Merge branch 'develop'

Author: IngoMeyer441

.gitlab-ci.yml

@@ -382,10 +382,38 @@ pre-package:
   - pipx install "briefcase==${BRIEFCASE_VERSION}"
   - export PATH="${HOME}/.local/bin:${PATH}"
   - python3 -m venv env
+  - ./env/bin/python3 -m pip install -U
+      pip
+      setuptools
+      wheel
+  # Latest pip versions on Debian 11 bullseye may throw encoding errors in `compileall.py` if not all modules can be
+  # byte-compiled (for example for PySide6). Therefore, patch the Python installation to use 'UTF-8' as fallback
+  # encoding.
+  - |-
+    if ! awk -F'=' '$1 == "VERSION_CODENAME" && $2 == "bullseye" { exit 1 }' /etc/os-release; then
+      pushd /usr/lib/python3.9
+    (
+      echo "--- compileall.py       2025-03-20 02:07:39.000000000 +0000";
+      echo "+++ compileall.py.patched       2025-04-29 10:11:00.568493043 +0000";
+      echo "@@ -252,9 +252,9 @@";
+      echo "                 else:";
+      echo "                     print('*** ', end='')";
+      echo "                 # escape non-printable characters in msg";
+      echo "-                msg = err.msg.encode(sys.stdout.encoding,";
+      echo "+                msg = err.msg.encode(sys.stdout.encoding if sys.stdout.encoding is not None else 'utf-8',";
+      echo "                                      errors='backslashreplace')";
+      echo "-                msg = msg.decode(sys.stdout.encoding)";
+      echo "+                msg = msg.decode(sys.stdout.encoding if sys.stdout.encoding is not None else 'utf-8')";
+      echo "                 print(msg)";
+      echo "             except (SyntaxError, UnicodeError, OSError) as e:";
+      echo "                 success = False";
+    ) | patch -N
+      popd
+    fi
   script:
   # Install the project in editable mode to force to build all C extenions in-place. Otherwise, they won't be packaged
   # by briefcase
-  - ./env/bin/python3 -m pip install -e .
+  - ./env/bin/python3 -m pip install --no-deps -e .
   - briefcase create linux system
   - briefcase build linux system
   - briefcase package linux system
@@ -419,6 +447,11 @@ package:ubuntu:24.10:
   image: ubuntu:24.10
 
 
+package:ubuntu:25.04:
+  extends: .package:debian
+  image: ubuntu:25.04
+
+
 .package:rhel:
   stage: package
   needs: ["pre-package"]
@@ -433,10 +466,14 @@ package:ubuntu:24.10:
   - pipx install "briefcase==${BRIEFCASE_VERSION}"
   - export PATH="${HOME}/.local/bin:${PATH}"
   - python3 -m venv env
+  - ./env/bin/python3 -m pip install -U
+      pip
+      setuptools
+      wheel
   script:
   # Install the project in editable mode to force to build all C extenions in-place. Otherwise, they won't be packaged
   # by briefcase
-  - ./env/bin/python3 -m pip install -e .
+  - ./env/bin/python3 -m pip install --no-deps -e .
   - briefcase create linux system
   - briefcase build linux system
   - briefcase package linux system
@@ -455,6 +492,11 @@ package:fedora:41:
   image: fedora:41
 
 
+package:fedora:42:
+  extends: .package:rhel
+  image: fedora:42
+
+
 package:opensuse:tumbleweed:
   stage: package
   image: opensuse/tumbleweed
@@ -468,10 +510,14 @@ package:opensuse:tumbleweed:
   - pipx install "briefcase==${BRIEFCASE_VERSION}"
   - export PATH="${HOME}/.local/bin:${PATH}"
   - python3 -m venv env
+  - ./env/bin/python3 -m pip install -U
+      pip
+      setuptools
+      wheel
   script:
   # Install the project in editable mode to force to build all C extenions in-place. Otherwise, they won't be packaged
   # by briefcase
-  - ./env/bin/python3 -m pip install -e .
+  - ./env/bin/python3 -m pip install --no-deps -e .
   - briefcase create linux system
   - briefcase build linux system
   - briefcase package linux system
@@ -500,10 +546,14 @@ package:flatpack:
   - pipx install "briefcase==${BRIEFCASE_VERSION}"
   - export PATH="${HOME}/.local/bin:${PATH}"
   - python3 -m venv env
+  - ./env/bin/python3 -m pip install -U
+      pip
+      setuptools
+      wheel
   script:
   # Install the project in editable mode to force to build all C extenions in-place. Otherwise, they won't be packaged
   # by briefcase
-  - ./env/bin/python3 -m pip install -e .
+  - ./env/bin/python3 -m pip install --no-deps -e .
   - briefcase create linux flatpak
   - briefcase build linux flatpak
   - briefcase package linux flatpak
@@ -575,6 +625,10 @@ package:macos:
   - ./create_icns.py pymoldyn/icon.png pymoldyn/icon.icns
   - GR_TEMPDIR="$(mktemp -d)"
   - python3 -m venv env
+  - ./env/bin/python3 -m pip install -U
+      pip
+      setuptools
+      wheel
   - GR_STABLE_VERSION="$(
       git ls-remote --tags "https://github.com/sciapp/gr" |
       awk 'match($2, /refs\/tags\/v[0-9]+\.[0-9]+\.[0-9]+$/) { print substr($2, RSTART + length("refs/tags/v")) }' |
@@ -587,7 +641,7 @@ package:macos:
   script:
   # Install the project in editable mode to force to build all C extenions in-place. Otherwise, they won't be packaged
   # by briefcase
-  - ./env/bin/python3 -m pip install -e .
+  - ./env/bin/python3 -m pip install --no-deps -e .
   - briefcase create
   # Force to use the universal GR binaries for x86_64 and arm64
   - rsync -a "${GR_TEMPDIR}/gr/" --exclude "Applications"
@@ -620,10 +674,14 @@ package:windows:
       -define "icon:auto-resize=16,32,48,64,128,256"
       pymoldyn/icon.ico
   - vcvars_cmd python -m venv env
+  - ./env/Scripts/python -m pip install -U
+      pip
+      setuptools
+      wheel
   script:
   # Install the project in editable mode to force to build all C extenions in-place. Otherwise, they won't be packaged
   # by briefcase
-  - ./env/Scripts/python -m pip install -e .
+  - ./env/Scripts/python -m pip install --no-deps -e .
   - vcvars_cmd python -m briefcase create
   - vcvars_cmd python -m briefcase build
   - vcvars_cmd python -m briefcase package --adhoc-sign

pymoldyn/_version.py

@@ -1,2 +1,2 @@
-__version_info__ = (0, 11, 0)
+__version_info__ = (0, 11, 1)
 __version__ = ".".join(map(str, __version_info__))

pymoldyn/gui/gl_widget.py

@@ -48,6 +48,7 @@ def __init__(self, parent, main_window):
         self.control = parent.control
         self.main_window = main_window
         self.setDisabled(True)
+        self.vis.repaint_callback = self.update
 
     @property
     def vis(self):

pymoldyn/visualization/visualization.py

@@ -22,7 +22,7 @@ class Visualization(object):
     Visualize Atoms and Cavities with GR3
     """
 
-    def __init__(self):
+    def __init__(self, repaint_callback=None):
         self.max_side_lengths = 1.0
         self.mat = np.eye(4)
         self.d = self.max_side_lengths * 2
@@ -37,7 +37,12 @@ def __init__(self):
         self.width = 0
         self.height = 0
         self.usecurrentframebuffer = False
+        if repaint_callback is not None:
+            self._repaint_callback = repaint_callback
+        else:
+            self._repaint_callback = lambda: self.paint(self.width, self.height)
         #  self.assigned_opengl_context = None
+        self._export_args = None
 
         self.results = None
         self.settings = VisualizationSettings()
@@ -58,7 +63,7 @@ def setresults(self, results):
         self.far = 6 * max_side_lengths
         self.create_scene()
         if self.width != 0 and self.height != 0:
-            self.paint(self.width, self.height)
+            self.repaint_callback()
         self.settings.visible_domain_indices = None
         self.settings.visible_surface_cavity_indices = None
         self.settings.visible_center_cavity_indices = None
@@ -270,23 +275,28 @@ def paint(self, width, height, usecurrentframebuffer=None, device_pixel_ratio=1)
             self.usecurrentframebuffer = usecurrentframebuffer
         if self.usecurrentframebuffer:
             gr3.usecurrentframebuffer()
-        gr3.drawimage(
-            0,
-            width * device_pixel_ratio,
-            0,
-            height * device_pixel_ratio,
-            width,
-            height,
-            gr3.GR3_Drawable.GR3_DRAWABLE_OPENGL,
-        )
+        if self._export_args is not None:
+            gr3.export(*self._export_args)
+            self._export_args = None
+        else:
+            gr3.drawimage(
+                0,
+                width * device_pixel_ratio,
+                0,
+                height * device_pixel_ratio,
+                width,
+                height,
+                gr3.GR3_Drawable.GR3_DRAWABLE_OPENGL,
+            )
 
     def save_screenshot(self, file_name, width=3840, height=2160, first=True, last=True):
         """
         Save a screenshot in the given resolution.
         ``first`` and ``last`` can be used to indicate if the first or last screenshot is taken when
         multiple images are saved in a loop for example.
         """
-        gr3.export(file_name, width, height)
+        self._export_args = (file_name, width, height)
+        self.repaint_callback()
 
     def get_object_at_2dposition(self, x, y):
         oid = gr3.c_int(0)
@@ -317,6 +327,14 @@ def get_object_at_3dposition(self, x, y, z):
             if 0.95 < distances[nearest_atom_index] / atom_radius < 1.05:
                 return ("atom", nearest_atom_index)
 
+    @property
+    def repaint_callback(self):
+        return self._repaint_callback
+
+    @repaint_callback.setter
+    def repaint_callback(self, repaint_callback):
+        self._repaint_callback = repaint_callback
+
 
 class VisualizationSettings(object):
     """