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# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack.package import *
class PyMeldmd(CMakePackage, PythonExtension, CudaPackage):
"""MELD is a tool for inferring the structure of
biomolecules from sparse, ambiguous, or noisy data."""
homepage = "http://meldmd.org/"
url = "https://github.com/maccallumlab/meld/archive/refs/tags/0.4.20.tar.gz"
license("LGPL-3.0-or-later")
version("0.6.1", sha256="aae8e5bfbdacc1e6de61768a3298314c51575cda477a511e98dc11f5730fd918")
version("0.4.20", sha256="8c8d2b713f8dc0ecc137d19945b3957e12063c8dda569696e47c8820eeac6c92")
extends("python")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("amber")
depends_on("openmm+cuda")
depends_on("py-netcdf4", type=("build", "run"))
# Meld uses np.bool, deprecated in py-numpy@1.24.0
# https://numpy.org/devdocs/release/1.24.0-notes.html
depends_on("py-numpy@:1.23", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-scikit-learn", type=("build", "run"))
depends_on("py-parmed", type=("build", "run"))
depends_on("py-tqdm", type=("build", "run"))
depends_on("py-mpi4py", type=("build", "run"))
depends_on("py-pip", type="build")
# C++ / CUDA
depends_on("eigen", type="link")
depends_on("swig@4.0", type="build")
def cmake_args(self):
args = []
args.append("-DOPENMM_DIR={0}".format(self.spec["openmm"].prefix))
return args
root_cmakelists_dir = "plugin"
@run_after("install")
def install_python(self):
args = std_pip_args + ["--prefix=" + prefix, "."]
pip(*args)
with working_dir(join_path(self.build_directory, "python")):
make("MeldPluginPatch")
pip(*args)
for _, _, files in os.walk(self.spec["openmm"].prefix.lib.plugins):
for f in files:
os.symlink(
join_path(self.spec["openmm"].prefix.lib.plugins, f),
join_path(self.prefix.lib.plugins, f),
)
def patch(self):
filter_file(
"# Compile the Python module.",
"# Compile the Python module.\n"
'add_custom_target(MeldPluginPatch DEPENDS "${WRAP_FILE}")',
"plugin/python/CMakeLists.txt",
string=True,
)
# Fixed, but not versioned yet:
# https://github.com/maccallumlab/meld/commit/afe4b0c199e3562d112af7825f8839e76067039c
filter_file(
"MAXFLOAT", "FLT_MAX", "plugin/platforms/cuda/src/kernels/computeMeld.cu", string=True
)
# API Change: https://github.com/openmm/openmm/releases/tag/7.6.0
if self.spec.satisfies("^openmm@7.6.0:"):
filter_file("simtk.openmm", "openmm", "plugin/python/meldplugin.i", string=True)
def setup_run_environment(self, env):
env.set("OPENMM_PLUGIN_DIR", self.prefix.lib.plugins)
@run_after("install")
@on_package_attributes(run_tests=True)
def install_test(self):
python("-m", "meld.test_install")
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