eccodes: update package (#28849)

* eccodes: modernize the package

* eccodes: add patch fixing location of NetCDF

* eccodes: add variant 'shared'

* eccodes: enable building with NAG compiler

* eccodes: add property 'libs'

* eccodes: add variant 'definitions'

* eccodes: add variant 'samples'

* eccodes: add variant 'tools'

1 files changed, 258 insertions, 52 deletions

diff --git a/var/spack/repos/builtin/packages/eccodes/package.py b/var/spack/repos/builtin/packages/eccodes/package.py
index 0791559a0b..0a70db94f7 100644
--- a/var/spack/repos/builtin/packages/eccodes/package.py
+++ b/var/spack/repos/builtin/packages/eccodes/package.py
@@ -3,8 +3,35 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-#
-from spack import *
+
+_definitions = {
+    # German Meteorological Service (Deutscher Wetterdienst, DWD):
+    'edzw': {
+        'conflicts': {'when': '@:2.19.1,2.22.0,2.24.0:'},
+        'resources': [
+            {
+                'when': '@2.20.0',
+                'url': 'http://opendata.dwd.de/weather/lib/grib/eccodes_definitions.edzw-2.20.0-1.tar.gz',
+                'sha256': 'a92932f8a13c33cba65d3a33aa06c7fb4a37ed12a78e9abe2c5e966402b99af4'
+            },
+            {
+                'when': '@2.21.0',
+                'url': 'http://opendata.dwd.de/weather/lib/grib/eccodes_definitions.edzw-2.21.0-3.tar.bz2',
+                'sha256': '046f1f6450abb3b44c31dee6229f4aab06ca0d3576e27e93e05ccb7cd6e2d9d9'
+            },
+            {
+                'when': '@2.22.1',
+                'url': 'http://opendata.dwd.de/weather/lib/grib/eccodes_definitions.edzw-2.22.1-1.tar.bz2',
+                'sha256': 'be73102a0dcabb236bacd2a70c7b5475f673fda91b49e34df61bef0fa5ad3389'
+            },
+            {
+                'when': '@2.23.0',
+                'url': 'http://opendata.dwd.de/weather/lib/grib/eccodes_definitions.edzw-2.23.0-4.tar.bz2',
+                'sha256': 'c5db32861c7d23410aed466ffef3ca661410d252870a3949442d3ecb176aa338'
+            }
+        ]
+    }
+}
 
 
 class Eccodes(CMakePackage):
@@ -28,6 +55,7 @@ class Eccodes(CMakePackage):
     version('2.5.0', sha256='18ab44bc444168fd324d07f7dea94f89e056f5c5cd973e818c8783f952702e4e')
     version('2.2.0', sha256='1a4112196497b8421480e2a0a1164071221e467853486577c4f07627a702f4c3')
 
+    variant('tools', default=False, description='Build the command line tools')
     variant('netcdf', default=False,
             description='Enable GRIB to NetCDF conversion tool')
     variant('jp2k', default='openjpeg', values=('openjpeg', 'jasper', 'none'),
@@ -45,6 +73,21 @@ class Eccodes(CMakePackage):
     variant('python', default=False,
             description='Enable the Python 2 interface')
     variant('fortran', default=False, description='Enable the Fortran support')
+    variant('shared', default=True,
+            description='Build shared versions of the libraries')
+
+    variant('definitions',
+            values=disjoint_sets(
+                ('auto',),
+                ('default',) + tuple(_definitions.keys()),
+            ).with_default('auto'),
+            description="List of definitions to install")
+
+    variant('samples',
+            values=disjoint_sets(
+                ('auto',), ('default',),
+            ).with_default('auto'),
+            description="List of samples to install")
 
     depends_on('netcdf-c', when='+netcdf')
     # Cannot be built with openjpeg@2.0.x.
@@ -66,9 +109,26 @@ class Eccodes(CMakePackage):
 
     depends_on('cmake@3.6:', type='build')
     depends_on('cmake@3.12:', when='@2.19:', type='build')
+
     conflicts('+openmp', when='+pthreads',
               msg='Cannot enable both POSIX threads and OMP')
 
+    conflicts('+netcdf', when='~tools',
+              msg='Cannot enable the NetCDF conversion tool '
+                  'when the command line tools are disabled')
+
+    conflicts('~tools', when='@:2.18.0',
+              msg='The command line tools can be disabled '
+                  'only starting version 2.19.0')
+
+    for center, definitions in _definitions.items():
+        kwargs = definitions.get('conflicts', None)
+        if kwargs:
+            conflicts('definitions={0}'.format(center), **kwargs)
+        for kwargs in definitions.get('resources', []):
+            resource(name=center, destination='spack-definitions',
+                     placement='definitions.{0}'.format(center), **kwargs)
+
     # Enforce linking against the specified JPEG2000 backend, see also
     # https://github.com/ecmwf/eccodes/commit/2c10828495900ff3d80d1e570fe96c1df16d97fb
     patch('openjpeg_jasper.patch', when='@:2.16')
@@ -76,6 +136,140 @@ class Eccodes(CMakePackage):
     # CMAKE_INSTALL_RPATH must be a semicolon-separated list.
     patch('cmake_install_rpath.patch', when='@:2.10')
 
+    # Fix a bug preventing cmake from finding NetCDF:
+    patch('https://github.com/ecmwf/ecbuild/commit/3916c7d22575c45166fcc89edcbe02a6e9b81aa2.patch',
+          sha256='857454528b666c52eb36ef3aa5d40ae018981b44e129bb8df3c2d3d560e3fa03',
+          when='@:2.4.0+netcdf')
+
+    @when('%nag+fortran')
+    def patch(self):
+        # A number of Fortran source files assume that the kinds of integer and
+        # real variables are specified in bytes. However, the NAG compiler
+        # accepts such code only with an additional compiler flag -kind=byte.
+        # We do not simply add the flag because all user applications would
+        # have to be compiled with this flag too, which goes against one of the
+        # purposes of using the NAG compiler: make sure the code does not
+        # contradict the Fortran standards. The following logic could have been
+        # implemented as regular patch files, which would, however, be quite
+        # large. We would also have to introduce several versions of each patch
+        # file to support different versions of the package.
+
+        patch_kind_files = ['fortran/eccodes_f90_head.f90',
+                            'fortran/eccodes_f90_tail.f90',
+                            'fortran/grib_f90_head.f90',
+                            'fortran/grib_f90_tail.f90',
+                            'fortran/grib_types.f90']
+
+        patch_unix_ext_files = []
+
+        if self.run_tests:
+            patch_kind_files.extend([
+                'examples/F90/grib_print_data.f90',
+                'examples/F90/grib_print_data_static.f90',
+                # Files that need patching only when the extended regression
+                # tests are enabled, which we disable unconditionally:
+                # 'examples/F90/bufr_attributes.f90',
+                # 'examples/F90/bufr_expanded.f90',
+                # 'examples/F90/bufr_get_keys.f90',
+                # 'examples/F90/bufr_read_scatterometer.f90',
+                # 'examples/F90/bufr_read_synop.f90',
+                # 'examples/F90/bufr_read_temp.f90',
+                # 'examples/F90/bufr_read_tempf.f90',
+                # 'examples/F90/bufr_read_tropical_cyclone.f90',
+                # 'examples/F90/grib_clone.f90',
+                # 'examples/F90/grib_get_data.f90',
+                # 'examples/F90/grib_nearest.f90',
+                # 'examples/F90/grib_precision.f90',
+                # 'examples/F90/grib_read_from_file.f90',
+                # 'examples/F90/grib_samples.f90',
+                # 'examples/F90/grib_set_keys.f90'
+            ])
+
+            patch_unix_ext_files.extend([
+                'examples/F90/bufr_ecc-1284.f90',
+                'examples/F90/grib_set_data.f90',
+                'examples/F90/grib_set_packing.f90',
+                # Files that need patching only when the extended regression
+                # tests are enabled, which we disable unconditionally:
+                # 'examples/F90/bufr_copy_data.f90',
+                # 'examples/F90/bufr_get_string_array.f90',
+                # 'examples/F90/bufr_keys_iterator.f90',
+                # 'examples/F90/get_product_kind.f90',
+                # 'examples/F90/grib_count_messages_multi.f90'
+            ])
+
+        kwargs = {'string': False, 'backup': False, 'ignore_absent': True}
+
+        # Return the kind and not the size:
+        filter_file(r'(^\s*kind_of_double\s*=\s*)(\d{1,2})(\s*$)',
+                    '\\1kind(real\\2)\\3',
+                    'fortran/grib_types.f90', **kwargs)
+        filter_file(r'(^\s*kind_of_\w+\s*=\s*)(\d{1,2})(\s*$)',
+                    '\\1kind(x\\2)\\3',
+                    'fortran/grib_types.f90', **kwargs)
+
+        # Replace integer kinds:
+        for size, r in [(2, 4), (4, 9), (8, 18)]:
+            filter_file(r'(^\s*integer\((?:kind=)?){0}(\).*)'.format(size),
+                        '\\1selected_int_kind({0})\\2'.format(r),
+                        *patch_kind_files, **kwargs)
+
+        # Replace real kinds:
+        for size, p, r in [(4, 6, 37), (8, 15, 307)]:
+            filter_file(r'(^\s*real\((?:kind=)?){0}(\).*)'.format(size),
+                        '\\1selected_real_kind({0}, {1})\\2'.format(p, r),
+                        *patch_kind_files, **kwargs)
+
+        # Enable getarg and exit subroutines:
+        filter_file(r'(^\s*program\s+\w+)(\s*$)',
+                    '\\1; use f90_unix_env; use f90_unix_proc\\2',
+                    *patch_unix_ext_files, **kwargs)
+
+    @property
+    def libs(self):
+        libraries = []
+
+        query_parameters = self.spec.last_query.extra_parameters
+
+        if 'shared' in query_parameters:
+            shared = True
+        elif 'static' in query_parameters:
+            shared = False
+        else:
+            shared = '+shared' in self.spec
+
+        # Return Fortran library if requested:
+        return_fortran = 'fortran' in query_parameters
+        # Return C library if either requested or the Fortran library is not
+        # requested (to avoid overlinking) or the static libraries are
+        # requested:
+        return_c = 'c' in query_parameters or not (return_fortran and shared)
+        # Return MEMFS library only if enabled and the static libraries are
+        # requested:
+        return_memfs = '+memfs' in self.spec and not shared
+
+        if return_fortran:
+            libraries.append('libeccodes_f90')
+
+        if return_c:
+            libraries.append('libeccodes')
+
+        if return_memfs:
+            libraries.append('libeccodes_memfs')
+
+        libs = find_libraries(
+            libraries, root=self.prefix, shared=shared, recursive=True
+        )
+
+        if libs and len(libs) == len(libraries):
+            return libs
+
+        msg = 'Unable to recursively locate {0} {1} libraries in {2}'
+        raise spack.error.NoLibrariesError(
+            msg.format('shared' if shared else 'static',
+                       self.spec.name,
+                       self.spec.prefix))
+
     @run_before('cmake')
     def check_fortran(self):
         if '+fortran' in self.spec and self.compiler.fc is None:
@@ -83,69 +277,81 @@ class Eccodes(CMakePackage):
                 'Fortran interface requires a Fortran compiler!')
 
     def cmake_args(self):
-        var_opt_list = [
-            ('+pthreads', 'ECCODES_THREADS'),
-            ('+openmp', 'ECCODES_OMP_THREADS'),
-            ('+memfs', 'MEMFS'),
-            ('+python',
-             'PYTHON2' if self.spec.satisfies('@2.20.0:') else 'PYTHON'),
-            ('+fortran', 'FORTRAN')]
-
-        args = ['-DENABLE_%s=%s' % (opt, 'ON' if var in self.spec else 'OFF')
-                for var, opt in var_opt_list]
-
-        args.extend(
-            ['-DENABLE_%s=%s' % (opt, 'ON' if self.run_tests else 'OFF')
-             for opt in ['TESTS',
-                         # Examples are not installed and are
-                         # just part of the test suite.
-                         'EXAMPLES']])
-
-        # Unconditionally disable the extended regression testing,
-        # which requires data downloads.
-        args.append('-DENABLE_EXTRA_TESTS=OFF')
+        jp2k = self.spec.variants['jp2k'].value
 
-        if '+netcdf' in self.spec:
-            args.extend(['-DENABLE_NETCDF=ON',
-                         # Prevent overriding by environment variable
-                         # HDF5_ROOT.
-                         '-DHDF5_ROOT=' + self.spec['hdf5'].prefix,
-                         # Prevent possible overriding by environment variables
-                         # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH.
-                         '-DNETCDF_PATH=' + self.spec['netcdf-c'].prefix])
-        else:
-            args.append('-DENABLE_NETCDF=OFF')
+        args = [
+            self.define_from_variant('ENABLE_BUILD_TOOLS', 'tools'),
+            self.define_from_variant('ENABLE_NETCDF', 'netcdf'),
+            self.define('ENABLE_JPG', jp2k != 'none'),
+            self.define('ENABLE_JPG_LIBJASPER', jp2k == 'jasper'),
+            self.define('ENABLE_JPG_LIBOPENJPEG', jp2k == 'openjpeg'),
+            self.define_from_variant('ENABLE_PNG', 'png'),
+            self.define_from_variant('ENABLE_AEC', 'aec'),
+            self.define_from_variant('ENABLE_ECCODES_THREADS', 'pthreads'),
+            self.define_from_variant('ENABLE_ECCODES_OMP_THREADS', 'openmp'),
+            self.define_from_variant('ENABLE_MEMFS', 'memfs'),
+            self.define_from_variant(
+                'ENABLE_PYTHON{0}'.format(
+                    '2' if self.spec.satisfies('@2.20.0:') else ''),
+                'python'),
+            self.define_from_variant('ENABLE_FORTRAN', 'fortran'),
+            self.define('BUILD_SHARED_LIBS',
+                        'BOTH' if '+shared' in self.spec else 'OFF'),
+            self.define('ENABLE_TESTS', self.run_tests),
+            # Examples are not installed and are just part of the test suite:
+            self.define('ENABLE_EXAMPLES', self.run_tests),
+            # Unconditionally disable the extended regression tests, since they
+            # download additional data (~134MB):
+            self.define('ENABLE_EXTRA_TESTS', False)
+        ]
 
-        jp2k = self.spec.variants['jp2k'].value
-        args.append('-DENABLE_JPG=' +
-                    ('OFF' if jp2k == 'none' else 'ON'))
-        args.append('-DENABLE_JPG_LIBJASPER=' +
-                    ('ON' if jp2k == 'jasper' else 'OFF'))
-        args.append('-DENABLE_JPG_LIBOPENJPEG=' +
-                    ('ON' if jp2k == 'openjpeg' else 'OFF'))
+        if '+netcdf' in self.spec:
+            args.extend([
+                # Prevent possible overriding by environment variables
+                # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH:
+                self.define('NETCDF_PATH', self.spec['netcdf-c'].prefix),
+                # Prevent overriding by environment variable HDF5_ROOT:
+                self.define('HDF5_ROOT', self.spec['hdf5'].prefix)])
 
         if jp2k == 'openjpeg':
-            args.append('-DOPENJPEG_PATH=' + self.spec['openjpeg'].prefix)
+            args.append(self.define('OPENJPEG_PATH',
+                                    self.spec['openjpeg'].prefix))
 
         if '+png' in self.spec:
-            args.extend(['-DENABLE_PNG=ON',
-                         '-DZLIB_ROOT=' + self.spec['zlib'].prefix])
-        else:
-            args.append('-DENABLE_PNG=OFF')
+            args.append(self.define('ZLIB_ROOT', self.spec['zlib'].prefix))
 
         if '+aec' in self.spec:
-            args.extend(['-DENABLE_AEC=ON',
-                         # Prevent overriding by environment variables
-                         # AEC_DIR and AEC_PATH.
-                         '-DAEC_DIR=' + self.spec['libaec'].prefix])
-        else:
-            args.append('-DENABLE_AEC=OFF')
+            # Prevent overriding by environment variables AEC_DIR and AEC_PATH:
+            args.append(self.define('AEC_DIR', self.spec['libaec'].prefix))
 
         if '^python' in self.spec:
-            args.append('-DPYTHON_EXECUTABLE:FILEPATH=' + python.path)
+            args.append(self.define('PYTHON_EXECUTABLE', python.path))
+
+        definitions = self.spec.variants['definitions'].value
+
+        if 'auto' not in definitions:
+            args.append(self.define('ENABLE_INSTALL_ECCODES_DEFINITIONS',
+                                    'default' in definitions))
+
+        samples = self.spec.variants['samples'].value
+
+        if 'auto' not in samples:
+            args.append(self.define('ENABLE_INSTALL_ECCODES_SAMPLES',
+                                    'default' in samples))
 
         return args
 
+    @run_after('install')
+    def install_extra_definitions(self):
+        noop = set(['auto', 'none', 'default'])
+        for center in self.spec.variants['definitions'].value:
+            if center not in noop:
+                center_dir = 'definitions.{0}'.format(center)
+                install_tree(
+                    join_path(self.stage.source_path,
+                              'spack-definitions', center_dir),
+                    join_path(self.prefix.share.eccodes, center_dir))
+
     def check(self):
         # https://confluence.ecmwf.int/display/ECC/ecCodes+installation
         with working_dir(self.build_directory):