`
- **Function mode**: Used by DataLab, shows function name → `"Normalize"`
### 5. ROI (Region of Interest) System
**Types of ROI**:
- **Signal**: `SegmentROI` (X interval)
- **Image**: `RectangularROI`, `CircularROI`, `PolygonalROI`
**Using ROIs in processing**:
```python
# Get data masked by ROI
data = obj.get_data(roi_index=0) # First ROI
data = obj.get_data() # All data (no ROI)
# ROI iteration
for roi_index, roi in enumerate(obj.roi):
masked_data = obj.get_data(roi_index)
# ... process masked_data ...
```
**ROI creation in detection functions**:
```python
from sigima.objects import create_image_roi_around_points
# Automatically create ROIs around detected features
coords = detect_peaks(image.data) # Returns N×2 array
rois = create_image_roi_around_points(coords, image,
relative_size=1.5)
result.roi = rois # Attach to result
```
## Common Tasks
### Adding a New Signal Processing Function
**Complete workflow**:
1. **Implement in `sigima/proc/signal/processing.py` (or appropriate module)**:
```python
from sigima.proc.decorator import computation_function
import sigima.params
@computation_function()
def my_feature(src: SignalObj, p: MyFeatureParam) -> SignalObj:
"""Apply my feature to signal.
Args:
src: Input signal
p: Feature parameters
Returns:
Processed signal
"""
dst = src.copy()
# Processing logic using src.x, src.y
dst.y = apply_my_algorithm(src.y, p.threshold)
FormatResultTitle.apply(dst, src, p)
return dst
```
2. **Define parameter class in same file**:
```python
class MyFeatureParam(gds.DataSet):
"""Parameters for my feature."""
threshold = gds.FloatItem("Threshold", default=0.5, min=0, max=1)
@staticmethod
def create(threshold: float = 0.5) -> MyFeatureParam:
return MyFeatureParam(threshold=threshold)
def generate_title(self) -> str:
return f"my_feature(thresh={self.threshold})"
```
3. **Export in `sigima/proc/signal/__init__.py`**:
```python
from sigima.proc.signal.processing import my_feature, MyFeatureParam
__all__ = [
# ... existing exports ...
"my_feature",
"MyFeatureParam",
]
```
4. **Re-export parameter in `sigima/params.py`**:
```python
from sigima.proc.signal import MyFeatureParam
__all__ = [
# ... existing params ...
"MyFeatureParam",
]
```
5. **Add tests in `sigima/tests/signal/`**:
```python
import sigima.proc.signal as sips
import sigima.params
from sigima.tests.data import get_test_signal
@pytest.mark.validation
def test_my_feature():
"""Test my_feature processing."""
src = get_test_signal("paracetamol.txt")
p = sigima.params.MyFeatureParam.create(threshold=0.5)
result = sips.my_feature(src, p)
assert result is not None
assert len(result.y) == len(src.y)
# Add assertions checking result correctness
```
6. **Document in Sphinx** (if public API):
```python
# Docstring already makes it appear in API docs
# Add usage example in doc/examples/ if complex
```
### Adding Low-Level NumPy Functions to `tools`
**When to use `tools` vs `proc`**:
- Use `tools` for **pure NumPy/SciPy algorithms** that don't need object context
- Use `proc` for functions that need **metadata, ROI, or object operations**
**Example**:
```python
# sigima/tools/signal/myalgorithm.py
import numpy as np
from sigima.tools.checks import check_1d_array
def my_numpy_function(y: np.ndarray, threshold: float) -> np.ndarray:
"""Low-level algorithm operating on NumPy arrays.
Args:
y: 1D NumPy array
threshold: Processing threshold
Returns:
Processed array
"""
check_1d_array(y) # Input validation
# ... pure NumPy processing ...
return result
```
**Export in `sigima/tools/signal/__init__.py`** and document intended usage.
### Handling Integer Signal Data
**Issue**: Integer arrays cause precision loss in computations.
**Solution**: Sigima automatically converts to `float64`:
```python
# This is handled automatically now
signal = SignalObj.create(x=np.array([1, 2, 3]),
y=np.array([10, 20, 30])) # int arrays
# Internally converted to float64
# Validation: If you need strict float checks
from sigima.tools.checks import check_1d_array
check_1d_array(y) # Allows float dtypes, raises for invalid types
```
### Working with ROI Boundaries
**Issue**: ROI extending beyond image causes `ValueError`.
**Solution**: Use `get_data()` which automatically clips:
```python
# Safe: Handles ROI clipping automatically
data = image.get_data(roi_index=0)
# Manual clipping (if needed in tools)
y0 = max(0, roi.y0)
y1 = min(image.data.shape[0], roi.y1)
x0 = max(0, roi.x0)
x1 = min(image.data.shape[1], roi.x1)
```
## Coding Conventions
### Type Annotations
```python
from __future__ import annotations
import numpy as np
from sigima.objects import SignalObj
def process(src: SignalObj, threshold: float) -> SignalObj:
"""Use forward references via __future__ import."""
pass
```
### Docstrings
**Google-style** with Args/Returns:
```python
def my_function(x: np.ndarray, param: int) -> np.ndarray:
"""One-line summary.
Longer description if needed.
Args:
x: Input array description
param: Parameter description
Returns:
Output array description
Raises:
ValueError: When input is invalid
"""
```
For continued lines in enumerations (args, returns), indent subsequent lines by 1 space:
```python
def compute_feature(obj: SignalObj, param: MyParam) -> SignalObj:
"""Compute feature on signal.
Args:
obj: Input signal object
param: Processing parameters, with a very long description that
continues on the next line.
Returns:
Processed signal object
"""
```
### Imports
**Order**: Standard → Third-party → Sigima
```python
from __future__ import annotations
import numpy as np
import scipy.signal as sps
from guidata.dataset import DataSet
from sigima.objects import SignalObj
from sigima.proc.decorator import computation_function
from sigima.tools.checks import check_1d_array
```
### Module Exports
**Always define `__all__`**:
```python
__all__ = [
"my_function",
"MyParam",
"AnotherFunction",
]
```
## Integration with DataLab
Sigima functions are **consumed by DataLab processors**:
1. **Sigima** implements computation: `sigima.proc.signal.my_feature()`
2. **DataLab** registers in processor: `self.register_1_to_1(sips.my_feature, ...)`
3. **DataLab** adds to menu: `self.processing_menu.addAction(act)`
**Testing flow**:
1. Test in **Sigima unit tests** (headless, fast)
2. Test in **DataLab integration tests** (GUI, full workflow)
## Key Files Reference
| File | Purpose |
|------|---------|
| `sigima/__init__.py` | Top-level exports (`SignalObj`, `ImageObj`, convenience functions) |
| `sigima/params.py` | Centralized parameter class exports (re-exports from `proc`) |
| `sigima/objects/signal/object.py` | `SignalObj` implementation |
| `sigima/objects/image/object.py` | `ImageObj` implementation |
| `sigima/proc/decorator.py` | `@computation_function` decorator system |
| `sigima/proc/signal/processing.py` | Signal processing functions (normalize, calibrate, etc.) |
| `sigima/proc/image/detection.py` | Image detection (blobs, peaks, contours) |
| `sigima/tools/checks.py` | Input validation (`check_1d_array`, `check_2d_array`) |
| `scripts/run_with_env.py` | Environment loader (always use for commands) |
| `.env` | Local PYTHONPATH for development |
## VS Code Tasks
`.vscode/tasks.json` provides shortcuts:
- **🧽🔦 Ruff**: Format + lint
- **🚀 Pytest**: Run tests (`--ff` flag)
- **📚 Compile translations**: Build .mo files
- **🔎 Scan translations**: Update .po files
## Release Classification
**Bug Fix** (1.0.x):
- Fixes incorrect behavior (e.g., ROI boundary clipping)
- Restores expected functionality (e.g., integer array conversion)
- Adds missing capability that should have existed (e.g., `replace_x_by_other_y`)
**Feature** (1.x.0):
- Entirely new computation type (e.g., new parametric images)
- New analysis methods
## Getting Help
- **Documentation**: https://sigima.readthedocs.io/
- **Issues**: https://github.com/DataLab-Platform/Sigima/issues
- **DataLab Integration**: https://datalab-platform.com/
---
**Remember**: Always use `scripts/run_with_env.py`, test headlessly with pytest, and export all parameters through `sigima.params`.
Sigima-1.1.1/.github/workflows/ 0000775 0000000 0000000 00000000000 15140133332 0016313 5 ustar 00root root 0000000 0000000 Sigima-1.1.1/.github/workflows/build_deploy.yml 0000664 0000000 0000000 00000001435 15140133332 0021514 0 ustar 00root root 0000000 0000000 name: Build and upload to PyPI
on:
release:
types: [published]
permissions:
contents: read
jobs:
deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.x'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install build guidata babel
- name: Compile translations
run: |
python -m guidata.utils.translations compile --name sigima --directory .
- name: Build package
run: python -m build
- name: Publish package
uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}
Sigima-1.1.1/.github/workflows/test.yml 0000664 0000000 0000000 00000012637 15140133332 0020026 0 ustar 00root root 0000000 0000000 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
# Inspired from https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html#github-actions
name: Install and Test on Ubuntu (latest)
on:
push:
branches: [ "main", "develop", "release" ]
pull_request:
branches: [ "main", "develop", "release" ]
workflow_dispatch:
inputs:
job_to_run:
description: 'Which job to run'
required: true
type: choice
options:
- 'all'
- 'build'
- 'build_latest'
default: 'all'
schedule:
# Only the "build_latest" job runs on schedule (see execution conditions below)
- cron: "0 5 * * 1"
jobs:
build:
if: ${{ (github.event_name == 'push' || github.event_name == 'pull_request') || (github.event_name == 'workflow_dispatch' && (github.event.inputs.job_to_run == 'all' || github.event.inputs.job_to_run == 'build')) }}
env:
DISPLAY: ':99.0'
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: ["3.9", "3.13"]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
sudo apt install libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 x11-utils
/sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX
python -m pip install --upgrade pip
python -m pip install ruff pytest
if [ "${{ github.ref_name }}" = "develop" ]; then
pip uninstall -y guidata
cd ..
git clone --depth 1 --branch develop https://github.com/PlotPyStack/guidata.git
cd Sigima
pip install -e ../guidata
# Install tomli for TOML parsing (safe if already present)
pip install tomli
# Extract dependencies and save to file, then install
python -c "import tomli; f=open('pyproject.toml','rb'); data=tomli.load(f); deps=[d for d in data['project']['dependencies'] if not any(p in d for p in ['guidata'])]; open('deps.txt','w').write('\n'.join(deps))"
pip install -r deps.txt
# Install Sigima without dependencies
pip install --no-deps .
elif [ "${{ github.ref_name }}" = "release" ]; then
pip uninstall -y guidata
cd ..
# Try cloning guidata from release, fallback to main or master
git clone --depth 1 --branch release https://github.com/PlotPyStack/guidata.git || git clone --depth 1 https://github.com/PlotPyStack/guidata.git || git clone --depth 1 --branch master https://github.com/PlotPyStack/guidata.git
cd Sigima
pip install -e ../guidata
# Install tomli for TOML parsing (safe if already present)
pip install tomli
# Extract dependencies and save to file, then install
python -c "import tomli; f=open('pyproject.toml','rb'); data=tomli.load(f); deps=[d for d in data['project']['dependencies'] if not any(p in d for p in ['guidata'])]; open('deps.txt','w').write('\n'.join(deps))"
pip install -r deps.txt
# Install Sigima without dependencies
pip install --no-deps .
else
# Install from PyPI normally for main branch
pip install .
fi
- name: Lint with Ruff
run: ruff check --output-format=github sigima
- name: Test with pytest
run: pytest -v --tb=long
build_latest:
if: ${{ github.event_name == 'schedule' || (github.event_name == 'workflow_dispatch' && (github.event.inputs.job_to_run == 'all' || github.event.inputs.job_to_run == 'build_latest')) }}
env:
DISPLAY: ':99.0'
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.13
uses: actions/setup-python@v5
with:
python-version: "3.13"
- name: Install dependencies (latest)
run: |
set -euxo pipefail
sudo apt-get update
sudo apt-get install -y \
libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \
libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 x11-utils
/sbin/start-stop-daemon --start --quiet \
--pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background \
--exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX
python -m pip install --upgrade pip
python -m pip install ruff pytest
# Install Sigima itself, but do NOT install its pinned deps
python -m pip install -e . --no-deps
# Extract dependency names from pyproject.toml and install latest versions
python -m pip install -U --upgrade-strategy eager $(python -c "import tomllib, re; print(' '.join(re.sub(r'[\[\]<>=!~,.\s].*$', '', d).strip() for d in tomllib.loads(open('pyproject.toml', 'rb').read().decode())['project']['dependencies']))")
- name: Lint with Ruff (latest)
run: ruff check --output-format=github sigima
- name: Test with pytest (latest)
run: pytest -v --tb=long
Sigima-1.1.1/.gitignore 0000664 0000000 0000000 00000012377 15140133332 0014720 0 ustar 00root root 0000000 0000000 # ---------------------------- Specific to this project --------------------------------
# Project specific
resources/*.png
doc.zip
releases/
/tutorialnotes*.md
doc/changelog.md
scenario_*.h5
# Windows specific
Thumbs.db
# Microsoft Visual Studio
*.pyproj
*.sln
# Sphinx documentation
doctmp/
.doctrees/
doc/install_requires.txt
doc/extras_require-dev.txt
doc/extras_require-doc.txt
doc/locale/pot/_sphinx_design_static/
# Backup files (e.g. created during merge conflicts)
*.bak
# ------------------ Template `Python.gitignore` from gitignore.io ---------------------
# Created by https://www.gitignore.io/api/python
### Python ###
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[codz]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
# *.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py.cover
.hypothesis/
.pytest_cache/
cover/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal
# Flask stuff:
instance/
.webassets-cache
# Scrapy stuff:
.scrapy
# Sphinx documentation
docs/_build/
doc/auto_examples/
doc/sg_execution_times.rst
# PyBuilder
.pybuilder/
target/
# Jupyter Notebook
.ipynb_checkpoints
# IPython
profile_default/
ipython_config.py
# pyenv
# For a library or package, you might want to ignore these files since the code is
# intended to run in multiple environments; otherwise, check them in:
# .python-version
# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock
# UV
# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
# This is especially recommended for binary packages to ensure reproducibility, and is more
# commonly ignored for libraries.
#uv.lock
# poetry
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
# This is especially recommended for binary packages to ensure reproducibility, and is more
# commonly ignored for libraries.
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
#poetry.lock
#poetry.toml
# pdm
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
# https://pdm-project.org/en/latest/usage/project/#working-with-version-control
#pdm.lock
#pdm.toml
.pdm-python
.pdm-build/
# pixi
# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
#pixi.lock
# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
# in the .venv directory. It is recommended not to include this directory in version control.
.pixi
# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
__pypackages__/
# Celery stuff
celerybeat-schedule
celerybeat.pid
# SageMath parsed files
*.sage.py
# Environments
.env
.envrc
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
# Spyder project settings
.spyderproject
.spyproject
# Rope project settings
.ropeproject
# mkdocs documentation
/site
# mypy
.mypy_cache/
.dmypy.json
dmypy.json
# Pyre type checker
.pyre/
# pytype static type analyzer
.pytype/
# Cython debug symbols
cython_debug/
# PyCharm
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/
# Abstra
# Abstra is an AI-powered process automation framework.
# Ignore directories containing user credentials, local state, and settings.
# Learn more at https://abstra.io/docs
.abstra/
# Visual Studio Code
# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
# and can be added to the global gitignore or merged into this file. However, if you prefer,
# you could uncomment the following to ignore the entire vscode folder
# .vscode/
# Ruff stuff:
.ruff_cache/
# PyPI configuration file
.pypirc
# Cursor
# Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
# refer to https://docs.cursor.com/context/ignore-files
.cursorignore
.cursorindexingignore
# Marimo
marimo/_static/
marimo/_lsp/
__marimo__/
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rev: v0.12.2
hooks:
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args: [ --fix ]
# Run the formatter.
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# Essential to be able to compare code side-by-side (`black` default setting)
# and best compromise to minimize file size
max-line-length=88
[TYPECHECK]
ignored-modules=qtpy.QtWidgets,qtpy.QtCore,qtpy.QtGui,cv2,plotpy._scaler,skimage.restoration,skimage.feature
[MESSAGES CONTROL]
disable=wrong-import-order
[DESIGN]
max-args=10 # default: 5
max-positional-arguments=11 # default: 5
max-attributes=12 # default: 7
max-branches=20 # default: 12
max-locals=20 # default: 15
min-public-methods=0 # default: 2
max-public-methods=25 # default: 20 Sigima-1.1.1/.readthedocs.yaml 0000664 0000000 0000000 00000001274 15140133332 0016151 0 ustar 00root root 0000000 0000000 # Read the Docs configuration file for Sphinx projects
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
version: 2
build:
os: ubuntu-22.04
tools:
python: "3.11"
apt_packages:
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sphinx:
configuration: doc/conf.py
formats:
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python:
install:
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path: .
extra_requirements:
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"python.analysis.autoFormatStrings": true,
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"python.testing.pytestPath": "pytest",
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} Sigima-1.1.1/.vscode/tasks.json 0000664 0000000 0000000 00000052511 15140133332 0016303 0 ustar 00root root 0000000 0000000 {
// See https://go.microsoft.com/fwlink/?LinkId=733558
// for the documentation about the tasks.json format
"version": "2.0.0",
"tasks": [
{
"label": "🧽 Ruff Formatter",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"ruff",
"format",
],
"options": {
"cwd": "${workspaceFolder}",
"statusbar": {
"hide": true,
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"group": {
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"presentation": {
"clear": true,
"echo": true,
"focus": false,
"panel": "dedicated",
"reveal": "always",
"showReuseMessage": true,
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"type": "shell",
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{
"label": "🔦 Ruff Linter",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"ruff",
"check",
"--fix",
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"options": {
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"echo": true,
"focus": false,
"panel": "dedicated",
"reveal": "always",
"showReuseMessage": true,
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"type": "shell",
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{
"label": "🧽🔦 Ruff",
"dependsOrder": "sequence",
"dependsOn": [
"🧽 Ruff Formatter",
"🔦 Ruff Linter",
],
"group": {
"kind": "build",
"isDefault": false,
},
"presentation": {
"clear": true,
"echo": true,
"focus": false,
"panel": "dedicated",
"reveal": "always",
"showReuseMessage": true,
},
"type": "shell",
},
{
"label": "🔦 Pylint",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"pylint",
"sigima",
"--disable=duplicate-code",
"--disable=fixme",
"--disable=too-many-arguments",
"--disable=too-many-branches",
"--disable=too-many-instance-attributes",
"--disable=too-many-lines",
"--disable=too-many-locals",
"--disable=too-many-public-methods",
"--disable=too-many-statements",
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"options": {
"cwd": "${workspaceFolder}",
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"group": {
"kind": "build",
"isDefault": true,
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"echo": true,
"focus": false,
"panel": "dedicated",
"reveal": "always",
"showReuseMessage": true,
},
"type": "shell",
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{
"label": "🚀 Pytest",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"pytest",
"--ff",
// "--gui",
// "--show-windows",
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"options": {
"cwd": "${workspaceFolder}",
"env": {
// "DEBUG": "1", // ☣️ Debug mode will reset .ini settings
"UNATTENDED": "1",
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{
"label": "sphinx-build",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"sphinx",
"build",
"doc",
"build/gettext",
"-b",
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"-W",
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"options": {
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"-m",
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"-d",
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"-p",
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"-l",
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"--no-obsolete",
"-w",
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{
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"${command:python.interpreterPath}",
"-m",
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"cleanup-doc",
"--directory",
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{
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"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"sphinx_intl",
"build",
"-d",
"doc/locale",
],
"options": {
"cwd": "${workspaceFolder}",
"statusbar": {
"hide": true,
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"clear": true,
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"focus": false,
"panel": "dedicated",
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"showReuseMessage": true,
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"type": "shell",
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{
"label": "🔎 Scan translations",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"guidata.utils.translations",
"scan",
"--name",
"sigima",
"--directory",
".",
"--copyright-holder",
"DataLab Platform Developers",
"--languages",
"fr",
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"panel": "dedicated",
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"showReuseMessage": true,
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"type": "shell",
"dependsOrder": "sequence",
"dependsOn": [
"cleanup-doc-translations",
],
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{
"label": "📚 Compile translations",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"guidata.utils.translations",
"compile",
"--name",
"sigima",
"--directory",
".",
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"panel": "dedicated",
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"type": "shell",
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"dependsOn": [
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{
"label": "Generate requirements",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"guidata.utils.genreqs",
"all",
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"options": {
"cwd": "${workspaceFolder}",
"statusbar": {
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"group": {
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"echo": true,
"focus": false,
"panel": "dedicated",
"reveal": "always",
"showReuseMessage": true,
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"type": "shell",
},
{
"label": "🧪 Coverage tests",
"type": "shell",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"coverage",
"run",
"-m",
"pytest",
"sigima",
],
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"cwd": "${workspaceFolder}",
"env": {
"COVERAGE_PROCESS_START": "${workspaceFolder}/.coveragerc",
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"statusbar": {
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"group": {
"kind": "test",
"isDefault": true,
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"presentation": {
"panel": "dedicated",
},
"problemMatcher": [],
},
{
"label": "📊 Coverage full",
"type": "shell",
"windows": {
"command": "${command:python.interpreterPath} -m coverage combine && ${command:python.interpreterPath} -m coverage html && start htmlcov\\index.html",
},
"linux": {
"command": "${command:python.interpreterPath} -m coverage combine && ${command:python.interpreterPath} -m coverage html && xdg-open htmlcov/index.html",
},
"osx": {
"command": "${command:python.interpreterPath} -m coverage combine && ${command:python.interpreterPath} -m coverage html && open htmlcov/index.html",
},
"options": {
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"env": {
"COVERAGE_PROCESS_START": "${workspaceFolder}/.coveragerc",
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"problemMatcher": [],
"dependsOrder": "sequence",
"dependsOn": [
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{
"label": "Update doc resources (statically generated)",
"type": "shell",
"command": "cmd",
"args": [
"/c",
"update_doc_resources.bat",
],
"options": {
"cwd": "scripts",
"env": {
"PYTHON": "${command:python.interpreterPath}",
"UNATTENDED": "1",
},
"statusbar": {
"hide": true,
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"group": {
"kind": "build",
"isDefault": false,
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"presentation": {
"echo": true,
"reveal": "always",
"focus": false,
"panel": "dedicated",
"showReuseMessage": true,
"clear": true,
},
"dependsOrder": "sequence",
"dependsOn": [
"Generate requirements",
],
},
{
"label": "Upgrade PlotPyStack",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"pip",
"install",
"--upgrade",
"pip",
"PythonQwt",
"guidata",
"PlotPy",
],
"options": {
"cwd": "${workspaceFolder}",
"statusbar": {
"hide": true,
},
},
"group": {
"kind": "build",
"isDefault": true,
},
"presentation": {
"echo": true,
"reveal": "always",
"focus": false,
"panel": "shared",
"showReuseMessage": true,
"clear": false,
},
"type": "shell",
},
{
"label": "🔁 Reinstall guidata/plotpy dev",
"type": "shell",
"windows": {
"command": ".venv/scripts/pip uninstall -y guidata plotpy; Remove-Item -Recurse -Force .venv/Lib/site-packages/guidata -ErrorAction SilentlyContinue; Remove-Item -Recurse -Force .venv/Lib/site-packages/plotpy -ErrorAction SilentlyContinue; .venv/scripts/pip install -e ../guidata; .venv/scripts/pip install -e ../plotpy",
},
"linux": {
"command": ".venv/bin/pip uninstall -y guidata plotpy && rm -rf .venv/lib/python*/site-packages/guidata && rm -rf .venv/lib/python*/site-packages/plotpy && .venv/bin/pip install -e ../guidata && .venv/bin/pip install -e ../plotpy",
},
"osx": {
"command": ".venv/bin/pip uninstall -y guidata plotpy && rm -rf .venv/lib/python*/site-packages/guidata && rm -rf .venv/lib/python*/site-packages/plotpy && .venv/bin/pip install -e ../guidata && .venv/bin/pip install -e ../plotpy",
},
"options": {
"cwd": "${workspaceFolder}",
"statusbar": {
"hide": true,
},
},
"presentation": {
"panel": "dedicated",
"reveal": "always",
},
"problemMatcher": [],
},
{
"label": "🧹 Clean Up",
"type": "shell",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"guidata.utils.cleanup"
],
"options": {
"cwd": "${workspaceFolder}"
},
"group": {
"kind": "build",
"isDefault": true
},
"presentation": {
"echo": true,
"reveal": "always",
"focus": false,
"panel": "shared",
"showReuseMessage": true,
"clear": false,
},
},
{
"label": "📚 Build doc",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"sphinx",
"build",
"doc",
"${workspaceFolder}/build/doc",
"-b",
"html",
"-D",
"language=fr",
// "-W",
],
"options": {
"cwd": "${workspaceFolder}",
},
"group": {
"kind": "build",
"isDefault": true,
},
"presentation": {
"clear": true,
"echo": true,
"focus": false,
"panel": "dedicated",
"reveal": "always",
"showReuseMessage": true,
},
"type": "shell",
"dependsOrder": "sequence",
"dependsOn": [
"Generate requirements",
],
},
{
"label": "🌐 Open HTML doc",
"type": "shell",
"windows": {
"command": "start build/doc/index.html",
},
"linux": {
"command": "xdg-open build/doc/index.html",
},
"osx": {
"command": "open build/doc/index.html",
},
"options": {
"cwd": "${workspaceFolder}",
},
"problemMatcher": [],
},
{
"label": "📦 Build package",
"type": "shell",
"command": "${command:python.interpreterPath}",
"args": [
"scripts/run_with_env.py",
"${command:python.interpreterPath}",
"-m",
"guidata.utils.securebuild",
"--prebuild",
"python -m guidata.utils.translations compile --name sigima --directory .",
],
"options": {
"cwd": "${workspaceFolder}",
},
"group": {
"kind": "build",
"isDefault": false,
},
"presentation": {
"clear": true,
"panel": "dedicated",
},
"problemMatcher": [],
"dependsOrder": "sequence",
"dependsOn": [
"🧹 Clean Up",
],
},
{
"label": "❔ Untracked files",
"type": "shell",
"command": "git ls-files --others | Where-Object { $_ -notmatch '^\\.' -and $_ -notmatch '^(build|dist|releases)/' -and $_ -notmatch '.(pyc|mo)$'}",
"options": {
"cwd": "${workspaceFolder}",
},
"group": {
"kind": "build",
"isDefault": true,
},
"presentation": {
"echo": true,
"reveal": "always",
"focus": false,
"panel": "dedicated",
"showReuseMessage": true,
"clear": true,
},
},
],
} Sigima-1.1.1/LICENSE 0000664 0000000 0000000 00000003000 15140133332 0013714 0 ustar 00root root 0000000 0000000 BSD 3-Clause License
Copyright (c) 2023, DataLab Platform Developers.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Sigima-1.1.1/MANIFEST.in 0000664 0000000 0000000 00000000116 15140133332 0014452 0 ustar 00root root 0000000 0000000 graft doc
graft sigima/locale
include CONTRIBUTING.md
include requirements.txt Sigima-1.1.1/README.md 0000664 0000000 0000000 00000016322 15140133332 0014201 0 ustar 00root root 0000000 0000000 # Sigima - Scientific Image and Signal Processing Library

[](./LICENSE)
[](https://pypi.org/project/sigima/)
[](https://github.com/DataLab-Platform/Sigima)
[](https://pypi.org/project/sigima/)
[](https://notebook.link/github/DataLab-Platform/Sigima/tree/main/notebooks/?path=notebooks/sigima_basic_example.ipynb)
**Sigima** is an **open-source Python library for scientific image and signal processing**,
designed as a modular and testable foundation for building advanced analysis pipelines.
🔬 Developed by the [DataLab Platform Developers](https://github.com/DataLab-Platform), Sigima powers the computation backend of [DataLab](https://datalab-platform.com/).
## 🚀 Try it Online
**Experience Sigima instantly in your browser** — no installation required!
[](https://notebook.link/github/DataLab-Platform/Sigima/tree/main/notebooks/?path=notebooks/sigima_basic_example.ipynb)
Click the badge above to open a basic example notebook in a live JupyterLite environment powered by [**notebook.link**](https://notebook.link/). This service, developed by [**QuantStack**](https://quantstack.net/), enables sharing and running Jupyter notebooks directly in the browser with zero setup.
Simply run the cells to explore:
- Creating signal and image objects
- Applying processing functions
- Visualizing results inline
---
## 🌟 Project & Sponsors
| Project/Sponsor | Description |
|---------------------|-------------|
|
| Open-source platform for scientific signal and image processing, powered by Sigima. |
|
| European non-profit supporting open-source and internet projects. Sigima has received funding from NLnet for its development, through the DataLab project. |
---
## ✨ Highlights
- Unified processing model for **1D signals** and **2D images**
- Works with **object-oriented wrappers** (`SignalObj`, `ImageObj`) extending NumPy arrays
- Includes common processing tasks: filtering, smoothing, binning, thresholding, labeling, etc.
- Structured for **testability**, **modularity**, and **headless usage**
- 100% **independent of GUI frameworks** (no Qt/PlotPyStack dependencies)
---
## 💡 Use cases
Sigima is meant to be:
- A **processing backend** for scientific/industrial tools
- A library to **build reproducible analysis pipelines**
- A component for **headless automation or remote execution**
- A testbed for **developing and validating new signal/image operations**
---
## 📖 Design Philosophy
The main goal of **Sigima** is to provide a unified, high-level API for handling and processing **1D signals** and **2D images**, through dedicated Python objects: `SignalObj` and `ImageObj`.
The library is organized to separate concerns clearly:
- `sigima.objects`: defines the object model for signals and images.
- `sigima.params`: contains parameter classes for configuring processing functions.
- `sigima.proc`: provides high-level processing functions that operate directly on `SignalObj` and `ImageObj` instances.
- `sigima.io`: handles input/output operations (CSV files, image formats, etc.) for signals and images.
- `sigima.tools`: contains **low-level, NumPy-based functions** that implement the core logic behind many processing routines.
This structure supports a **layered programming model**:
- Developers can use `computation` to process full signal/image objects in an object-oriented manner.
- Or they can directly use `tools` to process raw NumPy arrays — for instance, in custom tools or when integrating Sigima into other projects.
> ⚠️ `sigima.tools` is not intended as a general-purpose NumPy extension. Its purpose is to **fill in the gaps** of common scientific libraries (NumPy, SciPy, scikit-image, etc.), offering consistent tools for signal/image processing in the context of Sigima and similar projects.
---
## Usage Outside Sigima
Although Sigima is designed primarily for object-based processing, some of its core functions are useful on their own.
For instance, the [DataLab](https://datalab-platform.com) project — an open-source platform for signal/image processing — uses many functions from `sigima.tools` independently of the object model. This demonstrates how `sigima.tools` can serve as a **lightweight utility layer** in scientific and industrial Python applications, even when the object model is not used directly.
To maintain this flexibility and avoid confusion, the distinction between `tools` (array-based) and `computation` (object-based) is intentional and explicit.
---
## 📦 Installation
```bash
pip install sigima
```
Or in a development environment:
```bash
git clone https://github.com/DataLab-Platform/Sigima.git
cd Sigima
pip install -e .
```
---
## 📚 Documentation
📖 Full documentation (in progress) is available at:
👉
> Want to use Sigima inside DataLab with GUI tools?
> Check out the full platform: [DataLab](https://datalab-platform.com/)
---
## ⚙️ Architecture
Sigima is organized by data type:
```text
sigima/
├── tools/ # Low-level NumPy-based algorithms supporting some computation functions
├── proc/ # High-level processing functions operating on SignalObj/ImageObj
│ ├── base/ # Common processing functions
│ ├── signal/ # 1D signal processing
│ └── image/ # 2D image processing
```
Each domain provides:
- Low-level functions operating on NumPy arrays
- High-level functions operating on `SignalObj` or `ImageObj`
---
## 🧪 Testing
Sigima comes with unit tests based on `pytest`.
To run all tests:
```bash
pytest
```
To run GUI-assisted validation tests (optional):
```bash
pytest --gui
```
---
## 🧠 License
Sigima is distributed under the terms of the BSD 3-Clause license.
See [LICENSE](./LICENSE) for details.
---
## 🤝 Contributing
Bug reports, feature requests and pull requests are welcome!
See the [CONTRIBUTING](https://datalab-platform.com/en/contributing) guide to get started.
---





---
© DataLab Platform Developers
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Sigima-1.1.1/doc/_static/Sigima-Frontpage.png 0000664 0000000 0000000 00000167637 15140133332 0020777 0 ustar 00root root 0000000 0000000 PNG
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