Merge branch 'devel' into fix_470

Matthew · Matthew · commit bce30a6b2fa8 · 2025-11-18T17:15:28.000Z
diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
@@ -9,7 +9,18 @@ company supporting open-source development of fostering academic/industrial coll
 within the biomolecular simulation community. Our software is hosted via the `OpenBioSim`
 `GitHub <https://github.com/OpenBioSim/biosimspace>`__ organisation.
 
-`2025.2.0 <https://github.com/openbiosim/biosimspace/compare/2024.5.0...2025.2.0>`_ - Oct 08 2025
+`2025.3.0 <https://github.com/openbiosim/biosimspace/compare/2025.2.0...2025.3.0>`_ - Nov 10 2025
+-------------------------------------------------------------------------------------------------
+
+* Fixed bug that caused trajectory frame reconstruction to be skipped for perturbable systems (`#460 <https://github.com/OpenBioSim/biosimspace/pull/460>`__).
+* Fixed typo in RDKit ``rdMolDraw2D`` attribute name (`#463 <https://github.com/OpenBioSim/biosimspace/pull/463>`__).
+* Fix incorrect context manager name in node runner (`#463 <https://github.com/OpenBioSim/biosimspace/pull/463>`__).
+* Added functionality for quickly getting and setting the coordinates array of a :class:`System <BioSimSpace._SireWrappers.System>` (`#465 <https://github.com/OpenBioSim/biosimspace/pull/465>`__).
+* Reduce depdency import overheads by switching from module level imports to function and method level (`#466 <https://github.com/OpenBioSim/biosimspace/pull/466>`__).
+* Fully switch over to using the new Sire Python API naming convention, allowing BioSimSpace to be used within Sire (`#466 <https://github.com/OpenBioSim/biosimspace/pull/466>`__).
+* Fixed logic used for setting the GPU device index for :class:`Process.OpenMM <BioSimSpace.Process.OpenMM>` (`#468 <https://github.com/OpenBioSim/biosimspace/pull/468>`__).
+
+`2025.2.0 <https://github.com/openbiosim/biosimspace/compare/2025.1.0...2025.2.0>`_ - Oct 08 2025
 -------------------------------------------------------------------------------------------------
 
 * Add support for ``SOMD2`` FEP analysis using data frames with different numbers of samples (`#415 <https://github.com/OpenBioSim/biosimspace/pull/415>`__).
diff --git a/python/BioSimSpace/Convert/__init__.py b/python/BioSimSpace/Convert/__init__.py
@@ -29,7 +29,7 @@
     :toctree: generated/
 
     smiles
-    supported_formats
+    supportedFormats
     to
     toBioSimSpace
     toOpenMM
diff --git a/python/BioSimSpace/Process/_openmm.py b/python/BioSimSpace/Process/_openmm.py
@@ -2037,6 +2037,9 @@ def _add_config_platform(self):
                     "'CUDA' platform selected but 'CUDA_VISIBLE_DEVICES' "
                     "environment variable is unset. Defaulting to '0'."
                 )
+            else:
+                num_devices = len(cuda_devices.split(","))
+                cuda_devices = ",".join([str(x) for x in range(num_devices)])
             self.addToConfig("properties = {'CudaDeviceIndex': '%s'}" % cuda_devices)
         elif self._platform == "OPENCL":
             opencl_devices = _os.environ.get("OPENCL_VISIBLE_DEVICES")
@@ -2046,6 +2049,9 @@ def _add_config_platform(self):
                     "'OpenCL' platform selected but 'OPENCL_VISIBLE_DEVICES' "
                     "environment variable is unset. Defaulting to '0'."
                 )
+            else:
+                num_devices = len(opencl_devices.split(","))
+                opencl_devices = ",".join([str(x) for x in range(num_devices)])
             self.addToConfig(
                 "properties = {'OpenCLDeviceIndex': '%s'}" % opencl_devices
             )
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Convert/__init__.py b/python/BioSimSpace/Sandpit/Exscientia/Convert/__init__.py
@@ -29,7 +29,7 @@
     :toctree: generated/
 
     smiles
-    supported_formats
+    supportedFormats
     to
     toBioSimSpace
     toOpenMM
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
@@ -1984,6 +1984,9 @@ def _add_config_platform(self):
                     "'CUDA' platform selected but 'CUDA_VISIBLE_DEVICES' "
                     "environment variable is unset. Defaulting to '0'."
                 )
+            else:
+                num_devices = len(cuda_devices.split(","))
+                cuda_devices = ",".join([str(x) for x in range(num_devices)])
             self.addToConfig("properties = {'CudaDeviceIndex': '%s'}" % cuda_devices)
         elif self._platform == "OPENCL":
             opencl_devices = _os.environ.get("OPENCL_VISIBLE_DEVICES")
@@ -1993,6 +1996,9 @@ def _add_config_platform(self):
                     "'OpenCL' platform selected but 'OPENCL_VISIBLE_DEVICES' "
                     "environment variable is unset. Defaulting to '0'."
                 )
+            else:
+                num_devices = len(opencl_devices.split(","))
+                opencl_devices = ",".join([str(x) for x in range(num_devices)])
             self.addToConfig(
                 "properties = {'OpenCLDeviceIndex': '%s'}" % opencl_devices
             )
diff --git a/requirements.txt b/requirements.txt
@@ -1,10 +1,10 @@
 # BioSimSpace runtime requirements.
 
 # main
-#sire~=2025.2.0
+#sire~=2025.3.0
 
 # devel
-sire==2025.3.0.dev
+sire==2025.4.0.dev
 
 configargparse
 ipywidgets

Original file line number	Diff line number	Diff line change
`@@ -2037,6 +2037,9 @@ def _add_config_platform(self):`
`2037`	`2037`	`"'CUDA' platform selected but 'CUDA_VISIBLE_DEVICES' "`
`2038`	`2038`	`"environment variable is unset. Defaulting to '0'."`
`2039`	`2039`	`)`
	`2040`	`+ else:`
	`2041`	`+ num_devices = len(cuda_devices.split(","))`
	`2042`	`+ cuda_devices = ",".join([str(x) for x in range(num_devices)])`
`2040`	`2043`	`self.addToConfig("properties = {'CudaDeviceIndex': '%s'}" % cuda_devices)`
`2041`	`2044`	`elif self._platform == "OPENCL":`
`2042`	`2045`	`opencl_devices = _os.environ.get("OPENCL_VISIBLE_DEVICES")`
`@@ -2046,6 +2049,9 @@ def _add_config_platform(self):`
`2046`	`2049`	`"'OpenCL' platform selected but 'OPENCL_VISIBLE_DEVICES' "`
`2047`	`2050`	`"environment variable is unset. Defaulting to '0'."`
`2048`	`2051`	`)`
	`2052`	`+ else:`
	`2053`	`+ num_devices = len(opencl_devices.split(","))`
	`2054`	`+ opencl_devices = ",".join([str(x) for x in range(num_devices)])`
`2049`	`2055`	`self.addToConfig(`
`2050`	`2056`	`"properties = {'OpenCLDeviceIndex': '%s'}" % opencl_devices`
`2051`	`2057`	`)`
Original file line number	Diff line number	Diff line change
`@@ -1984,6 +1984,9 @@ def _add_config_platform(self):`
`1984`	`1984`	`"'CUDA' platform selected but 'CUDA_VISIBLE_DEVICES' "`
`1985`	`1985`	`"environment variable is unset. Defaulting to '0'."`
`1986`	`1986`	`)`
	`1987`	`+ else:`
	`1988`	`+ num_devices = len(cuda_devices.split(","))`
	`1989`	`+ cuda_devices = ",".join([str(x) for x in range(num_devices)])`
`1987`	`1990`	`self.addToConfig("properties = {'CudaDeviceIndex': '%s'}" % cuda_devices)`
`1988`	`1991`	`elif self._platform == "OPENCL":`
`1989`	`1992`	`opencl_devices = _os.environ.get("OPENCL_VISIBLE_DEVICES")`
`@@ -1993,6 +1996,9 @@ def _add_config_platform(self):`
`1993`	`1996`	`"'OpenCL' platform selected but 'OPENCL_VISIBLE_DEVICES' "`
`1994`	`1997`	`"environment variable is unset. Defaulting to '0'."`
`1995`	`1998`	`)`
	`1999`	`+ else:`
	`2000`	`+ num_devices = len(opencl_devices.split(","))`
	`2001`	`+ opencl_devices = ",".join([str(x) for x in range(num_devices)])`
`1996`	`2002`	`self.addToConfig(`
`1997`	`2003`	`"properties = {'OpenCLDeviceIndex': '%s'}" % opencl_devices`
`1998`	`2004`	`)`