feat(ambertools): copy package from upstream

packages/ambertools/package.py

+# Copyright 2013-2024 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)
+
+from spack.package import *
+
+
+class Ambertools(CMakePackage):
+    """AmberTools is a free, useful standalone package and a prerequisite
+    for installing Amber itself. The AmberTools suite is free of charge,
+    and its components are mostly released under the GNU General Public
+    License (GPL). A few components are included that are in the public
+    domain or which have other, open-source, licenses. The libsander and
+    libpbsa libraries use the LGPL license."""
+
+    homepage = "https://ambermd.org/AmberTools.php"
+    url = "https://ambermd.org/downloads/AmberTools22jlmrcc.tar.bz2"
+
+    maintainers("d-beltran")
+
+    version("22jlmrcc", sha256="1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121")
+
+    depends_on("flex", type="build")
+    depends_on("bison", type="build")
+    depends_on("tcsh", type="build")
+    depends_on("zlib", type=("build", "run"))
+    depends_on("bzip2", type=("build", "run"))
+    depends_on("blas", type=("build", "run"))
+    depends_on("lapack", type=("build", "run"))
+    depends_on("arpack-ng", type=("build", "run"))
+    depends_on("netcdf-c", type=("build", "run"))
+    depends_on("netcdf-fortran", type=("build", "run"))
+    depends_on("fftw", type=("build", "run"))
+    depends_on("readline", type=("build", "run"))
+    depends_on("netlib-xblas~plain_blas", type=("build", "run"))
+    # Specific variants needed for boost according to build logs
+    depends_on(
+        "boost+thread+system+program_options+iostreams+regex+timer+chrono+filesystem+graph",
+        type=("build", "run"),
+    )
+    # Python dependencies
+    depends_on("python@3.8:3.10 +tkinter", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+
+    def cmake_args(self):
+        # Translated from ambertools build/run_cmake script
+        # We also add the TRUST_SYSTEM_LIBS argument mentioned in the ambertools guide
+        #   https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Guide-to-Options
+        args = [
+            self.define("COMPILER", "GNU"),
+            self.define("MPI", False),
+            self.define("CUDA", False),
+            self.define("INSTALL_TESTS", True),
+            self.define("DOWNLOAD_MINICONDA", False),
+            self.define("TRUST_SYSTEM_LIBS", True),
+            # This is to avoid the x11 (X11_Xext_LIB) error
+            # It is equivalent to the "-noX11" flag accoridng to the docs:
+            # https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
+            self.define("BUILD_GUI", False),
+        ]
+        return args
+
+    def setup_run_environment(self, env):
+        env.set("AMBER_PREFIX", self.prefix)
+        env.set("AMBERHOME", self.prefix)
+
+    def setup_build_environment(self, env):
+        env.set("AMBER_PREFIX", self.prefix)
+        env.set("AMBERHOME", self.prefix)
+
+    @run_after("install")
+    @on_package_attributes(run_tests=True)
+    def check_install(self):
+        make("test.serial")
+
+    # Temporarily copy netcdf.h header file to netcdf-fortran/include to pass the Ambertools
+    # cmake check (quickest fix, will probably cause problems, needs to change)
+    @run_before("cmake")
+    def fix_check(self):
+        cp = Executable("cp")
+        cp(
+            self.spec["netcdf-c"].headers.directories[0] + "/netcdf.h",
+            self.spec["netcdf-fortran"].headers.directories[0],
+        )