Flann package (#3966)

* Initial attempt at flann packaging.

Python2 somehow works. Python3 does not.  Still debugging their
obscure setup.py configuration.

* Flann good enough. Python3 broken but close.

Flake8 checks in place.  Unsure about CMAKE_BUILD_TYPE and default
spack behavior.

* spack uses RelWithDebInfo as default build type.

* builds py2/3, but direct site-packages install

* prefix working, empty python install dir

* flann package +python installs correctly

* str format {0} instead of {}

* potential doctest fix

* consistency of build env with PythonPackage

* fix python again, test deptype todo, build type

* potentially enable matlab, untested

1 files changed, 141 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/flann/package.py b/var/spack/repos/builtin/packages/flann/package.py
new file mode 100644
index 0000000000..bb7af21fa9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flann/package.py
@@ -0,0 +1,141 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Flann(CMakePackage):
+    """FLANN is a library for performing fast approximate nearest neighbor
+    searches in high dimensional spaces. It contains a collection of
+    algorithms we found to work best for nearest neighbor search and a system
+    for automatically choosing the best algorithm and optimum parameters
+    depending on the dataset.
+
+    FLANN is written in C++ and contains bindings for the following languages:
+    C, MATLAB and Python.
+    """
+
+    homepage = "http://www.cs.ubc.ca/research/flann/"
+    url      = "https://github.com/mariusmuja/flann/archive/1.9.1.tar.gz"
+
+    version('1.9.1', '73adef1c7bf8e8b978987e7860926ea6')
+    version('1.8.5', '02a81640b1e9c11796a0413976dc11f5')
+    version('1.8.4', '774b74580e3cbc5b0d45c6ec345a64ae')
+    version('1.8.1', '1f51500e172f5e11fbda05f033858eb6')
+    version('1.8.0', '473150f592c2997e32d5ce31fd3c19a2')
+
+    # Options available in the CMakeLists.txt
+    # Language bindings
+    variant("python",   default=False,
+            description="Build the Python bindings. "
+                        "Module: pyflann.")
+    variant("matlab",   default=False, description="Build the Matlab bindings.")
+    # default to true for C because it's a C++ library, nothing extra needed
+    variant("c",        default=True,  description="Build the C bindings.")
+
+    # Must build C bindings for Python / Matlab
+    conflicts("+python", when="~c")
+    conflicts("+matlab", when="~c")
+
+    # Additional options
+    variant("cuda",     default=False, description="Build the CUDA library.")
+    variant("examples", default=False, description="Build the examples.")
+    variant("doc",      default=False, description="Build the documentation.")
+    variant("openmp",   default=True,  description="Use OpenMP multi-threading.")
+    # mpi and hdf5 are the bread and butter of this library, use 'em
+    variant("mpi",      default=True,  description="Use MPI.")
+    variant("hdf5",     default=True,  description="Enable HDF5 support.")
+
+    # Dependencies
+    extends("python",      when="+python")
+    depends_on("py-numpy", when="+python", type=("build", "run"))
+    depends_on("matlab",   when="+matlab", type=("build", "run"))
+    depends_on("cuda",     when="+cuda")
+    depends_on("mpi",      when="+mpi")
+    depends_on("hdf5",     when="+hdf5")
+    # HDF5_IS_PARALLEL actually comes from hdf5+mpi
+    # https://github.com/mariusmuja/flann/blob/06a49513138009d19a1f4e0ace67fbff13270c69/CMakeLists.txt#L108-L112
+    depends_on("boost+mpi+system+serialization+thread", when="+mpi ^hdf5+mpi")
+
+    # Doc deps
+    depends_on("latex", when="+doc")
+
+    # Example uses hdf5.
+    depends_on("hdf5", when="+examples")
+
+    def patch(self):
+        # Fix up the python setup.py call inside the install(CODE
+        filter_file("setup.py install",
+                    'setup.py --no-user-cfg install --prefix=\\"{0}\\"'.format(
+                        self.prefix
+                    ),
+                    "src/python/CMakeLists.txt")
+        # Fix the install location so that spack activate works
+        filter_file("share/flann/python",
+                    site_packages_dir,
+                    "src/python/CMakeLists.txt")
+        # Hack. Don't install setup.py
+        filter_file("install( FILES",
+                    "# install( FILES",
+                    "src/python/CMakeLists.txt", string=True)
+
+    # TODO: revisit after https://github.com/LLNL/spack/issues/1279
+    # depends_on('hdf5', type='test')
+    # depends_on('gtest', type='test')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = []
+
+        # Language bindings. Many default to true in CMakeLists, bypass all
+        c_bind = "ON" if "+c" in spec else "OFF"
+        args.append("-DBUILD_C_BINDINGS:BOOL={0}".format(c_bind))
+
+        py_bind = "ON" if "+python" in spec else "OFF"
+        args.append("-DBUILD_PYTHON_BINDINGS:BOOL={0}".format(py_bind))
+
+        mat_bind = "ON" if "+matlab" in spec else "OFF"
+        args.append("-DBUILD_MATLAB_BINDINGS:BOOL={0}".format(mat_bind))
+
+        # Extra options
+        cuda_lib = "ON" if "+cuda" in spec else "OFF"
+        args.append("-DBUILD_CUDA_LIB:BOOL={0}".format(cuda_lib))
+
+        examples = "ON" if "+examples" in spec else "OFF"
+        args.append("-DBUILD_EXAMPLES:BOOL={0}".format(examples))
+
+        use_openmp = "ON" if "+openmp" in spec else "OFF"
+        args.append("-DUSE_OPENMP:BOOL={0}".format(use_openmp))
+
+        use_mpi = "ON" if "+mpi" in spec else "OFF"
+        args.append("-DUSE_MPI:BOOL={0}".format(use_mpi))
+
+        # Configure the proper python executable
+        if "+python" in spec:
+            args.append(
+                "-DPYTHON_EXECUTABLE={0}".format(spec["python"].command.path)
+            )
+
+        return args