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Analysis fixes #83

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merged 2 commits into from
May 16, 2024
Merged

Analysis fixes #83

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5c5abf2
Update gmx commands
hp115 May 15, 2024
9974eb1
update install script
hp115 May 16, 2024
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10 changes: 9 additions & 1 deletion install.sh
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Original file line number Diff line number Diff line change
@@ -1,3 +1,11 @@
#!/bin/bash

pipx install --python python3.9 --force $1 .
# optional pipx arguments can be passed as the first argument
# e.g. ./install.sh --verbose --editable

# Remove existing installs
pipx uninstall ClayCodeTests > /dev/null 2>&1
pipx uninstall ClayCode > /dev/null 2>&1

# Install the package
pipx install --python python3.10 --force $1 .
3 changes: 2 additions & 1 deletion package/ClayCode/core/gmx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -259,14 +259,15 @@ def get_mdp_parameter_file(
file_or_str=mdp_str,
freeze_dims=freeze_dims,
)
if define is not None:
if define is not None and not isinstance(define, bool):
if isinstance(define, str):
define_str = f"-D{define}"
else:
for definition in define:
define_str = " ".join(
list(map(lambda d: f"-D{d}", definition))
)
pass
mdp_str = set_mdp_parameter("define", define_str, mdp_str)
mdp_str = re.sub(
"(^|\n)[^\n]*?\s*?=\s*?\n",
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