Merge branch 'main' into develop

# Conflicts:
#	doc/locale/fr/LC_MESSAGES/contributing/changelog.po

Author: PierreRaybaut

CHANGELOG.md

@@ -28,7 +28,9 @@ See DataLab [roadmap page](https://datalab-platform.com/en/contributing/roadmap.
 
 🛠️ Bug fixes:
 
+* Fixed [Issue #233](https://github.com/DataLab-Platform/DataLab/issues/233) - Hard crash when trying to activate the curve stats tool on a zero signal
 * Fixed [Issue #184](https://github.com/DataLab-Platform/DataLab/issues/184) - Curve marker style unexpectedly changes to "Square" after validating "Parameters…" dialog
+* Fixed [Issue #117](https://github.com/DataLab-Platform/DataLab/issues/117) - DataLab's signal moving median crashes on Linux with `mode='mirror'`: `free(): invalid next size (normal)` (this is a bug in SciPy v1.15.0 to v1.15.2, which was fixed in SciPy v1.15.3)
 
 ℹ️ Other changes:
 

cdl/core/gui/docks.py

@@ -63,26 +63,58 @@
     from plotpy.styles import BaseImageParam
 
 
-def fwhm_info(x, y):
-    """Return FWHM information string"""
-    try:
-        with warnings.catch_warnings(record=True) as w:
-            x0, _y0, x1, _y1 = fwhm((x, y), "zero-crossing")
-            wstr = " ⚠️" if w else ""
-    except ValueError:
-        return "🛑"
-    return f"{x1 - x0:g}{wstr}"
-
-
-CURVESTATSTOOL_LABELFUNCS = (
-    ("%g < x < %g", lambda *args: (np.nanmin(args[0]), np.nanmax(args[0]))),
-    ("%g < y < %g", lambda *args: (np.nanmin(args[1]), np.nanmax(args[1]))),
-    ("<y>=%g", lambda *args: np.nanmean(args[1])),
-    ("σ(y)=%g", lambda *args: np.nanstd(args[1])),
-    ("∑(y)=%g", lambda *args: spt.trapezoid(args[1])),
-    ("∫ydx=%g<br>", lambda *args: spt.trapezoid(args[1], args[0])),
-    ("FWHM = %s", fwhm_info),
-)
+class CurveStatsToolFunctions:
+    """Statistical functions for CurveStatsTool"""
+
+    @classmethod
+    def set_labelfuncs(cls, statstool: CurveStatsTool) -> None:
+        """Set label functions for CurveStatsTool"""
+        labelfuncs = (
+            ("%g &lt; x &lt; %g", lambda *args: cls.nan_min_max(args[0])),
+            ("%g &lt; y &lt; %g", lambda *args: cls.nan_min_max(args[1])),
+            ("&lt;y&gt;=%g", lambda *args: cls.nan_mean(args[1])),
+            ("σ(y)=%g", lambda *args: cls.nan_std(args[1])),
+            ("∑(y)=%g", lambda *args: spt.trapezoid(args[1])),
+            ("∫ydx=%g<br>", lambda *args: spt.trapezoid(args[1], args[0])),
+            ("FWHM = %s", cls.fwhm_info),
+        )
+        statstool.set_labelfuncs(labelfuncs)
+
+    @staticmethod
+    def nan_min_max(arr: np.ndarray) -> tuple[float, float]:
+        """Return min/max tuple"""
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", RuntimeWarning)
+            min_val = np.nanmin(arr)
+            max_val = np.nanmax(arr)
+        return (min_val, max_val)
+
+    @staticmethod
+    def nan_mean(arr: np.ndarray) -> float:
+        """Return mean value, ignoring NaNs"""
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", RuntimeWarning)
+            mean_val = np.nanmean(arr)
+        return mean_val
+
+    @staticmethod
+    def nan_std(arr: np.ndarray) -> float:
+        """Return standard deviation, ignoring NaNs"""
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", RuntimeWarning)
+            std_val = np.nanstd(arr)
+        return std_val
+
+    @staticmethod
+    def fwhm_info(x, y):
+        """Return FWHM information string"""
+        try:
+            with warnings.catch_warnings(record=True) as w:
+                x0, _y0, x1, _y1 = fwhm((x, y), "zero-crossing")
+                wstr = " ⚠️" if w else ""
+        except (ValueError, ZeroDivisionError):
+            return "🛑"
+        return f"{x1 - x0:g}{wstr}"
 
 
 def get_more_image_stats(
@@ -245,7 +277,7 @@ def __register_other_tools(self) -> None:
         if self.options.type == PlotType.CURVE:
             mgr.register_curve_tools()
             statstool = mgr.get_tool(CurveStatsTool)
-            statstool.set_labelfuncs(CURVESTATSTOOL_LABELFUNCS)
+            CurveStatsToolFunctions.set_labelfuncs(statstool)
         else:
             mgr.register_image_tools()
             # Customizing the ImageStatsTool

cdl/core/remote.py

@@ -27,6 +27,7 @@
 import guidata.dataset as gds
 import numpy as np
 from guidata.io import JSONReader, JSONWriter
+from packaging.version import Version
 from qtpy import QtCore as QC
 
 import cdl
@@ -36,7 +37,6 @@
 from cdl.core.model.image import ImageObj, create_image
 from cdl.core.model.signal import SignalObj, create_signal
 from cdl.env import execenv
-from cdl.utils.misc import is_version_at_least
 
 if TYPE_CHECKING:
     from cdl.core.gui.main import CDLMainWindow
@@ -798,14 +798,14 @@ def __connect_to_server(self) -> None:
             version = self.get_version()
         except ConnectionRefusedError as exc:
             raise ConnectionRefusedError("DataLab is currently not running") from exc
-        # If DataLab version is not compatible with this client, show a warning using
-        # standard `warnings` module:
-        minor_version = ".".join(cdl.__version__.split(".")[:2])
-        if not is_version_at_least(version, minor_version):
+        # If DataLab version is not compatible with this client, show a warning
+        server_ver = Version(version)
+        client_ver = Version(cdl.__version__)
+        if server_ver < client_ver:
             warnings.warn(
-                f"DataLab server version ({version}) may not be fully compatible with "
-                f"this DataLab client version ({cdl.__version__}).\n"
-                f"Please upgrade the server to {minor_version} or higher."
+                f"DataLab server version ({server_ver}) may not be fully compatible "
+                f"with this DataLab client version ({client_ver}).\n"
+                f"Please upgrade the server to {client_ver} or higher."
             )
 
     def connect(

cdl/tests/features/common/stats_tools_unit_test.py

@@ -15,6 +15,7 @@
 import numpy as np
 import plotpy
 from guidata.qthelpers import exec_dialog, qt_app_context
+from packaging.version import Version
 from plotpy.constants import PlotType
 from plotpy.tests.unit.utils import drag_mouse
 from plotpy.tools import CurveStatsTool, ImageStatsTool
@@ -23,7 +24,6 @@
 import cdl.obj
 from cdl.core.gui.docks import DataLabPlotWidget
 from cdl.tests.data import create_multigauss_image, create_paracetamol_signal
-from cdl.utils.misc import compare_versions
 
 
 def simulate_stats_tool(
@@ -42,7 +42,7 @@ def simulate_stats_tool(
     klass = CurveStatsTool if plot_type == PlotType.CURVE else ImageStatsTool
     stattool = widget.get_manager().get_tool(klass)
     stattool.activate()
-    if compare_versions(plotpy.__version__, "<", "2.4"):
+    if Version(plotpy.__version__) < Version("2.4"):
         qapp = QW.QApplication.instance()
         drag_mouse(widget, qapp, x_path, y_path)
     else:

cdl/tests/features/signals/processing_unit_test.py

@@ -21,8 +21,10 @@
 
 import numpy as np
 import pytest
+import scipy
 import scipy.ndimage as spi
 import scipy.signal as sps
+from packaging.version import Version
 
 import cdl.algorithms.coordinates
 import cdl.computation.signal as cps
@@ -316,6 +318,10 @@ def test_signal_moving_average() -> None:
 
 
 @pytest.mark.validation
+@pytest.mark.skipif(
+    Version("1.15.0") <= Version(scipy.__version__) <= Version("1.15.2"),
+    reason="Skipping test: scipy median_filter is broken in 1.15.0-1.15.2",
+)
 def test_signal_moving_median() -> None:
     """Validation test for the signal moving median processing."""
     src = get_test_signal("paracetamol.txt")

cdl/utils/misc.py

@@ -39,66 +39,3 @@ def go_to_error(text: str) -> None:
         args = Conf.console.external_editor_args.get().format(**fdict).split(" ")
         editor_path = Conf.console.external_editor_path.get()
         subprocess.run([editor_path] + args, shell=True, check=False)
-
-
-def is_version_at_least(version1: str, version2: str) -> bool:
-    """
-    Compare two version strings to check if the first version is at least
-    equal to the second. Limit the comparison to the minor version (e.g. 1.2.3 -> 1.2).
-
-    Args:
-        version1 (str): The first version string.
-        version2 (str): The second version string.
-
-    Returns:
-        bool: True if version1 is greater than or equal to version2, False otherwise.
-
-    .. note::
-
-        Development, alpha, beta, and rc versions are considered to be equal
-        to the corresponding release version.
-    """
-    # Split the version strings into parts
-    parts1 = [part.strip() for part in version1.split(".")]
-    parts2 = [part.strip() for part in version2.split(".")]
-
-    for part1, part2 in zip(parts1, parts2):
-        if part1.isdigit() and part2.isdigit():
-            if int(part1) > int(part2):
-                return True
-            if int(part1) < int(part2):
-                return False
-        elif part1 > part2:
-            return True
-        elif part1 < part2:
-            return False
-
-    return len(parts1) >= len(parts2)
-
-
-def compare_versions(version1: str, operator: str, version2: str) -> bool:
-    """Compare module version with the given version.
-
-    Args:
-        version1: Version to compare (e.g., "1.2.3")
-        operator: Comparison operator (e.g., "==", "<", ">", "<=", ">=")
-        version2: Version to compare with (e.g., "1.2.3")
-
-    Returns:
-        True if the comparison is successful, False otherwise.
-    """
-    specs1, specs2 = version1.split("."), version2.split(".")
-    assert len(specs2) <= len(specs1)
-    specs2 = specs2[: len(specs1)]
-    tuple1, tuple2 = tuple(map(int, specs1)), tuple(map(int, specs2))
-    if operator == "==":
-        return tuple1 == tuple2
-    if operator == "<":
-        return tuple1 < tuple2
-    if operator == ">":
-        return tuple1 > tuple2
-    if operator == "<=":
-        return tuple1 <= tuple2
-    if operator == ">=":
-        return tuple1 >= tuple2
-    raise ValueError("Invalid operator")

doc/locale/fr/LC_MESSAGES/contributing/changelog.po

@@ -84,9 +84,15 @@ msgstr "Ces méthodes sont internes et utilisées par des développeurs avancés
 msgid "This closes [Issue #180](https://github.com/DataLab-Platform/DataLab/issues/180) - Rationalize `BaseProcessor` method names for core processing types"
 msgstr "Ceci corrige l'[Issue #180](https://github.com/DataLab-Platform/DataLab/issues/180) - Rationaliser les noms de méthodes `BaseProcessor` pour les types de traitement de base"
 
+msgid "Fixed [Issue #233](https://github.com/DataLab-Platform/DataLab/issues/233) - Hard crash when trying to activate the curve stats tool on a zero signal"
+msgstr "Correction de l'[Issue #233](https://github.com/DataLab-Platform/DataLab/issues/233) - Plantage sévère lors de l'activation de l'outil de statistiques de courbe sur un signal nul"
+
 msgid "Fixed [Issue #184](https://github.com/DataLab-Platform/DataLab/issues/184) - Curve marker style unexpectedly changes to \"Square\" after validating \"Parameters…\" dialog"
 msgstr "Correction de l'[Issue #184](https://github.com/DataLab-Platform/DataLab/issues/184) - Le style du marqueur de courbe change de manière inattendue en \"Carré\" après validation de la boîte de dialogue \"Paramètres…\""
 
+msgid "Fixed [Issue #117](https://github.com/DataLab-Platform/DataLab/issues/117) - DataLab's signal moving median crashes on Linux with `mode='mirror'`: `free(): invalid next size (normal)` (this is a bug in SciPy v1.15.0 to v1.15.2, which was fixed in SciPy v1.15.3)"
+msgstr "Correction de l'[Issue #117](https://github.com/DataLab-Platform/DataLab/issues/117) - Le filtre médian mobile de DataLab plante sur Linux avec `mode='mirror'` : `free(): invalid next size (normal)` (il s'agit d'un bug dans SciPy v1.15.0 à v1.15.2, qui a été corrigé dans SciPy v1.15.3)"
+
 msgid "ℹ️ Other changes:"
 msgstr "ℹ️ Autres changements :"
 

pyproject.toml

@@ -42,11 +42,12 @@ requires-python = ">=3.9, <4"
 dependencies = [
     "guidata >= 3.10",
     "PlotPy >= 2.7.4",
-    "SciPy >= 1.5, < 1.15.0",
+    "SciPy >= 1.5",
     "scikit-image >= 0.18",
     "pandas >= 1.2",
     "PyWavelets >= 1.1",
     "psutil >= 5.7",
+    "packaging >= 20.0",
 ]
 dynamic = ["version"]