Fix issue #124

.github/workflows/devel.yaml

@@ -13,7 +13,7 @@ jobs:
       max-parallel: 9
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
@@ -22,14 +22,14 @@ jobs:
           # Exclude all but the latest Python from all but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.8"
+            python-version: "3.9"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.8"
+            python-version: "3.9"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.9"
+            python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.9"
+            python-version: "3.10"
     environment:
       name: biosimspace-build
     defaults:

.github/workflows/pr.yaml

@@ -12,7 +12,7 @@ jobs:
       max-parallel: 9
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
@@ -22,14 +22,14 @@ jobs:
           # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.8"
+            python-version: "3.9"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.8"
+            python-version: "3.9"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.9"
+            python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.9"
+            python-version: "3.10"
     environment:
       name: biosimspace-build
     defaults:

python/BioSimSpace/Process/_gromacs.py

@@ -286,10 +286,15 @@ def _generate_config(self):
         """Generate GROMACS configuration file strings."""
 
         # Check whether the system contains periodic box information.
-        # For now, well not attempt to generate a box if the system property
-        # is missing. If no box is present, we'll assume a non-periodic simulation.
-        if "space" in self._system._sire_object.propertyKeys():
-            has_box = True
+        space_prop = self._property_map.get("space", "space")
+        if space_prop in self._system._sire_object.propertyKeys():
+            try:
+                # Make sure that we have a periodic box. The system will now have
+                # a default cartesian space.
+                box = self._system._sire_object.property(space_prop)
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
             has_box = False

python/BioSimSpace/Process/_openmm.py

@@ -283,10 +283,14 @@ def _generate_config(self):
         prop = self._property_map.get("space", "space")
 
         # Check whether the system contains periodic box information.
-        # For now, we'll not attempt to generate a box if the system property
-        # is missing. If no box is present, we'll assume a non-periodic simulation.
         if prop in self._system._sire_object.propertyKeys():
-            has_box = True
+            try:
+                # Make sure that we have a periodic box. The system will now have
+                # a default cartesian space.
+                box = self._system._sire_object.property(prop)
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
             has_box = False

python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py

@@ -285,7 +285,13 @@ def _generate_config(self):
         # For now, we'll not attempt to generate a box if the system property
         # is missing. If no box is present, we'll assume a non-periodic simulation.
         if prop in self._system._sire_object.propertyKeys():
-            has_box = True
+            try:
+                # Make sure that we have a periodic box. The system will now have
+                # a default cartesian space.
+                box = self._system._sire_object.property(prop)
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
             has_box = False

python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py

@@ -39,7 +39,13 @@ def __init__(self, system, protocol, explicit_dummies=False):
     def _has_box(self):
         """Return whether the current system has a box."""
         if "space" in self.system._sire_object.propertyKeys():
-            has_box = True
+            try:
+                # Make sure that we have a periodic box. The system will now have
+                # a default cartesian space.
+                box = self.system._sire_object.property("space")
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
             has_box = False

python/BioSimSpace/_Config/_config.py

@@ -91,10 +91,18 @@ def hasBox(self):
         """
         space_prop = self._property_map.get("space", "space")
         if space_prop in self._system._sire_object.propertyKeys():
-            return True
+            try:
+                # Make sure that we have a periodic box. The system will now have
+                # a default cartesian space.
+                box = self._system._sire_object.property(space_prop)
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
+            has_box = False
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
-            return False
+
+        return has_box
 
     def hasWater(self):
         """