89 lines
3.2 KiB
Python
89 lines
3.2 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os
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from spack.package import *
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class PyMeldmd(CMakePackage, PythonExtension, CudaPackage):
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"""MELD is a tool for inferring the structure of
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biomolecules from sparse, ambiguous, or noisy data."""
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homepage = "http://meldmd.org/"
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url = "https://github.com/maccallumlab/meld/archive/refs/tags/0.4.20.tar.gz"
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license("LGPL-3.0-or-later")
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version("0.6.1", sha256="aae8e5bfbdacc1e6de61768a3298314c51575cda477a511e98dc11f5730fd918")
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version("0.4.20", sha256="8c8d2b713f8dc0ecc137d19945b3957e12063c8dda569696e47c8820eeac6c92")
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extends("python")
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depends_on("python@3.6:", type=("build", "run"))
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depends_on("py-setuptools", type="build")
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depends_on("amber")
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depends_on("openmm+cuda")
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depends_on("py-netcdf4", type=("build", "run"))
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# Meld uses np.bool, deprecated in py-numpy@1.24.0
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# https://numpy.org/devdocs/release/1.24.0-notes.html
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depends_on("py-numpy@:1.23", type=("build", "run"))
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depends_on("py-scipy", type=("build", "run"))
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depends_on("py-scikit-learn", type=("build", "run"))
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depends_on("py-parmed", type=("build", "run"))
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depends_on("py-tqdm", type=("build", "run"))
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depends_on("py-mpi4py", type=("build", "run"))
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depends_on("py-pip", type="build")
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# C++ / CUDA
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depends_on("eigen", type="link")
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depends_on("swig@4.0", type="build")
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def cmake_args(self):
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args = []
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args.append("-DOPENMM_DIR={0}".format(self.spec["openmm"].prefix))
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return args
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root_cmakelists_dir = "plugin"
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@run_after("install")
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def install_python(self):
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args = std_pip_args + ["--prefix=" + prefix, "."]
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pip(*args)
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with working_dir(join_path(self.build_directory, "python")):
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make("MeldPluginPatch")
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pip(*args)
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for _, _, files in os.walk(self.spec["openmm"].prefix.lib.plugins):
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for f in files:
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os.symlink(
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join_path(self.spec["openmm"].prefix.lib.plugins, f),
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join_path(self.prefix.lib.plugins, f),
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)
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def patch(self):
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filter_file(
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"# Compile the Python module.",
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"# Compile the Python module.\n"
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'add_custom_target(MeldPluginPatch DEPENDS "${WRAP_FILE}")',
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"plugin/python/CMakeLists.txt",
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string=True,
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)
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# Fixed, but not versioned yet:
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# https://github.com/maccallumlab/meld/commit/afe4b0c199e3562d112af7825f8839e76067039c
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filter_file(
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"MAXFLOAT", "FLT_MAX", "plugin/platforms/cuda/src/kernels/computeMeld.cu", string=True
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)
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# API Change: https://github.com/openmm/openmm/releases/tag/7.6.0
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if self.spec.satisfies("^openmm@7.6.0:"):
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filter_file("simtk.openmm", "openmm", "plugin/python/meldplugin.i", string=True)
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def setup_run_environment(self, env):
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env.set("OPENMM_PLUGIN_DIR", self.prefix.lib.plugins)
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@run_after("install")
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@on_package_attributes(run_tests=True)
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def install_test(self):
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python("-m", "meld.test_install")
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