Merge pull request #42 from OpenBioSim/fix_backport

Backport fixes in to main
OpenBioSim · Apr 18, 2023 · 52d3a82 · 52d3a82
2 parents 083dc3e + d29bfa2
commit 52d3a82
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Showing 7 changed files with 8 additions and 10 deletions.
diff --git a/python/BioSimSpace/Protocol/_equilibration.py b/python/BioSimSpace/Protocol/_equilibration.py
@@ -36,7 +36,7 @@
 from ._protocol import Protocol as _Protocol
 
 
-class Equilibration(_PositionRestraintMixin):
+class Equilibration(_Protocol, _PositionRestraintMixin):
     """A class for storing equilibration protocols."""
 
     def __init__(
@@ -168,7 +168,7 @@ def _get_parm(self):
             f"pressure={self._pressure}, "
             f"report_interval={self._report_interval}, "
             f"restart_interval={self._restart_interval}, "
-            f"restart={self._restart}, " + _PositionRestraintMixin._get_parm(self)
+            + _PositionRestraintMixin._get_parm(self)
         )
 
     def __str__(self):

diff --git a/python/BioSimSpace/Protocol/_free_energy_mixin.py b/python/BioSimSpace/Protocol/_free_energy_mixin.py
@@ -30,10 +30,8 @@
 
 from .. import Types as _Types
 
-from ._protocol import Protocol as _Protocol
 
-
-class _FreeEnergyMixin(_Protocol):
+class _FreeEnergyMixin:
     """A mixin for alchemical free energy protocols."""
 
     def __init__(

diff --git a/python/BioSimSpace/Protocol/_minimisation.py b/python/BioSimSpace/Protocol/_minimisation.py
@@ -34,7 +34,7 @@
 from ._protocol import Protocol as _Protocol
 
 
-class Minimisation(_PositionRestraintMixin):
+class Minimisation(_Protocol, _PositionRestraintMixin):
     """A class for storing minimisation protocols."""
 
     def __init__(

diff --git a/python/BioSimSpace/Protocol/_position_restraint_mixin.py b/python/BioSimSpace/Protocol/_position_restraint_mixin.py
@@ -29,10 +29,8 @@
 from .. import Types as _Types
 from .. import Units as _Units
 
-from ._protocol import Protocol as _Protocol
 
-
-class _PositionRestraintMixin(_Protocol):
+class _PositionRestraintMixin:
     """A mixin for applying position restraints to other protocols."""
 
     # Supported restraint keywords.

diff --git a/python/BioSimSpace/Protocol/_production.py b/python/BioSimSpace/Protocol/_production.py
@@ -36,7 +36,7 @@
 from ._protocol import Protocol as _Protocol
 
 
-class Production(_PositionRestraintMixin):
+class Production(_Protocol, _PositionRestraintMixin):
     """A class for storing production protocols."""
 
     def __init__(

diff --git a/test/IO/test_tuple.py b/test/IO/test_tuple.py
@@ -1,5 +1,6 @@
 import BioSimSpace as BSS
 
+
 def test_tuple():
     """Check that we can read from a tuple of files."""
     BSS.IO.readMolecules(("test/input/ala.crd", "test/input/ala.top"))
diff --git a/test/Sandpit/Exscientia/IO/test_tuple.py b/test/Sandpit/Exscientia/IO/test_tuple.py
@@ -1,5 +1,6 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
+
 def test_tuple():
     """Check that we can read from a tuple of files."""
     BSS.IO.readMolecules(("test/input/ala.crd", "test/input/ala.top"))