def test_get_batch_command(cli_runner, monkeypatch, tmpdir):
"""Test that the get_engine_command works correctly.
It should exit if no batching system was found.
"""
# The following was taken from the basic testing example from the Click
# documentation: http://click.pocoo.org/6/testing/#basic-testing
# We need to do this, because `get_engine_command()` uses `click.echo` to
# display an error message and we want to test its value.
@click.group()
def test_cli():
pass
@test_cli.command()
def test():
get_batch_command()
# Test fail state
output = 'ERROR Was not able to find a batch system. ' \
'Are you trying to use this package on a host with a queuing system?\n'
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 1
assert result.output == output
# Test non-fail state
monkeypatch.setattr('mdbenchmark.submit.glob', lambda x: ['qsub'])
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 0
def test_submit_resubmit(cli_runner, monkeypatch, tmpdir, data):
"""Test that we cannot submit a benchmark system that was already submitted,
unless we force it.
"""
with tmpdir.as_cwd():
# Test that we get an error if we try to point the submit function to
# an non-existent path.
result = cli_runner.invoke(cli, ["submit", "--directory=look_here/"],
"--yes")
assert result.exit_code == 1
assert result.output == "ERROR No benchmarks found.\n"
# Test that we get an error if we try to start benchmarks that were
# already started once.
result = cli_runner.invoke(
cli,
[
"submit", "--directory={}".format(
data["analyze-files-gromacs"]), "--yes"
],
)
df = pd.read_csv(data["analyze-files-gromacs-consolidated.csv"],
index_col=0)
s = PrintDataFrame(df, False)
output = "ERROR All generated benchmarks were already started once. You can force a restart with --force.\n"
assert result.exit_code == 1
assert result.output == output
# Test that we can force restart already run benchmarks.
# Monkeypatch a few functions
monkeypatch.setattr("subprocess.call", lambda x: True)
monkeypatch.setattr("mdbenchmark.cli.submit.get_batch_command",
lambda: "sbatch")
monkeypatch.setattr("mdbenchmark.cli.submit.detect_md_engine",
lambda x: gromacs)
monkeypatch.setattr("mdbenchmark.submit.cleanup_before_restart",
lambda engine, sim: True)
output = (
"Benchmark Summary:\n" + s +
"\nThe above benchmarks will be submitted.\n" +
"Submitting a total of 5 benchmarks.\n" +
"Submitted all benchmarks. Run mdbenchmark analyze once they are finished to get the results.\n"
)
result = cli_runner.invoke(
cli,
[
"submit",
"--directory={}".format(data["analyze-files-gromacs"]),
"--force",
"--yes",
],
)
assert result.exit_code == 0
assert result.output == output
def test_generate_console_messages(cli_runner, monkeypatch, tmpdir):
"""Test that the CLI for generate prints all error messages as expected."""
with tmpdir.as_cwd():
# monkeypatch the output of the available modules
monkeypatch.setattr('mdbenchmark.mdengines.get_available_modules',
lambda: {'gromacs': ['2016']})
# Test that we get an error when not supplying a file name
result = cli_runner.invoke(
cli.cli, ['generate', '--module=gromacs/2016', '--host=draco'])
output = 'Usage: cli generate [OPTIONS]\n\nError: Invalid value for ' \
'"-n" / "--name": Please specifiy the name of your input files.'
# Test error message if the TPR file does not exist
result = cli_runner.invoke(
cli.cli,
['generate', '--module=gromacs/2016', '--host=draco', '--name=md'])
output = 'ERROR File md.tpr does not exist, but is needed for GROMACS benchmarks.\n'
assert result.exit_code == 1
assert result.output == output
with open('protein.tpr', 'w') as fh:
fh.write('This is a dummy tpr!')
# Test that the minimal number of nodes must be bigger than the maximal number
result = cli_runner.invoke(cli.cli, [
'generate', '--module=gromacs/2016', '--host=draco',
'--name=protein', '--min-nodes=6', '--max-nodes=4'
])
output = 'Usage: cli generate [OPTIONS]\n\nError: Invalid value for ' \
'"--min-nodes": The minimal number of nodes needs to be smaller ' \
'than the maximal number.\n'
assert result.exit_code == 2
assert result.output == output
# Test error message if we pass an invalid template name
result = cli_runner.invoke(cli.cli, [
'generate', '--module=gromacs/2016', '--host=minerva',
'--name=protein'
])
output = 'Could not find template for host \'minerva\'.\n' \
'Available host templates:\n' \
'draco\n' \
'hydra\n'
assert result.exit_code == 0
assert result.output == output
# Test error message if we do not pass any module name
result = cli_runner.invoke(
cli.cli, ['generate', '--host=draco', '--name=protein'])
output = 'Usage: cli generate [OPTIONS]\n\nError: Invalid value for ' \
'"-m" / "--module": Please specify which MD engine module ' \
'to use for the benchmarks.\n'
assert result.exit_code == 2
assert result.output == output
def test_normalize_modules(cli_runner, monkeypatch, tmpdir):
"""Test that normalize modules works as expected."""
@click.group()
def test_cli():
pass
# Test the warning when we skip the validation
@test_cli.command()
def skip_validation():
normalize_modules(modules=['gromacs/2016.4'], skip_validation=True)
result = cli_runner.invoke(test_cli, ['skip_validation'])
assert result.exit_code == 0
assert result.output == 'WARNING Not performing module name validation.\n'
# Test the warning when we do not skip the validation
@test_cli.command()
def do_not_skip_validation():
normalize_modules(modules=['gromacs/2016.4'], skip_validation=False)
result = cli_runner.invoke(test_cli, ['do_not_skip_validation'])
assert result.exit_code == 0
assert result.output == 'WARNING Cannot locate modules available on this host. ' \
'Not performing module name validation.\n'
@test_cli.command()
def test_normalize():
normalize_modules(modules=['gromacs/doesnotexist'],
skip_validation=False)
with tmpdir.as_cwd():
for k, v in DIR_STRUCTURE.items():
for k2, v2 in v.items():
os.makedirs(os.path.join(k, k2))
for v3 in v2:
open(os.path.join(k, k2, v3), 'a').close()
# Prepare path variable that we are going to monkeypatch for
# `get_available_modules`
dirs = ':'.join(
[os.path.join(os.getcwd(), x) for x in os.listdir(os.getcwd())])
monkeypatch.setenv('MODULEPATH', dirs)
modules = get_available_modules()
output = 'WARNING We have problems finding all of your requested modules on this host.\n' \
'We were not able to find the following modules for MD engine gromacs: ' \
'doesnotexist.\n' \
'Available modules are:\n' \
'gromacs/2016.4\n' \
'gromacs/2018.1\n' \
'gromacs/5.1.4-plumed2.3\n\n'
result = cli_runner.invoke(test_cli, ['test_normalize'])
assert result.exit_code == 0
assert result.output == output
def test_analyze_namd_file(cli_runner, tmpdir):
"""Test that we check the `.namd` file as expected."""
@click.group()
def test_cli():
pass
@test_cli.command()
def test():
with open('md.namd') as fh:
namd.analyze_namd_file(fh)
with tmpdir.as_cwd():
# Make sure that we do not throw any error when everything is fine!
with open('md.namd', 'w') as fh:
fh.write('dummy file')
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 0
assert result.output == ''
# Assert that we fail, when a relative path is given.
with open('md.namd', 'w') as fh:
fh.write('parameters ./relative/path/')
output = 'ERROR No absolute path detected in NAMD file!\n'
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 1
assert result.output == output
# Fail if we do not give ANY absolute path.
with open('md.namd', 'w') as fh:
fh.write('parameters abc')
output = 'ERROR No absolute path detected in NAMD file!\n'
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 1
assert result.output == output
# Fail if we do not give ANY absolute path.
with open('md.namd', 'w') as fh:
fh.write('coordinates ../another/relative/path')
output = 'ERROR Relative file paths are not allowed in NAMD files!\n'
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 1
assert result.output == output
# Fail if we do not give ANY absolute path.
with open('md.namd', 'w') as fh:
fh.write('structure $')
output = 'ERROR Variable Substitutions are not allowed in NAMD files!\n'
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 1
assert result.output == output
def test_submit_resubmit(cli_runner, monkeypatch, tmpdir, data):
"""Test that we cannot submit a benchmark system that was already submitted,
unless we force it.
"""
# Define dummy function, so we can monkeypatch `subprocess.call` and
# `mdbenchmark.utils.cleanup_before_restart`.
def call(arg):
return DummyEngine
with tmpdir.as_cwd():
# Test that we get an error if we try to point the submit function to
# an non-existent path.
result = cli_runner.invoke(cli.cli, [
'submit',
'--directory=look_here/',
])
assert result.exit_code == 1
assert result.output == 'ERROR No benchmarks found.\n'
# Test that we get an error if we try to start benchmarks that were
# already started once.
result = cli_runner.invoke(cli.cli, [
'submit',
'--directory={}'.format(data['analyze-files-gromacs']),
])
assert result.exit_code == 1
assert result.output == 'ERROR All generated benchmarks were already' \
' started once. You can force a restart with' \
' --force.\n'
# Test that we can force restart already run benchmarks.
# Monkeypatch a few functions
monkeypatch.setattr('subprocess.call', call)
monkeypatch.setattr('mdbenchmark.submit.get_batch_command',
lambda: 'sbatch')
# We need to patch the cleanup, as we otherwise delete our own test
# files
monkeypatch.setattr('mdbenchmark.submit.detect_md_engine', call)
output = 'Submitting a total of 5 benchmarks.\n' \
'Submitted all benchmarks. Run mdbenchmark analyze once' \
' they are finished to get the results.\n'
result = cli_runner.invoke(cli.cli, [
'submit', '--directory={}'.format(data['analyze-files-gromacs']),
'--force'
])
assert result.exit_code == 0
assert result.output == output
def test_generate_simple_input(cli_runner, generate_output, module, extensions, tmpdir):
"""Test that we can generate benchmarks for all supported MD engines w/o module validation."""
with tmpdir.as_cwd():
for ext in extensions:
open("protein.{}".format(ext), "a").close()
result = cli_runner.invoke(
cli.cli,
[
"generate",
"--module={}".format(module),
"--host=draco",
"--max-nodes=4",
"--gpu",
"--no-cpu",
"--name=protein",
"--yes",
],
)
output = generate_output().format(module)
output = (
"WARNING Cannot locate modules available on this host. "
"Not performing module name validation.\n" + output
)
if "namd" in module:
output = NAMD_WARNING_FORMATTED + output
# Test that we get a warning, if no module name validation is performed.
assert result.exit_code == 0
assert result.output == output
def test_generate_unsupported_engine(cli_runner, monkeypatch, tmpdir):
"""Make sure we throw the correct error, when passed an unsupported MD engine."""
with tmpdir.as_cwd():
for k, v in DIR_STRUCTURE.items():
for k2, v2 in v.items():
os.makedirs(os.path.join(k, k2))
for v3 in v2:
open(os.path.join(k, k2, v3), "a").close()
# Prepare path variable that we are going to monkeypatch for
# `mdengines.get_available_modules`
dirs = ":".join([os.path.join(os.getcwd(), x) for x in os.listdir(os.getcwd())])
monkeypatch.setenv("MODULEPATH", dirs)
supported_engines = ", ".join(sorted([x for x in SUPPORTED_ENGINES]))
output = (
"ERROR There is currently no support for 'doesnotexist'. "
"Supported MD engines are: {}.\n".format(supported_engines)
)
result = cli_runner.invoke(
cli.cli,
[
"generate",
"--module=doesnotexist/version",
"--host=draco",
"--name=protein",
"--yes",
],
)
assert result.exit_code == 1
assert result.output == output
def test_generate_namd_experimental_warning(cli_runner, monkeypatch, tmpdir):
"""Test that we print the NAMD experimental warning."""
with tmpdir.as_cwd():
for f in ["md.namd", "md.psf", "md.pdb"]:
open(f, "a").close()
# monkeypatch the output of the available modules
monkeypatch.setattr(
"mdbenchmark.mdengines.get_available_modules", lambda: {"namd": ["123"]}
)
result = cli_runner.invoke(
cli, ["generate", "--module=namd/123", "--host=draco", "--name=md", "--yes"]
)
output1 = (
"WARNING NAMD support is experimental. "
"All input files must be in the current directory. "
"Parameter paths must be absolute. Only crude file checks are performed! "
"If you use the --gpu option make sure you use the GPU compatible NAMD module!\n"
"Creating benchmark system for namd/123.\n"
)
bundle = dtr.discover()
df = DataFrameFromBundle(bundle)
df = ConsolidateDataFrame(df)
test_output = "Benchmark Summary:\n" + PrintDataFrame(df, False) + "\n"
output2 = (
"Generating the above benchmarks.\n"
"Finished generating all benchmarks.\nYou can "
"now submit the jobs with mdbenchmark submit.\n"
)
output = output1 + test_output + output2
assert result.exit_code == 0
assert result.output == output
def test_plot_module_only(cli_runner, tmpdir, module, data):
"""Test plotting function with one given engine or module.
"""
with tmpdir.as_cwd():
if module in ["gromacs", "namd"]:
output = (
"Plotting GPU and CPU data.\n"
"Plotting all hosts in input file.\n"
"Plotting all modules for engine '{}'.\n"
"Your file was saved as 'testpng.png' in the working directory.\n"
.format(module))
else:
output = (
"Plotting GPU and CPU data.\n"
"Plotting all hosts in input file.\n"
"Plotting module '{}'.\n"
"Your file was saved as 'testpng.png' in the working directory.\n"
.format(module))
result = cli_runner.invoke(
cli.cli,
[
"plot",
"--csv={}".format(data["test.csv"]),
"--module={}".format(module),
"--output-name=testpng",
],
)
assert result.exit_code == 0
assert result.output == output
assert os.path.exists("testpng.png")
def test_plot_output_type(cli_runner, tmpdir, data, output_type):
"""check whether output types are constructed correctly.
"""
with tmpdir.as_cwd():
output = (
"All modules will be plotted.\n"
"All hosts will be plotted.\n"
"A total of 2 runs will be plotted.\n"
"Your file was saved as 'test.{}' in the working directory.\n".
format(output_type))
output = ("Plotting GPU and CPU data.\n"
"Plotting all hosts in input file.\n"
"Plotting all modules in your input data.\n"
"Your file was saved as 'testfile.{}' in the working "
"directory.\n".format(output_type))
result = cli_runner.invoke(
cli.cli,
[
"plot",
"--csv={}".format(data["test.csv"]),
"--output-name=testfile",
"--output-format={}".format(output_type),
],
)
assert result.output == output
assert result.exit_code == 0
def test_guess_ncores(cli_runner, monkeypatch):
"""Test that we can guess the correct number of cores on the supported
systems.
"""
def dummy(arg):
return 'ABC'
monkeypatch.setattr('mdbenchmark.utils.sys.platform', 'linux')
monkeypatch.setattr(
'mdbenchmark.utils._cat_proc_cpuinfo_grep_query_sort_uniq', dummy)
assert utils.guess_ncores() == 9
monkeypatch.setattr('mdbenchmark.utils.sys.platform', 'darwin')
monkeypatch.setattr('mdbenchmark.utils.mp.cpu_count', lambda: 10)
assert utils.guess_ncores() == 5
@click.group()
def test_cli():
pass
@test_cli.command()
def test():
utils.guess_ncores()
monkeypatch.setattr('mdbenchmark.utils.sys.platform', 'starlord')
output = 'WARNING Could not guess number of physical cores. ' \
'Assuming there is only 1 core per node.\n'
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 0
assert result.output == output
def test_analze_namd(cli_runner, tmpdir, data):
with tmpdir.as_cwd():
result = cli_runner.invoke(
cli.cli,
['analyze', '--directory={}'.format(data['analyze-files-namd'])])
assert result.exit_code == 0
assert result.output == """ module nodes ns/day run time [min] gpu host ncores
def test_plot_gpu(cli_runner, tmpdir, data):
"""Test gpu flage without any host or module.
"""
with tmpdir.as_cwd():
output = (
"Plotting GPU and CPU data.\n"
"Plotting all hosts in input file.\n"
"Plotting all modules in your input data.\n"
"Your file was saved as 'testpng.png' in the working directory.\n")
result = cli_runner.invoke(
cli.cli,
[
"plot",
"--csv={}".format(data["test.csv"]),
"--gpu",
"--output-name=testpng",
"--output-format=png",
],
)
assert result.exit_code == 0
assert result.output == output
assert os.path.exists("testpng.png")
def test_plot_host_only(cli_runner, tmpdir, host, data):
"""Test plotting function with one given host.
"""
with tmpdir.as_cwd():
output = (
"Plotting GPU and CPU data.\n"
"Data for the following hosts will be plotted: {}\n"
"Plotting all modules in your input data.\n"
"Your file was saved as 'testpng.png' in the working directory.\n".
format(host))
result = cli_runner.invoke(
cli.cli,
[
"plot",
"--csv={}".format(data["test.csv"]),
"--host={}".format(host),
"--output-name=testpng",
"--output-format=png",
],
)
assert result.exit_code == 0
assert result.output == output
assert os.path.exists("testpng.png")
def test_analyze_console_messages(cli_runner, tmpdir):
"""Test that the CLI for analyze prints all error messages as expected."""
with tmpdir.as_cwd():
# Test error message if the TPR file does not exist
result = cli_runner.invoke(cli, ["analyze", "--directory=look_here/"])
output = "ERROR There is no data for the given path.\n"
assert result.exit_code == 1
assert result.output == output
def test_aliasedgroup_unknown_command(cli_runner):
"""Test that we return an error, when invoking an unknown command."""
result = cli_runner.invoke(cli, ["unknown_command"])
assert result.exit_code == 2
output = ("Usage: cli [OPTIONS] COMMAND [ARGS]...\n"
'Try "cli --help" for help.\n\n'
"Error: Sub command unknown: unknown_command\n")
assert result.output == output
def test_analyze_gromacs(cli_runner, tmpdir, data):
"""Test that the output is OK when all outputs are fine."""
with tmpdir.as_cwd():
result = cli_runner.invoke(cli.cli, [
'analyze',
'--directory={}'.format(data['analyze-files-gromacs']),
])
assert result.exit_code == 0
assert result.output == """ module nodes ns/day run time [min] gpu host ncores
def test_prepare_module_name(cli_runner):
"""Test that prepare_module_name works as expected."""
@click.group()
def test_cli():
pass
@test_cli.command()
def test_wrong_module_name():
prepare_module_name('gromacs-2016.4')
@test_cli.command()
def test_correct_module_name():
prepare_module_name('gromacs/2016.4')
result = cli_runner.invoke(test_cli, ['test_wrong_module_name'])
assert result.exit_code == 1
assert result.output == 'ERROR We were not able to determine the module name.\n'
result = cli_runner.invoke(test_cli, ['test_correct_module_name'])
assert result.exit_code == 0
def test_analyze_gromacs(cli_runner, tmpdir, data):
"""Test that the output is OK when all outputs are fine."""
with tmpdir.as_cwd():
result = cli_runner.invoke(cli, [
"analyze", "--directory={}".format(data["analyze-files-gromacs"])
])
df = pd.read_csv(data["analyze-files-gromacs.csv"])
test_output = PrintDataFrame(df, False) + "\n"
assert result.exit_code == 0
assert result.output == test_output
def test_analyze_namd(cli_runner, tmpdir, data):
with tmpdir.as_cwd():
result = cli_runner.invoke(
cli,
["analyze", "--directory={}".format(data["analyze-files-namd"])])
bundle = dtr.discover(data["analyze-files-namd"])
df = DataFrameFromBundle(bundle)
test_output = PrintDataFrame(df, False) + "\n"
assert result.exit_code == 0
assert result.output == test_output
def test_analyze_with_errors(cli_runner, tmpdir, data):
"""Test that we warn the user of errors in the output files. Also test that we
show a question mark instead of a float in the corresponding cell.
"""
with tmpdir.as_cwd():
result = cli_runner.invoke(cli.cli, [
'analyze',
'--directory={}'.format(data['analyze-files-w-errors']),
])
assert result.exit_code == 0
assert result.output == """WARNING We were not able to gather informations for all systems. Systems marked with question marks have either crashed or were not started yet.
def test_analyze_many_rows(cli_runner, tmpdir, datafiles):
"""Test that pandas does not limit the number of printed rows."""
with tmpdir.as_cwd():
open("protein.tpr", "a").close()
result = cli_runner.invoke(
cli.cli,
[
"generate",
"--module=gromacs/2016.3",
"--host=draco",
"--max-nodes=64",
"--name=protein",
"--yes",
],
)
result = cli_runner.invoke(cli.cli, ["analyze", "--directory=draco_gromacs"])
df = pd.read_csv(datafiles["analyze-many-rows.csv"], index_col=0)
test_output = PrintDataFrame(df, False) + "\n"
assert result.exit_code == 0
assert result.output == test_output
def test_check_file_extension(cli_runner, tmpdir):
"""Test that we check for all files needed to run NAMD benchmarks."""
@click.group()
def test_cli():
pass
@test_cli.command()
def test():
namd.check_input_file_exists('md')
output = 'ERROR File md.namd does not exist, but is needed for NAMD benchmarks.\n'
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 1
assert result.output == output
NEEDED_FILES = ['md.namd', 'md.psf', 'md.pdb']
with tmpdir.as_cwd():
# Create files first
for fn in NEEDED_FILES:
with open(fn, 'w') as fh:
fh.write('dummy file')
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 0
def test_analyze_plot(cli_runner, tmpdir, data):
with tmpdir.as_cwd():
result = cli_runner.invoke(cli.cli, [
'analyze',
'--directory={}'.format(data['analyze-files-gromacs'], '--plot'),
])
assert result.exit_code == 0
assert result.output == """ module nodes ns/day run time [min] gpu host ncores
0 gromacs/2016.3 1 98.147 15 False draco 32
1 gromacs/2016.3 2 178.044 15 False draco 64
2 gromacs/2016.3 3 226.108 15 False draco 96
3 gromacs/2016.3 4 246.973 15 False draco 128
4 gromacs/2016.3 5 254.266 15 False draco 160
"""
os.path.isfile("runtimes.pdf")
def test_analyze_with_errors(cli_runner, tmpdir, data):
"""Test that we warn the user of errors in the output files. Also test that we
show a question mark instead of a float in the corresponding cell.
"""
with tmpdir.as_cwd():
result = cli_runner.invoke(cli, [
"analyze", "--directory={}".format(data["analyze-files-w-errors"])
])
bundle = dtr.discover(data["analyze-files-w-errors"])
df = DataFrameFromBundle(bundle)
df = df.replace(np.nan, "?")
test_output = PrintDataFrame(df, False) + "\n"
assert result.exit_code == 0
assert result.output == test_output
def test_analyze_plot(cli_runner, tmpdir, data):
with tmpdir.as_cwd():
result = cli_runner.invoke(
cli.cli,
[
"analyze",
"--directory={}".format(data["analyze-files-gromacs"], "--plot"),
],
)
bundle = dtr.discover(data["analyze-files-gromacs"])
df = DataFrameFromBundle(bundle)
test_output = PrintDataFrame(df, False) + "\n"
assert result.exit_code == 0
assert result.output == test_output
os.path.isfile("runtimes.pdf")
def test_generate_simple_input_with_cpu_gpu(
cli_runner,
generate_output_create,
generate_output_finish,
generate_output_table,
module,
extensions,
tmpdir,
):
"""Test that we can generate benchmarks for CPUs and GPUs at once."""
with tmpdir.as_cwd():
for ext in extensions:
open("protein.{}".format(ext), "a").close()
result = cli_runner.invoke(
cli.cli,
[
"generate",
"--module={}".format(module),
"--template=draco",
"--max-nodes=4",
"--gpu",
"--name=protein",
"--yes",
],
)
output = generate_output_create(gpu=False).format(module)
output = (
"WARNING Cannot locate modules available on this host. "
"Not performing module name validation.\n" + output
)
output += generate_output_create(gpu=True).format(module)
output += generate_output_table(True)
output += generate_output_finish
if "namd" in module:
output = NAMD_WARNING_FORMATTED + output
# Test that we get a warning, if no module name validation is performed.
assert result.exit_code == 0
assert result.output == output
def test_validation(monkeypatch, tmpdir, cli_runner):
"""Test that we retrieve the correct module versions.
Names are retrieved from a given path and the module names and versions
are validated.
"""
@click.group()
def test_cli():
pass
@test_cli.command()
def test():
validate_module_name('wrong-format')
with tmpdir.as_cwd():
for k, v in DIR_STRUCTURE.items():
for k2, v2 in v.items():
os.makedirs(os.path.join(k, k2))
for v3 in v2:
open(os.path.join(k, k2, v3), 'a').close()
# Prepare path variable that we are going to monkeypatch for
# `get_available_modules`
dirs = ':'.join(
[os.path.join(os.getcwd(), x) for x in os.listdir(os.getcwd())])
monkeypatch.setenv('MODULEPATH', dirs)
modules = get_available_modules()
# Assert that the correct modules and their versions are returned.
assert set(modules['gromacs']) == set(
['2016.4', '5.1.4-plumed2.3', '2018.1'])
assert set(modules['namd']) == set(['123', '456'])
# Make sure we return a boolean if the module is available or not.
assert not validate_module_name('gromacs/123', modules)
assert validate_module_name('gromacs/2018.1', modules)
output = 'ERROR We were not able to determine the module name.\n'
result = cli_runner.invoke(test_cli, ['test'])
assert result.exit_code == 1
assert result.output == output
def test_submit_test_prompt_no(cli_runner, tmpdir, data):
"""Test whether prompt answer no works."""
with tmpdir.as_cwd():
result = cli_runner.invoke(
cli.cli,
["submit", "--directory={}".format(data["analyze-files-gromacs"])],
input="n\n",
)
df = pd.read_csv(data["analyze-files-gromacs-consolidated.csv"],
index_col=0)
s = PrintDataFrame(df, False)
output = (
"Benchmark Summary:\n" + s +
"\nThe above benchmarks will be submitted. Continue? [y/N]: n\n" +
"ERROR Exiting. No benchmarks submitted.\n")
assert result.exit_code == 1
assert result.output == output