Merge branch 'develop' into visualization_table_error

# Conflicts:
#	src/petab_gui/controllers/table_controllers.py

Author: PaulJonasJost

.github/workflows/ci.yml

@@ -22,3 +22,46 @@ jobs:
 
     - name: Run pre-commit hooks
       run: pre-commit run --all-files
+
+  launch:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11', '3.13']
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v5
+
+    - name: Prepare Python
+      uses: actions/setup-python@v6
+      with:
+          python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y xvfb libegl1 libqt6gui6 libxcb-cursor0
+
+    - name: Install PEtabGUI
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+
+    - name: Launch GUI
+      # Ensure that we can launch the GUI
+      run: |
+        echo "Launching Xvfb"
+        Xvfb :99 -screen 0 1920x1200x24 &
+        export DISPLAY=:99
+        echo "Running petab_gui --version"
+        petab_gui --version
+        echo "Running petab_gui without arguments"
+        petab_gui &
+        echo $! > petabgui_pid.txt
+        sleep 10
+        kill $(cat petabgui_pid.txt)
+        echo "Running petab_gui with example problem"
+        petab_gui example/problem.yaml &
+        echo $! > petabgui_pid.txt
+        sleep 10
+        kill $(cat petabgui_pid.txt)

.github/workflows/python-publish.yml

@@ -21,6 +21,9 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          # Fetch full history for setuptools-scm
+          fetch-depth: 0
 
       - uses: actions/setup-python@v5
         with:
@@ -56,7 +59,8 @@ jobs:
       # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
       # ALTERNATIVE: exactly, uncomment the following line instead:
       # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
-
+    env:
+      SETUPTOOLS_SCM_OVERRIDES_FOR_PETAB_GUI: '{"local_scheme": "no-local-version"}'
     steps:
       - name: Retrieve release distributions
         uses: actions/download-artifact@v4

.readthedocs.yaml

@@ -22,3 +22,10 @@ build:
   os: "ubuntu-24.04"
   tools:
     python: "3.11"
+  jobs:
+    post_checkout:
+      # Avoid setuptools-scm dirty Git index issues
+      - git reset --hard HEAD
+      - git clean -fdx
+      # Enforce fail_on_shallow for setuptools-scm
+      - export SETUPTOOLS_SCM_OVERRIDES_FOR_${READTHEDOCS_PROJECT//-/_}='{scm.git.pre_parse="fail_on_shallow"}'

README.md

@@ -21,7 +21,7 @@ pip install petab_gui
 To install the latest development version from GitHub, run:
 
 ```bash
-    pip3 install git+https://github.com/PaulJonasJost/PEtab_GUI/
+pip install git+https://github.com/PaulJonasJost/PEtab_GUI/
 ```
 
 ### From a local copy
@@ -52,7 +52,7 @@ The PEtabGUI provides a Python-based graphical user interface that simplifies
 the creation, editing, and validation of PEtab parameter estimation problems.
 
 - **Unified Environment**
-  - Integrates all PEtab components (SBML/PySB models, conditions, observables,
+  - Integrates all PEtab components (SBML models, conditions, observables,
     measurements, parameters, and visualization files).
   - Supports drag-and-drop import of YAML or individual component files.
   - Automatically resolves mismatches and converts matrix-format experimental data

docs/source/conf.py

@@ -2,6 +2,7 @@
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
+from importlib.metadata import version as get_version
 
 rst_prolog = """
 .. |petab_doc_url| replace:: https://petab.readthedocs.io/en/latest/index.html
@@ -13,7 +14,7 @@
 project = "PEtab GUI"
 copyright = "2025, Paul Jonas Jost, Frank T. Bergmann"
 author = "Paul Jonas Jost, Frank T. Bergmann"
-release = "0.1.3"
+release: str = get_version("petab-gui")
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/source/contributing.rst

@@ -42,7 +42,7 @@ Filing an Issue
 ----------------
 
 If you encounter any bugs or have feature requests, please file an issue on GitHub.
-[Open a new issue](https://github.com/PaulJonasJost/PEtab_GUI/issues/new/choose).
+`Open a new issue <https://github.com/PaulJonasJost/PEtab_GUI/issues/new/choose>`__.
 
 When filing an issue, provide as much detail as possible,
 including steps to reproduce the issue, expected behavior, and any relevant logs or screenshots.

docs/source/index.rst

@@ -55,3 +55,4 @@ To get started with PEtab GUI, check out the :doc:`installation instructions <re
    :caption: Development
 
    GitHub Repository <https://github.com/PaulJonasJost/PEtab_GUI>
+   contributing

src/petab_gui/controllers/mother_controller.py

@@ -858,11 +858,15 @@ def check_model(self):
 
             # Log the consistency check result
             if not failed:
-                self.logger.log_message("Model is consistent.", color="green")
+                self.logger.log_message(
+                    "PEtab problem has no errors.", color="green"
+                )
                 for model in self.model.pandas_models.values():
                     model.reset_invalid_cells()
             else:
-                self.logger.log_message("Model is inconsistent.", color="red")
+                self.logger.log_message(
+                    "PEtab problem has errors.", color="red"
+                )
         except Exception as e:
             msg = f"PEtab linter failed at some point: {filtered_error(e)}"
             self.logger.log_message(msg, color="red")

src/petab_gui/controllers/table_controllers.py

@@ -77,7 +77,7 @@ def __init__(
         self.undo_stack = undo_stack
         self.model.undo_stack = undo_stack
         self.check_petab_lint_mode = True
-        if model.table_type in ["simulation"]:
+        if model.table_type in ["simulation", "visualization"]:
             self.check_petab_lint_mode = False
         self.mother_controller = mother_controller
         self.view.table_view.setModel(self.proxy_model)
@@ -1341,3 +1341,61 @@ def check_petab_lint(
             capture_handler.get_formatted_messages()
         )
         raise ValueError(captured_output)
+
+    def setup_completers(self):
+        """Set completers for the visualization table."""
+        table_view = self.view.table_view
+        # plotTypeSimulation
+        index = self.model.return_column_index("plotTypeSimulation")
+        if index and index > -1:
+            self.completers["plotTypeSimulation"] = ComboBoxDelegate(
+                ["LinePlot", "BarPlot", "ScatterPlot"]
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["plotTypeSimulation"]
+            )
+        # plotTypeData
+        index = self.model.return_column_index("plotTypeData")
+        if index and index > -1:
+            self.completers["plotTypeData"] = ComboBoxDelegate(
+                ["MeanAndSD", "MeanAndSEM", "replicate", "provided"]
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["plotTypeData"]
+            )
+        # datasetId
+        index = self.model.return_column_index("datasetId")
+        if index and index > -1:
+            self.completers["datasetId"] = ColumnSuggestionDelegate(
+                self.mother_controller.model.measurement, "datasetId"
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["datasetId"]
+            )
+        # yValues
+        index = self.model.return_column_index("yValues")
+        if index and index > -1:
+            self.completers["yValues"] = ColumnSuggestionDelegate(
+                self.mother_controller.model.observable, "observableId"
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["yValues"]
+            )
+        # xScale
+        index = self.model.return_column_index("xScale")
+        if index and index > -1:
+            self.completers["xScale"] = ComboBoxDelegate(
+                ["lin", "log", "log10", "order"]
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["xScale"]
+            )
+        # yScale
+        index = self.model.return_column_index("yScale")
+        if index and index > -1:
+            self.completers["yScale"] = ComboBoxDelegate(
+                ["lin", "log", "log10", "order"]
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["yScale"]
+            )

src/petab_gui/models/pandas_table_model.py

@@ -377,7 +377,7 @@ def _set_data_single(self, index, value):
             if error:
                 self.new_log_message.emit(
                     f"Column '{column_name}' expects a value of type "
-                    f"{expected_type}, but got '{value}'",
+                    f"{expected_type.__name__}, but got '{value}'",
                     "red",
                 )
                 return False
@@ -670,7 +670,9 @@ def return_column_index(self, column_name):
         Returns:
             int: The view column index for the given column name, or -1
         """
-        pass
+        if column_name in self._data_frame.columns:
+            return self._data_frame.columns.get_loc(column_name)
+        return -1
 
     def unique_values(self, column_name):
         """Return a list of unique values in a specified column.
@@ -1115,12 +1117,6 @@ def get_default_values(self, index, changed: dict | None = None):
         else:
             command.redo()
 
-    def return_column_index(self, column_name):
-        """Return the index of a column."""
-        if column_name in self._data_frame.columns:
-            return self._data_frame.columns.get_loc(column_name)
-        return -1
-
 
 class ObservableModel(IndexedPandasTableModel):
     """Table model for the observable data."""