Merge branch 'develop'

Author: PierreRaybaut

.github/workflows/build.yml

@@ -16,7 +16,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Build wheels
-        run: pipx run cibuildwheel==2.20.0
+        run: pipx run cibuildwheel==2.21.2
 
       - uses: actions/upload-artifact@v4
         with:

.github/workflows/build_deploy.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.20.0
+        uses: pypa/cibuildwheel@v2.21.2
 
       - uses: actions/upload-artifact@v4
         with:

.github/workflows/test.yml

@@ -3,13 +3,13 @@
 
 # Inspired from https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html#github-actions
 
-name: Python package
+name: Build, install and test
 
 on:
   push:
-    branches: [ "master" ]
+    branches: [ "master", "develop" ]
   pull_request:
-    branches: [ "master" ]
+    branches: [ "master", "develop" ]
 
 jobs:
   build:
@@ -21,12 +21,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.11", "3.12"]
+        python-version: ["3.9", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

CHANGELOG.md

@@ -1,5 +1,31 @@
 # Changelog #
 
+## Version 2.7.0 ##
+
+Supported versions of Python have been updated (drop support for Python 3.8, add support for Python 3.13):
+
+* PlotPy < 2.7.0: Python 3.8, 3.9, 3.10, 3.11 and 3.12
+* PlotPy >= 2.7.0: Python 3.9, 3.10, 3.11, 3.12 and 3.13
+
+Other dependencies have been updated:
+
+* Updated versions to those available at the time of the release of the oldest supported Python version (3.9)
+* Exception: Cython 3.0 is required for Python 3.13
+
+💥 New features / Enhancements:
+
+* Added `AnnotatedPolygon` annotation to items
+* Added `make.annotated_polygon` function to `plotpy.builder` module
+* Customization of annotation information:
+  * Added `info_callback` argument to all annotation class constructors
+  * Added `set_info_callback` method to all annotation classes
+  * The `info_callback` is a function that takes the annotation object and returns a string with the information to display
+  * Default `info_callback` is redirected to the `get_infos` method of the annotation object (this makes the feature backward compatible)
+
+🛠️ Bug fixes:
+
+* Fixed `pydicom` support: use `dcmread` instead of `read_file` to read DICOM files
+
 ## Version 2.6.3 ##
 
 🧯 In this release, test coverage is 79%.

doc/dev/platforms.rst

@@ -7,16 +7,17 @@ The following sections describe the reference platforms for the project.
 
 .. note::
 
-    The officially supported Python versions are 3.8, 3.9 and 3.10.
-    However, the project should work on any earlier Python 3 version.
+    The officially supported Python versions are 3.9, 3.10, 3.11, 3.12 and 3.13.
 
     The officially supported Qt binding is PyQt5. However, efforts have been
     made and will continue to be made to support PyQt6 and PySide6 as well.
 
     The project is currently tested on the following platforms:
 
     * Microsoft Windows 10 (64-bit)
+    * Microsoft Windows 11 (64-bit)
     * CentOS Stream 8.8 (64-bit)
+    * Ubuntu 22.04 LTS (64-bit)
 
     However, it should work on any other platform supported by its dependencies.
 

doc/features/items/builder.rst

@@ -12,4 +12,4 @@ used to simplify the creation of plot items.
    :members:
 
 .. autoclass:: plotpy.builder.PlotBuilder
-   :members: widget,dialog,window,gridparam,grid,mcurve,pcurve,curve,merror,perror,error,histogram,phistogram,range,vcursor,hcursor,xcursor,marker,image,maskedimage,maskedxyimage,rgbimage,quadgrid,pcolor,trimage,xyimage,imagefilter,contours,histogram2D,rectangle,ellipse,polygon,circle,segment,svg,annotated_point,annotated_rectangle,annotated_ellipse,annotated_circle,annotated_segment,label,legend,info_label,range_info_label,computation,computations,computation2d,computations2d
+   :members: widget,dialog,window,gridparam,grid,mcurve,pcurve,curve,merror,perror,error,histogram,phistogram,range,vcursor,hcursor,xcursor,marker,image,maskedimage,maskedxyimage,rgbimage,quadgrid,pcolor,trimage,xyimage,imagefilter,contours,histogram2D,rectangle,ellipse,polygon,circle,segment,svg,annotated_point,annotated_rectangle,annotated_ellipse,annotated_circle,annotated_segment,annotated_polygon,label,legend,info_label,range_info_label,computation,computations,computation2d,computations2d

doc/features/items/overview.rst

@@ -75,6 +75,7 @@ The following annotation items are available:
 * :py:class:`.AnnotatedObliqueRectangle`
 * :py:class:`.AnnotatedEllipse`
 * :py:class:`.AnnotatedCircle`
+* :py:class:`.AnnotatedPolygon`
 
 Labels
 ^^^^^^

doc/features/items/reference.rst

@@ -124,6 +124,8 @@ Annotations
    :members:
 .. autoclass:: plotpy.items.AnnotatedCircle
    :members:
+.. autoclass:: plotpy.items.AnnotatedPolygon
+   :members:
 
 Labels
 ^^^^^^

doc/features/tools/reference.rst

@@ -58,7 +58,7 @@ Shape tools
 
 .. autoclass:: plotpy.tools.MultiLineTool
    :members:
-.. autoclass:: plotpy.tools.FreeFormTool
+.. autoclass:: plotpy.tools.PolygonTool
    :members:
 .. autoclass:: plotpy.tools.LabelTool
    :members:
@@ -84,6 +84,8 @@ Shape tools
    :members:
 .. autoclass:: plotpy.tools.AnnotatedSegmentTool
    :members:
+.. autoclass:: plotpy.tools.AnnotatedPolygonTool
+   :members:
 .. autoclass:: plotpy.tools.HRangeTool
    :members:
 

doc/intro/motivation.rst

@@ -13,7 +13,7 @@ From a developer point of view, PlotPy V2 is a major overhaul of PlotPy V1:
   all over the codebase
 
 .. note::
-    PlotPy V2 is fully typed using Python 3.8+ type annotations.
+    PlotPy V2 is fully typed using Python type annotations.
     This means that you can use your IDE to get autocompletion and type checking
     (e.g. with VSCode, Visual Studio, etc.).
     This is a major improvement when you write code using PlotPy V2:

doc/requirements.rst

@@ -8,20 +8,20 @@ The :mod:`plotpy` package requires the following Python modules:
       - Version
       - Summary
     * - Python
-      - >=3.8, <4
+      - >=3.9, <4
       - Python programming language
     * - guidata
-      - >=3.4
+      - >=3.7
       - Automatic GUI generation for easy dataset editing and display
     * - PythonQwt
-      - >=0.12.1
+      - >=0.14
       - Qt plotting widgets for Python
-    * - NumPy
-      - >=1.17
-      - Fundamental package for array computing in Python
     * - SciPy
-      - >=1.3
+      - >=1.5
       - Fundamental algorithms for scientific computing in Python
+    * - scikit-image
+      -  >= 0.18
+      - Image processing in Python
     * - Pillow
       - 
       - Python Imaging Library (Fork)

doc/update_requirements.py

@@ -15,5 +15,5 @@
 
 if __name__ == "__main__":
     print("Updating requirements.rst file...", end=" ")
-    gen_module_req_rst(plotpy, ["Python>=3.8", "PyQt5>=5.11"])
+    gen_module_req_rst(plotpy, ["Python>=3.9", "PyQt5>=5.11"])
     print("done.")

plotpy/__init__.py

@@ -20,7 +20,7 @@
 .. _GitHub: https://github.com/PierreRaybaut/plotpy
 """
 
-__version__ = "2.6.3"
+__version__ = "2.7.0"
 __VERSION__ = tuple([int(number) for number in __version__.split(".")])
 
 # --- Important note: DATAPATH and LOCALEPATH are used by guidata.configtools

plotpy/builder/annotation.py

@@ -27,6 +27,7 @@
     AnnotatedCircle,
     AnnotatedEllipse,
     AnnotatedPoint,
+    AnnotatedPolygon,
     AnnotatedRectangle,
     AnnotatedSegment,
 )
@@ -126,10 +127,7 @@ def annotated_point(
     def __annotated_shape(
         self,
         shapeclass,
-        x0,
-        y0,
-        x1,
-        y1,
+        points,
         title,
         subtitle,
         show_label,
@@ -153,7 +151,10 @@ def __annotated_shape(
             readonly=readonly,
             private=private,
         )
-        shape = shapeclass(x0, y0, x1, y1, param)
+        if isinstance(points, np.ndarray):
+            shape = shapeclass(points, annotationparam=param)
+        else:
+            shape = shapeclass(*points, annotationparam=param)
         shape.set_style("plot", "shape/drag")
         return shape
 
@@ -195,12 +196,10 @@ def annotated_rectangle(
         Returns:
             :py:class:`.AnnotatedRectangle` object
         """
+        points = x0, y0, x1, y1
         return self.__annotated_shape(
             AnnotatedRectangle,
-            x0,
-            y0,
-            x1,
-            y1,
+            points,
             title,
             subtitle,
             show_label,
@@ -259,12 +258,10 @@ def annotated_ellipse(
         Returns:
             :py:class:`.AnnotatedEllipse` object
         """
+        points = x0, y0, x1, y1
         item = self.__annotated_shape(
             AnnotatedEllipse,
-            x0,
-            y0,
-            x1,
-            y1,
+            points,
             title,
             subtitle,
             show_label,
@@ -318,12 +315,10 @@ def annotated_circle(
         Returns:
             :py:class:`.AnnotatedCircle` object
         """
+        points = x0, y0, x1, y1
         return self.__annotated_shape(
             AnnotatedCircle,
-            x0,
-            y0,
-            x1,
-            y1,
+            points,
             title,
             subtitle,
             show_label,
@@ -374,12 +369,57 @@ def annotated_segment(
         Returns:
             :py:class:`.AnnotatedSegment` object
         """
+        points = x0, y0, x1, y1
         return self.__annotated_shape(
             AnnotatedSegment,
-            x0,
-            y0,
-            x1,
-            y1,
+            points,
+            title,
+            subtitle,
+            show_label,
+            show_computations,
+            show_subtitle,
+            format,
+            uncertainty,
+            transform_matrix,
+            readonly,
+            private,
+        )
+
+    def annotated_polygon(
+        self,
+        points: np.ndarray,
+        title: str | None = None,
+        subtitle: str | None = None,
+        show_label: bool | None = None,
+        show_computations: bool | None = None,
+        show_subtitle: bool | None = None,
+        format: str | None = None,
+        uncertainty: float | None = None,
+        transform_matrix: np.ndarray | None = None,
+        readonly: bool | None = None,
+        private: bool | None = None,
+    ) -> AnnotatedPolygon:
+        """Make an annotated polygon `plot item`
+
+        Args:
+            points: polygon points
+            title: label name. Default is None
+            subtitle: label subtitle. Default is None
+            show_label: show label. Default is None
+            show_computations: show computations. Default is None
+            show_subtitle: show subtitle. Default is None
+            format: string formatting. Default is None
+            uncertainty: measurement relative uncertainty. Default is None
+            transform_matrix: transform matrix. Default is None
+            readonly: readonly. Default is None
+            private: private. Default is None
+
+        Returns:
+            :py:class:`.AnnotatedPolygon` object
+        """
+        return self.__annotated_shape(
+            AnnotatedPolygon,
+            points,
             title,
             subtitle,
             show_label,

plotpy/builder/image.py

@@ -226,9 +226,9 @@ def image(
         if isinstance(filename, str) and filename.lower().endswith(".dcm"):
             # pylint: disable=import-outside-toplevel
             # pylint: disable=import-error
-            from pydicom import dicomio  # type:ignore
+            from pydicom import dcmread  # type:ignore
 
-            template = dicomio.read_file(filename, stop_before_pixels=True, force=True)
+            template = dcmread(filename, stop_before_pixels=True, force=True)
             ipp = getattr(template, "ImagePositionPatient", ["0", "0", "0"])
             pxs = getattr(template, "PixelSpacing", ["1", "1"])
             ipx, ipy = float(ipp[0]), float(ipp[1])

plotpy/builder/shape.py

@@ -179,7 +179,8 @@ def svg(
         assert shape in ("circle", "rectangle", "square")
         assert isinstance(fname_or_data, (str, bytes))
         if isinstance(fname_or_data, str):
-            data = open(fname_or_data, "rb").read()
+            with open(fname_or_data, "rb") as file:
+                data = file.read()
         else:
             data = fname_or_data
         shapeklass = {