Small fixes (#484)

* Fix errors when loading strain designs

* New FBA error message with community editions

* Better handling of community edition errors

* Add XLSX generation with all in and out fluxes

* Fix missing newline character in net conversion

* Refactoring; More community errors; Qt fix

* More to core_gui

* Remove special Gurobi handling; Point size fix

* Better language

* Remove edge error case; Import fix

* simplification

* Fix RGB color function argument typing

---------

Co-authored-by: axelvonkamp <[email protected]>

cnapy/appdata.py

@@ -189,13 +189,13 @@ def compute_color_heat(self, value: Tuple[float, float], low, high):
                 h = 255
             else:
                 h = mean * 255 / high
-            return QColor.fromRgb(255-h, 255, 255 - h)
+            return QColor.fromRgbF(255-h, 255, 255 - h)
         else:
             if low == 0.0:
                 h = 255
             else:
                 h = mean * 255 / low
-            return QColor.fromRgb(255, 255 - h, 255 - h)
+            return QColor.fromRgbF(255, 255 - h, 255 - h)
 
     def low_and_high(self) -> Tuple[int, int]:
         low = 0

cnapy/application.py

@@ -71,7 +71,7 @@ def __init__(self):
         self.qapp.setStyle("fusion")
         config_file_version = self.read_config()
         font = self.qapp.font()
-        font.setPointSize(self.appdata.font_size)
+        font.setPointSizeF(self.appdata.font_size)
         self.qapp.setFont(font)
         self.window = MainWindow(self.appdata)
         self.appdata.window = self.window

cnapy/core.py

@@ -4,13 +4,11 @@
 from collections import defaultdict
 from typing import Dict, Tuple, List
 from collections import Counter
-import gurobipy
 import numpy
 import cobra
 from cobra.util.array import create_stoichiometric_matrix
 from cobra.core.dictlist import DictList
 from optlang.symbolics import Zero, Add
-from qtpy.QtWidgets import QMessageBox
 
 import efmtool_link.efmtool4cobra as efmtool4cobra
 import efmtool_link.efmtool_extern as efmtool_extern
@@ -369,17 +367,3 @@ def replace_ids(dict_list: DictList, annotation_key: str, unambiguous_only: bool
                 pass
         if len(candidates) > 0 and old_id == entry.id:
             print("Could not find a new ID for", entry.id, "in", candidates)
-
-# TODO: should not be in the core module
-def model_optimization_with_exceptions(model: cobra.Model):
-    try:
-        return model.optimize()
-    except gurobipy.GurobiError as error:
-        msgBox = QMessageBox()
-        msgBox.setWindowTitle("Gurobi Error!")
-        msgBox.setText("Calculation failed due to the following Gurobi solver error " +\
-                       "(if this error cannot be resolved,\ntry using a different solver by changing " +\
-                       "it under 'Config->Configure cobrapy'):\n"+error.message+\
-                       "\nNOTE: Another error message will follow, you can safely ignore it.")
-        msgBox.setIcon(QMessageBox.Warning)
-        msgBox.show()

cnapy/core_gui.py

@@ -0,0 +1,37 @@
+import gurobipy
+import io
+import traceback
+import cobra
+from qtpy.QtWidgets import QMessageBox
+
+
+def except_likely_community_model_error() -> None:
+    """Shows a message in the case that using a (size-limited) community edition solver version probably caused an error."""
+    community_error_text = "Solver error. One possible reason: You set CPLEX or Gurobi as solver although you only use their\n"+\
+                            "Community edition which only work for small models. To solve this, either follow the instructions under\n"+\
+                            "'Config->Configure IBM CPLEX full version' or 'Config->Configure Gurobi full version', or use a different solver such as GLPK."
+    msgBox = QMessageBox()
+    msgBox.setWindowTitle("Error")
+    msgBox.setText(community_error_text)
+    msgBox.setIcon(QMessageBox.Warning)
+    msgBox.exec()
+
+
+def get_last_exception_string() -> str:
+    output = io.StringIO()
+    traceback.print_exc(file=output)
+    return output.getvalue()
+
+
+def has_community_error_substring(string: str) -> bool:
+    return ("Model too large for size-limited license" in string) or ("1016: Community Edition" in string)
+
+
+def model_optimization_with_exceptions(model: cobra.Model) -> None:
+    try:
+        return model.optimize()
+    except Exception:
+        exstr = get_last_exception_string()
+        # Check for substrings of Gurobi and CPLEX community edition errors
+        if has_community_error_substring(exstr):
+            except_likely_community_model_error()