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Backport fixes from PR #463 #464

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Merged
lohedges merged 1 commit into from
Oct 22, 2025
Merged

Backport fixes from PR #463 #464

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2 changes: 1 addition & 1 deletion python/BioSimSpace/Align/_align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2450,7 +2450,7 @@ def _draw_molecules(

# standard settings for visualization
d2d.drawOptions().useBWAtomPalette()
d2d.drawOptions().continousHighlight = False
d2d.drawOptions().continuousHighlight = False
d2d.drawOptions().setHighlightColour(highlight_color)
d2d.drawOptions().addAtomIndices = True
d2d.DrawMolecules(
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8 changes: 6 additions & 2 deletions python/BioSimSpace/Node/_node.py
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Expand Up @@ -105,7 +105,8 @@ def run(name, args={}, work_dir=None):
work_dir : str, optional
The working directory in which to run the node. If not specified,
the current working directory is used.
the current working directory is used. Note that inputs should
use absolute paths if this is set.
Returns
-------
Expand Down Expand Up @@ -142,7 +143,7 @@ def run(name, args={}, work_dir=None):
else:
full_name += ".py"

with _Utils.chdir(work_dir):
with _Utils.cd(work_dir):
# Write a YAML configuration file for the BioSimSpace node.
if len(args) > 0:
with open("input.yaml", "w") as file:
Expand Down Expand Up @@ -196,6 +197,9 @@ def setNodeDirectory(dir):
if not _os.path.isdir(dir):
raise IOError("Node directory '%s' doesn't exist!" % dir)

# Use the absolute path.
dir = _os.path.abspath(dir)

global _node_dir
_node_dir = dir

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8 changes: 6 additions & 2 deletions python/BioSimSpace/Sandpit/Exscientia/Node/_node.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,8 @@ def run(name, args={}, work_dir=None):
work_dir : str, optional
The working directory in which to run the node. If not specified,
the current working directory is used.
the current working directory is used. Note that inputs should
use absolute paths if this is set.
Returns
-------
Expand Down Expand Up @@ -142,7 +143,7 @@ def run(name, args={}, work_dir=None):
else:
full_name += ".py"

with _Utils.chdir(work_dir):
with _Utils.cd(work_dir):
# Write a YAML configuration file for the BioSimSpace node.
if len(args) > 0:
with open("input.yaml", "w") as file:
Expand Down Expand Up @@ -196,6 +197,9 @@ def setNodeDirectory(dir):
if not _os.path.isdir(dir):
raise IOError("Node directory '%s' doesn't exist!" % dir)

# Use the absolute path.
dir = _os.path.abspath(dir)

global _node_dir
_node_dir = dir

Expand Down