def suite():
"""Return all easyblock --module-only tests."""
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=['--prefix=%s' % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'external_modules_metadata': {},
# enable --force --module-only
'force': True,
'module_only': True,
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob('%s/*/*.py' % easyblocks_path)
easyblocks = [
eb for eb in all_pys
if os.path.basename(eb) != '__init__.py' and '/test/' not in eb
]
# filter out no longer supported easyblocks, or easyblocks that are tested in a different way
excluded_easyblocks = ['versionindependendpythonpackage.py']
easyblocks = [
e for e in easyblocks if os.path.basename(e) not in excluded_easyblocks
]
# add dummy PrgEnv-gnu/1.2.3 module, required for testing CrayToolchain easyblock
write_file(os.path.join(TMPDIR, 'modules', 'all', 'PrgEnv-gnu', '1.2.3'),
"#%Module")
for easyblock in easyblocks:
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
if os.path.basename(easyblock) == 'systemcompiler.py':
# use GCC as name when testing SystemCompiler easyblock
exec(
"def innertest(self): template_module_only_test(self, '%s', name='GCC', version='system')"
% easyblock)
elif os.path.basename(easyblock) == 'craytoolchain.py':
# make sure that a (known) PrgEnv is included as a dependency
extra_txt = 'dependencies = [("PrgEnv-gnu/1.2.3", EXTERNAL_MODULE)]'
exec(
"def innertest(self): template_module_only_test(self, '%s', extra_txt='%s')"
% (easyblock, extra_txt))
else:
exec("def innertest(self): template_module_only_test(self, '%s')" %
easyblock)
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % '_'.join(
easyblock.replace('.py', '').split('/'))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
def suite():
"""Return all easyblock --module-only tests."""
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=['--prefix=%s' % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'external_modules_metadata': {},
# enable --force --module-only
'force': True,
'module_only': True,
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob('%s/*/*.py' % easyblocks_path)
easyblocks = [eb for eb in all_pys if os.path.basename(eb) != '__init__.py' and '/test/' not in eb]
# filter out no longer supported easyblocks, or easyblocks that are tested in a different way
excluded_easyblocks = ['versionindependendpythonpackage.py']
easyblocks = [e for e in easyblocks if os.path.basename(e) not in excluded_easyblocks]
# add dummy PrgEnv-* modules, required for testing CrayToolchain easyblock
for prgenv in ['PrgEnv-cray', 'PrgEnv-gnu', 'PrgEnv-intel', 'PrgEnv-pgi']:
write_file(os.path.join(TMPDIR, 'modules', 'all', prgenv, '1.2.3'), "#%Module")
for easyblock in easyblocks:
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
if os.path.basename(easyblock) == 'systemcompiler.py':
# use GCC as name when testing SystemCompiler easyblock
exec("def innertest(self): template_module_only_test(self, '%s', name='GCC', version='system')" % easyblock)
elif os.path.basename(easyblock) == 'systemmpi.py':
# use OpenMPI as name when testing SystemMPI easyblock
exec("def innertest(self): template_module_only_test(self, '%s', name='OpenMPI', version='system')" %
easyblock)
elif os.path.basename(easyblock) == 'craytoolchain.py':
# make sure that a (known) PrgEnv is included as a dependency
extra_txt = 'dependencies = [("PrgEnv-gnu/1.2.3", EXTERNAL_MODULE)]'
exec("def innertest(self): template_module_only_test(self, '%s', extra_txt='%s')" % (easyblock, extra_txt))
else:
exec("def innertest(self): template_module_only_test(self, '%s')" % easyblock)
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % '_'.join(easyblock.replace('.py', '').split('/'))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
def suite():
"""Return all easyblock --module-only tests."""
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=['--prefix=%s' % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
# enable --force --module-only
'force': True,
'module_only': True,
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob('%s/*/*.py' % easyblocks_path)
easyblocks = [eb for eb in all_pys if os.path.basename(eb) != '__init__.py' and '/test/' not in eb]
# filter out no longer supported easyblocks, or easyblocks that are tested in a different way
excluded_easyblocks = ['versionindependendpythonpackage.py']
easyblocks = [e for e in easyblocks if os.path.basename(e) not in excluded_easyblocks]
for easyblock in easyblocks:
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
if os.path.basename(easyblock) == 'systemcompiler.py':
# use GCC as name when testing SystemCompiler easyblock
exec("def innertest(self): template_module_only_test(self, '%s', name='GCC', version='system')" % easyblock)
else:
exec("def innertest(self): template_module_only_test(self, '%s')" % easyblock)
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % '_'.join(easyblock.replace('.py', '').split('/'))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
class InitTest(TestCase):
""" Baseclass for easyblock testcases """
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
del eb_go
def write_ec(self,
easyblock,
name='foo',
version='1.3.2',
toolchain=None,
extratxt=''):
""" create temporary easyconfig file """
if toolchain is None:
toolchain = 'SYSTEM'
txt = '\n'.join([
'easyblock = "%s"',
'name = "%s"' % name,
'version = "%s"' % version,
'homepage = "http://example.com"',
'description = "Dummy easyconfig file."',
'toolchain = %s' % toolchain,
'sources = []',
extratxt,
])
write_file(self.eb_file, txt % easyblock)
def setUp(self):
"""Setup test."""
self.log = fancylogger.getLogger("EasyblocksInitTest", fname=False)
fd, self.eb_file = tempfile.mkstemp(prefix='easyblocks_init_test_',
suffix='.eb')
os.close(fd)
def tearDown(self):
"""Cleanup."""
try:
os.remove(self.eb_file)
except OSError as err:
self.log.error("Failed to remove %s: %s" % (self.eb_file, err))
def setUp(self):
"""Set up testcase."""
super(EnhancedTestCase, self).setUp()
# make sure option parser doesn't pick up any cmdline arguments/options
while len(sys.argv) > 1:
sys.argv.pop()
# keep track of log handlers
log = fancylogger.getLogger(fname=False)
self.orig_log_handlers = log.handlers[:]
log.info("setting up test %s" % self.id())
self.orig_tmpdir = tempfile.gettempdir()
# use a subdirectory for this test (which we can clean up easily after the test completes)
self.test_prefix = set_tmpdir()
self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
fd, self.logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')
os.close(fd)
self.cwd = os.getcwd()
# keep track of original environment to restore
self.orig_environ = copy.deepcopy(os.environ)
# keep track of original environment/Python search path to restore
self.orig_sys_path = sys.path[:]
testdir = os.path.dirname(os.path.abspath(__file__))
self.test_sourcepath = os.path.join(testdir, 'sandbox', 'sources')
os.environ['EASYBUILD_SOURCEPATH'] = self.test_sourcepath
os.environ['EASYBUILD_PREFIX'] = self.test_prefix
self.test_buildpath = tempfile.mkdtemp()
os.environ['EASYBUILD_BUILDPATH'] = self.test_buildpath
self.test_installpath = tempfile.mkdtemp()
os.environ['EASYBUILD_INSTALLPATH'] = self.test_installpath
# make sure that the tests only pick up easyconfigs provided with the tests
os.environ['EASYBUILD_ROBOT_PATHS'] = os.path.join(testdir, 'easyconfigs', 'test_ecs')
# make sure no deprecated behaviour is being triggered (unless intended by the test)
self.orig_current_version = eb_build_log.CURRENT_VERSION
self.disallow_deprecated_behaviour()
init_config()
import easybuild
# try to import easybuild.easyblocks(.generic) packages
# it's OK if it fails here, but important to import first before fiddling with sys.path
try:
import easybuild.easyblocks
import easybuild.easyblocks.generic
except ImportError:
pass
# add sandbox to Python search path, update namespace packages
sys.path.append(os.path.join(testdir, 'sandbox'))
# required to make sure the 'easybuild' dir in the sandbox is picked up;
# this relates to the other 'reload' statements below
reload(easybuild)
# required to 'reset' easybuild.tools.module_naming_scheme namespace
reload(easybuild.tools)
reload(easybuild.tools.module_naming_scheme)
# remove any entries in Python search path that seem to provide easyblocks (except the sandbox)
for path in sys.path[:]:
if os.path.exists(os.path.join(path, 'easybuild', 'easyblocks', '__init__.py')):
if not os.path.samefile(path, os.path.join(testdir, 'sandbox')):
sys.path.remove(path)
# hard inject location to (generic) test easyblocks into Python search path
# only prepending to sys.path is not enough due to 'pkgutil.extend_path' in easybuild/easyblocks/__init__.py
easybuild.__path__.insert(0, os.path.join(testdir, 'sandbox', 'easybuild'))
import easybuild.easyblocks
test_easyblocks_path = os.path.join(testdir, 'sandbox', 'easybuild', 'easyblocks')
easybuild.easyblocks.__path__.insert(0, test_easyblocks_path)
reload(easybuild.easyblocks)
import easybuild.easyblocks.generic
test_easyblocks_path = os.path.join(test_easyblocks_path, 'generic')
easybuild.easyblocks.generic.__path__.insert(0, test_easyblocks_path)
reload(easybuild.easyblocks.generic)
# save values of $PATH & $PYTHONPATH, so they can be restored later
# this is important in case EasyBuild was installed as a module, since that module may be unloaded,
# for example due to changes to $MODULEPATH in case EasyBuild was installed in a module hierarchy
# cfr. https://github.com/easybuilders/easybuild-framework/issues/1685
self.env_path = os.environ.get('PATH')
self.env_pythonpath = os.environ.get('PYTHONPATH')
self.modtool = modules_tool()
self.reset_modulepath([os.path.join(testdir, 'modules')])
reset_module_caches()
class EasyConfigTest(TestCase):
"""Baseclass for easyconfig testcases."""
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'check_osdeps': False,
'external_modules_metadata': {},
'force': True,
'optarch': 'test',
'robot_path': get_paths_for("easyconfigs")[0],
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
del eb_go
# put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains
TMPDIR = tempfile.mkdtemp()
os.environ['MODULEPATH'] = TMPDIR
write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n')
log = fancylogger.getLogger("EasyConfigTest", fname=False)
# make sure a logger is present for main
main._log = log
ordered_specs = None
parsed_easyconfigs = []
def process_all_easyconfigs(self):
"""Process all easyconfigs and resolve inter-easyconfig dependencies."""
# all available easyconfig files
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path)
# parse all easyconfigs if they haven't been already
if not self.parsed_easyconfigs:
for spec in specs:
self.parsed_easyconfigs.extend(process_easyconfig(spec))
# filter out external modules
for ec in self.parsed_easyconfigs:
for dep in ec['dependencies'][:]:
if dep.get('external_module', False):
ec['dependencies'].remove(dep)
self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs,
retain_all_deps=True)
def test_dep_graph(self):
"""Unit test that builds a full dependency graph."""
# pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6
if LooseVersion(
sys.version) >= LooseVersion('2.6') and single_tests_ok:
# temporary file for dep graph
(hn, fn) = tempfile.mkstemp(suffix='.dot')
os.close(hn)
if self.ordered_specs is None:
self.process_all_easyconfigs()
dep_graph(fn, self.ordered_specs)
try:
os.remove(fn)
except OSError, err:
log.error("Failed to remove %s: %s" % (fn, err))
else:
class EasyConfigTest(TestCase):
"""Baseclass for easyconfig testcases."""
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'check_osdeps': False,
'external_modules_metadata': {},
'force': True,
'optarch': 'test',
'robot_path': get_paths_for("easyconfigs")[0],
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
del eb_go
# put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains
TMPDIR = tempfile.mkdtemp()
os.environ['MODULEPATH'] = TMPDIR
write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n')
log = fancylogger.getLogger("EasyConfigTest", fname=False)
# make sure a logger is present for main
eb_main._log = log
ordered_specs = None
parsed_easyconfigs = []
def process_all_easyconfigs(self):
"""Process all easyconfigs and resolve inter-easyconfig dependencies."""
# all available easyconfig files
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path)
# parse all easyconfigs if they haven't been already
if not self.parsed_easyconfigs:
for spec in specs:
self.parsed_easyconfigs.extend(process_easyconfig(spec))
# filter out external modules
for ec in self.parsed_easyconfigs:
for dep in ec['dependencies'][:]:
if dep.get('external_module', False):
ec['dependencies'].remove(dep)
self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs,
modules_tool(),
retain_all_deps=True)
def test_dep_graph(self):
"""Unit test that builds a full dependency graph."""
# pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6
if LooseVersion(
sys.version) >= LooseVersion('2.6') and single_tests_ok:
# temporary file for dep graph
(hn, fn) = tempfile.mkstemp(suffix='.dot')
os.close(hn)
if self.ordered_specs is None:
self.process_all_easyconfigs()
dep_graph(fn, self.ordered_specs)
remove_file(fn)
else:
print "(skipped dep graph test)"
def test_conflicts(self):
"""Check whether any conflicts occur in software dependency graphs."""
if not single_tests_ok:
print "(skipped conflicts test)"
return
if self.ordered_specs is None:
self.process_all_easyconfigs()
self.assertFalse(
check_conflicts(self.ordered_specs,
modules_tool(),
check_inter_ec_conflicts=False),
"No conflicts detected")
def test_dep_versions_per_toolchain_generation(self):
"""
Check whether there's only one dependency version per toolchain generation actively used.
This is enforced to try and limit the chance of running into conflicts when multiple modules built with
the same toolchain are loaded together.
"""
if self.ordered_specs is None:
self.process_all_easyconfigs()
def get_deps_for(ec):
"""Get list of (direct) dependencies for specified easyconfig."""
deps = []
for dep in ec['ec']['dependencies']:
dep_mod_name = dep['full_mod_name']
deps.append((dep['name'], dep['version'], dep['versionsuffix'],
dep_mod_name))
res = [
x for x in self.ordered_specs
if x['full_mod_name'] == dep_mod_name
]
if len(res) == 1:
deps.extend(get_deps_for(res[0]))
else:
raise EasyBuildError(
"Failed to find %s in ordered list of easyconfigs",
dep_mod_name)
return deps
def check_dep_vars(dep, dep_vars):
"""Check whether available variants of a particular dependency are acceptable or not."""
# 'guilty' until proven 'innocent'
res = False
# filter out binutils with empty versionsuffix which is used to build toolchain compiler
if dep == 'binutils' and len(dep_vars) > 1:
empty_vsuff_vars = [
v for v in dep_vars.keys() if v.endswith('versionsuffix: ')
]
if len(empty_vsuff_vars) == 1:
dep_vars = dict((k, v) for (k, v) in dep_vars.items()
if k != empty_vsuff_vars[0])
# multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools
elif dep == 'HTSlib' and len(dep_vars) > 1:
for key, ecs in dep_vars.items():
# filter out HTSlib variants that are only used as dependency for BCFtools with same version
htslib_ver = re.search('^version: (?P<ver>[^;]+);',
key).group('ver')
if all(
ec.startswith('BCFtools-%s-' % htslib_ver)
for ec in ecs):
dep_vars.pop(key)
# filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains
elif dep in ['FFTW', 'imkl']:
serial_vsuff_vars = [
v for v in dep_vars.keys()
if v.endswith('versionsuffix: -serial')
]
if len(serial_vsuff_vars) == 1:
dep_vars = dict((k, v) for (k, v) in dep_vars.items()
if k != serial_vsuff_vars[0])
# for some dependencies, we allow exceptions for software that depends on a particular version,
# as long as that's indicated by the versionsuffix
elif dep in ['Boost', 'R', 'PLUMED'] and len(dep_vars) > 1:
for key in dep_vars.keys():
dep_ver = re.search('^version: (?P<ver>[^;]+);',
key).group('ver')
# filter out dep version if all easyconfig filenames using it include specific dep version
if all(
re.search('-%s-%s' % (dep, dep_ver), v)
for v in dep_vars[key]):
dep_vars.pop(key)
# always retain at least one dep variant
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:
key1, key2 = sorted(dep_vars.keys())
ver1, ver2 = [k.split(';')[0] for k in [key1, key2]]
if ver1.startswith(ver2):
dep_vars.pop(key2)
elif ver2.startswith(ver1):
dep_vars.pop(key1)
# filter out variants that are specific to a particular version of CUDA
cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v]
if len(dep_vars) > len(cuda_dep_vars):
for key in dep_vars.keys():
if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key):
dep_vars.pop(key)
# some software packages require an old version of a particular dependency
old_dep_versions = {
# libxc (CP2K & ABINIT require libxc 2.x or 3.x)
'libxc': r'[23]\.',
# OPERA requires SAMtools 0.x
'SAMtools': r'0\.',
# Kraken 1.0 requires Jellyfish 1.x
'Jellyfish': r'1\.',
}
if dep in old_dep_versions and len(dep_vars) > 1:
for key in dep_vars.keys():
# filter out known old dependency versions
if re.search('^version: %s' % old_dep_versions[dep], key):
dep_vars.pop(key)
# only single variant is always OK
if len(dep_vars) == 1:
res = True
elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']:
# for Python & Tkinter, it's OK to have on 2.x and one 3.x version
v2_dep_vars = [
x for x in dep_vars.keys() if x.startswith('version: 2.')
]
v3_dep_vars = [
x for x in dep_vars.keys() if x.startswith('version: 3.')
]
if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1:
res = True
# two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix)
elif len(dep_vars) == 2:
py2_dep_vars = [
x for x in dep_vars.keys()
if '; versionsuffix: -Python-2.' in x
]
py3_dep_vars = [
x for x in dep_vars.keys()
if '; versionsuffix: -Python-3.' in x
]
if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1:
res = True
return res
# some software also follows <year>{a,b} versioning scheme,
# which throws off the pattern matching done below for toolchain versions
false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]')
# restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a)
# and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x
for pattern in [
'201[89][ab]', '20[2-9][0-9][ab]', 'GCCcore-[7-9]\.[0-9]'
]:
all_deps = {}
regex = re.compile('^.*-(?P<tc_gen>%s).*\.eb$' % pattern)
# collect variants for all dependencies of easyconfigs that use a toolchain that matches
for ec in self.ordered_specs:
ec_file = os.path.basename(ec['spec'])
# take into account software which also follows a <year>{a,b} versioning scheme
ec_file = false_positives_regex.sub('', ec_file)
res = regex.match(ec_file)
if res:
tc_gen = res.group('tc_gen')
all_deps_tc_gen = all_deps.setdefault(tc_gen, {})
for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(
ec):
dep_variants = all_deps_tc_gen.setdefault(dep_name, {})
# a variant is defined by version + versionsuffix
variant = "version: %s; versionsuffix: %s" % (
dep_ver, dep_versuff)
# keep track of which easyconfig this is a dependency
dep_variants.setdefault(variant, set()).add(ec_file)
# check which dependencies have more than 1 variant
multi_dep_vars, multi_dep_vars_msg = [], ''
for tc_gen in sorted(all_deps.keys()):
for dep in sorted(all_deps[tc_gen].keys()):
dep_vars = all_deps[tc_gen][dep]
if not check_dep_vars(dep, dep_vars):
multi_dep_vars.append(dep)
multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (
len(dep_vars), dep)
multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen
multi_dep_vars_msg += '\n* '.join(
"%s as dep for %s" % v
for v in sorted(dep_vars.items()))
multi_dep_vars_msg += '\n'
error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (
regex.pattern, multi_dep_vars_msg)
self.assertFalse(multi_dep_vars, error_msg)
def test_sanity_check_paths(self):
"""Make sure specified sanity check paths adher to the requirements."""
if self.ordered_specs is None:
self.process_all_easyconfigs()
for ec in self.parsed_easyconfigs:
ec_scp = ec['ec']['sanity_check_paths']
if ec_scp != {}:
# if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements
# both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list
error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (
ec['spec'], ec_scp)
self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'],
error_msg)
self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg)
self.assertTrue(isinstance(ec_scp['files'], list), error_msg)
self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg)
def test_easyconfig_locations(self):
"""Make sure all easyconfigs files are in the right location."""
easyconfig_dirs_regex = re.compile(
r'/easybuild/easyconfigs/[0a-z]/[^/]+$')
topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
for (dirpath, _, filenames) in os.walk(topdir):
# ignore git/svn dirs & archived easyconfigs
if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath:
continue
# check whether list of .eb files is non-empty
easyconfig_files = [fn for fn in filenames if fn.endswith('eb')]
if easyconfig_files:
# check whether path matches required pattern
if not easyconfig_dirs_regex.search(dirpath):
# only exception: TEMPLATE.eb
if not (dirpath.endswith('/easybuild/easyconfigs')
and filenames == ['TEMPLATE.eb']):
self.assertTrue(
False,
"List of easyconfig files in %s is empty: %s" %
(dirpath, filenames))
def check_sha256_checksums(self, changed_ecs):
"""Make sure changed easyconfigs have SHA256 checksums in place."""
# list of software for which checksums can not be required,
# e.g. because 'source' files need to be constructed manually
whitelist = ['Kent_tools-*', 'MATLAB-*', 'OCaml-*']
# the check_sha256_checksums function (again) creates an EasyBlock instance
# for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter
# is updated in place (sources for components are added the 'parent' sources) in Bundle's __init__;
# therefore, we need to reset 'sources' to an empty list here if Bundle is used...
for ec in changed_ecs:
if ec['easyblock'] == 'Bundle':
ec['sources'] = []
# filter out deprecated easyconfigs
retained_changed_ecs = []
for ec in changed_ecs:
if not ec['deprecated']:
retained_changed_ecs.append(ec)
checksum_issues = check_sha256_checksums(retained_changed_ecs,
whitelist=whitelist)
self.assertTrue(
len(checksum_issues) == 0,
"No checksum issues:\n%s" % '\n'.join(checksum_issues))
def check_python_packages(self, changed_ecs):
"""Several checks for easyconfigs that install (bundles of) Python packages."""
# MATLAB-Engine, PyTorch do not support installation with 'pip'
whitelist_pip = ['MATLAB-Engine-*', 'PyTorch-*']
failing_checks = []
for ec in changed_ecs:
ec_fn = os.path.basename(ec.path)
easyblock = ec.get('easyblock')
exts_defaultclass = ec.get('exts_defaultclass')
download_dep_fail = ec.get('download_dep_fail')
exts_download_dep_fail = ec.get('exts_download_dep_fail')
use_pip = ec.get('use_pip')
# download_dep_fail should be set when using PythonPackage
if easyblock == 'PythonPackage':
if not download_dep_fail:
failing_checks.append("'download_dep_fail' set in %s" %
ec_fn)
# use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs)
if easyblock in ['PythonBundle', 'PythonPackage']:
if not use_pip and not any(
re.match(regex, ec_fn) for regex in whitelist_pip):
failing_checks.append("'use_pip' set in %s" % ec_fn)
# download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set
if easyblock == 'PythonBundle':
if download_dep_fail or exts_download_dep_fail:
fail = "'*download_dep_fail' set in %s (shouldn't, since PythonBundle easyblock is used)" % ec_fn
failing_checks.append(fail)
elif exts_defaultclass == 'PythonPackage':
# bundle of Python packages should use PythonBundle
if easyblock == 'Bundle':
fail = "'PythonBundle' easyblock is used for bundle of Python packages in %s" % ec_fn
failing_checks.append(fail)
else:
# both download_dep_fail and use_pip should be set via exts_default_options
# when installing Python packages as extensions
exts_default_options = ec.get('exts_default_options', {})
for key in ['download_dep_fail', 'use_pip']:
if not exts_default_options.get(key):
failing_checks.append(
"'%s' set in exts_default_options in %s" %
(key, ec_fn))
# if Python is a dependency, that should be reflected in the versionsuffix
if any(dep['name'] == 'Python' for dep in ec['dependencies']):
if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+',
ec['versionsuffix']):
failing_checks.append(
"'-Python-%%(pyver)s' included in versionsuffix in %s"
% ec_fn)
self.assertFalse(failing_checks, '\n'.join(failing_checks))
def test_changed_files_pull_request(self):
"""Specific checks only done for the (easyconfig) files that were changed in a pull request."""
# $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR
if re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST',
'(none)')):
# target branch should be anything other than 'master';
# usually is 'develop', but could also be a release branch like '3.7.x'
travis_branch = os.environ.get('TRAVIS_BRANCH', None)
if travis_branch and travis_branch != 'master':
if not self.parsed_easyconfigs:
self.process_all_easyconfigs()
# relocate to top-level directory of repository to run 'git diff' command
top_dir = os.path.dirname(
os.path.dirname(get_paths_for('easyconfigs')[0]))
cwd = change_dir(top_dir)
# get list of changed easyconfigs
cmd = "git diff --name-only --diff-filter=AM %s...HEAD" % travis_branch
out, ec = run_cmd(cmd, simple=False)
changed_ecs_filenames = [
os.path.basename(f) for f in out.strip().split('\n')
if f.endswith('.eb')
]
print("\nList of changed easyconfig files in this PR: %s" %
'\n'.join(changed_ecs_filenames))
change_dir(cwd)
# grab parsed easyconfigs for changed easyconfig files
changed_ecs = []
for ec_fn in changed_ecs_filenames:
match = None
for ec in self.parsed_easyconfigs:
if os.path.basename(ec['spec']) == ec_fn:
match = ec['ec']
break
if match:
changed_ecs.append(match)
else:
# if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR...
# so as a last resort, try to find the easyconfig file in __archive__
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/__archive__/*/*/%s' %
(easyconfigs_path, ec_fn))
if len(specs) == 1:
ec = process_easyconfig(specs[0])[0]
changed_ecs.append(ec['ec'])
else:
error_msg = "Failed to find parsed easyconfig for %s" % ec_fn
error_msg += " (and could not isolate it in easyconfigs archive either)"
self.assertTrue(False, error_msg)
# run checks on changed easyconfigs
self.check_sha256_checksums(changed_ecs)
self.check_python_packages(changed_ecs)
def test_zzz_cleanup(self):
"""Dummy test to clean up global temporary directory."""
shutil.rmtree(self.TMPDIR)
def test_toolchain_external_modules(self):
"""Test use of Toolchain easyblock with external modules."""
external_modules = [
'gcc/8.3.0', 'openmpi/4.0.2', 'openblas/0.3.7', 'fftw/3.3.8',
'scalapack/2.0.2'
]
external_modules_metadata = {
# all metadata for gcc/8.3.0
'gcc/8.3.0': {
'name': ['GCC'],
'version': ['8.3.0'],
'prefix': '/software/gcc/8.3.0',
},
# only name/version for openmpi/4.0.2
'openmpi/4.0.2': {
'name': ['OpenMPI'],
'version': ['4.0.2'],
},
# only name/prefix for openblas/0.3.7
'openblas/0.3.7': {
'name': ['OpenBLAS'],
'prefix': '/software/openblas/0.3.7',
},
# only version/prefix for fftw/3.3.8 (no name)
'fftw/3.3.8': {
'version': ['3.3.8'],
'prefix': '/software/fftw/3.3.8',
},
# no metadata for scalapack/2.0.2
}
# initialize configuration
cleanup()
eb_go = eboptions.parse_options(
args=['--installpath=%s' % self.tmpdir])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'external_modules_metadata': external_modules_metadata,
'valid_module_classes': config.module_classes(),
}
config.init_build_options(build_options=build_options)
set_tmpdir()
del eb_go
modtool = modules_tool()
# make sure no $EBROOT* or $EBVERSION* environment variables are set in current environment
for key in os.environ:
if any(key.startswith(x) for x in ['EBROOT', 'EBVERSION']):
del os.environ[key]
# create dummy module file for each of the external modules
test_mod_path = os.path.join(self.tmpdir, 'modules', 'all')
for mod in external_modules:
write_file(os.path.join(test_mod_path, mod), "#%Module")
modtool.use(test_mod_path)
# test easyconfig file to install toolchain that uses external modules,
# and enables set_env_external_modules
test_ec_path = os.path.join(self.tmpdir, 'test.eb')
test_ec_txt = '\n'.join([
"easyblock = 'Toolchain'",
"name = 'test-toolchain'",
"version = '1.2.3'",
"homepage = 'https://example.com'",
"description = 'just a test'",
"toolchain = SYSTEM",
"dependencies = [",
" ('gcc/8.3.0', EXTERNAL_MODULE),",
" ('openmpi/4.0.2', EXTERNAL_MODULE),",
" ('openblas/0.3.7', EXTERNAL_MODULE),",
" ('fftw/3.3.8', EXTERNAL_MODULE),",
" ('scalapack/2.0.2', EXTERNAL_MODULE),",
"]",
"set_env_external_modules = True",
"moduleclass = 'toolchain'",
])
write_file(test_ec_path, test_ec_txt)
test_ec = process_easyconfig(test_ec_path)[0]
# create easyblock & install module via run_all_steps
tc_inst = get_easyblock_instance(test_ec)
self.assertTrue(isinstance(tc_inst, Toolchain))
self.mock_stdout(True)
tc_inst.run_all_steps(False)
self.mock_stdout(False)
# make sure expected module file exists
test_mod = os.path.join(test_mod_path, 'test-toolchain', '1.2.3')
if get_module_syntax() == 'Lua':
test_mod += '.lua'
self.assertTrue(os.path.exists(test_mod))
# load test-toolchain/1.2.3 module to get environment variable to check for defined
modtool.load(['test-toolchain/1.2.3'])
# check whether expected environment variables are defined
self.assertEqual(os.environ.pop('EBROOTGCC'), '/software/gcc/8.3.0')
self.assertEqual(os.environ.pop('EBVERSIONGCC'), '8.3.0')
self.assertEqual(os.environ.pop('EBVERSIONOPENMPI'), '4.0.2')
self.assertEqual(os.environ.pop('EBROOTOPENBLAS'),
'/software/openblas/0.3.7')
undefined_env_vars = [
'EBROOTOPENMPI', # no prefix in metadata
'EBVERSIONOPENBLAS' # no version in metadata
'EBROOTFFTW',
'EBVERSIONFFTW', # no name in metadata
'EBROOTSCALAPACK',
'EBVERSIONSCALAPACK', # no metadata
]
for env_var in undefined_env_vars:
self.assertTrue(os.getenv(env_var) is None)
# make sure no unexpected $EBROOT* or $EBVERSION* environment variables were defined
del os.environ['EBROOTTESTMINTOOLCHAIN']
del os.environ['EBVERSIONTESTMINTOOLCHAIN']
extra_eb_env_vars = []
for key in os.environ:
if any(key.startswith(x) for x in ['EBROOT', 'EBVERSION']):
extra_eb_env_vars.append(key)
self.assertEqual(extra_eb_env_vars, [])
def setUp(self):
"""Set up testcase."""
super(EnhancedTestCase, self).setUp()
# keep track of log handlers
log = fancylogger.getLogger(fname=False)
self.orig_log_handlers = log.handlers[:]
log.info("setting up test %s" % self.id())
self.orig_tmpdir = tempfile.gettempdir()
# use a subdirectory for this test (which we can clean up easily after the test completes)
self.test_prefix = set_tmpdir()
self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
fd, self.logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')
os.close(fd)
self.cwd = os.getcwd()
# keep track of original environment to restore
self.orig_environ = copy.deepcopy(os.environ)
# keep track of original environment/Python search path to restore
self.orig_sys_path = sys.path[:]
testdir = os.path.dirname(os.path.abspath(__file__))
self.test_sourcepath = os.path.join(testdir, 'sandbox', 'sources')
os.environ['EASYBUILD_SOURCEPATH'] = self.test_sourcepath
os.environ['EASYBUILD_PREFIX'] = self.test_prefix
self.test_buildpath = tempfile.mkdtemp()
os.environ['EASYBUILD_BUILDPATH'] = self.test_buildpath
self.test_installpath = tempfile.mkdtemp()
os.environ['EASYBUILD_INSTALLPATH'] = self.test_installpath
# make sure that the tests only pick up easyconfigs provided with the tests
os.environ['EASYBUILD_ROBOT_PATHS'] = os.path.join(testdir, 'easyconfigs')
# make sure no deprecated behaviour is being triggered (unless intended by the test)
# trip *all* log.deprecated statements by setting deprecation version ridiculously high
self.orig_current_version = eb_build_log.CURRENT_VERSION
os.environ['EASYBUILD_DEPRECATED'] = '10000000'
init_config()
# remove any entries in Python search path that seem to provide easyblocks
for path in sys.path[:]:
if os.path.exists(os.path.join(path, 'easybuild', 'easyblocks', '__init__.py')):
sys.path.remove(path)
# add test easyblocks to Python search path and (re)import and reload easybuild modules
import easybuild
sys.path.append(os.path.join(testdir, 'sandbox'))
reload(easybuild)
import easybuild.easyblocks
reload(easybuild.easyblocks)
import easybuild.easyblocks.generic
reload(easybuild.easyblocks.generic)
reload(easybuild.tools.module_naming_scheme) # required to run options unit tests stand-alone
modtool = modules_tool()
# purge out any loaded modules with original $MODULEPATH before running each test
modtool.purge()
self.reset_modulepath([os.path.join(testdir, 'modules')])
def setUp(self):
"""Set up testcase."""
super(EnhancedTestCase, self).setUp()
# make sure option parser doesn't pick up any cmdline arguments/options
while len(sys.argv) > 1:
sys.argv.pop()
# keep track of log handlers
log = fancylogger.getLogger(fname=False)
self.orig_log_handlers = log.handlers[:]
log.info("setting up test %s" % self.id())
self.orig_tmpdir = tempfile.gettempdir()
# use a subdirectory for this test (which we can clean up easily after the test completes)
self.test_prefix = set_tmpdir()
self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
fd, self.logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')
os.close(fd)
self.cwd = os.getcwd()
# keep track of original environment to restore
self.orig_environ = copy.deepcopy(os.environ)
# keep track of original environment/Python search path to restore
self.orig_sys_path = sys.path[:]
testdir = os.path.dirname(os.path.abspath(__file__))
self.test_sourcepath = os.path.join(testdir, 'sandbox', 'sources')
os.environ['EASYBUILD_SOURCEPATH'] = self.test_sourcepath
os.environ['EASYBUILD_PREFIX'] = self.test_prefix
self.test_buildpath = tempfile.mkdtemp()
os.environ['EASYBUILD_BUILDPATH'] = self.test_buildpath
self.test_installpath = tempfile.mkdtemp()
os.environ['EASYBUILD_INSTALLPATH'] = self.test_installpath
# make sure that the tests only pick up easyconfigs provided with the tests
os.environ['EASYBUILD_ROBOT_PATHS'] = os.path.join(testdir, 'easyconfigs')
# make sure no deprecated behaviour is being triggered (unless intended by the test)
# trip *all* log.deprecated statements by setting deprecation version ridiculously high
self.orig_current_version = eb_build_log.CURRENT_VERSION
os.environ['EASYBUILD_DEPRECATED'] = '10000000'
init_config()
import easybuild
# try to import easybuild.easyblocks(.generic) packages
# it's OK if it fails here, but important to import first before fiddling with sys.path
try:
import easybuild.easyblocks
import easybuild.easyblocks.generic
except ImportError:
pass
# add sandbox to Python search path, update namespace packages
sys.path.append(os.path.join(testdir, 'sandbox'))
# workaround for bug in recent setuptools version (19.4 and newer, atleast until 20.3.1)
# injecting <prefix>/easybuild is required to avoid a ValueError being thrown by fixup_namespace_packages
# cfr. https://bitbucket.org/pypa/setuptools/issues/520/fixup_namespace_packages-may-trigger
for path in sys.path[:]:
if os.path.exists(os.path.join(path, 'easybuild', 'easyblocks', '__init__.py')):
# keep track of 'easybuild' paths to inject into sys.path later
sys.path.append(os.path.join(path, 'easybuild'))
# required to make sure the 'easybuild' dir in the sandbox is picked up;
# this relates to the other 'reload' statements below
reload(easybuild)
# this is strictly required to make the test modules in the sandbox available, due to declare_namespace
fixup_namespace_packages(os.path.join(testdir, 'sandbox'))
# remove any entries in Python search path that seem to provide easyblocks (except the sandbox)
for path in sys.path[:]:
if os.path.exists(os.path.join(path, 'easybuild', 'easyblocks', '__init__.py')):
if not os.path.samefile(path, os.path.join(testdir, 'sandbox')):
sys.path.remove(path)
# hard inject location to (generic) test easyblocks into Python search path
# only prepending to sys.path is not enough due to 'declare_namespace' in easybuild/easyblocks/__init__.py
import easybuild.easyblocks
reload(easybuild.easyblocks)
test_easyblocks_path = os.path.join(testdir, 'sandbox', 'easybuild', 'easyblocks')
easybuild.easyblocks.__path__.insert(0, test_easyblocks_path)
import easybuild.easyblocks.generic
reload(easybuild.easyblocks.generic)
test_easyblocks_path = os.path.join(test_easyblocks_path, 'generic')
easybuild.easyblocks.generic.__path__.insert(0, test_easyblocks_path)
# save values of $PATH & $PYTHONPATH, so they can be restored later
# this is important in case EasyBuild was installed as a module, since that module may be unloaded,
# for example due to changes to $MODULEPATH in case EasyBuild was installed in a module hierarchy
# cfr. https://github.com/hpcugent/easybuild-framework/issues/1685
self.env_path = os.environ['PATH']
self.env_pythonpath = os.environ['PYTHONPATH']
self.modtool = modules_tool()
self.reset_modulepath([os.path.join(testdir, 'modules')])
reset_module_caches()
import test.framework.repository as r
import test.framework.robot as robot
import test.framework.run as run
import test.framework.scripts as sc
import test.framework.systemtools as s
import test.framework.toolchain as tc
import test.framework.toolchainvariables as tcv
import test.framework.toy_build as t
import test.framework.type_checking as et
import test.framework.tweak as tw
import test.framework.variables as v
import test.framework.yeb as y
# make sure temporary files can be created/used
try:
set_tmpdir(raise_error=True)
except EasyBuildError, err:
sys.stderr.write(
"No execution rights on temporary files, specify another location via $TMPDIR: %s\n"
% err)
sys.exit(1)
# initialize logger for all the unit tests
fd, log_fn = tempfile.mkstemp(prefix='easybuild-tests-', suffix='.log')
os.close(fd)
os.remove(log_fn)
fancylogger.logToFile(log_fn)
log = fancylogger.getLogger()
# call suite() for each module and then run them all
# note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
def suite():
"""Return all easyblock --module-only tests."""
def make_inner_test(easyblock, **kwargs):
def innertest(self):
template_module_only_test(self, easyblock, **kwargs)
return innertest
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=['--prefix=%s' % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'external_modules_metadata': {},
# enable --force --module-only
'force': True,
'module_only': True,
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob('%s/*/*.py' % easyblocks_path)
easyblocks = [
eb for eb in all_pys
if os.path.basename(eb) != '__init__.py' and '/test/' not in eb
]
# filter out no longer supported easyblocks, or easyblocks that are tested in a different way
excluded_easyblocks = ['versionindependendpythonpackage.py']
easyblocks = [
e for e in easyblocks if os.path.basename(e) not in excluded_easyblocks
]
# add dummy PrgEnv-* modules, required for testing CrayToolchain easyblock
for prgenv in ['PrgEnv-cray', 'PrgEnv-gnu', 'PrgEnv-intel', 'PrgEnv-pgi']:
write_file(os.path.join(TMPDIR, 'modules', 'all', prgenv, '1.2.3'),
"#%Module")
# add foo/1.3.2.1.1 module, required for testing ModuleAlias easyblock
write_file(os.path.join(TMPDIR, 'modules', 'all', 'foo', '1.2.3.4.5'),
"#%Module")
for easyblock in easyblocks:
eb_fn = os.path.basename(easyblock)
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
if eb_fn == 'systemcompiler.py':
# use GCC as name when testing SystemCompiler easyblock
innertest = make_inner_test(easyblock,
name='GCC',
version='system')
elif eb_fn == 'systemmpi.py':
# use OpenMPI as name when testing SystemMPI easyblock
innertest = make_inner_test(easyblock,
name='OpenMPI',
version='system')
elif eb_fn == 'craytoolchain.py':
# make sure that a (known) PrgEnv is included as a dependency
extra_txt = 'dependencies = [("PrgEnv-gnu/1.2.3", EXTERNAL_MODULE)]'
innertest = make_inner_test(easyblock,
name='CrayCC',
extra_txt=extra_txt)
elif eb_fn == 'modulerc.py':
# exactly one dependency is included with ModuleRC generic easyblock (and name must match)
extra_txt = 'dependencies = [("foo", "1.2.3.4.5")]'
innertest = make_inner_test(easyblock,
name='foo',
version='1.2.3.4',
extra_txt=extra_txt)
elif eb_fn == 'intel_compilers.py':
# custom easyblock for intel-compilers (oneAPI) requires v2021.x or newer
innertest = make_inner_test(easyblock,
name='intel-compilers',
version='2021.1')
elif eb_fn == 'openssl_wrapper.py':
# easyblock to create OpenSSL wrapper expects an OpenSSL version
innertest = make_inner_test(easyblock,
name='OpenSSL-wrapper',
version='1.1')
elif eb_fn == 'ucx_plugins.py':
# install fake ucx_info command (used in make_module_extra)
tmpdir = tempfile.mkdtemp()
install_fake_command('ucx_info', FAKE_UCX_INFO, tmpdir)
innertest = make_inner_test(easyblock,
name='UCX-CUDA',
tmpdir=tmpdir)
else:
# Make up some unique name
innertest = make_inner_test(easyblock,
name=eb_fn.replace('.', '-') + '-sw')
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % '_'.join(
easyblock.replace('.py', '').split('/'))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
class EasyConfigTest(TestCase):
"""Baseclass for easyconfig testcases."""
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'check_osdeps': False,
'external_modules_metadata': {},
'force': True,
'local_var_naming_check': 'error',
'optarch': 'test',
'robot_path': get_paths_for("easyconfigs")[0],
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
del eb_go
# put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains
TMPDIR = tempfile.mkdtemp()
os.environ['MODULEPATH'] = TMPDIR
write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n')
log = fancylogger.getLogger("EasyConfigTest", fname=False)
# make sure a logger is present for main
eb_main._log = log
ordered_specs = None
parsed_easyconfigs = []
def process_all_easyconfigs(self):
"""Process all easyconfigs and resolve inter-easyconfig dependencies."""
# all available easyconfig files
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path)
# parse all easyconfigs if they haven't been already
if not EasyConfigTest.parsed_easyconfigs:
for spec in specs:
EasyConfigTest.parsed_easyconfigs.extend(process_easyconfig(spec))
# filter out external modules
for ec in EasyConfigTest.parsed_easyconfigs:
for dep in ec['dependencies'][:]:
if dep.get('external_module', False):
ec['dependencies'].remove(dep)
EasyConfigTest.ordered_specs = resolve_dependencies(EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
def test_dep_graph(self):
"""Unit test that builds a full dependency graph."""
# pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6
if LooseVersion(sys.version) >= LooseVersion('2.6') and single_tests_ok:
# temporary file for dep graph
(hn, fn) = tempfile.mkstemp(suffix='.dot')
os.close(hn)
if EasyConfigTest.ordered_specs is None:
self.process_all_easyconfigs()
dep_graph(fn, EasyConfigTest.ordered_specs)
remove_file(fn)
else:
print("(skipped dep graph test)")
def test_conflicts(self):
"""Check whether any conflicts occur in software dependency graphs."""
if not single_tests_ok:
print("(skipped conflicts test)")
return
if EasyConfigTest.ordered_specs is None:
self.process_all_easyconfigs()
self.assertFalse(check_conflicts(EasyConfigTest.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
"No conflicts detected")
def check_dep_vars(self, dep, dep_vars):
"""Check whether available variants of a particular dependency are acceptable or not."""
# 'guilty' until proven 'innocent'
res = False
# filter out wrapped Java versions
# 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)
if dep == 'Java':
dep_vars_to_check = sorted(dep_vars.keys())
retained_dep_vars = []
while dep_vars_to_check:
dep_var = dep_vars_to_check.pop()
dep_var_version = dep_var.split(';')[0]
# remove dep vars wrapped by current dep var
dep_vars_to_check = [x for x in dep_vars_to_check if not x.startswith(dep_var_version + '.')]
retained_dep_vars = [x for x in retained_dep_vars if not x.startswith(dep_var_version + '.')]
retained_dep_vars.append(dep_var)
for key in list(dep_vars.keys()):
if key not in retained_dep_vars:
del dep_vars[key]
# filter out binutils with empty versionsuffix which is used to build toolchain compiler
if dep == 'binutils' and len(dep_vars) > 1:
empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')]
if len(empty_vsuff_vars) == 1:
dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0])
# multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools;
# same goes for WRF and WPS
for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS')]:
if dep == dep_name and len(dep_vars) > 1:
for key in list(dep_vars):
ecs = dep_vars[key]
# filter out dep variants that are only used as dependency for parent with same version
dep_ver = re.search('^version: (?P<ver>[^;]+);', key).group('ver')
if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1:
dep_vars.pop(key)
# multiple versions of Boost is OK as long as they are deps for a matching Boost.Python
if dep == 'Boost' and len(dep_vars) > 1:
for key in list(dep_vars):
ecs = dep_vars[key]
# filter out Boost variants that are only used as dependency for Boost.Python with same version
boost_ver = re.search('^version: (?P<ver>[^;]+);', key).group('ver')
if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs):
dep_vars.pop(key)
# filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains
if dep in ['FFTW', 'imkl']:
serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')]
if len(serial_vsuff_vars) == 1:
dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0])
# for some dependencies, we allow exceptions for software that depends on a particular version,
# as long as that's indicated by the versionsuffix
if dep in ['ASE', 'Boost', 'Java', 'Lua', 'PLUMED', 'R', 'TensorFlow'] and len(dep_vars) > 1:
for key in list(dep_vars):
dep_ver = re.search('^version: (?P<ver>[^;]+);', key).group('ver')
# use version of Java wrapper rather than full Java version
if dep == 'Java':
dep_ver = '.'.join(dep_ver.split('.')[:2])
# filter out dep version if all easyconfig filenames using it include specific dep version
if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]):
dep_vars.pop(key)
# always retain at least one dep variant
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 list(dep_vars):
if '; versionsuffix: -Python-2' in key:
dep_vars.pop(key)
# always retain at least one variant
if len(dep_vars) == 1:
break
# filter out variants that are specific to a particular version of CUDA
cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v]
if len(dep_vars) > len(cuda_dep_vars):
for key in list(dep_vars):
if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key):
dep_vars.pop(key)
# some software packages require an old version of a particular dependency
old_dep_versions = {
# libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k
# (Qiskit depends on PySCF)
'libxc': (r'[23]\.', ['ABINIT-', 'AtomPAW-', 'CP2K-', 'GPAW-', 'horton-', 'PySCF-', 'Qiskit-', 'WIEN2k-']),
# OPERA requires SAMtools 0.x
'SAMtools': (r'0\.', ['ChimPipe-0.9.5', 'Cufflinks-2.2.1', 'OPERA-2.0.6']),
# Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x)
'Jellyfish': (r'1\.', ['Kraken-1.', 'Roary-3.12.0', 'metaWRAP-1.2']),
# EMAN2 2.3 requires Boost(.Python) 1.64.0
'Boost': ('1.64.0;', ['Boost.Python-1.64.0-', 'EMAN2-2.3-']),
'Boost.Python': ('1.64.0;', ['EMAN2-2.3-']),
}
if dep in old_dep_versions and len(dep_vars) > 1:
for key in list(dep_vars):
version_pattern, parents = old_dep_versions[dep]
# filter out known old dependency versions
if re.search('^version: %s' % version_pattern, key):
# only filter if the easyconfig using this dep variants is known
if all(any(x.startswith(p) for p in parents) for x in dep_vars[key]):
dep_vars.pop(key)
# only single variant is always OK
if len(dep_vars) == 1:
res = True
elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']:
# for Python & Tkinter, it's OK to have on 2.x and one 3.x version
v2_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 2.')]
v3_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 3.')]
if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1:
res = True
# two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix)
elif len(dep_vars) == 2:
py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x]
py3_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-3.' in x]
if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1:
res = True
return res
def test_check_dep_vars(self):
"""Test check_dep_vars utility method."""
# one single dep version: OK
self.assertTrue(self.check_dep_vars('testdep', {
'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb', 'bar-4.5.6.eb'],
}))
self.assertTrue(self.check_dep_vars('testdep', {
'version: 1.2.3; versionsuffix: -test': ['foo-1.2.3.eb', 'bar-4.5.6.eb'],
}))
# two or more dep versions (no special case: not OK)
self.assertFalse(self.check_dep_vars('testdep', {
'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'],
'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'],
}))
self.assertFalse(self.check_dep_vars('testdep', {
'version: 0.0; versionsuffix:': ['foobar-0.0.eb'],
'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'],
'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'],
}))
# Java is a special case, with wrapped Java versions
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
}))
# two Java wrappers is not OK
self.assertFalse(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6.eb'],
}))
# OK to have two or more wrappers if versionsuffix is used to indicate exception
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
}))
# versionsuffix must be there for all easyconfigs to indicate exception
self.assertFalse(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'],
}))
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
'version: 12.1.6; versionsuffix:': ['foobar-0.0-Java-12.eb'],
'version: 12; versionsuffix:': ['foobar-0.0-Java-12.eb'],
}))
# strange situation: odd number of Java versions
# not OK: two Java wrappers (and no versionsuffix to indicate exception)
self.assertFalse(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6.eb'],
}))
# OK because of -Java-11 versionsuffix
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
}))
# not OK: two Java wrappers (and no versionsuffix to indicate exception)
self.assertFalse(self.check_dep_vars('Java', {
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6.eb'],
}))
# OK because of -Java-11 versionsuffix
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
}))
# two different versions of Boost is not OK
self.assertFalse(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'],
}))
# a different Boost version that is only used as dependency for a matching Boost.Python is fine
self.assertTrue(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'],
'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'],
}))
self.assertTrue(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018b.eb'],
'version: 1.66.0; versionsuffix:': ['Boost.Python-1.66.0-gompi-2019a.eb'],
'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'],
}))
self.assertFalse(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'],
'version: 1.66.0; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'],
}))
self.assertTrue(self.check_dep_vars('Boost', {
'version: 1.63.0; versionsuffix: -Python-2.7.14': ['EMAN2-2.21a-foss-2018a-Python-2.7.14-Boost-1.63.0.eb'],
'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018a.eb'],
'version: 1.66.0; versionsuffix:': ['BLAST+-2.7.1-foss-2018a.eb'],
}))
self.assertTrue(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': [
'Boost.Python-1.64.0-gompi-2019a.eb',
'EMAN2-2.3-foss-2019a-Python-2.7.15.eb',
],
'version: 1.70.0; versionsuffix:': [
'BLAST+-2.9.0-gompi-2019a.eb',
'Boost.Python-1.70.0-gompi-2019a.eb',
],
}))
def test_dep_versions_per_toolchain_generation(self):
"""
Check whether there's only one dependency version per toolchain generation actively used.
This is enforced to try and limit the chance of running into conflicts when multiple modules built with
the same toolchain are loaded together.
"""
if EasyConfigTest.ordered_specs is None:
self.process_all_easyconfigs()
def get_deps_for(ec):
"""Get list of (direct) dependencies for specified easyconfig."""
deps = []
for dep in ec['ec']['dependencies']:
dep_mod_name = dep['full_mod_name']
deps.append((dep['name'], dep['version'], dep['versionsuffix'], dep_mod_name))
res = [x for x in EasyConfigTest.ordered_specs if x['full_mod_name'] == dep_mod_name]
if len(res) == 1:
deps.extend(get_deps_for(res[0]))
else:
raise EasyBuildError("Failed to find %s in ordered list of easyconfigs", dep_mod_name)
return deps
# some software also follows <year>{a,b} versioning scheme,
# which throws off the pattern matching done below for toolchain versions
false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]')
# restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a)
# and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x
for pattern in ['201[89][ab]', '20[2-9][0-9][ab]', 'GCCcore-[7-9]\.[0-9]']:
all_deps = {}
regex = re.compile('^.*-(?P<tc_gen>%s).*\.eb$' % pattern)
# collect variants for all dependencies of easyconfigs that use a toolchain that matches
for ec in EasyConfigTest.ordered_specs:
ec_file = os.path.basename(ec['spec'])
# take into account software which also follows a <year>{a,b} versioning scheme
ec_file = false_positives_regex.sub('', ec_file)
res = regex.match(ec_file)
if res:
tc_gen = res.group('tc_gen')
all_deps_tc_gen = all_deps.setdefault(tc_gen, {})
for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(ec):
dep_variants = all_deps_tc_gen.setdefault(dep_name, {})
# a variant is defined by version + versionsuffix
variant = "version: %s; versionsuffix: %s" % (dep_ver, dep_versuff)
# keep track of which easyconfig this is a dependency
dep_variants.setdefault(variant, set()).add(ec_file)
# check which dependencies have more than 1 variant
multi_dep_vars, multi_dep_vars_msg = [], ''
for tc_gen in sorted(all_deps.keys()):
for dep in sorted(all_deps[tc_gen].keys()):
dep_vars = all_deps[tc_gen][dep]
if not self.check_dep_vars(dep, dep_vars):
multi_dep_vars.append(dep)
multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (len(dep_vars), dep)
multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen
multi_dep_vars_msg += '\n* '.join("%s as dep for %s" % v for v in sorted(dep_vars.items()))
multi_dep_vars_msg += '\n'
error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (regex.pattern, multi_dep_vars_msg)
self.assertFalse(multi_dep_vars, error_msg)
def test_sanity_check_paths(self):
"""Make sure specified sanity check paths adher to the requirements."""
if EasyConfigTest.ordered_specs is None:
self.process_all_easyconfigs()
for ec in EasyConfigTest.parsed_easyconfigs:
ec_scp = ec['ec']['sanity_check_paths']
if ec_scp != {}:
# if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements
# both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list
error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (ec['spec'], ec_scp)
self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'], error_msg)
self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg)
self.assertTrue(isinstance(ec_scp['files'], list), error_msg)
self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg)
def test_easyconfig_locations(self):
"""Make sure all easyconfigs files are in the right location."""
easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$')
topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
for (dirpath, _, filenames) in os.walk(topdir):
# ignore git/svn dirs & archived easyconfigs
if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath:
continue
# check whether list of .eb files is non-empty
easyconfig_files = [fn for fn in filenames if fn.endswith('eb')]
if easyconfig_files:
# check whether path matches required pattern
if not easyconfig_dirs_regex.search(dirpath):
# only exception: TEMPLATE.eb
if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']):
self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames))
def check_sha256_checksums(self, changed_ecs):
"""Make sure changed easyconfigs have SHA256 checksums in place."""
# list of software for which checksums can not be required,
# e.g. because 'source' files need to be constructed manually
whitelist = ['Kent_tools-*', 'MATLAB-*', 'OCaml-*']
# the check_sha256_checksums function (again) creates an EasyBlock instance
# for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter
# is updated in place (sources for components are added the 'parent' sources) in Bundle's __init__;
# therefore, we need to reset 'sources' to an empty list here if Bundle is used...
# likewise for 'patches' and 'checksums'
for ec in changed_ecs:
if ec['easyblock'] == 'Bundle':
ec['sources'] = []
ec['patches'] = []
ec['checksums'] = []
# filter out deprecated easyconfigs
retained_changed_ecs = []
for ec in changed_ecs:
if not ec['deprecated']:
retained_changed_ecs.append(ec)
checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist)
self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues))
def check_python_packages(self, changed_ecs, added_ecs_filenames):
"""Several checks for easyconfigs that install (bundles of) Python packages."""
# These packages do not support installation with 'pip'
whitelist_pip = [r'MATLAB-Engine-.*', r'PyTorch-.*', r'Meld-.*']
failing_checks = []
for ec in changed_ecs:
ec_fn = os.path.basename(ec.path)
easyblock = ec.get('easyblock')
exts_defaultclass = ec.get('exts_defaultclass')
exts_default_options = ec.get('exts_default_options', {})
download_dep_fail = ec.get('download_dep_fail')
exts_download_dep_fail = ec.get('exts_download_dep_fail')
use_pip = ec.get('use_pip')
# download_dep_fail should be set when using PythonPackage
if easyblock == 'PythonPackage':
if download_dep_fail is None:
failing_checks.append("'download_dep_fail' set in %s" % ec_fn)
# use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs)
if easyblock in ['PythonBundle', 'PythonPackage']:
if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip):
failing_checks.append("'use_pip' set in %s" % ec_fn)
# download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set
if easyblock == 'PythonBundle':
if download_dep_fail or exts_download_dep_fail:
fail = "'*download_dep_fail' set in %s (shouldn't, since PythonBundle easyblock is used)" % ec_fn
failing_checks.append(fail)
elif exts_defaultclass == 'PythonPackage':
# bundle of Python packages should use PythonBundle
if easyblock == 'Bundle':
fail = "'PythonBundle' easyblock is used for bundle of Python packages in %s" % ec_fn
failing_checks.append(fail)
else:
# both download_dep_fail and use_pip should be set via exts_default_options
# when installing Python packages as extensions
for key in ['download_dep_fail', 'use_pip']:
if exts_default_options.get(key) is None:
failing_checks.append("'%s' set in exts_default_options in %s" % (key, ec_fn))
# if Python is a dependency, that should be reflected in the versionsuffix
# Tkinter is an exception, since its version always matches the Python version anyway
if any(dep['name'] == 'Python' for dep in ec['dependencies']) and ec.name != 'Tkinter':
if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']):
msg = "'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn
# This is only a failure for newly added ECs, not for existing ECS
# As that would probably break many ECs
if ec_fn in added_ecs_filenames:
failing_checks.append(msg)
else:
print('\nNote: Failed non-critical check: ' + msg)
# require that running of "pip check" during sanity check is enabled via sanity_pip_check
if use_pip and easyblock in ['PythonBundle', 'PythonPackage']:
sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check')
if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip):
failing_checks.append("sanity_pip_check is enabled in %s" % ec_fn)
self.assertFalse(failing_checks, '\n'.join(failing_checks))
def check_sanity_check_paths(self, changed_ecs):
"""Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock."""
# PythonBundle & PythonPackage already have a decent customised sanity_check_paths
# BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check.
whitelist = ['CrayToolchain', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain', 'BuildEnv']
# Autotools & (recent) GCC are just bundles (Autotools: Autoconf+Automake+libtool, GCC: GCCcore+binutils)
bundles_whitelist = ['Autotools', 'GCC']
failing_checks = []
for ec in changed_ecs:
easyblock = ec.get('easyblock')
if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'):
if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist):
pass
else:
ec_fn = os.path.basename(ec.path)
failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn)
self.assertFalse(failing_checks, '\n'.join(failing_checks))
def check_https(self, changed_ecs):
"""Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://)."""
whitelist = [
'Kaiju', # invalid certificate at https://kaiju.binf.ku.dk
'libxml2', # https://xmlsoft.org works, but invalid certificate
'p4vasp', # https://www.p4vasp.at doesn't work
'ITSTool', # https://itstool.org/ doesn't work
'UCX-', # bad certificate for https://www.openucx.org
]
http_regex = re.compile('http://[^"\'\n]+', re.M)
failing_checks = []
for ec in changed_ecs:
ec_fn = os.path.basename(ec.path)
# skip whitelisted easyconfigs
if any(ec_fn.startswith(x) for x in whitelist):
continue
# ignore commented out lines in easyconfig files when checking for http:// URLs
ec_txt = '\n'.join(l for l in ec.rawtxt.split('\n') if not l.startswith('#'))
for http_url in http_regex.findall(ec_txt):
https_url = http_url.replace('http://', 'https://')
try:
https_url_works = bool(urlopen(https_url, timeout=5))
except Exception:
https_url_works = False
if https_url_works:
failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url))
self.assertFalse(failing_checks, '\n'.join(failing_checks))
def test_changed_files_pull_request(self):
"""Specific checks only done for the (easyconfig) files that were changed in a pull request."""
def get_eb_files_from_diff(diff_filter):
cmd = "git diff --name-only --diff-filter=%s %s...HEAD" % (diff_filter, target_branch)
out, ec = run_cmd(cmd, simple=False)
return [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')]
# $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR
travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '(none)'))
# when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request'
github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request'
if travis_pr_test or github_pr_test:
# target branch should be anything other than 'master';
# usually is 'develop', but could also be a release branch like '3.7.x'
if travis_pr_test:
target_branch = os.environ.get('TRAVIS_BRANCH', None)
else:
target_branch = os.environ.get('GITHUB_BASE_REF', None)
if target_branch is None:
self.assertTrue(False, "Failed to determine target branch for current pull request.")
if target_branch != 'master':
if not EasyConfigTest.parsed_easyconfigs:
self.process_all_easyconfigs()
# relocate to top-level directory of repository to run 'git diff' command
top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0]))
cwd = change_dir(top_dir)
# get list of changed easyconfigs
changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M')
added_ecs_filenames = get_eb_files_from_diff(diff_filter='A')
if changed_ecs_filenames:
print("\nList of changed easyconfig files in this PR: %s" % '\n'.join(changed_ecs_filenames))
if added_ecs_filenames:
print("\nList of added easyconfig files in this PR: %s" % '\n'.join(added_ecs_filenames))
change_dir(cwd)
# grab parsed easyconfigs for changed easyconfig files
changed_ecs = []
for ec_fn in changed_ecs_filenames + added_ecs_filenames:
match = None
for ec in EasyConfigTest.parsed_easyconfigs:
if os.path.basename(ec['spec']) == ec_fn:
match = ec['ec']
break
if match:
changed_ecs.append(match)
else:
# if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR...
# so as a last resort, try to find the easyconfig file in __archive__
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn))
if len(specs) == 1:
ec = process_easyconfig(specs[0])[0]
changed_ecs.append(ec['ec'])
else:
error_msg = "Failed to find parsed easyconfig for %s" % ec_fn
error_msg += " (and could not isolate it in easyconfigs archive either)"
self.assertTrue(False, error_msg)
# run checks on changed easyconfigs
self.check_sha256_checksums(changed_ecs)
self.check_python_packages(changed_ecs, added_ecs_filenames)
self.check_sanity_check_paths(changed_ecs)
self.check_https(changed_ecs)
def test_zzz_cleanup(self):
"""Dummy test to clean up global temporary directory."""
shutil.rmtree(self.TMPDIR)
import test.framework.run as run
import test.framework.scripts as sc
import test.framework.style as st
import test.framework.systemtools as s
import test.framework.toolchain as tc
import test.framework.toolchainvariables as tcv
import test.framework.toy_build as t
import test.framework.type_checking as et
import test.framework.tweak as tw
import test.framework.variables as v
import test.framework.yeb as y
# make sure temporary files can be created/used
try:
set_tmpdir(raise_error=True)
except EasyBuildError, err:
sys.stderr.write("No execution rights on temporary files, specify another location via $TMPDIR: %s\n" % err)
sys.exit(1)
# initialize logger for all the unit tests
fd, log_fn = tempfile.mkstemp(prefix='easybuild-tests-', suffix='.log')
os.close(fd)
os.remove(log_fn)
fancylogger.logToFile(log_fn)
log = fancylogger.getLogger()
# call suite() for each module and then run them all
# note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
tests = [gen, bl, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc,
tw, p, i, pkg, d, env, et, y, st]
def setUp(self):
"""Set up testcase."""
super(EnhancedTestCase, self).setUp()
# make sure option parser doesn't pick up any cmdline arguments/options
while len(sys.argv) > 1:
sys.argv.pop()
# keep track of log handlers
log = fancylogger.getLogger(fname=False)
self.orig_log_handlers = log.handlers[:]
log.info("setting up test %s" % self.id())
self.orig_tmpdir = tempfile.gettempdir()
# use a subdirectory for this test (which we can clean up easily after the test completes)
self.test_prefix = set_tmpdir()
self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
fd, self.logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')
os.close(fd)
self.cwd = os.getcwd()
# keep track of original environment to restore
self.orig_environ = copy.deepcopy(os.environ)
# keep track of original environment/Python search path to restore
self.orig_sys_path = sys.path[:]
testdir = os.path.dirname(os.path.abspath(__file__))
self.test_sourcepath = os.path.join(testdir, 'sandbox', 'sources')
os.environ['EASYBUILD_SOURCEPATH'] = self.test_sourcepath
os.environ['EASYBUILD_PREFIX'] = self.test_prefix
self.test_buildpath = tempfile.mkdtemp()
os.environ['EASYBUILD_BUILDPATH'] = self.test_buildpath
self.test_installpath = tempfile.mkdtemp()
os.environ['EASYBUILD_INSTALLPATH'] = self.test_installpath
# make sure that the tests only pick up easyconfigs provided with the tests
os.environ['EASYBUILD_ROBOT_PATHS'] = os.path.join(
testdir, 'easyconfigs')
# make sure no deprecated behaviour is being triggered (unless intended by the test)
# trip *all* log.deprecated statements by setting deprecation version ridiculously high
self.orig_current_version = eb_build_log.CURRENT_VERSION
os.environ['EASYBUILD_DEPRECATED'] = '10000000'
init_config()
import easybuild
# try to import easybuild.easyblocks(.generic) packages
# it's OK if it fails here, but important to import first before fiddling with sys.path
try:
import easybuild.easyblocks
import easybuild.easyblocks.generic
except ImportError:
pass
# add sandbox to Python search path, update namespace packages
sys.path.append(os.path.join(testdir, 'sandbox'))
# workaround for bug in recent setuptools version (19.4 and newer, atleast until 20.3.1)
# injecting <prefix>/easybuild is required to avoid a ValueError being thrown by fixup_namespace_packages
# cfr. https://bitbucket.org/pypa/setuptools/issues/520/fixup_namespace_packages-may-trigger
for path in sys.path[:]:
if os.path.exists(
os.path.join(path, 'easybuild', 'easyblocks',
'__init__.py')):
# keep track of 'easybuild' paths to inject into sys.path later
sys.path.append(os.path.join(path, 'easybuild'))
# required to make sure the 'easybuild' dir in the sandbox is picked up;
# this relates to the other 'reload' statements below
reload(easybuild)
# this is strictly required to make the test modules in the sandbox available, due to declare_namespace
fixup_namespace_packages(os.path.join(testdir, 'sandbox'))
# remove any entries in Python search path that seem to provide easyblocks (except the sandbox)
for path in sys.path[:]:
if os.path.exists(
os.path.join(path, 'easybuild', 'easyblocks',
'__init__.py')):
if not os.path.samefile(path, os.path.join(testdir,
'sandbox')):
sys.path.remove(path)
# hard inject location to (generic) test easyblocks into Python search path
# only prepending to sys.path is not enough due to 'declare_namespace' in easybuild/easyblocks/__init__.py
import easybuild.easyblocks
reload(easybuild.easyblocks)
test_easyblocks_path = os.path.join(testdir, 'sandbox', 'easybuild',
'easyblocks')
easybuild.easyblocks.__path__.insert(0, test_easyblocks_path)
import easybuild.easyblocks.generic
reload(easybuild.easyblocks.generic)
test_easyblocks_path = os.path.join(test_easyblocks_path, 'generic')
easybuild.easyblocks.generic.__path__.insert(0, test_easyblocks_path)
self.modtool = modules_tool()
self.reset_modulepath([os.path.join(testdir, 'modules')])
reset_module_caches()
def setUp(self):
"""Set up testcase."""
super(EnhancedTestCase, self).setUp()
# keep track of log handlers
log = fancylogger.getLogger(fname=False)
self.orig_log_handlers = log.handlers[:]
log.info("setting up test %s" % self.id())
self.orig_tmpdir = tempfile.gettempdir()
# use a subdirectory for this test (which we can clean up easily after the test completes)
self.test_prefix = set_tmpdir()
self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
fd, self.logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')
os.close(fd)
self.cwd = os.getcwd()
# keep track of original environment to restore
self.orig_environ = copy.deepcopy(os.environ)
# keep track of original environment/Python search path to restore
self.orig_sys_path = sys.path[:]
testdir = os.path.dirname(os.path.abspath(__file__))
self.test_sourcepath = os.path.join(testdir, 'sandbox', 'sources')
os.environ['EASYBUILD_SOURCEPATH'] = self.test_sourcepath
os.environ['EASYBUILD_PREFIX'] = self.test_prefix
self.test_buildpath = tempfile.mkdtemp()
os.environ['EASYBUILD_BUILDPATH'] = self.test_buildpath
self.test_installpath = tempfile.mkdtemp()
os.environ['EASYBUILD_INSTALLPATH'] = self.test_installpath
# make sure that the tests only pick up easyconfigs provided with the tests
os.environ['EASYBUILD_ROBOT_PATHS'] = os.path.join(
testdir, 'easyconfigs')
# make sure no deprecated behaviour is being triggered (unless intended by the test)
# trip *all* log.deprecated statements by setting deprecation version ridiculously high
self.orig_current_version = eb_build_log.CURRENT_VERSION
os.environ['EASYBUILD_DEPRECATED'] = '10000000'
init_config()
# remove any entries in Python search path that seem to provide easyblocks
for path in sys.path[:]:
if os.path.exists(
os.path.join(path, 'easybuild', 'easyblocks',
'__init__.py')):
sys.path.remove(path)
# add test easyblocks to Python search path and (re)import and reload easybuild modules
import easybuild
sys.path.append(os.path.join(testdir, 'sandbox'))
reload(easybuild)
import easybuild.easyblocks
reload(easybuild.easyblocks)
import easybuild.easyblocks.generic
reload(easybuild.easyblocks.generic)
reload(easybuild.tools.module_naming_scheme
) # required to run options unit tests stand-alone
modtool = modules_tool()
# purge out any loaded modules with original $MODULEPATH before running each test
modtool.purge()
self.reset_modulepath([os.path.join(testdir, 'modules')])
