Various updates to the NCO package and dependencies (#2639)

* Remove +mpi variant from NCO

* Update NCO deps to AutotoolsPackage

* Update the other NetCDF packages to AutotoolsPackage

* ANTLR has a nolink deptype on java, don't worry about csharp

* Remove restrictions from NCO package, fix homepage

* Add version 4.6.3 of NCO

* Missed AutotoolsPackage for NetCDF-CXX4

* NetCDF tests fail when run in parallel

* Remove commented out dependency

* Add documentation dependency

var/spack/repos/builtin/packages/antlr/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class Antlr(Package):
+class Antlr(AutotoolsPackage):
     """ANTLR (ANother Tool for Language Recognition) is a powerful parser
     generator for reading, processing, executing, or translating structured
     text or binary files. It's widely used to build languages, tools, and
@@ -35,9 +35,6 @@ class Antlr(Package):
     homepage = "http://www.antlr.org"
     url      = "https://github.com/antlr/antlr/tarball/v2.7.7"
 
-    # NOTE: This requires that a system Java be available.
-    # Spack does not yet know how to install Java compilers
-
     # Notes from http://nco.sourceforge.net/#bld
     # The first steps to build (i.e., compile, for the most part) NCO from
     # source code are to install the pre-requisites: ANTLR version 2.7.7
@@ -52,27 +49,18 @@ class Antlr(Package):
     # Unpatched version
     # url='http://dust.ess.uci.edu/nco/antlr-2.7.7.tar.gz')
 
-    variant('cxx', default=False, description='Enable ANTLR for C++')
+    variant('cxx',    default=True,  description='Enable ANTLR for C++')
-    variant('java', default=False, description='Enable ANTLR for Java')
+    variant('java',   default=False, description='Enable ANTLR for Java')
     variant('python', default=False, description='Enable ANTLR for Python')
-    variant('csharp', default=False, description='Enable ANTLR for Csharp')
 
-    def install(self, spec, prefix):
+    extends('python', when='+python')
-        # Check for future enabling of variants
+    depends_on('jdk', type='nolink', when='+java')
-        for v in ('+java', '+python', '+csharp'):
-            if v in spec:
-                raise Error(
-                    ('Illegal variant %s; ' % v) + 'for now, '
-                    'Spack only knows how to build antlr or antlr+cxx')
 
-        config_args = [
+    def configure_args(self):
-            '--prefix=%s' % prefix,
+        spec = self.spec
-            '--%s-cxx' % ('enable' if '+cxx' in spec else 'disable'),
-            '--%s-java' % ('enable' if '+java' in spec else 'disable'),
-            '--%s-python' % ('enable' if '+python' in spec else 'disable'),
-            '--%s-csharp' % ('enable' if '+csharp' in spec else 'disable')]
 
-        # which('autoreconf')('-iv')
+        return [
-        configure(*config_args)
+            '--{0}-cxx'.format('enable' if '+cxx' in spec else 'disable'),
-        make()
+            '--{0}-java'.format('enable' if '+java' in spec else 'disable'),
-        make("install")
+            '--{0}-python'.format('enable' if '+python' in spec else 'disable')
+        ]

var/spack/repos/builtin/packages/expat/package.py

@@ -25,19 +25,9 @@
 from spack import *
 
 
-class Expat(Package):
+class Expat(AutotoolsPackage):
-    """<eXpat/> is an XML parser library written in C"""
+    """Expat is an XML parser library written in C."""
     homepage = "http://expat.sourceforge.net/"
+    url = "http://downloads.sourceforge.net/project/expat/expat/2.2.0/expat-2.2.0.tar.bz2"
 
-    version('2.2.0', '2f47841c829facb346eb6e3fab5212e2',
+    version('2.2.0', '2f47841c829facb346eb6e3fab5212e2')
-            url="http://downloads.sourceforge.net/project/expat/expat/2.2.0/expat-2.2.0.tar.bz2")
-    version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd',
-            url="http://downloads.sourceforge.net/project/expat/expat/2.1.0/expat-2.1.0.tar.gz")
-
-    def install(self, spec, prefix):
-        configure('--prefix={0}'.format(prefix))
-
-        make()
-        if self.run_tests:
-            make('check')
-        make('install')

var/spack/repos/builtin/packages/nco/package.py

@@ -29,35 +29,27 @@ class Nco(AutotoolsPackage):
     """The NCO toolkit manipulates and analyzes data stored in
     netCDF-accessible formats"""
 
-    homepage = "https://sourceforge.net/projects/nco"
+    homepage = "http://nco.sourceforge.net/"
     url      = "https://github.com/nco/nco/archive/4.6.2.tar.gz"
 
+    version('4.6.3', '0e1d6616c65ed3a30c54cc776da4f987')
     version('4.6.2', 'b7471acf0cc100343392f4171fb56113')
     version('4.6.1', 'ef43cc989229c2790a9094bd84728fd8')
     version('4.5.5', '9f1f1cb149ad6407c5a03c20122223ce')
 
+    variant('doc', default=False, description='Build/install NCO TexInfo-based documentation')
+
     # See "Compilation Requirements" at:
     # http://nco.sourceforge.net/#bld
-    variant('mpi', default=True)
-
     depends_on('netcdf')
     depends_on('antlr@2.7.7+cxx')  # required for ncap2
     depends_on('gsl')              # desirable for ncap2
     depends_on('udunits2')         # allows dimensional unit transformations
-    # depends_on('opendap')        # enables network transparency
 
-    @AutotoolsPackage.precondition('configure')
+    depends_on('flex', type='build')
-    def validate(self):
+    depends_on('bison', type='build')
-        """Ensures that dependents were built with the right variants."""
+    depends_on('texinfo@4.12:', type='build', when='+doc')
-        # Workaround until variant forwarding works properly
-        spec = self.spec
-        if '+mpi' in spec and spec.satisfies('^netcdf~mpi'):
-            raise RuntimeError('Invalid spec. Package netcdf requires '
-                               'netcdf+mpi, but spec asked for netcdf~mpi.')
 
     def configure_args(self):
-        return [
+        spec = self.spec
-            '--disable-openmp',  # TODO: Make this a variant
+        return ['--{0}-doc'.format('enable' if '+doc' in spec else 'disable')]
-            '--disable-dap',     # TODO: Make this a variant
-            '--disable-esmf'
-        ]

var/spack/repos/builtin/packages/netcdf-cxx/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class NetcdfCxx(Package):
+class NetcdfCxx(AutotoolsPackage):
     """Deprecated C++ compatibility bindings for NetCDF.
     These do NOT read or write NetCDF-4 files, and are no longer
     maintained by Unidata.  Developers should migrate to current
@@ -37,8 +37,3 @@ class NetcdfCxx(Package):
     version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c')
 
     depends_on('netcdf')
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-        make()
-        make("install")

var/spack/repos/builtin/packages/netcdf-cxx4/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class NetcdfCxx4(Package):
+class NetcdfCxx4(AutotoolsPackage):
     """C++ interface for NetCDF4"""
     homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "https://www.github.com/unidata/netcdf-cxx4/tarball/v4.3.0"
@@ -34,11 +34,8 @@ class NetcdfCxx4(Package):
     version('4.2.1', 'd019853802092cf686254aaba165fc81')
 
     depends_on('netcdf')
-    depends_on("autoconf", type='build')
+    depends_on('autoconf', type='build')
 
-    def install(self, spec, prefix):
+    def autoreconf(self, spec, prefix):
         # Rebuild to prevent problems of inconsistency in git repo
         which('autoreconf')('-ivf')
-        configure('--prefix=%s' % prefix)
-        make()
-        make("install")

var/spack/repos/builtin/packages/netcdf-fortran/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class NetcdfFortran(Package):
+class NetcdfFortran(AutotoolsPackage):
     """Fortran interface for NetCDF4"""
 
     homepage = "http://www.unidata.ucar.edu/software/netcdf"
@@ -35,8 +35,3 @@ class NetcdfFortran(Package):
     version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
 
     depends_on('netcdf')
-
-    def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
-        make()
-        make("install")

var/spack/repos/builtin/packages/netcdf/package.py

@@ -25,12 +25,10 @@
 from spack import *
 
 
-class Netcdf(Package):
+class Netcdf(AutotoolsPackage):
     """NetCDF is a set of software libraries and self-describing,
-       machine-independent data formats that support the creation, access,
+    machine-independent data formats that support the creation, access,
-       and sharing of array-oriented scientific data.
+    and sharing of array-oriented scientific data."""
-
-    """
 
     homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz"
@@ -82,7 +80,8 @@ def patch(self):
         ff.filter(r'^(#define\s+NC_MAX_VARS\s+)\d+(.*)$',
                   r'\1{0}\2'.format(max_vars))
 
-    def install(self, spec, prefix):
+    def configure_args(self):
+        spec = self.spec
         # Workaround until variant forwarding works properly
         if '+mpi' in spec and spec.satisfies('^hdf5~mpi'):
             raise RuntimeError('Invalid spec. Package netcdf requires '
@@ -95,7 +94,6 @@ def install(self, spec, prefix):
         LIBS     = []
 
         config_args = [
-            "--prefix=%s" % prefix,
             "--enable-fsync",
             "--enable-v2",
             "--enable-utilities",
@@ -168,10 +166,8 @@ def install(self, spec, prefix):
         config_args.append('LDFLAGS=%s'  % ' '.join(LDFLAGS))
         config_args.append('LIBS=%s'     % ' '.join(LIBS))
 
-        configure(*config_args)
+        return config_args
-        make()
 
-        if self.run_tests:
+    def check(self):
-            make("check")
+        # h5_test fails when run in parallel
-
+        make('check', parallel=False)
-        make("install")

var/spack/repos/builtin/packages/texinfo/package.py

@@ -26,24 +26,18 @@
 from spack import *
 
 
-class Texinfo(Package):
+class Texinfo(AutotoolsPackage):
     """Texinfo is the official documentation format of the GNU project.
 
     It was invented by Richard Stallman and Bob Chassell many years ago,
     loosely based on Brian Reid's Scribe and other formatting languages
-    of the time. It is used by many non-GNU projects as well.FIXME: put a
+    of the time. It is used by many non-GNU projects as well."""
-    proper description of your package here.
 
-    """
     homepage = "https://www.gnu.org/software/texinfo/"
     url      = "http://ftp.gnu.org/gnu/texinfo/texinfo-6.0.tar.gz"
 
+    version('6.3', '9b08daca9bf8eccae9b0f884aba41f9e')
     version('6.0', 'e1a2ef5dce5018b53f0f6eed45b247a7')
     version('5.2', '1b8f98b80a8e6c50422125e07522e8db')
     version('5.1', '54e250014fe698fb4832016158747c03')
     version('5.0', '918432285abe6fe96c98355594c5656a')
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-        make()
-        make("install")

var/spack/repos/builtin/packages/udunits2/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class Udunits2(Package):
+class Udunits2(AutotoolsPackage):
     """Automated units conversion"""
 
     homepage = "http://www.unidata.ucar.edu/software/udunits"
@@ -35,7 +35,5 @@ class Udunits2(Package):
 
     depends_on('expat')
 
-    def install(self, spec, prefix):
+    depends_on('bison', type='build')
-        configure("--prefix=%s" % prefix)
+    depends_on('flex',  type='build')
-        make()
-        make("install")