def test_scripts(datadir_factory, printer):
datadir = datadir_factory.mkdatadir(f'../_examples/{EXAMPLE}')
with chdir(datadir):
run(['python', 'source/make_orchestrator.py', '1', '10', '10', '3'], )
def test_runs(datadir_factory, printer):
datadir = datadir_factory.mkdatadir(f'../_examples/{EXAMPLE}')
with chdir(datadir):
run([
'bash',
'_tangle_source/run0.bash',
], )
def test_run_passes_stdout_and_stderr_if_not_captured():
with patch('subprocess.Popen') as Popen:
Popen.return_value.returncode = 0
Popen.return_value.communicate.return_value = (None, None)
run.run(sentinel.cmd, capture_stdout=False, capture_stderr=False)
Popen.assert_called_with(sentinel.cmd,
stdin=None,
stdout=None,
stderr=None)
def test_run_logs_stdout_on_failure():
cmd = get_python_cmd('sys.stdout.write("stdout")', exit_code=1)
with mock.patch('pytest_shutil.run.log') as log:
with pytest.raises(subprocess.CalledProcessError):
with no_cov():
run.run(cmd, capture_stdout=True)
expected = 'Command failed: "%s"\nstdout' % " ".join(cmd)
log.error.assert_called_with(expected)
def test_run_logs_stdout_on_failure():
cmd = get_python_cmd('sys.stdout.write("stdout")', exit_code=1)
with mock.patch('pytest_shutil.run.log') as log:
with pytest.raises(subprocess.CalledProcessError):
with no_cov():
run.run(cmd, capture_stdout=True)
expected = 'Command failed: "%s"\nstdout' % " ".join(cmd)
log.error.assert_called_with(expected)
def test_run_passes_stderr_if_not_captured():
cmd = get_python_cmd('sys.stderr.write("stderr")')
cmd = ", ".join(['\'%s\'' % s for s in cmd])
with no_cov():
p = subprocess.Popen([sys.executable, '-c', """from pytest_shutil import run
run.run([%s], capture_stderr=False)""" % cmd], stderr=subprocess.PIPE)
_, err = p.communicate()
assert p.returncode == 0
assert 'stderr' in err.decode('utf-8')
def test_run_logs_stderr_on_failure():
cmd = get_python_cmd('sys.stderr.write("stderr")', exit_code=1)
with mock.patch('pytest_shutil.run.log') as log:
with pytest.raises(subprocess.CalledProcessError):
with no_cov():
run.run(cmd, capture_stderr=True)
expected = 'Command failed: "%s"\nstderr' % " ".join(cmd)
assert log.error.call_count == 1
assert log.error.call_args[0][0].startswith(expected)
def test_run_logs_stderr_on_failure():
cmd = get_python_cmd('sys.stderr.write("stderr")', exit_code=1)
with mock.patch('pytest_shutil.run.log') as log:
with pytest.raises(subprocess.CalledProcessError):
with no_cov():
run.run(cmd, capture_stderr=True)
expected = 'Command failed: "%s"\nstderr' % " ".join(cmd)
assert log.error.call_count == 1
assert log.error.call_args[0][0].startswith(expected)
def test_trivial_run(datadir_factory, printer):
example = "Lennard_Jones_Pair"
datadir = datadir_factory.mkdatadir(f'../_examples/{example}')
with chdir(datadir):
run(['python',
'source/trivial_run.py',
],
)
def test_run_passes_stdout_if_not_captured():
cmd = get_python_cmd('sys.stdout.write("stdout")')
cmd = ", ".join(['\'%s\'' % s for s in cmd])
with no_cov():
p = subprocess.Popen([
sys.executable, '-c',
"""from pytest_shutil import run
run.run([%s], capture_stdout=False)""" % cmd
],
stdout=subprocess.PIPE)
out, _ = p.communicate()
assert p.returncode == 0
assert out.decode('utf-8') == 'stdout'
def test_reference(datadir_factory):
datadir = Path(
datadir_factory.mkdatadir('../_tangled_docs/info/reference'))
with chdir(datadir):
out = run([
'python',
'decision_fields_0.py',
], )
out = run([
'python',
'record_fields_0.py',
], )
def test_no_env_ok_if_not_exists():
if TEMP_NAME in os.environ:
del os.environ[TEMP_NAME]
with env.no_env(TEMP_NAME):
out = run.run('env', capture_stdout=True)
for o in out.split('\n'):
if o.startswith(TEMP_NAME):
assert False, '%s found in os.environ' % TEMP_NAME
assert TEMP_NAME not in os.environ
def test_no_env_ok_if_not_exists():
if TEMP_NAME in os.environ:
del os.environ[TEMP_NAME]
with env.no_env(TEMP_NAME):
out = run.run('env', capture_stdout=True)
for o in out.split('\n'):
if o.startswith(TEMP_NAME):
assert False, '%s found in os.environ' % TEMP_NAME
assert TEMP_NAME not in os.environ
def test_readme(datadir_factory):
datadir = Path(datadir_factory.mkdatadir('../_tangled_docs/README'))
with chdir(datadir):
out = run([
'bash',
'check_installation.bash',
], )
def test_set_env_ok_if_not_exists():
if TEMP_NAME in os.environ:
del os.environ[TEMP_NAME]
with env.set_env(TEMP_NAME, 'anything'):
out = run.run('env', capture_stdout=True)
for o in out.split('\n'):
if o.startswith(TEMP_NAME):
assert o == '%s=anything' % TEMP_NAME
break
else:
assert False, '%s not found in os.environ' % TEMP_NAME
def test_set_env_ok_if_not_exists():
if TEMP_NAME in os.environ:
del os.environ[TEMP_NAME]
with env.set_env(TEMP_NAME, 'anything'):
out = run.run('env', capture_stdout=True)
for o in out.split('\n'):
if o.startswith(TEMP_NAME):
assert o == '%s=anything' % TEMP_NAME
break
else:
assert False, '%s not found in os.environ' % TEMP_NAME
def test_quick_start(datadir_factory):
datadir = Path(
datadir_factory.mkdatadir('../_tangled_docs/info/quick_start'))
with chdir(datadir):
out = run([
'bash',
'test_drive.bash',
], )
out = run([
'python',
'noresampler_example.py',
], )
out = run([
'bash',
'noresampler_example.bash',
], )
def test_we(datadir_factory, printer):
datadir = datadir_factory.mkdatadir(f'../_examples/{EXAMPLE}')
with chdir(datadir):
with check:
printer("running CPU-NoResampler")
run([
'python', 'source/we.py', '2', '2', '10', '1', 'CPU',
'NoResampler'
], )
printer("running CPU-REVOResampler")
with check:
print("CPU-REVOResampler")
run([
'python', 'source/we.py', '2', '2', '10', '1', 'CPU',
'REVOResampler'
], )
printer("running CPU-WExploreResampler")
with check:
print("CPU_WExploreResampler")
run([
'python', 'source/we.py', '2', '2', '10', '1', 'CPU',
'WExploreResampler'
], )
def test_subprocecmdline():
ev = os.environ[TEMP_NAME] = 'junk_name'
try:
with env.no_env(TEMP_NAME):
out = run.run('env', capture_stdout=True)
for o in out.split('\n'):
if o.startswith(TEMP_NAME):
assert False, '%s found in os.environ' % TEMP_NAME
assert os.environ[TEMP_NAME] == ev
finally:
if TEMP_NAME in os.environ:
del os.environ[TEMP_NAME]
def test_subprocecmdline():
ev = os.environ[TEMP_NAME] = 'junk_name'
try:
with env.no_env(TEMP_NAME):
out = run.run('env', capture_stdout=True)
for o in out.split('\n'):
if o.startswith(TEMP_NAME):
assert False, '%s found in os.environ' % TEMP_NAME
assert os.environ[TEMP_NAME] == ev
finally:
if TEMP_NAME in os.environ:
del os.environ[TEMP_NAME]
def test_tutorial(datadir_factory, printer):
tutorial = "data_analysis"
datadir = datadir_factory.mkdatadir(f'../_tutorials/{tutorial}')
assert (datadir / "README.ipynb").is_file()
assert (datadir / "input").is_dir()
with chdir(datadir):
run([
'python',
'_tangle_source/README.py',
], )
assert (datadir / '_output/results_run1.wepy.h5').exists()
assert (datadir / '_output/results_run2.wepy.h5').exists()
assert (datadir / '_output/results_run3.wepy.h5').exists()
assert (datadir / '_output/lj-pair.pdb').exists()
assert (datadir / '_output/lj-pair_walker_lineage').exists()
def test_scripts(datadir_factory, printer):
datadir = datadir_factory.mkdatadir(f'../_examples/{EXAMPLE}')
with chdir(datadir):
run(['python', 'source/rw_conventional.py', '1', '10', '10', '3'], )
run(['python', 'source/rw_revo.py', '1', '10', '10', '3'], )
run(['python', 'source/rw_wexplore.py', '1', '10', '10', '3'], )
def test_run0(datadir_factory, printer):
tutorial = "extended_test_drive"
datadir = datadir_factory.mkdatadir(f'../_tutorials/{tutorial}')
with chdir(datadir):
# check that the help message runs
run([
'bash',
'_tangle_source/run-help.bash',
], )
# default Run with WExplore
run0_out = run([
'bash',
'_tangle_source/run0.bash',
], )
with check:
assert (
datadir /
'_tangle_source/expected_run0_ls.txt').read_text() == run0_out
assert (datadir / '_output/run0/root.wepy.h5').exists()
assert (datadir / '_output/run0/root.dash.org').exists()
assert (datadir / '_output/run0/root.init_top.pdb').exists()
assert (datadir / '_output/run0/root.walkers.dcd').exists()
# REVO run
run([
'bash',
'_tangle_source/revo_run.bash',
], )
assert (datadir / '_output/revo_run/root.wepy.h5').exists()
assert (datadir / '_output/revo_run/root.dash.org').exists()
assert (datadir / '_output/revo_run/root.init_top.pdb').exists()
assert (datadir / '_output/revo_run/root.walkers.dcd').exists()
# No run
run([
'bash',
'_tangle_source/no_run.bash',
], )
assert (datadir / '_output/no_run/root.wepy.h5').exists()
assert (datadir / '_output/no_run/root.dash.org').exists()
assert (datadir / '_output/no_run/root.init_top.pdb').exists()
assert (datadir / '_output/no_run/root.walkers.dcd').exists()
## analysis
# part 0
analysis0_out = run([
'python',
'_tangle_source/analysis0.py',
], )
assert (datadir / '_output/run0/traj0.dcd').exists()
assert (datadir / "_output/run0/last_cycle.dcd").exists()
with check:
assert (datadir / '_tangle_source/test_analysis_0.txt').read_text() == \
analysis0_out.strip()
def test_we_analysis(datadir_factory, printer):
example = "Lennard_Jones_Pair"
datadir = datadir_factory.mkdatadir(f'../_examples/{example}')
printer("Testing from inside test_we_analysis")
with chdir(datadir):
printer(f"Datadir: {datadir}")
printer(f"Current dir: {os.getcwd()}")
out = run([
"python",
"source/we.py",
"10", '100', "10"])
printer(out)
assert (datadir / "_output/we/results.wepy.h5").is_file()
assert (datadir / "_output/we/wepy.dash.org").is_file()
out = run([
"python",
"source/compute_distance_observable.py",
])
printer(out)
out = run([
"python",
"source/state_network.py",
])
printer(out)
assert (datadir / "_output/state.dcd").is_file()
assert (datadir / "_output/random_macrostates.csn.gexf").is_file()
### Tangled sources
out = run([
"python",
"_tangle_source/inspect_observable.py",
])
printer(out)
out = run([
"bash",
"./_tangle_source/run0.bash",
]
)
printer(out)
out = run([
"bash",
"./_tangle_source/run1.bash",
]
)
def test_run_raises_on_failure():
cmd = get_python_cmd(exit_code=1)
with pytest.raises(subprocess.CalledProcessError):
with no_cov():
run.run(cmd)
def test_sim_maker_run(datadir_factory, printer):
example = "Lennard_Jones_Pair"
datadir = datadir_factory.mkdatadir(f'../_examples/{example}')
with chdir(datadir):
run(['python',
'source/sim_maker_run.py',
'2', '100', '10', '1', 'Reference', 'NoResampler'],
)
run(['python',
'source/sim_maker_run.py',
'2', '100', '10', '1', 'Reference', 'WExploreResampler'],
)
run(['python',
'source/sim_maker_run.py',
'2', '100', '10', '1', 'Reference', 'REVOResampler'],
)
run(['python',
'source/sim_maker_run.py',
'2', '100', '10', '1', 'CPU', 'NoResampler'],
)
run(['python',
'source/sim_maker_run.py',
'2', '100', '10', '1', 'CPU', 'WExploreResampler'],
)
run(['python',
'source/sim_maker_run.py',
'2', '100', '10', '1', 'CPU', 'REVOResampler'],
)
def test_run_raises_on_failure():
cmd = get_python_cmd(exit_code=1)
with pytest.raises(subprocess.CalledProcessError):
with no_cov():
run.run(cmd)
def test_run_passes_stdout_and_stderr_if_not_captured():
with patch('subprocess.Popen') as Popen:
Popen.return_value.returncode = 0
Popen.return_value.communicate.return_value = (None, None)
run.run(sentinel.cmd, capture_stdout=False, capture_stderr=False)
Popen.assert_called_with(sentinel.cmd, stdin=None, stdout=None, stderr=None)