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Fix #5360: Deprecate the GROMACS patch #5365

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Fix #5360: Deprecate the GROMACS patch #5365

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6a520f7
Deprecate the GROMACS patch with build and runtime warnings
JiwaniZakir Apr 2, 2026
8cf10ef
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 2, 2026
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4 changes: 4 additions & 0 deletions source/gmx/CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
message(
DEPRECATION
"The GROMACS plugin is deprecated and will be removed in a future version. "
"See https://arxiv.org/abs/2602.02234 for a third-party alternative.")
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Copilot AI Apr 2, 2026

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The PR description says the deprecation warning appears when the GROMACS plugin is enabled, but this message(DEPRECATION ...) will fire whenever source/gmx is configured. In source/CMakeLists.txt the gmx/ subdirectory is added unconditionally for non-Python C++ builds (around lines 565–567), so this warning will show up even for builds that don’t intend to use GROMACS. Consider adding an explicit CMake option to enable/disable the GROMACS plugin and only emitting the deprecation warning when that option is ON (and/or only adding the subdirectory when enabled).

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Copilot AI Apr 2, 2026

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Using message(DEPRECATION ...) can hard-fail configuration for users/CI that set CMAKE_ERROR_DEPRECATED=ON. If the goal is to warn while still allowing builds during the deprecation window, consider either emitting a message(WARNING ...) instead, or conditionally downgrading to WARNING when CMAKE_ERROR_DEPRECATED is enabled so downstreams don’t get an unexpected configure error.

Suggested change
message(
DEPRECATION
"The GROMACS plugin is deprecated and will be removed in a future version. "
"See https://arxiv.org/abs/2602.02234 for a third-party alternative.")
if(CMAKE_ERROR_DEPRECATED)
message(
WARNING
"The GROMACS plugin is deprecated and will be removed in a future version. "
"See https://arxiv.org/abs/2602.02234 for a third-party alternative.")
else()
message(
DEPRECATION
"The GROMACS plugin is deprecated and will be removed in a future version. "
"See https://arxiv.org/abs/2602.02234 for a third-party alternative.")
endif()

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message(STATUS "Build GROMACS plugin")

file(GLOB PATCH_VERSIONS patches/*)
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2 changes: 2 additions & 0 deletions source/gmx/dp_gmx_patch
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
#!/bin/bash
echo "WARNING: The GROMACS patch in deepmd-kit is deprecated and will be removed in a future version." >&2
echo "WARNING: See https://arxiv.org/abs/2602.02234 for a third-party alternative." >&2
DEEPMD_PATCH_SCRIPT_DIR=$(dirname $(readlink -f "$0"))
DEEPMD_PATCH_ROOT=${DEEPMD_PATCH_SCRIPT_DIR}/../share/deepmd_gromacs_patches
VERSION="NULL"
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