Offboarding after Save

src/petab_gui/controllers/mother_controller.py

@@ -42,6 +42,7 @@
     process_file,
 )
 from ..views import TaskBar
+from ..views.other_views import NextStepsPanel
 from .logger_controller import LoggerController
 from .sbml_controller import SbmlController
 from .table_controllers import (
@@ -150,6 +151,11 @@ def __init__(self, view, model: PEtabModel):
         }
         self.sbml_checkbox_states = {"sbml": False, "antimony": False}
         self.unsaved_changes = False
+        # Next Steps Panel
+        self.next_steps_panel = NextStepsPanel(self.view)
+        self.next_steps_panel.dont_show_again_changed.connect(
+            self._handle_next_steps_dont_show_again
+        )
         self.filter = QLineEdit()
         self.filter_active = {}  # Saves which tables the filter applies to
         self.actions = self.setup_actions()
@@ -509,6 +515,12 @@ def setup_actions(self):
             )
         )
 
+        # Show next steps panel action
+        actions["next_steps"] = QAction(
+            qta.icon("mdi6.lightbulb-on"), "Possible next steps...", self.view
+        )
+        actions["next_steps"].triggered.connect(self._show_next_steps_panel)
+
         # Undo / Redo
         actions["undo"] = QAction(qta.icon("mdi6.undo"), "&Undo", self.view)
         actions["undo"].setShortcut(QKeySequence.Undo)
@@ -612,6 +624,14 @@ def save_model(self):
             "Save Project",
             f"Project saved successfully to {file_name}",
         )
+
+        # Show next steps panel if not disabled
+        dont_show = settings_manager.get_value(
+            "next_steps/dont_show_again", False, bool
+        )
+        if not dont_show:
+            self.next_steps_panel.show_panel()
+
         return True
 
     def save_single_table(self):
@@ -1502,6 +1522,26 @@ def about(self):
             f"<a href='file://{config_file}'>{config_file}</a></small>",
         )
 
+    def _show_next_steps_panel(self):
+        """Show the next steps panel (ignores 'don't show again' preference)."""
+        # Sync checkbox state with current settings
+        dont_show = settings_manager.get_value(
+            "next_steps/dont_show_again", False, bool
+        )
+        self.next_steps_panel.set_dont_show_again(dont_show)
+        self.next_steps_panel.show_panel()
+
+    def _handle_next_steps_dont_show_again(self, dont_show: bool):
+        """Handle the 'don't show again' checkbox state change.
+
+        Connected to the next steps panel's dont_show_again_changed signal.
+        Persists the user's preference to settings.
+
+        Args:
+            dont_show: Whether to suppress the panel on future saves
+        """
+        settings_manager.set_value("next_steps/dont_show_again", dont_show)
+
     def get_current_problem(self):
         """Get the current PEtab problem from the model."""
         return self.model.current_petab_problem

src/petab_gui/views/other_views.py

@@ -1,12 +1,16 @@
 """Collection of other views aside from the main ones."""
 
+from PySide6.QtCore import Qt, Signal
 from PySide6.QtWidgets import (
+    QCheckBox,
     QComboBox,
     QDialog,
+    QFrame,
     QHBoxLayout,
     QLabel,
     QLineEdit,
     QPushButton,
+    QTextBrowser,
     QVBoxLayout,
 )
 
@@ -59,8 +63,273 @@ def __init__(
         btns.addWidget(ok)
         lay.addLayout(btns)
 
-    def get_result(self) -> tuple[str | None, str | None]:
+    def get_result(self) -> tuple[str | None, str | None, str]:
         dose = self._dose.currentText() or None
         time_text = (self._time.text() or "").strip() or None
         preeq = (self._preeq_edit.text() or "").strip()
         return dose, time_text, preeq
+
+
+class NextStepsPanel(QDialog):
+    """Non-modal panel showing possible next steps after saving."""
+
+    dont_show_again_changed = Signal(bool)
+
+    # Styling constants
+    MIN_WIDTH = 450
+    MAX_WIDTH = 600
+    MIN_HEIGHT = 360
+    FRAME_PADDING = 8
+    FRAME_BORDER_RADIUS = 4
+    LAYOUT_MARGIN = 12
+    LAYOUT_SPACING = 10
+
+    # Card background colors
+    COLOR_BENCHMARK = "rgba(255, 193, 7, 0.08)"
+    COLOR_PYPESTO = "rgba(100, 149, 237, 0.08)"
+    COLOR_COPASI = "rgba(169, 169, 169, 0.08)"
+    COLOR_OTHER_TOOLS = "rgba(144, 238, 144, 0.08)"
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setWindowTitle("Possible next steps")
+        self.setModal(False)
+        self.setMinimumWidth(self.MIN_WIDTH)
+        self.setMaximumWidth(self.MAX_WIDTH)
+        self.setMinimumHeight(self.MIN_HEIGHT)
+
+        # Main layout
+        main_layout = QVBoxLayout(self)
+        main_layout.setContentsMargins(
+            self.LAYOUT_MARGIN,
+            self.LAYOUT_MARGIN,
+            self.LAYOUT_MARGIN,
+            self.LAYOUT_MARGIN,
+        )
+        main_layout.setSpacing(self.LAYOUT_SPACING)
+
+        # Description
+        desc = QLabel(
+            "This parameter estimation problem can now be used in the following tools:"
+        )
+        desc.setWordWrap(True)
+        main_layout.addWidget(desc)
+
+        # Main suggestions
+        suggestions_layout = QVBoxLayout()
+        suggestions_layout.setSpacing(8)
+
+        # Benchmark Collection action
+        benchmark_frame = self._create_tool_card(
+            bg_color=self.COLOR_BENCHMARK,
+            html_content=(
+                '<p style="margin:0; line-height:1.3;">'
+                "<b>📚 Contribute to Benchmark Collection</b><br/>"
+                "Share your publsihed PEtab problem with the community to "
+                "validate it, enable reproducibility, and support "
+                "benchmarking.<br/>"
+                '<a href="https://github.com/Benchmarking-Initiative/'
+                'Benchmark-Models-PEtab">Benchmark Collection</a></p>'
+            ),
+        )
+        suggestions_layout.addWidget(benchmark_frame)
+
+        # pyPESTO action
+        pypesto_frame = self._create_tool_card(
+            bg_color=self.COLOR_PYPESTO,
+            html_content=(
+                '<p style="margin:0; line-height:1.3;">'
+                "<b>▶ Parameter Estimation with pyPESTO</b><br/>"
+                "Use pyPESTO for parameter estimation, uncertainty analysis, "
+                "and model selection.<br/>"
+                '<a href="https://pypesto.readthedocs.io/en/latest/example/'
+                'petab_import.html">pyPESTO documentation</a></p>'
+            ),
+        )
+        suggestions_layout.addWidget(pypesto_frame)
+
+        # COPASI action
+        copasi_frame = self._create_tool_card(
+            bg_color=self.COLOR_COPASI,
+            html_content=(
+                '<p style="margin:0; line-height:1.3;">'
+                "<b>⚙ Advanced Model Adaptation and Simulation</b><br/>"
+                "Use COPASI for further model adjustment and advanced "
+                "simulation with a graphical interface.<br/>"
+                '<a href="https://copasi.org">COPASI website</a></p>'
+            ),
+        )
+        suggestions_layout.addWidget(copasi_frame)
+
+        main_layout.addLayout(suggestions_layout)
+
+        # Collapsible section for other tools
+        self._other_tools_btn = QPushButton(
+            "📊 ▶ Other tools supporting PEtab"
+        )
+        self._other_tools_btn.setCheckable(True)
+        self._other_tools_btn.setFlat(True)
+        self._other_tools_btn.setStyleSheet(
+            "QPushButton { text-align: left; padding: 6px; "
+            "font-weight: normal; }"
+            "QPushButton:checked { font-weight: bold; }"
+        )
+        self._other_tools_btn.clicked.connect(self._toggle_other_tools)
+        main_layout.addWidget(self._other_tools_btn)
+
+        # Other tools frame (initially hidden)
+        self._other_tools_frame = QFrame()
+        self._other_tools_frame.setStyleSheet(
+            f"QFrame {{ background-color: {self.COLOR_OTHER_TOOLS}; "
+            f"border-radius: {self.FRAME_BORDER_RADIUS}px; "
+            f"padding: {self.FRAME_PADDING}px; }}"
+        )
+        self._other_tools_frame.setVisible(False)
+        other_tools_layout = QVBoxLayout(self._other_tools_frame)
+        other_tools_layout.setContentsMargins(
+            self.FRAME_PADDING,
+            self.FRAME_PADDING,
+            self.FRAME_PADDING,
+            self.FRAME_PADDING,
+        )
+        other_tools_layout.setSpacing(4)
+
+        # Framing text
+        framing_text = QLabel("Additional tools in the PEtab ecosystem:")
+        framing_text.setWordWrap(True)
+        other_tools_layout.addWidget(framing_text)
+
+        other_tools_text = QTextBrowser()
+        other_tools_text.setOpenExternalLinks(True)
+        other_tools_text.setMaximumHeight(120)
+        other_tools_text.setFrameStyle(QFrame.NoFrame)
+        other_tools_text.setStyleSheet(
+            "QTextBrowser { background: transparent; }"
+        )
+        other_tools_text.setVerticalScrollBarPolicy(
+            Qt.ScrollBarPolicy.ScrollBarAsNeeded
+        )
+        other_tools_text.setHtml(
+            '<ul style="margin:4px 0; padding-left: 20px; '
+            'line-height: 1.6;">'
+            '<li style="margin-bottom: 4px;">'
+            '<a href="https://amici.readthedocs.io/en/latest/examples/'
+            'example_petab/petab.html">AMICI</a> - '
+            "Efficient simulation and sensitivity analysis</li>"
+            '<li style="margin-bottom: 4px;">'
+            '<a href="https://sebapersson.github.io/PEtab.jl/stable/">'
+            "PEtab.jl</a> - "
+            "High-performance Julia parameter estimation</li>"
+            '<li style="margin-bottom: 4px;">'
+            '<a href="https://github.com/Data2Dynamics/d2d/wiki">'
+            "Data2Dynamics</a> - "
+            "MATLAB-based comprehensive modeling framework</li>"
+            '<li style="margin-bottom: 4px;">'
+            '<a href="https://petab.readthedocs.io/en/latest/v1/'
+            'software_support.html">PEtab documentation</a> - '
+            "Full list of supporting tools</li>"
+            "</ul>"
+        )
+        other_tools_layout.addWidget(other_tools_text)
+
+        main_layout.addWidget(self._other_tools_frame)
+
+        # Spacer
+        main_layout.addStretch()
+
+        # Reassurance text
+        reassurance = QLabel(
+            "<small><i>You can always access this dialog from the "
+            "Help menu.</i></small>"
+        )
+        reassurance.setWordWrap(True)
+        reassurance.setStyleSheet("QLabel { color: gray; padding: 0; }")
+        main_layout.addWidget(reassurance)
+
+        # Bottom section with checkbox and close button
+        bottom_layout = QHBoxLayout()
+        bottom_layout.setSpacing(8)
+
+        self._dont_show_checkbox = QCheckBox("Don't show after saving")
+        self._dont_show_checkbox.toggled.connect(
+            self.dont_show_again_changed.emit
+        )
+        bottom_layout.addWidget(self._dont_show_checkbox)
+
+        bottom_layout.addStretch()
+
+        close_btn = QPushButton("Close")
+        close_btn.clicked.connect(self.close)
+        close_btn.setDefault(True)
+        bottom_layout.addWidget(close_btn)
+
+        main_layout.addLayout(bottom_layout)
+
+    def _create_tool_card(
+        self, bg_color: str, html_content: str, scrollbar_policy=None
+    ) -> QFrame:
+        """Create a styled card for displaying tool information.
+
+        Args:
+            bg_color: Background color for the frame (rgba string)
+            html_content: HTML content to display in the text browser
+            scrollbar_policy: Optional scrollbar policy (defaults to AlwaysOff)
+
+        Returns:
+            Configured QFrame containing the tool information
+        """
+        frame = QFrame()
+        frame.setStyleSheet(
+            f"QFrame {{ background-color: {bg_color}; "
+            f"border-radius: {self.FRAME_BORDER_RADIUS}px; "
+            f"padding: {self.FRAME_PADDING}px; }}"
+        )
+        layout = QVBoxLayout(frame)
+        layout.setContentsMargins(
+            self.FRAME_PADDING,
+            self.FRAME_PADDING,
+            self.FRAME_PADDING,
+            self.FRAME_PADDING,
+        )
+        layout.setSpacing(4)
+
+        text_browser = QTextBrowser()
+        text_browser.setOpenExternalLinks(True)
+        text_browser.setFrameStyle(QFrame.NoFrame)
+        text_browser.setStyleSheet("QTextBrowser { background: transparent; }")
+        if scrollbar_policy is None:
+            scrollbar_policy = Qt.ScrollBarPolicy.ScrollBarAlwaysOff
+        text_browser.setVerticalScrollBarPolicy(scrollbar_policy)
+        text_browser.setHtml(html_content)
+        layout.addWidget(text_browser)
+
+        return frame
+
+    def _toggle_other_tools(self, checked):
+        """Toggle visibility of other tools section."""
+        self._other_tools_frame.setVisible(checked)
+        # Update button text to show expand/collapse state
+        arrow = "▼" if checked else "▶"
+        icon = "📊"
+        self._other_tools_btn.setText(
+            f"{icon} {arrow} Other tools supporting PEtab"
+        )
+        # Adjust window size
+        self.adjustSize()
+
+    def set_dont_show_again(self, dont_show: bool):
+        """Set the 'don't show again' checkbox state."""
+        self._dont_show_checkbox.setChecked(dont_show)
+
+    def show_panel(self):
+        """Show the panel and center it on the parent."""
+        if self.parent():
+            # Center on parent window
+            parent_geo = self.parent().geometry()
+            self.move(
+                parent_geo.center().x() - self.width() // 2,
+                parent_geo.center().y() - self.height() // 2,
+            )
+        self.show()
+        self.raise_()
+        self.activateWindow()

src/petab_gui/views/task_bar.py

@@ -139,6 +139,8 @@ def __init__(self, parent, actions):
 
         # Add actions to the menu for re-adding tables
         self.menu.addAction(actions["open_documentation"])
+        self.menu.addAction(actions["next_steps"])
+        self.menu.addSeparator()
         self.menu.addAction(actions["whats_this"])
         self.menu.addAction(actions["about"])