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06a5646
Add style check for easyconfigs
wpoely86 Feb 17, 2016
dd95739
Rename function
wpoely86 Feb 17, 2016
276f17a
Add test for style
wpoely86 Feb 17, 2016
9e92dab
Update test easyconfig to pass style check
wpoely86 Feb 18, 2016
d482ff2
Fix remarks
wpoely86 Feb 18, 2016
adac638
Make function private
wpoely86 Feb 18, 2016
9056d23
Fix checksums for tests
wpoely86 Feb 25, 2016
fbac45a
Merge branch 'develop' into style
wpoely86 Feb 25, 2016
6e62431
Fix style
wpoely86 Feb 25, 2016
613fdcf
Fix remarks
wpoely86 Feb 26, 2016
286c0e9
Typo
wpoely86 Feb 26, 2016
4604134
Fix style of test easyconfigs
wpoely86 Feb 26, 2016
04548c9
Fix remarks for tests
wpoely86 Feb 26, 2016
d434485
Print message for custom style checks
wpoely86 Feb 26, 2016
fce593f
Add documentation
wpoely86 Feb 26, 2016
215f7ad
Fix checksums
wpoely86 Feb 26, 2016
34315fa
Fix again...
wpoely86 Feb 26, 2016
74a8cf4
Final checksum fix.
wpoely86 Feb 26, 2016
41651bf
Mutiline description in yeb file
wpoely86 Feb 26, 2016
529af5c
Revert line change in test easyconfigs.
wpoely86 Feb 29, 2016
a7991b4
Merge branch 'develop' into style
wpoely86 Nov 24, 2016
210cc17
Fix author tag
wpoely86 Nov 24, 2016
5a51dee
Add pep8 to travis.yml
wpoely86 Nov 24, 2016
e1bf239
Some style changes
wpoely86 Nov 24, 2016
854f1dc
Fix remarks
wpoely86 Nov 29, 2016
5e047ca
Fix imports and order
wpoely86 Nov 29, 2016
d92bb09
Fix more remarks
wpoely86 Nov 29, 2016
a12c72c
Use constants and refactor
wpoely86 Nov 29, 2016
795048f
Drop unneeded comment
wpoely86 Nov 29, 2016
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113 changes: 113 additions & 0 deletions easybuild/framework/easyconfig/style.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,113 @@
##
# Copyright 2016 Ghent University
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2016-2016 (makes updating trivial next year)

#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (http://www.herculesstichting.be/in_English)
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FWO ;)

# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
#
# http://github.com/hpcugent/easybuild
#
# EasyBuild is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation v2.
#
# EasyBuild 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
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with EasyBuild. If not, see <http://www.gnu.org/licenses/>.
##
"""
Style tests for easyconfig files using pep8.
@author: Ward Poelmans (Ghent University)
"""

import re
from vsc.utils import fancylogger

from easybuild.tools.utilities import only_if_module_is_available

try:
import pep8
except ImportError:
pass

_log = fancylogger.getLogger('easyconfig.style', fname=False)
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why add a logger if you're not using it?

(don't remove it, use it below :))



# any function starting with _eb_check_ will be added to the tests
# if the test number is added to the select list. The test number is
# definied as AXXX where A is either E or W and XXX is a 3 digit number.
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the "A is either E or W" bit is confusing :)

# It should be mentioned in the docstring as a single word.
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on a separate line?

# Read the pep8 docs to understand the arguments of these functions
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pointer to pep8 docs?

def _eb_check_trailing_whitespace(physical_line, lines, line_number, total_lines):
"""
W299
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why 299?

shouldn't be define our own range like 9xy (or whatever other range that is not used by PEP8)?

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Well, there is a structure in the codes: https://pep8.readthedocs.org/en/latest/intro.html#error-codes

Warn about trailing whitespace, expect for the description and comments.
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except

This differs from the standard trailing whitespace check as that
will warn for any trailing whitespace.
"""
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doc args?

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I can copy & paste the pep8 docs but I prefer not to. The names are already quite clear and the precise meaning should be looked up in the url above

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please refer to the right place in the pep8 docs in the docstring; the comments won't show up in the auto-generated API documentation for EB we'll have at easybuild.readthedocs.org someday...

comment_re = re.compile('^\s*#')
if comment_re.match(physical_line):
return None
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not a big fan of inline returns (we rarely do this in the current codebase, I'd prefer sticking to that)

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It's much more readable in this way. Inline returns are not bad.


result = pep8.trailing_whitespace(physical_line)
if result:
result = (result[0], result[1].replace("W291", "W299"))
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ideally, we only have the "W299" string in a single place

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it should be in the docs as well, so it's gonna be here twice.

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can we string template a docstring? :P

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just tested this, templating on a docstring doesn't really work...


# if the warning is about the multiline string of description
# we will not issue a warning
keys_re = re.compile("^(?P<key>[a-z_]+)\s*=\s*")

for line in reversed(lines[0:line_number]):
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the 0 is useless, use [:line_number]

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why reversed btw?

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good question, I think to have a hit quicker? Not sure anymore.

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a no, it's because of the break

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well, since even you're forgetting it easily, add a comment above this line why the search is reversed...

res = keys_re.match(line)
if res:
if res.group("key") == "description":
return None
else:
break
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so, always break? and use result = None above => one less inline return :)

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what this does is: find the last key = value going back from the current line to the first one. It's a description, we pass the test else we return the default pep8 test.

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I understand, but stick to a single return:

for line in reversed(lines[:line_number]):
    res = keys_re.match(line)
    if res and res.group("key") == "description":
        result = None
        break

return result


return result


@only_if_module_is_available('pep8')
def style_conformance(lst_easyconfigs, verbose=False):
"""
Check the given list of easyconfigs for style
@param lst_easyconfigs list of file paths to easyconfigs
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why lst_?

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list

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easyconfig_s_ makes it clear it's a list?

let's not start using Hungarian syntax, we don't do it anywhere else in the codebase...

@param verbose print our statistics and be verbose about the errors and warning
@return the number of warnings and errors
"""
# importing autopep8 changes some pep8 functions.
# We reload it to be sure to get the real pep8 functions.
reload(pep8)

# register the extra checks before using pep8:
# any function in this module starting with `_eb_check_` will be used.
cands = globals()
for check_function in sorted([cands[f] for f in cands if callable(cands[f]) and f.startswith('_eb_check_')]):
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eb_check_ should be a constant?

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if you really want too but I don't see the point. These functions should 'private' to this file.

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sure, but eb_check_ is what we call a 'magic string'

right now, it's sort of OK, since it's only used here (and in the function names, but there you can't use a constant anyway)

but we should definitely not start using it in other places, like log messages

in fact... I'd like to see a log message, or maybe even a print, for a list of checks functions being performed?

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@wpoely86 let's flesh out _eb_check_ as a constant

pep8.register_check(check_function)

pep8style = pep8.StyleGuide(quiet=False, config_file=None)
options = pep8style.options
options.max_line_length = 120
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add a comment above to explain why (and what the default is)

# we ignore some tests
# note that W291 has be replaced by our custom W299
options.ignore = ('E402', # import not on top
'W291', # replaced by W299
'E501', # line too long
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please fix style, indent by 4 spaces

)
options.verbose = int(verbose)
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just make the default value 0?

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it is 0?


result = pep8style.check_files(lst_easyconfigs)

if verbose:
result.print_statistics()

return result.total_errors
2 changes: 1 addition & 1 deletion test/framework/easyconfig.py
Original file line number Diff line number Diff line change
Expand Up @@ -303,7 +303,7 @@ def test_exts_list(self):
' "source_urls": [("http://example.com", "suffix")],'
' "patches": ["toy-0.0.eb"],', # dummy patch to avoid downloading fail
' "checksums": [',
' "a5464d79c2c8d4935e383ebd070b305e",', # MD5 checksum for source (gzip-1.4.eb)
' "9e9485921c6afe15f62aedfead2c8f6e",', # MD5 checksum for source (gzip-1.4.eb)
' "fad34da3432ee2fd4d6554b86c8df4bf",', # MD5 checksum for patch (toy-0.0.eb)
' ],',
' }),',
Expand Down
36 changes: 18 additions & 18 deletions test/framework/easyconfigs/GCC-4.6.3.eb
Original file line number Diff line number Diff line change
@@ -1,29 +1,29 @@
# should be EB_GCC, but OK for testing purposes
easyblock = 'EB_toy'

name="GCC"
version='4.6.3'
name = "GCC"
version = '4.6.3'

homepage='http://gcc.gnu.org/'
description="The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...)."
homepage = 'http://gcc.gnu.org/'
description = "The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...)."

toolchain={'name': 'dummy','version': 'dummy'}
toolchain = {'name': 'dummy', 'version': 'dummy'}

sources=['%s-%s.tar.gz'%(name.lower(),version),
'gmp-5.0.4.tar.bz2',
'mpfr-3.0.1.tar.gz',
'mpc-0.9.tar.gz',
]
source_urls=['http://ftpmirror.gnu.org/%(name)s/%(name)s-%(version)s' % {'name':name.lower(), 'version':version}, # GCC auto-resolving HTTP mirror
'http://ftpmirror.gnu.org/gmp', # idem for GMP
'http://ftpmirror.gnu.org/mpfr', # idem for MPFR
'http://www.multiprecision.org/mpc/download', # MPC official
sources = ['%s-%s.tar.gz' % (name.lower(), version),
'gmp-5.0.4.tar.bz2',
'mpfr-3.0.1.tar.gz',
'mpc-0.9.tar.gz',
]
source_urls = ['http://ftpmirror.gnu.org/%(name)s/%(name)s-%(version)s' % {'name': name.lower(), 'version': version}, # GCC auto-resolving HTTP mirror
'http://ftpmirror.gnu.org/gmp', # idem for GMP
'http://ftpmirror.gnu.org/mpfr', # idem for MPFR
'http://www.multiprecision.org/mpc/download', # MPC official
]
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fix with 'correct' indent style?


languages=['c', 'c++', 'fortran', 'lto']
languages = ['c', 'c++', 'fortran', 'lto']

## compiler class
moduleclass='compiler'
# compiler class
moduleclass = 'compiler'

# building GCC sometimes fails if make parallelism is too high, so let's limit it
maxparallel=4
maxparallel = 4
8 changes: 4 additions & 4 deletions test/framework/easyconfigs/GCC-4.7.2.eb
Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,10 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj
toolchain = {'name': 'dummy', 'version': 'dummy'}

source_urls = [
'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror
'http://ftpmirror.gnu.org/gmp', # idem for GMP
'http://ftpmirror.gnu.org/mpfr', # idem for MPFR
'http://www.multiprecision.org/mpc/download', # MPC official
'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror
'http://ftpmirror.gnu.org/gmp', # idem for GMP
'http://ftpmirror.gnu.org/mpfr', # idem for MPFR
'http://www.multiprecision.org/mpc/download', # MPC official
]
sources = [
SOURCELOWER_TAR_GZ,
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"'
installopts = threading + " PREFIX=%(installdir)s"

# extensive testing can be enabled by uncommenting the line below
#runtest = 'PATH=.:$PATH lapack-timing'
# runtest = 'PATH=.:$PATH lapack-timing'

sanity_check_paths = {
'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h',
Expand Down
6 changes: 3 additions & 3 deletions test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.6.4.eb
Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,9 @@ else:
sanity_check_paths = {
'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] +
["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90",
"mpi", "ompitrace", "open-pal",
"open-rte", "vt", "vt-hyb",
"vt-mpi", "vt-mpi-unify"]] +
"mpi", "ompitrace", "open-pal",
"open-rte", "vt", "vt-hyb",
"vt-mpi", "vt-mpi-unify"]] +
["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif",
"mpif-mpi-io", "mpi", "mpi_portable_platform"]],
'dirs': ["include/openmpi/ompi/mpi/cxx"],
Expand Down
6 changes: 3 additions & 3 deletions test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.7.2.eb
Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,9 @@ else:
sanity_check_paths = {
'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] +
["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90",
"mpi", "ompitrace", "open-pal",
"open-rte", "vt", "vt-hyb",
"vt-mpi", "vt-mpi-unify"]] +
"mpi", "ompitrace", "open-pal",
"open-rte", "vt", "vt-hyb",
"vt-mpi", "vt-mpi-unify"]] +
["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif",
"mpif-mpi-io", "mpi", "mpi_portable_platform"]],
'dirs': ["include/openmpi/ompi/mpi/cxx"],
Expand Down
19 changes: 9 additions & 10 deletions test/framework/easyconfigs/Python-2.7.10-ictce-4.1.13.eb
Original file line number Diff line number Diff line change
Expand Up @@ -19,14 +19,14 @@ sources = [SOURCE_TGZ]
# python needs bzip2 to build the bz2 package
# commented out for testing to avoid having to add them all - dependencies are tested in other files
dependencies = [
# ('bzip2', '1.0.6'),
# ('zlib', '1.2.8'),
# ('libreadline', '6.3'),
# ('ncurses', '5.9'),
# ('SQLite', '3.8.10.2'),
# ('Tk', '8.6.4', '-no-X11'),
# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's
# nice to have an up to date openssl for security reasons
# ('bzip2', '1.0.6'),
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single space after #?

# ('zlib', '1.2.8'),
# ('libreadline', '6.3'),
# ('ncurses', '5.9'),
# ('SQLite', '3.8.10.2'),
# ('Tk', '8.6.4', '-no-X11'),
# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's
# nice to have an up to date openssl for security reasons
]

# fixme: tuple values; see issue #1442
Expand All @@ -47,7 +47,7 @@ exts_list = [
['numpy', numpyversion, {
'source_urls': [['http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download']],
'patches': [
'numpy-1.8.0-mkl.patch', # % numpyversion,
'numpy-1.8.0-mkl.patch', # % numpyversion,
],
}],
['scipy', scipyversion, {
Expand Down Expand Up @@ -123,4 +123,3 @@ exts_list = [
]

moduleclass = 'lang'

4 changes: 2 additions & 2 deletions test/framework/easyconfigs/SQLite-3.8.10.2-GCC-4.7.2.eb
Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,8 @@ sources = ['sqlite-autoconf-%s.tar.gz' % version_str]

# commented out for testing to avoid having to add them all - dependencies are tested in other files
dependencies = [
# ('libreadline', '6.3'),
# ('Tcl', '8.6.4'),
# ('libreadline', '6.3'),
# ('Tcl', '8.6.4'),
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single space after #

]

parallel = 1
Expand Down
4 changes: 2 additions & 2 deletions test/framework/easyconfigs/SQLite-3.8.10.2-gompi-1.4.10.eb
Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,8 @@ sources = ['sqlite-autoconf-%s.tar.gz' % version_str]

# commented out for testing to avoid having to add them all - dependencies are tested in other files
dependencies = [
# ('libreadline', '6.3'),
# ('Tcl', '8.6.4'),
# ('libreadline', '6.3'),
# ('Tcl', '8.6.4'),
]

parallel = 1
Expand Down
4 changes: 2 additions & 2 deletions test/framework/easyconfigs/SQLite-3.8.10.2-goolf-1.4.10.eb
Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,8 @@ sources = ['sqlite-autoconf-%s.tar.gz' % version_str]

# commented out for testing to avoid having to add them all - dependencies are tested in other files
dependencies = [
# ('libreadline', '6.3'),
# ('Tcl', '8.6.4'),
# ('libreadline', '6.3'),
# ('Tcl', '8.6.4'),
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single space after #

]

parallel = 1
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff)

dependencies = [(blaslib, blasver, blassuff)]

## parallel build tends to fail, so disabling it
# parallel build tends to fail, so disabling it
parallel = 1

moduleclass = 'numlib'
4 changes: 2 additions & 2 deletions test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,10 @@ homepage = "http://www.gzip.org/"
description = "gzip (GNU zip) is a popular data compression program as a replacement for compress"

# test toolchain specification
toolchain = {'name': 'GCC','version': '4.6.3'}
toolchain = {'name': 'GCC', 'version': '4.6.3'}

# source tarball filename
sources = ['%s-%s.tar.gz'%(name,version)]
sources = ['%s-%s.tar.gz' % (name, version)]
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%(version)s etc? ;)


# download location for source files
source_urls = [GNU_SOURCE]
Expand Down
2 changes: 1 addition & 1 deletion test/framework/easyconfigs/gzip-1.4-broken.eb
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ homepage = "http://www.gzip.org/"
description = "gzip (GNU zip) is a popular data compression program as a replacement for compress"

# test toolchain specification
toolchain = {'name':'dummy','version':'dummy'}
toolchain = {'name': 'dummy', 'version': 'dummy'}

# source tarball filename
sources = [SOURCE_TAR_GZ]
Expand Down
2 changes: 1 addition & 1 deletion test/framework/easyconfigs/gzip-1.4.eb
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ homepage = "http://www.gzip.org/"
description = "gzip (GNU zip) is a popular data compression program as a replacement for compress"

# test toolchain specification
toolchain = {'name':'dummy','version':'dummy'}
toolchain = {'name': 'dummy', 'version': 'dummy'}

# source tarball filename
sources = [SOURCE_TAR_GZ]
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2 changes: 1 addition & 1 deletion test/framework/easyconfigs/hwloc-1.6.2-GCC-4.6.4.eb
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide
information about modern computing hardware so as to exploit it accordingly and efficiently."""

toolchain = {'name': 'GCC', 'version': '4.6.4'}

source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/']
sources = [SOURCE_TAR_GZ]

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2 changes: 1 addition & 1 deletion test/framework/easyconfigs/hwloc-1.6.2-GCC-4.7.2.eb
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide
information about modern computing hardware so as to exploit it accordingly and efficiently."""

toolchain = {'name': 'GCC', 'version': '4.7.2'}

source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/']
sources = [SOURCE_TAR_GZ]

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Expand Up @@ -19,7 +19,7 @@ versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver)

dependencies = [
('GCCcore', gccver),
# ('binutils', binutilsver, '', ('GCCcore', gccver)),
# ('binutils', binutilsver, '', ('GCCcore', gccver)),
]

# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver)

dependencies = [
('GCCcore', gccver),
# ('binutils', binutilsver, '', ('GCCcore', gccver)),
# ('binutils', binutilsver, '', ('GCCcore', gccver)),
]

# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources
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