{bio}[foss/2018b] AFNI v18.3.00, tcsh v6.20.00

easybuild/easyconfigs/a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb

@@ -0,0 +1,63 @@
+easyblock = 'ConfigureMake'
+
+name = 'AFNI'
+version = '18.3.00'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://afni.nimh.nih.gov/'
+description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data -
+ a technique for mapping human brain activity."""
+
+toolchain = {'name': 'foss', 'version': '2018b'}
+toolchainopts = {'openmp': True, 'pic': True}
+
+source_urls = ['https://github.com/afni/afni/archive/']
+sources = ['AFNI_%(version)s.tar.gz']
+patches = ['AFNI-18.1.09_omp-pragma-statement-fix.patch']
+checksums = [
+    '01ecba09b1dfe270937f8cde204c18f38f9c4d543b1af3a7ccb17b04688f632d',  # AFNI_18.3.00.tar.gz
+    '8b739ddc09d6e398ac7fa86d89f6a02f26f2b58b17caea627d5c07de5282aab2',  # AFNI-18.1.09_omp-pragma-statement-fix.patch
+]
+
+builddependencies = [('M4', '1.4.18')]
+
+dependencies = [
+    ('tcsh', '6.20.00'),
+    ('Python', '3.6.6'),
+    ('X11', '20180604'),
+    ('motif', '2.3.8'),
+    ('R', '3.5.1'),
+    ('PyQt5', '5.11.3', versionsuffix),
+    ('expat', '2.2.5'),
+    ('libpng', '1.6.34'),
+    ('libjpeg-turbo', '2.0.0'),
+    ('GSL', '2.5'),
+    ('GLib', '2.54.3'),  # must match version used in Qt5 (via PyQt5)
+    ('zlib', '1.2.11'),
+]
+
+skipsteps = ['configure', 'install']
+
+prebuildopts = "cd src && cp Makefile.linux_openmp_64 Makefile && "
+buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)sm" '
+buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" '
+buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)sm '
+buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"'
+buildopts += ' INSTALLDIR=%(installdir)s'
+
+parallel = 1
+
+modextrapaths = {'PATH': ['']}
+
+sanity_check_paths = {
+    'files': ['afni'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb

@@ -0,0 +1,41 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit
+# Authors::   Valentin Plugaru <valentin.plugaru@gmail.com>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html
+##
+easyblock = 'ConfigureMake'
+
+name = 'tcsh'
+version = '6.20.00'
+
+homepage = 'http://www.tcsh.org'
+description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). 
+ It is a command language interpreter usable both as an interactive login shell and a shell script command 
+ processor. It includes a command-line editor, programmable word completion, spelling correction, a history 
+ mechanism, job control and a C-like syntax."""
+
+toolchain = {'name': 'GCCcore', 'version': '7.3.0'}
+
+source_urls = [
+    'ftp://ftp.astron.com/pub/%(namelower)s',
+    'ftp://ftp.astron.com/pub/%(namelower)s/old',
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b89de7064ab54dac454a266cfe5d8bf66940cb5ed048d0c30674ea62e7ecef9d']
+
+builddependencies = [('binutils', '2.30')]
+
+dependencies = [('ncurses', '6.1')]
+
+sanity_check_paths = {
+    'files': ["bin/tcsh"],
+    'dirs': []
+}
+
+moduleclass = 'tools'

test/easyconfigs/easyconfigs.py

@@ -27,8 +27,6 @@
 
 @author: Kenneth Hoste (Ghent University)
 """
-
-import copy
 import glob
 import os
 import re
@@ -37,25 +35,22 @@
 import tempfile
 from distutils.version import LooseVersion
 from vsc.utils import fancylogger
-from vsc.utils.missing import nub
 from unittest import TestCase, TestLoader, main
 
-import easybuild.main as main
+import easybuild.main as eb_main
 import easybuild.tools.options as eboptions
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig.default import DEFAULT_CONFIG
 from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS
-from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for, resolve_template
 from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tools import check_sha256_checksums, dep_graph, get_paths_for, process_easyconfig
 from easybuild.tools import config
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import change_dir, write_file
+from easybuild.tools.filetools import change_dir, remove_file, write_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
-from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.robot import check_conflicts, resolve_dependencies
@@ -98,7 +93,7 @@ class EasyConfigTest(TestCase):
     log = fancylogger.getLogger("EasyConfigTest", fname=False)
 
     # make sure a logger is present for main
-    main._log = log
+    eb_main._log = log
     ordered_specs = None
     parsed_easyconfigs = []
 
@@ -134,10 +129,7 @@ def test_dep_graph(self):
 
             dep_graph(fn, self.ordered_specs)
 
-            try:
-                os.remove(fn)
-            except OSError, err:
-                log.error("Failed to remove %s: %s" % (fn, err))
+            remove_file(fn)
         else:
             print "(skipped dep graph test)"
 
@@ -215,6 +207,15 @@ def check_dep_vars(dep, dep_vars):
                     if len(dep_vars) == 1:
                         break
 
+                # filter R dep for a specific version of Python 2.x
+                if dep == 'R' and len(dep_vars) > 1:
+                    for key in dep_vars.keys():
+                        if '; versionsuffix: -Python-2' in key:
+                            dep_vars.pop(key)
+                        # always retain at least one variant
+                        if len(dep_vars) == 1:
+                            break
+
             # filter out Java 'wrapper'
             # i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181)
             elif dep == 'Java' and len(dep_vars) == 2:
@@ -397,6 +398,7 @@ def test_zzz_cleanup(self):
         """Dummy test to clean up global temporary directory."""
         shutil.rmtree(self.TMPDIR)
 
+
 def template_easyconfig_test(self, spec):
     """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ..."""
 
@@ -435,7 +437,7 @@ def template_easyconfig_test(self, spec):
     # check that automagic fallback to ConfigureMake isn't done (deprecated behaviour)
     fn = os.path.basename(spec)
     error_msg = "%s relies on automagic fallback to ConfigureMake, should use easyblock = 'ConfigureMake' instead" % fn
-    self.assertTrue(easyblock or not app_class is ConfigureMake, error_msg)
+    self.assertTrue(easyblock or app_class is not ConfigureMake, error_msg)
 
     app = app_class(ec)
 
@@ -467,7 +469,7 @@ def template_easyconfig_test(self, spec):
         if ec['toolchain']['version'] == 'system':
             binutils_complete_dependencies = ['M4', 'Bison', 'flex', 'help2man', 'zlib', 'binutils']
             requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies)
-            
+
         # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled)
         requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components'))
 
@@ -486,7 +488,7 @@ def template_easyconfig_test(self, spec):
             patch_full = os.path.join(specdir, patch)
             msg = "Patch file %s is available for %s" % (patch_full, specfn)
             self.assertTrue(os.path.isfile(patch_full), msg)
-    ext_patches = []
+
     for ext in ec['exts_list']:
         if isinstance(ext, (tuple, list)) and len(ext) == 3:
             self.assertTrue(isinstance(ext[2], dict), "3rd element of extension spec is a dictionary")
@@ -598,5 +600,6 @@ def suite():
     print "Found %s easyconfigs..." % cnt
     return TestLoader().loadTestsFromTestCase(EasyConfigTest)
 
+
 if __name__ == '__main__':
     main()