feat: Launch PartSeg GUI from napari (#581)

Author: Czaki

.github/workflows/test_napari_widgets.yml

@@ -55,7 +55,7 @@ jobs:
         uses: GabrielBB/xvfb-action@v1
         timeout-minutes: 60
         with:
-          run: tox
+          run: python -m tox
         env:
           PLATFORM: ${{ matrix.platform }}
           NAPARI: ${{ matrix.napari_version }}

package/PartSeg/_launcher/main_window.py

@@ -3,7 +3,7 @@
 import warnings
 from functools import partial
 
-from qtpy.QtCore import QSize, Qt, QThread
+from qtpy.QtCore import QSize, Qt, QThread, Signal
 from qtpy.QtGui import QIcon
 from qtpy.QtWidgets import QGridLayout, QMainWindow, QMessageBox, QProgressBar, QToolButton, QWidget
 
@@ -39,10 +39,11 @@ def run(self):
             self.result = partial(main_window, settings=settings, initial_image=im)
 
 
-class MainWindow(QMainWindow):
-    def __init__(self, title):
-        super().__init__()
-        self.setWindowTitle(title)
+class PartSegGUILauncher(QWidget):
+    launched = Signal()
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
         self.lib_path = ""
         self.final_title = ""
         analysis_icon = QIcon(os.path.join(icons_dir, "icon.png"))
@@ -66,28 +67,10 @@ def __init__(self, title):
         layout.addWidget(self.progress, 0, 0, 1, 2)
         layout.addWidget(self.analysis_button, 1, 1)
         layout.addWidget(self.mask_button, 1, 0)
-        widget = QWidget()
-        widget.setLayout(layout)
-        self.setCentralWidget(widget)
-        self.setWindowIcon(analysis_icon)
-        self.prepare = None
-        self.wind = None
-        self._update_theme()
-
-    def _update_theme(self):
-        napari_settings = napari_get_settings(state_store.save_folder)
-        with warnings.catch_warnings():
-            warnings.simplefilter("ignore", FutureWarning)
-            theme = get_theme(napari_settings.appearance.theme)
-        # TODO understand qss overwrite mechanism
-        self.setStyleSheet(napari_template(get_stylesheet(), **theme))
-
-    def _launch_begin(self):
-        self.progress.setVisible(True)
-        self.progress.setRange(0, 0)
-        self.analysis_button.setDisabled(True)
-        self.mask_button.setDisabled(True)
-        import_config()
+        self.setLayout(layout)
+        self.prepare = Prepare("")
+        self.prepare.finished.connect(self.launch)
+        self.wind = []
 
     def launch_analysis(self):
         self._launch_begin()
@@ -97,8 +80,7 @@ def launch_analysis(self):
     def _launch_analysis(self):
         self.lib_path = "PartSeg._roi_analysis.main_window"
         self.final_title = f"{APP_NAME} {ANALYSIS_NAME}"
-        self.prepare = Prepare(self.lib_path)
-        self.prepare.finished.connect(self.launch)
+        self.prepare.module = self.lib_path
 
     def launch_mask(self):
         self._launch_begin()
@@ -108,28 +90,56 @@ def launch_mask(self):
     def _launch_mask(self):
         self.lib_path = "PartSeg._roi_mask.main_window"
         self.final_title = f"{APP_NAME} {MASK_NAME}"
-        self.prepare = Prepare(self.lib_path)
-        self.prepare.finished.connect(self.launch)
+        self.prepare.module = self.lib_path
+
+    def _launch_begin(self):
+        self.progress.setVisible(True)
+        self.progress.setRange(0, 0)
+        self.analysis_button.setDisabled(True)
+        self.mask_button.setDisabled(True)
+        import_config()
 
     def window_shown(self):
-        self.close()
+        self.progress.setHidden(True)
+        self.analysis_button.setEnabled(True)
+        self.mask_button.setEnabled(True)
+        self.launched.emit()
 
     def launch(self):
-        if self.prepare.result is None:
+        if self.prepare.result is None:  # pragma: no cover
             self.close()
             return
-        if self.prepare.errors:
+        if self.prepare.errors:  # pragma: no cover
             errors_message = QMessageBox()
             errors_message.setText("There are errors during start")
             errors_message.setInformativeText(
                 "During load saved state some of data could not be load properly\n"
                 "The files has prepared backup copies in  state directory (Help > State directory)"
             )
             errors_message.setStandardButtons(QMessageBox.Ok)
-            text = "\n".join("File: " + x[0] + "\n" + str(x[1]) for x in self.prepare.errors)
+            text = "\n".join(f"File: {x[0]}" + "\n" + str(x[1]) for x in self.prepare.errors)
 
             errors_message.setDetailedText(text)
             errors_message.exec_()
         wind = self.prepare.result(title=self.final_title, signal_fun=self.window_shown)
         wind.show()
-        self.wind = wind
+        self.wind.append(wind)
+
+
+class MainWindow(QMainWindow):
+    def __init__(self, title):
+        super().__init__()
+        self.setWindowTitle(title)
+        widget = PartSegGUILauncher(self)
+        widget.launched.connect(self.close)
+        self.setCentralWidget(widget)
+        self.setWindowIcon(QIcon(os.path.join(icons_dir, "icon.png")))
+        self._update_theme()
+
+    def _update_theme(self):
+        napari_settings = napari_get_settings(state_store.save_folder)
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", FutureWarning)
+            theme = get_theme(napari_settings.appearance.theme)
+        # TODO understand qss overwrite mechanism
+        self.setStyleSheet(napari_template(get_stylesheet(), **theme))

package/PartSeg/common_gui/algorithms_description.py

@@ -140,6 +140,7 @@ def from_algorithm_property(cls, ob):
                 possible_values=ob.possible_values,
                 help_text=ob.help_text,
                 per_dimension=ob.per_dimension,
+                mgi_options=ob.mgi_options,
             )
         if isinstance(ob, str):
             return QLabel(ob)
@@ -189,7 +190,7 @@ def _get_field_from_value_type(cls, ap: AlgorithmProperty):
         elif issubclass(ap.value_type, BaseModel):
             res = FieldsList([cls.from_algorithm_property(x) for x in base_model_to_algorithm_property(ap.value_type)])
         else:
-            res = create_widget(value=ap.default_value, annotation=ap.value_type, options={})
+            res = create_widget(value=ap.default_value, annotation=ap.value_type, options=ap.mgi_options)
         return res
 
     def _get_field(self) -> typing.Union[QWidget, Widget]:
@@ -202,7 +203,7 @@ def _get_field(self) -> typing.Union[QWidget, Widget]:
             self.per_dimension = True
             res = ListInput(prop, 3)
         elif not inspect.isclass(self.value_type):
-            res = create_widget(value=self.default_value, annotation=self.value_type, options={})
+            res = create_widget(value=self.default_value, annotation=self.value_type, options=self.mgi_options)
         elif hasattr(self.value_type, "get_object"):
             res = self.value_type.get_object()
         else:

package/PartSeg/plugins/napari_widgets/__init__.py

@@ -1,5 +1,6 @@
 from napari_plugin_engine import napari_hook_implementation
 
+from PartSeg._launcher.main_window import PartSegGUILauncher
 from PartSeg.plugins.napari_widgets.mask_create_widget import MaskCreate
 from PartSeg.plugins.napari_widgets.roi_extraction_algorithms import ROIAnalysisExtraction, ROIMaskExtraction
 from PartSeg.plugins.napari_widgets.search_label_widget import SearchLabel
@@ -37,3 +38,8 @@ def napari_experimental_provide_dock_widget4():
 @napari_hook_implementation(specname="napari_experimental_provide_dock_widget")
 def napari_experimental_provide_dock_widget5():
     return SearchLabel
+
+
+@napari_hook_implementation(specname="napari_experimental_provide_dock_widget")
+def napari_experimental_provide_dock_widget6():
+    return PartSegGUILauncher

package/PartSegCore/algorithm_describe_base.py

@@ -46,6 +46,7 @@ def __init__(
         value_type=None,
         help_text="",
         per_dimension=False,
+        mgi_options=None,
         **kwargs,
     ):
         if "property_type" in kwargs:
@@ -68,6 +69,7 @@ def __init__(
         self.possible_values = possible_values
         self.help_text = help_text
         self.per_dimension = per_dimension
+        self.mgi_options = mgi_options if mgi_options is not None else {}
         if self.value_type is list and default_value not in possible_values:
             raise ValueError(f"default_value ({default_value}) should be one of possible values ({possible_values}).")
 
@@ -583,6 +585,7 @@ def _field_to_algorithm_property(name: str, field: "ModelField"):
         value_type=value_type,
         possible_values=possible_values,
         help_text=help_text,
+        mgi_options=field.field_info.extra.get("options", {}),
     )
 
 

package/tests/test_PartSeg/test_main_windows.py

@@ -1,11 +1,15 @@
+# pylint: disable=R0201
 import platform
 import sys
+from functools import partial
 
 import pytest
 import qtpy
 from qtpy.QtCore import QCoreApplication
 
 from PartSeg._launcher.main_window import MainWindow as LauncherMainWindow
+from PartSeg._launcher.main_window import PartSegGUILauncher
+from PartSeg._launcher.main_window import Prepare as LauncherPrepare
 from PartSeg._roi_analysis import main_window as analysis_main_window
 from PartSeg._roi_mask import main_window as mask_main_window
 
@@ -57,13 +61,13 @@ def test_open_mask(self, qtbot, monkeypatch, tmp_path):
         monkeypatch.setattr(mask_main_window, "CONFIG_FOLDER", str(tmp_path))
         if platform.system() == "Linux" and (GITHUB_ACTIONS or TRAVIS):
             monkeypatch.setattr(mask_main_window.MainWindow, "show", empty)
-        main_window = LauncherMainWindow("Launcher")
+        main_window = PartSegGUILauncher()
         qtbot.addWidget(main_window)
-        main_window._launch_mask()
         with qtbot.waitSignal(main_window.prepare.finished, timeout=10**4):
-            main_window.prepare.start()
+            main_window.launch_mask()
         QCoreApplication.processEvents()
-        main_window.wind.hide()
+        qtbot.add_widget(main_window.wind[0])
+        main_window.wind[0].hide()
         qtbot.wait(50)
 
     # @pytest.mark.skipif((platform.system() == "Linux") and CI_BUILD, reason="vispy problem")
@@ -74,13 +78,18 @@ def test_open_analysis(self, qtbot, monkeypatch, tmp_path):
         monkeypatch.setattr(analysis_main_window, "CONFIG_FOLDER", str(tmp_path))
         if platform.system() in {"Darwin", "Linux"} and (GITHUB_ACTIONS or TRAVIS):
             monkeypatch.setattr(analysis_main_window.MainWindow, "show", empty)
-        main_window = LauncherMainWindow("Launcher")
+        main_window = PartSegGUILauncher()
         qtbot.addWidget(main_window)
-        main_window._launch_analysis()
         with qtbot.waitSignal(main_window.prepare.finished):
-            main_window.prepare.start()
+            main_window.launch_analysis()
         QCoreApplication.processEvents()
         qtbot.wait(50)
-        qtbot.addWidget(main_window.wind)
-        main_window.wind.hide()
+        qtbot.add_widget(main_window.wind[0])
+        main_window.wind[0].hide()
         qtbot.wait(50)
+
+    def test_prepare(self):
+        prepare = LauncherPrepare("PartSeg._roi_analysis.main_window")
+        prepare.run()
+        assert isinstance(prepare.result, partial)
+        assert prepare.result.func is analysis_main_window.MainWindow

package/tests/test_PartSegCore/test_algorithm_describe_base.py

@@ -247,6 +247,14 @@ class ModelWithPosition(BBaseModel):
     assert property_list[2].name == "field2"
 
 
+def test_base_model_to_algorithm_property_magicgui_parameters():
+    class BBaseModel(BaseModel):
+        field1: int = Field(1, options={"a": 1, "b": 2})
+
+    prop = base_model_to_algorithm_property(BBaseModel)[0]
+    assert prop.mgi_options == {"a": 1, "b": 2}
+
+
 class TestAlgorithmDescribeBase:
     def test_old_style_algorithm(self):
         class SampleAlgorithm(AlgorithmDescribeBase):

tox.ini

@@ -25,14 +25,7 @@ NAPARI =
     napari414: 414
     napari415: 415
     repo: repo
-PLATFORM =
-    ubuntu-latest: linux
-    ubuntu-16.04: linux
-    ubuntu-18.04: linux
-    ubuntu-20.04: linux
-    windows-latest: windows
-    macos-latest: macos
-    macos-11: macos
+
 
 [base]
 deps =