Examples

MANIFEST.in

@@ -1,5 +1,7 @@
-include  example/*.csv
-include  example/*.tsv
-include  example/*.xml
+include  example/*/*.csv
+include  example/*/*.tsv
+include  example/*/*.xml
+include  example/*/*.yaml
+include  example/*/*.yml
 exclude .git_archival.txt
 exclude .gitattributes

example/simple_conversion_measurements.tsv

@@ -0,0 +1,11 @@
+time	obs_A	obs_B
+0	10.1	0.1
+2	8.0	 2.1
+4	6.8	 3.4
+6	5.6	 4.6
+8	4.4	 5.4
+10	3.8	 6.4
+12	3.1	 7.2
+15	2.3	 7.9
+18	1.6	 8.2
+20	1.3	 8.5

pyproject.toml

@@ -56,6 +56,7 @@ include-package-data = true
 
 [tool.setuptools.package-data]
 "petab_gui.assets" = ["PEtab.png"]
+"petab_gui.example" = ["*/*.yaml", "*/*.yml", "*/*.tsv", "*/*.csv", "*/*.xml", "*/*.sbml"]
 
 [tool.setuptools_scm]
 

src/petab_gui/controllers/mother_controller.py

@@ -308,6 +308,23 @@ def setup_actions(self):
         actions["add"].triggered.connect(
             partial(self.open_file, mode="append")
         )
+        # Load Examples
+        actions["load_example_boehm"] = QAction(
+            qta.icon("mdi6.book-open-page-variant"),
+            "Load Example: Boehm",
+            self.view,
+        )
+        actions["load_example_boehm"].triggered.connect(
+            partial(self.load_example, "Boehm")
+        )
+        actions["load_example_simple"] = QAction(
+            qta.icon("mdi6.book-open-page-variant"),
+            "Load Example: Simple Conversion",
+            self.view,
+        )
+        actions["load_example_simple"].triggered.connect(
+            partial(self.load_example, "Simple_Conversion")
+        )
         # Save
         actions["save"] = QAction(
             qta.icon("mdi6.content-save-all"), "&Save As...", self.view
@@ -1072,6 +1089,69 @@ def new_file(self):
         self.view.plot_dock.plot_it()
         self.unsaved_changes_change(False)
 
+    def load_example(self, example_name):
+        """Load an internal example PEtab problem.
+
+        Parameters
+        ----------
+        example_name : str
+            Name of the example subdirectory (e.g., "Boehm", "Simple_Conversion").
+
+        Finds and loads the example dataset from the package directory.
+        No internet connection required - the example is bundled with the package.
+        """
+        try:
+            # Use importlib.resources to access packaged example files
+            from importlib.resources import files
+
+            example_files = files("petab_gui.example")
+
+            # Check if the example package exists
+            if not example_files.is_dir():
+                error_msg = (
+                    "Could not find the example dataset. "
+                    "The example folder may not be properly installed."
+                )
+                self.logger.log_message(error_msg, color="red")
+                QMessageBox.warning(self.view, "Example Not Found", error_msg)
+                return
+
+            # Get the problem.yaml file path for the specified example
+            yaml_file = example_files.joinpath(example_name, "problem.yaml")
+
+            # For importlib.resources, we need to handle this differently
+            # in Python 3.9+ we can use as_file context manager
+            from importlib.resources import as_file
+
+            with as_file(yaml_file) as yaml_path:
+                if not yaml_path.exists():
+                    error_msg = f"Example '{example_name}' not found or problem.yaml file is missing."
+                    self.logger.log_message(error_msg, color="red")
+                    QMessageBox.warning(
+                        self.view, "Example Invalid", error_msg
+                    )
+                    return
+
+                # Load the example
+                self.logger.log_message(
+                    f"Loading '{example_name}' example dataset...",
+                    color="blue",
+                )
+                self.open_yaml_and_load_files(str(yaml_path))
+
+        except ModuleNotFoundError as e:
+            error_msg = (
+                "Example dataset not found. It may not be installed properly. "
+                f"Error: {str(e)}"
+            )
+            self.logger.log_message(error_msg, color="red")
+            QMessageBox.warning(self.view, "Example Not Found", error_msg)
+        except Exception as e:
+            error_msg = f"Failed to load example: {str(e)}"
+            self.logger.log_message(error_msg, color="red")
+            logging.exception("Full traceback for load example error:")
+            QMessageBox.critical(self.view, "Error Loading Example", error_msg)
+
     def check_model(self):
         """Check the consistency of the model. And log the results."""
         capture_handler = CaptureLogHandler()

src/petab_gui/example/Simple_Conversion/conditions.tsv

@@ -0,0 +1,2 @@
+conditionId	conditionName
+cond_1

src/petab_gui/example/Simple_Conversion/measurements.tsv

@@ -0,0 +1,21 @@
+observableId	simulationConditionId	time	measurement
+obs_A	cond_1	0.0	10.1
+obs_A	cond_1	2.0	8.0
+obs_A	cond_1	4.0	6.8
+obs_A	cond_1	6.0	5.6
+obs_A	cond_1	8.0	4.4
+obs_A	cond_1	10.0	3.8
+obs_A	cond_1	12.0	3.1
+obs_A	cond_1	15.0	2.3
+obs_A	cond_1	18.0	1.6
+obs_A	cond_1	20.0	1.3
+obs_B	cond_1	0.0	0.1
+obs_B	cond_1	2.0	2.1
+obs_B	cond_1	4.0	3.4
+obs_B	cond_1	6.0	4.6
+obs_B	cond_1	8.0	5.4
+obs_B	cond_1	10.0	6.4
+obs_B	cond_1	12.0	7.2
+obs_B	cond_1	15.0	7.9
+obs_B	cond_1	18.0	8.2
+obs_B	cond_1	20.0	8.5

src/petab_gui/example/Simple_Conversion/model.xml

@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="SimpleConversion" id="SimpleConversion">
+    <listOfCompartments>
+      <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="A" compartment="default_compartment" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="B" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k_conversion" value="0.1" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="conversion" reversible="true">
+        <listOfReactants>
+          <speciesReference species="A" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="B" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> k_conversion </ci>
+              <ci> A </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>

src/petab_gui/example/Simple_Conversion/observables.tsv

@@ -0,0 +1,3 @@
+observableId	observableFormula	noiseFormula
+obs_A	A	0.5
+obs_B	B	0.5

src/petab_gui/example/Simple_Conversion/parameters.tsv

@@ -0,0 +1,2 @@
+parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
+k_conversion	log10	0.001	100.0	0.1	1

src/petab_gui/example/Simple_Conversion/problem.yaml

@@ -0,0 +1,11 @@
+parameter_file: parameters.tsv
+format_version: 1
+problems:
+- condition_files:
+  - conditions.tsv
+  measurement_files:
+  - measurements.tsv
+  sbml_files:
+  - model.xml
+  observable_files:
+  - observables.tsv

src/petab_gui/example/__init__.py

@@ -0,0 +1,5 @@
+"""Example PEtab dataset bundled with PEtab GUI.
+
+This package contains an example PEtab problem that can be loaded
+without an internet connection.
+"""

src/petab_gui/views/task_bar.py

@@ -52,6 +52,8 @@ def __init__(self, parent, actions):
         self.menu.addAction(actions["new"])
         self.menu.addAction(actions["open"])
         self.menu.addAction(actions["add"])
+        self.menu.addAction(actions["load_example_boehm"])
+        self.menu.addAction(actions["load_example_simple"])
         self.menu.addAction(actions["save"])
         self.menu.addMenu(actions["recent_files"])
         self.menu.addSeparator()