Fix/pip installability

cnapy/gui_elements/main_window.py

@@ -46,7 +46,12 @@
 from cnapy.gui_elements.configuration_cplex import CplexConfigurationDialog
 from cnapy.gui_elements.configuration_cplex_new import CplexNewConfigurationDialog
 from cnapy.gui_elements.configuration_gurobi import GurobiConfigurationDialog
-from cnapy.gui_elements.thermodynamics_dialog import ThermodynamicAnalysisTypes, ThermodynamicDialog
+from cnapy.gui_elements.thermodynamics_dialog import (
+    ThermodynamicAnalysisTypes,
+    ThermodynamicDialog,
+    COBRAK_AVAILABLE,
+    COBRAK_IMPORT_ERROR,
+)
 import cnapy.utils as utils
 
 SBML_suffixes = "*.xml *.sbml *.xml.gz *.sbml.gz *.xml.zip *.sbml.zip"
@@ -424,6 +429,18 @@ def __init__(self, appdata: AppData, project_path: str | None, scenario_path: st
         bottleneck_action.triggered.connect(self.perform_bottleneck_analysis)
         self.thermodynamic_menu.addAction(bottleneck_action)
 
+        # These three analyses require the optional COBRA-k package. When it is not
+        # installed, grey the entries out and explain via tooltip instead of letting
+        # the user open a dialog that cannot run. (perform_* still guard defensively.)
+        if not COBRAK_AVAILABLE:
+            for _cobrak_action in (optmdf_action, tfba_action, bottleneck_action):
+                _cobrak_action.setEnabled(False)
+                _cobrak_action.setToolTip(
+                    "Requires the optional COBRA-k package "
+                    "(install with: pip install cnapy[thermodynamics])"
+                )
+            self.thermodynamic_menu.setToolTipsVisible(True)
+
         self.thermodynamic_menu.addSeparator()
 
         dG0_menu = self.thermodynamic_menu.addMenu("Load dG'° values [in kJ/mol] (replacing all current values)...")
@@ -2163,8 +2180,29 @@ def set_status_unknown(self):
         self.solver_status_symbol.setStyleSheet("color: black")
         self.solver_status_symbol.setText("?")
 
+    def _require_cobrak(self) -> bool:
+        """Warn (and return False) if the optional COBRA-k package is missing.
+
+        The thermodynamic methods depend on cobrak, which is an optional
+        dependency. Guarding here lets CNApy run even when it is not installed.
+        """
+        if COBRAK_AVAILABLE:
+            return True
+        QMessageBox.warning(
+            self,
+            "COBRA-k not installed",
+            "The thermodynamic analyses require the optional 'cobrak' (COBRA-k) "
+            "package, which is not installed.\n\n"
+            "Install it with 'pip install cnapy[thermodynamics]' or from "
+            "https://github.com/klamt-lab/COBRA-k\n\n"
+            f"Import error: {COBRAK_IMPORT_ERROR}",
+        )
+        return False
+
     @Slot()
     def perform_optmdfpathway(self):
+        if not self._require_cobrak():
+            return
         # Has to be in self to keep computation thread
         self.optmdfpathway_dialog = ThermodynamicDialog(
             self.appdata,
@@ -2175,6 +2213,8 @@ def perform_optmdfpathway(self):
 
     @Slot()
     def perform_thermodynamic_fba(self):
+        if not self._require_cobrak():
+            return
         # Has to be in self to keep computation thread
         self.thermodynamic_fba_dialog = ThermodynamicDialog(
             self.appdata,
@@ -2185,6 +2225,8 @@ def perform_thermodynamic_fba(self):
 
     @Slot()
     def perform_bottleneck_analysis(self):
+        if not self._require_cobrak():
+            return
         # Has to be in self to keep computation thread
         self.bottleneck_dialog = ThermodynamicDialog(
             self.appdata,

cnapy/gui_elements/thermodynamics_dialog.py

@@ -18,11 +18,22 @@
 from cnapy.gui_elements.central_widget import CentralWidget
 from cnapy.gui_elements.solver_buttons import get_solver_buttons
 from enum import Enum
-from cobrak.constants import LNCONC_VAR_PREFIX, DF_VAR_PREFIX, MDF_VAR_ID, ALL_OK_KEY, OBJECTIVE_VAR_NAME, TERMINATION_CONDITION_KEY
-from cobrak.dataclasses import ExtraLinearConstraint, Solver
-from cobrak.lps import perform_lp_optimization, perform_lp_thermodynamic_bottleneck_analysis
-from cobrak.io import load_annotated_cobrapy_model_as_cobrak_model
-from cobrak.cobrapy_model_functionality import get_fullsplit_cobra_model
+# cobrak (COBRA-k) powers the thermodynamic methods but is treated as an optional
+# dependency so CNApy can be installed and started even when cobrak is unavailable
+# in the environment. Import it lazily and gate the "Thermodynamic analyses" menu
+# actions on COBRAK_AVAILABLE (see main_window.py). Enable the feature with
+# `pip install cnapy[thermodynamics]`.
+try:
+    from cobrak.constants import LNCONC_VAR_PREFIX, DF_VAR_PREFIX, MDF_VAR_ID, ALL_OK_KEY, OBJECTIVE_VAR_NAME, TERMINATION_CONDITION_KEY
+    from cobrak.dataclasses import ExtraLinearConstraint, Solver
+    from cobrak.lps import perform_lp_optimization, perform_lp_thermodynamic_bottleneck_analysis
+    from cobrak.io import load_annotated_cobrapy_model_as_cobrak_model
+    from cobrak.cobrapy_model_functionality import get_fullsplit_cobra_model
+    COBRAK_AVAILABLE = True
+    COBRAK_IMPORT_ERROR = ""
+except ModuleNotFoundError as _cobrak_err:
+    COBRAK_AVAILABLE = False
+    COBRAK_IMPORT_ERROR = str(_cobrak_err)
 
 
 

pyproject.toml

@@ -34,9 +34,16 @@ dependencies = [
     "openpyxl",
     "jpype1==1.5.0",
     "setuptools",
-    "cobrak==0.0.10",
+    "nest_asyncio",
 ]
 
+[project.optional-dependencies]
+# COBRA-k powers the thermodynamic analyses. It is kept as an optional extra rather
+# than a hard dependency so that a plain `pip install cnapy` always succeeds and the
+# GUI starts, even if cobrak cannot be installed in a given environment. Enable the
+# feature with `pip install cnapy[thermodynamics]`.
+thermodynamics = ["cobrak>=0.0.11"]
+
 [project.scripts]
 cnapy = "cnapy.__main__:main_cnapy"
 [project.urls]