def test_merge_docker(self):
"""merge primitives"""
r = []
r.append(runscript(commands=['a', 'b']))
r.append(runscript(commands=['c']))
merged = r[0].merge(r)
self.assertEqual(str(merged), 'ENTRYPOINT ["a"]')
def test_merge_singularity(self):
"""merge primitives"""
r = []
r.append(runscript(commands=['a', 'b']))
r.append(runscript(commands=['c']))
merged = r[0].merge(r)
self.assertEqual(str(merged), '%runscript\n a\n b\n exec c')
def test_allsections_singularity(self):
"""One of each SCI-f section type"""
s = scif(name='foo')
s += copy(src='file', dest='/tmp/file')
s += comment('My app')
s += environment(variables={'ONE': '1'})
s += label(metadata={'A': 'B'})
s += runscript(commands=['default_program'])
s += shell(commands=['build_cmds'])
s += shell(commands=['test_program'], _test=True)
self.assertEqual(
str(s), r'''%appenv foo
export ONE=1
%appfiles foo
file /tmp/file
%apphelp foo
My app
%appinstall foo
for f in /.singularity.d/env/*; do . $f; done
build_cmds
%applabels foo
A B
%apprun foo
exec default_program "$@"
%apptest foo
test_program''')
def __scif_recipe(self):
"""Generate the SCI-F recipe instructions, merging primitives of the
same type because SCI-F does not support duplicate
sections."""
recipe = []
if self.__appenv:
appenv = self.__appenv[0].merge(self.__appenv, _app=self.__name)
recipe.append(appenv)
if self.__appfiles:
appfiles = self.__appfiles[0].merge(self.__appfiles,
_app=self.__name)
recipe.append(appfiles)
if self.__apphelp:
apphelp = self.__apphelp[0].merge(self.__apphelp, _app=self.__name)
recipe.append(apphelp)
if self.__appinstall:
_appenv = False
if hpccm.config.g_ctype == container_type.SINGULARITY:
# If the container type is Singularity, load the
# general container environment
_appenv = True
appinstall = self.__appinstall[0].merge(self.__appinstall,
_app=self.__name,
_appenv=_appenv)
recipe.append(appinstall)
if self.__applabels:
applabels = self.__applabels[0].merge(self.__applabels,
_app=self.__name)
recipe.append(applabels)
if self.__apprun:
apprun = self.__apprun[0].merge(self.__apprun, _app=self.__name)
recipe.append(apprun)
else:
# Shell one liner to run a command if specified,
# otherwise start a shell
recipe.append(
runscript(commands=[
'eval "if [[ $# -eq 0 ]]; then exec /bin/bash; else exec $@; fi"'
],
_args=False,
_app=self.__name,
_exec=False))
if self.__apptest:
apptest = self.__apptest[0].merge(self.__apptest,
_app=self.__name,
_test=True)
recipe.append(apptest)
return recipe
def __instructions(self):
self += comment('OpenGeoSys build from repo {0}, branch {1}'.format(
self.__repo, self.__branch))
self += packages(ospackages=self.__ospackages)
self += shell(
commands=self.__commands,
_arguments='--mount=type=bind,target=/scif/apps/ogs/src,rw')
self += runscript(commands=['ogs'])
if self.__environment_variables:
self += environment(variables=self.__environment_variables)
if self.__labels:
self += label(metadata=self.__labels)
def test_allsections_docker(self):
"""One of each SCI-f section type"""
# See comment in the test_defaults_docker test case
scif_file = tempfile.NamedTemporaryFile(delete=False, suffix='.scif')
s = scif(name='foo', file=scif_file.name)
s += copy(src='file', dest='/tmp/file')
s += comment('My app')
s += environment(variables={'ONE': '1'})
s += label(metadata={'A': 'B'})
s += runscript(commands=['default_program'])
s += shell(commands=['build_cmds'])
s += shell(commands=['test_program'], _test=True)
str(s) # Force writing the SCI-F recipe file
# slurp file content
with open(scif_file.name) as f:
content = f.read()
try:
os.unlink(scif_file.name)
except WindowsError:
# WindowsError: [Error 32] The process cannot access the file
# because it is being used by another process
pass
self.assertEqual(
content, r'''%appenv foo
export ONE=1
%appfiles foo
file /tmp/file
%apphelp foo
My app
%appinstall foo
build_cmds
%applabels foo
A B
%apprun foo
exec default_program "$@"
%apptest foo
test_program''')
def build(container_format='singularity',
os_release='ubuntu',
os_version='20.04',
conda_packages=['conda', 'numpy', 'scipy', 'pandas'],
python_version='3.9.1',
channels=['anaconda', 'defaults', 'conda-forge'],
anaconda_version='4.9.2'):
config.set_container_format(container_format)
image = f'{os_release}:{os_version}'
stage0 = Stage(name='stage0')
stage0 += baseimage(image=image, _bootstrap='docker')
stage0 += environment(variables={
'LC_ALL': 'en_AU.UTF-8',
'LANGUAGE': 'en_AU.UTF-8',
})
stage0 += label(metadata={
'maintainer': 'Luhan Cheng',
'email': '*****@*****.**'
})
stage0 += shell(commands=[
'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash'
])
stage0 += packages(apt=[
'wget', 'git', 'software-properties-common', 'build-essential',
'locales'
])
stage0 += shell(commands=['locale-gen en_AU.UTF-8'])
stage0 += conda(eula=True,
packages=[f'python={python_version}'] + conda_packages,
channels=channels,
version=anaconda_version)
stage0 += environment(variables=from_prefix('/usr/local/anaconda'))
stage0 += runscript(commands=[
'source /usr/local/anaconda/etc/profile.d/conda.sh',
'/usr/local/anaconda/bin/python3 $*'
])
return stage0
def test_multiple_docker(self):
"""List of commands specified"""
cmds = ['a', 'b', 'c']
s = runscript(commands=cmds)
self.assertEqual(str(s), 'ENTRYPOINT ["a"]')
def test_multiple_noexec_singularity(self):
"""exec option"""
cmds = ['a', 'b', 'c']
s = runscript(commands=cmds, _exec=False)
self.assertEqual(str(s), '%runscript\n a\n b\n c')
def test_empty(self):
"""No commands specified"""
s = runscript()
self.assertEqual(str(s), '')
def test_apprun_multiple_singularity(self):
"""List of commands specified"""
cmds = ['a', 'b', 'c']
s = runscript(commands=cmds, _app='foo')
self.assertEqual(str(s), '%apprun foo\n a\n b\n exec c')
def test_apprun_docker(self):
"""apprun not implemented in Docker"""
cmds = ['a', 'b', 'c']
s = runscript(commands=cmds, _app='foo')
self.assertEqual(str(s), 'ENTRYPOINT ["a"]')
def test_multiple_singularity(self):
"""List of commands specified"""
cmds = ['a arga', 'b argb', 'c']
s = runscript(commands=cmds)
self.assertEqual(str(s),
'%runscript\n a arga\n b argb\n exec c')
def test_bash(self):
"""Single command specified"""
cmd = ['z']
s = runscript(commands=cmd)
self.assertEqual(str(s), '')
def test_single_singularity(self):
"""Single command specified"""
cmd = ['z']
s = runscript(commands=cmd)
self.assertEqual(str(s), '%runscript\n exec z')
def test_single_docker(self):
"""Single command specified"""
cmd = ['z arg1 arg2']
s = runscript(commands=cmd)
self.assertEqual(str(s), 'ENTRYPOINT ["z", "arg1", "arg2"]')
def test_invalid_ctype(self):
"""Invalid container type specified"""
s = runscript(commands=['a'])
with self.assertRaises(RuntimeError):
str(s)
