bb70e6ffcd
Bug fixes for package netcdf-cxx4 so that it builds on macOS semi case-sensitive filesystems; this includes additional changes to build netcdf-cxx4 consistently with netcdf-fortran. * netcdf-fortran: remove unused config_flags * netcdf-fortran: avoid building without the optimization flags * netcdf-cxx4: do not enforce autoreconf. This was a rudiment from the times when the package was fetched with git, which broke timestamp order of the automatically generated Autoconf files. * netcdf-cxx4: inject PIC flags for C++ when '+pic' * netcdf-cxx4: inject C/CXXFLAGS via the wrapper * netcdf-cxx4: fix the underlinking problem for platforms other than darwin (add netcdf-c libs netcdf-cxx4 ldlibs flags) * netcdf-cxx4: remove redundant extension of CPPFLAGS * netcdf-cxx4: only need to use MPI compiler wrapper when building C (vs both C and C++) * netcdf-cxx4: remove variant 'static' This makes it consistent with other packages from the NetCDF constellation: always build the static libraries and additionally build the shared ones when '+shared'. * netcdf-cxx4: do not configure --with/--without-pic. This makes it consistent with other packages from the NetCDF constellation: build the shared libraries with the PIC flag and the static ones without it (the default for Autotools) when '~pic', and build the static libraries with PIC when '+pic' (to make them injectable into other shared libraries). * netcdf-cxx4: run the tests serially * netcdf-cxx4: build the plugins only when the tests are run Co-authored-by: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
211 lines
9.4 KiB
Python
211 lines
9.4 KiB
Python
# Copyright 2013-2022 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 glob
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import os
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from shutil import Error, copyfile
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from spack import *
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class NetcdfFortran(AutotoolsPackage):
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"""NetCDF (network Common Data Form) is a set of software libraries and
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machine-independent data formats that support the creation, access, and
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sharing of array-oriented scientific data. This is the Fortran
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distribution."""
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homepage = "https://www.unidata.ucar.edu/software/netcdf"
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url = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.5.3.tar.gz"
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maintainers = ['skosukhin', 'WardF']
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version('4.5.3', sha256='123a5c6184336891e62cf2936b9f2d1c54e8dee299cfd9d2c1a1eb05dd668a74')
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version('4.5.2', sha256='b959937d7d9045184e9d2040a915d94a7f4d0185f4a9dceb8f08c94b0c3304aa')
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version('4.4.5', sha256='2467536ce29daea348c736476aa8e684c075d2f6cab12f3361885cb6905717b8')
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version('4.4.4', sha256='b2d395175f8d283e68c8be516e231a96b191ade67ad0caafaf7fa01b1e6b5d75')
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version('4.4.3', sha256='330373aa163d5931e475b5e83da5c1ad041e855185f24e6a8b85d73b48d6cda9')
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variant('pic', default=True,
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description='Produce position-independent code (for shared libs)')
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variant('shared', default=True, description='Enable shared library')
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variant('doc', default=False, description='Enable building docs')
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depends_on('netcdf-c')
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depends_on('doxygen', when='+doc', type='build')
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# The default libtool.m4 is too old to handle NAG compiler properly:
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# https://github.com/Unidata/netcdf-fortran/issues/94
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# Moreover, Libtool can't handle '-pthread' flag coming from libcurl,
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# doesn't inject convenience libraries into the shared ones, and is unable
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# to detect NAG when it is called with an MPI wrapper.
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patch('nag_libtool_2.4.2.patch', when='@:4.4.4%nag')
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patch('nag_libtool_2.4.6.patch', when='@4.4.5:%nag')
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# Enable 'make check' for NAG, which is too strict.
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patch('nag_testing.patch', when='@4.4.5%nag')
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# File fortran/nf_logging.F90 is compiled without -DLOGGING, which leads
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# to missing symbols in the library. Additionally, the patch enables
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# building with NAG, which refuses to compile empty source files (see also
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# comments in the patch):
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patch('logging.patch', when='@:4.4.5')
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# Prevent excessive linking to system libraries. Without this patch the
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# library might get linked to the system installation of libcurl. See
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# https://github.com/Unidata/netcdf-fortran/commit/0a11f580faebbc1c4dce68bf5135709d1c7c7cc1#diff-67e997bcfdac55191033d57a16d1408a
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patch('excessive_linking.patch', when='@4.4.5')
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# Parallel builds do not work in the fortran directory. This patch is
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# derived from https://github.com/Unidata/netcdf-fortran/pull/211
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patch('no_parallel_build.patch', when='@4.5.2')
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def flag_handler(self, name, flags):
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if name == 'cflags':
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if '+pic' in self.spec:
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flags.append(self.compiler.cc_pic_flag)
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elif name == 'fflags':
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if '+pic' in self.spec:
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flags.append(self.compiler.f77_pic_flag)
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if self.spec.satisfies('%gcc@10:'):
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# https://github.com/Unidata/netcdf-fortran/issues/212
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flags.append('-fallow-argument-mismatch')
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elif self.compiler.name == 'cce':
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# Cray compiler generates module files with uppercase names by
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# default, which is not handled by the makefiles of
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# NetCDF-Fortran:
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# https://github.com/Unidata/netcdf-fortran/pull/221.
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# The following flag forces the compiler to produce module
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# files with lowercase names.
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flags.append('-ef')
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# Note that cflags and fflags should be added by the compiler wrapper
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# and not on the command line to avoid overriding the default
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# compilation flags set by the configure script:
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return flags, None, None
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@property
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def libs(self):
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libraries = ['libnetcdff']
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query_parameters = self.spec.last_query.extra_parameters
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if 'shared' in query_parameters:
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shared = True
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elif 'static' in query_parameters:
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shared = False
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else:
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shared = '+shared' in self.spec
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libs = find_libraries(
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libraries, root=self.prefix, shared=shared, recursive=True
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)
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if libs:
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return libs
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msg = 'Unable to recursively locate {0} {1} libraries in {2}'
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raise spack.error.NoLibrariesError(
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msg.format('shared' if shared else 'static',
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self.spec.name,
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self.spec.prefix))
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def configure_args(self):
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config_args = self.enable_or_disable('shared')
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config_args.append('--enable-static')
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# We need to build with MPI wrappers if either of the parallel I/O
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# features is enabled in netcdf-c:
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# https://www.unidata.ucar.edu/software/netcdf/docs/building_netcdf_fortran.html
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netcdf_c_spec = self.spec['netcdf-c']
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if '+mpi' in netcdf_c_spec or '+parallel-netcdf' in netcdf_c_spec:
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config_args.append('CC=%s' % self.spec['mpi'].mpicc)
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config_args.append('FC=%s' % self.spec['mpi'].mpifc)
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config_args.append('F77=%s' % self.spec['mpi'].mpif77)
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if '+doc' in self.spec:
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config_args.append('--enable-doxygen')
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else:
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config_args.append('--disable-doxygen')
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return config_args
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@run_after('configure')
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def patch_libtool(self):
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"""AOCC support for NETCDF-F"""
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if '%aocc' in self.spec:
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# Libtool does not fully support the compiler toolchain, therefore
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# we have to patch the script. The C compiler normally gets
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# configured correctly, the variables of interest in the
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# 'BEGIN LIBTOOL CONFIG' section are set to non-empty values and,
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# therefore, are not affected by the replacements below. A more
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# robust solution would be to extend the filter_file function with
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# an additional argument start_at and perform the replacements
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# between the '# ### BEGIN LIBTOOL TAG CONFIG: FC' and
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# '# ### END LIBTOOL TAG CONFIG: FC' markers for the Fortran
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# compiler, and between the '# ### BEGIN LIBTOOL TAG CONFIG: F77'
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# and '# ### END LIBTOOL TAG CONFIG: F77' markers for the Fortran 77
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# compiler.
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# How to pass a linker flag through the compiler:
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filter_file(r'^wl=""$',
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'wl="{0}"'.format(self.compiler.linker_arg),
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'libtool')
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# Additional compiler flags for building library objects (we need
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# this to enable shared libraries when building with ~pic). Note
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# that the following will set fc_pic_flag for both FC and F77, which
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# in the case of AOCC, should not be a problem. If it is, the
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# aforementioned modification of the filter_file function could be
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# a solution.
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filter_file(r'^pic_flag=""$',
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'pic_flag=" {0}"'.format(self.compiler.fc_pic_flag),
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'libtool')
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# The following is supposed to tell the compiler to use the GNU
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# linker. However, the replacement does not happen (at least for
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# NetCDF-Fortran 4.5.3) because the replaced substring (i.e. the
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# first argument passed to the filter_file function) is not present
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# in the file. The flag should probably be added to 'ldflags' in the
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# flag_handler method above (another option is to add the flag to
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# 'ldflags' in compilers.yaml automatically as it was done for other
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# flags in https://github.com/spack/spack/pull/22219).
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filter_file(
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r'\${wl}-soname \$wl\$soname',
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r'-fuse-ld=ld -Wl,-soname,\$soname',
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'libtool', string=True)
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# TODO: resolve the NAG-related issues in a similar way: remove the
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# respective patch files and tune the generated libtool script instead.
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@when('@:4.4.5')
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def check(self):
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with working_dir(self.build_directory):
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make('check', parallel=False)
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@run_after('install')
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def cray_module_filenames(self):
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# Cray compiler searches for module files with uppercase names by
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# default and with lowercase names when the '-ef' flag is specified.
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# To avoid warning messages when compiler user applications in both
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# cases, we create copies of all '*.mod' files in the prefix/include
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# with names in upper- and lowercase.
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if self.spec.compiler.name != 'cce':
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return
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with working_dir(self.spec.prefix.include):
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for f in glob.glob('*.mod'):
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name, ext = os.path.splitext(f)
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try:
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# Create a copy with uppercase name:
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copyfile(f, name.upper() + ext)
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except Error:
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# Assume that the exception tells us that the file with
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# uppercase name already exists. Try to create a file with
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# lowercase name then:
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try:
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copyfile(f, name.lower() + ext)
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except Error:
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pass
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