Merge branch 'develop' of C:/Dev/Projets/DataLab into develop

Author: PierreRaybaut

.github/workflows/test_pyqt5.yml

@@ -36,14 +36,21 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install ruff pytest
         pip install PyQt5
-        pip install .
         if [ "${{ github.ref_name }}" = "develop" ]; then
-           pip uninstall -y guidata
+           # Install development versions of key dependencies first
            pip install git+https://github.com/PlotPyStack/guidata.git@develop
-           pip uninstall -y plotpy
            pip install git+https://github.com/PlotPyStack/plotpy.git@develop
-           pip uninstall -y sigima
            pip install git+https://github.com/DataLab-Platform/Sigima.git@develop
+           # 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','PlotPy','Sigima'])]; open('deps.txt','w').write('\n'.join(deps))"
+           pip install -r deps.txt
+           # Install DataLab 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 datalab

.vscode/tasks.json

@@ -476,17 +476,19 @@
         {
             "label": "🧹 Clean Up",
             "type": "shell",
-            "command": "cmd",
+            "command": "${command:python.interpreterPath}",
             "args": [
-                "/c",
-                "clean_up.bat",
+                "scripts/run_with_env.py",
+                "${command:python.interpreterPath}",
+                "-m",
+                "guidata.utils.cleanup",
             ],
             "options": {
-                "cwd": "scripts",
+                "cwd": "${workspaceFolder}"
             },
             "group": {
                 "kind": "build",
-                "isDefault": true,
+                "isDefault": true
             },
             "presentation": {
                 "echo": true,
@@ -505,7 +507,7 @@
                 "cwd": "scripts",
                 "env": {
                     "PYTHON": "${command:python.interpreterPath}",
-                    "RELEASE": "1",
+                    // "RELEASE": "1",
                     "UNATTENDED": "1",
                 },
                 "statusbar": {
@@ -571,7 +573,7 @@
                 "env": {
                     "PYTHON": "${command:python.interpreterPath}",
                     "QT_COLOR_MODE": "light",
-                    "RELEASE": "1",
+                    // "RELEASE": "1",
                     "UNATTENDED": "1",
                 },
                 "statusbar": {
@@ -778,7 +780,7 @@
                 "cwd": "scripts",
                 "env": {
                     "PYTHON": "${command:python.interpreterPath}",
-                    "RELEASE": "1",
+                    // "RELEASE": "1",
                     "UNATTENDED": "1",
                 },
                 "statusbar": {
@@ -820,7 +822,7 @@
                 "cwd": "scripts",
                 "env": {
                     "PYTHON": "${command:python.interpreterPath}",
-                    "RELEASE": "1",
+                    // "RELEASE": "1",
                     "UNATTENDED": "1",
                 },
             },

datalab/gui/processor/image.py

@@ -21,10 +21,10 @@
 from sigima.objects import (
     ImageObj,
     ImageROI,
-    NormalDistributionParam,
+    NormalDistribution2DParam,
     PoissonDistribution2DParam,
     ROI2DParam,
-    UniformDistributionParam,
+    UniformDistribution2DParam,
 )
 from sigima.objects.scalar import GeometryResult
 from sigima.proc.decorator import ComputationMetadata
@@ -416,7 +416,7 @@ def register_computations(self) -> None:
         self.register_1_to_1(
             sigima_image.add_gaussian_noise,
             _("Add Gaussian noise"),
-            NormalDistributionParam,
+            NormalDistribution2DParam,
         )
         self.register_1_to_1(
             sigima_image.add_poisson_noise,
@@ -426,7 +426,7 @@ def register_computations(self) -> None:
         self.register_1_to_1(
             sigima_image.add_uniform_noise,
             _("Add uniform noise"),
-            UniformDistributionParam,
+            UniformDistribution2DParam,
         )
         # Noise reduction
         self.register_1_to_1(

datalab/gui/processor/signal.py

@@ -17,12 +17,12 @@
 import sigima.proc.signal as sigima_signal
 from guidata.qthelpers import exec_dialog
 from sigima.objects import (
-    NormalDistributionParam,
+    NormalDistribution1DParam,
     PoissonDistribution1DParam,
     ROI1DParam,
     SignalObj,
     SignalROI,
-    UniformDistributionParam,
+    UniformDistribution1DParam,
     create_signal,
 )
 from sigima.objects.scalar import GeometryResult, TableResult
@@ -213,7 +213,7 @@ def register_computations(self) -> None:
         self.register_1_to_1(
             sigima_signal.add_gaussian_noise,
             _("Add Gaussian noise"),
-            NormalDistributionParam,
+            NormalDistribution1DParam,
         )
         self.register_1_to_1(
             sigima_signal.add_poisson_noise,
@@ -223,7 +223,7 @@ def register_computations(self) -> None:
         self.register_1_to_1(
             sigima_signal.add_uniform_noise,
             _("Add uniform noise"),
-            UniformDistributionParam,
+            UniformDistribution1DParam,
         )
         # Noise reduction
         self.register_1_to_1(

datalab/tests/features/common/table_results_app_test.py

@@ -9,7 +9,7 @@
 from __future__ import annotations
 
 import numpy as np
-from sigima.objects import NormalDistributionParam
+from sigima.objects import NormalDistribution1DParam
 from sigima.tests import data as test_data
 
 from datalab.adapters_metadata.table_adapter import TableAdapter
@@ -30,7 +30,7 @@ def test_table_results():
     obj2 = create_image_with_table_results()
     with datalab_test_app_context() as win:
         panel = win.signalpanel
-        noiseparam = NormalDistributionParam()
+        noiseparam = NormalDistribution1DParam()
         for sigma in np.linspace(0.0, 0.5, 11):
             noiseparam.sigma = sigma
             sig = test_data.create_noisy_signal(noiseparam=noiseparam)

datalab/tests/features/signal/fitdialog_unit_test.py

@@ -9,7 +9,7 @@
 # guitest: show
 
 from guidata.qthelpers import qt_app_context
-from sigima.objects import NormalDistributionParam
+from sigima.objects import NormalDistribution1DParam
 from sigima.tests.data import create_noisy_signal, get_test_signal
 from sigima.tests.helpers import get_default_test_name
 from sigima.tools.signal.peakdetection import peak_indices
@@ -29,7 +29,7 @@ def test_fit_dialog():
         )
 
         # Gaussian curve fitting test
-        noiseparam = NormalDistributionParam.create(sigma=5.0)
+        noiseparam = NormalDistribution1DParam.create(sigma=5.0)
         sig = create_noisy_signal(noiseparam)
         x, y = sig.x, sig.y
         execenv.print(fdlg.gaussianfit(x, y))

datalab/tests/scenarios/common.py

@@ -198,7 +198,9 @@ def run_signal_computations(
     roi = sigima.objects.create_signal_roi([i1, i2], indices=True)
     panel.processor.compute_roi_extraction(roi)
 
-    sig = create_noisy_signal(sigima.objects.NormalDistributionParam.create(sigma=5.0))
+    sig = create_noisy_signal(
+        sigima.objects.NormalDistribution1DParam.create(sigma=5.0)
+    )
     panel.add_object(sig)
     param = sigima.params.PolynomialFitParam()
     panel.processor.compute_polyfit(param)

doc/images/shots/i_help.png

@@ -17,7 +17,7 @@ The `datalab-platform` package requires the following Python modules:
       -  >= 2.7.4
       - Curve and image plotting tools for Python/Qt applications
     * - Sigima
-      -  >= 0.1.0
+      -  >= 1.0.0a0
       - Scientific computing engine for 1D signals and 2D images, part of the DataLab open-source platform.
     * - NumPy
       -  >= 1.22
@@ -64,25 +64,25 @@ Optional modules for development:
       - Version
       - Summary
     * - build
-      - 
+      -
       - A simple, correct Python build frontend
     * - babel
-      - 
+      -
       - Internationalization utilities
     * - Coverage
-      - 
+      -
       - Code coverage measurement for Python
     * - pyinstaller
       -  >= 6.0
       - PyInstaller bundles a Python application and all its dependencies into a single package.
     * - pylint
-      - 
+      -
       - python code static checker
     * - ruff
-      - 
+      -
       - An extremely fast Python linter and code formatter, written in Rust.
     * - pre-commit
-      - 
+      -
       - A framework for managing and maintaining multi-language pre-commit hooks.
 
 Optional modules for building the documentation:
@@ -95,25 +95,25 @@ Optional modules for building the documentation:
       - Version
       - Summary
     * - sphinx
-      - 
+      -
       - Python documentation generator
     * - sphinx_intl
-      - 
+      -
       - Sphinx utility that make it easy to translate and to apply translation.
     * - sphinx-sitemap
-      - 
+      -
       - Sitemap generator for Sphinx
     * - myst_parser
-      - 
+      -
       - An extended [CommonMark](https://spec.commonmark.org/) compliant parser,
     * - sphinx_design
-      - 
+      -
       - A sphinx extension for designing beautiful, view size responsive web components.
     * - sphinx-copybutton
-      - 
+      -
       - Add a copy button to each of your code cells.
     * - pydata-sphinx-theme
-      - 
+      -
       - Bootstrap-based Sphinx theme from the PyData community
 
 Optional modules for running test suite:
@@ -126,8 +126,8 @@ Optional modules for running test suite:
       - Version
       - Summary
     * - pytest
-      - 
+      -
       - pytest: simple powerful testing with Python
     * - pytest-xvfb
-      - 
+      -
       - A pytest plugin to run Xvfb (or Xephyr/Xvnc) for tests.