def test_main_help(self, script_runner: ScriptRunner) -> None:
"""Test help option.
GIVEN the main command-line interface
WHEN the '-h' or '--help' argument is provided
THEN the help screen should appear
Parameters
----------
script_runner : ScriptRunner
Command-line runner
"""
result = script_runner.run(
"qaa",
"-h",
)
result2 = script_runner.run(
"qaa",
"--help",
)
assert "Usage:" in result.stdout
assert result.success
assert result.stdout == result2.stdout
def test_reindex(script_runner: ScriptRunner, asset_dir: Path,
reindex_data: Path, tmp_path: Path, docker_from: str):
ret = script_runner.run('bldr', 'reindex', docker_from, '--local-repo-dir',
reindex_data)
assert ret.success, "reindex command should be succeded"
assert ret.stderr == '', "nothing should be written to stderr"
expected_packages_content = asset_dir.joinpath(
'test-reindex-data', 'Packages.correct').read_text()
assert reindex_data.joinpath('Packages').read_text(
) == expected_packages_content, 'Generated Packages file should be identical to Packages.correct'
expected_sources_content = asset_dir.joinpath(
'test-reindex-data', 'Sources.correct').read_text()
assert reindex_data.joinpath('Sources').read_text(
) == expected_sources_content, 'Generated Sources file should be identical to Sources.correct'
def test_command_help(script_runner: ScriptRunner):
ret = script_runner.run('bldr', 'build', '--help')
assert ret.success
argument_list = [
'docker_from',
'package',
'--snapshot',
'--shell',
'--deb-build-options',
'--local-repo-dir',
'--nocache',
'--container-env',
'--hooks-dir',
]
for argument in argument_list:
assert argument in ret.stdout
def test_pca(self, script_runner: ScriptRunner, tmp_path: Path) -> None:
"""Test pca subcommand.
GIVEN a trajectory file
WHEN invoking the pca subcommand
THEN an several files will be written
Parameters
----------
script_runner : ScriptRunner
Command-line runner
tmp_path : Path
Temporary directory
"""
logfile = tmp_path.joinpath("pca.log")
result = script_runner.run(
"qaa",
"pca",
"-s",
TOPWW,
"-f",
TRJWW,
"-o",
tmp_path.as_posix(),
"-l",
logfile.as_posix(),
"-m",
"ca",
"--verbose",
)
assert result.success
assert logfile.exists()
# Test whether text data file exists
data = tmp_path.joinpath("projection.csv")
assert data.exists()
assert data.stat().st_size > 0
# Test whether binary data file exists
bin_data = tmp_path.joinpath("projection.npy")
assert bin_data.exists()
assert bin_data.stat().st_size > 0
assert tmp_path.joinpath("explained_variance_ratio.png").exists()
def test_help(self, script_runner: ScriptRunner) -> None:
"""Test help output.
GIVEN the cluster subcommand
WHEN the help option is invoked
THEN the help output should be displayed
Parameters
----------
script_runner : ScriptRunner
Command-line runner
"""
result = script_runner.run(
"qaa",
"plot",
"-h",
)
assert result.success
def test_failed_build(script_runner: ScriptRunner, asset_dir: Path,
docker_from: str, local_repo_dir: Path):
ret = script_runner.run('bldr',
'build',
docker_from,
"--local-repo-dir",
str(local_repo_dir),
cwd=asset_dir.joinpath('never-builds'))
assert not ret.success, "build command should be failed"
assert ret.stderr == '', "nothing should be written to stderr"
assert local_repo_dir.joinpath(
"Packages").is_file(), "Packages file should exist"
assert local_repo_dir.joinpath(
"Sources").is_file(), "Sources file should exist"
assert local_repo_dir.joinpath(
"Packages").stat().st_size == 0, "Packages file should be empty"
assert local_repo_dir.joinpath(
"Sources").stat().st_size == 0, "Sources file should be empty"
def test_graph_parser(
train_config: pathlib.Path,
treebank: pathlib.Path,
script_runner: pytest_console_scripts.ScriptRunner,
tmp_path: pathlib.Path,
):
ret = script_runner.run(
"graph_parser",
str(train_config),
"--train_file",
str(treebank),
"--dev_file",
str(treebank),
"--pred_file",
str(treebank),
"--out_dir",
str(tmp_path),
)
assert ret.success
def test_build(script_runner: ScriptRunner, asset_dir: Path, docker_from: str,
local_repo_dir: Path):
ret = script_runner.run('bldr',
'build',
docker_from,
"--local-repo-dir",
str(local_repo_dir),
cwd=asset_dir.joinpath('example-lang-C'))
assert ret.success, "build command should be succeded"
assert 'Your deb files are at' in ret.stdout
assert ret.stderr == '', "nothing should be written to stderr"
assert local_repo_dir.joinpath(
"Packages").is_file(), "Packages file should exist"
assert local_repo_dir.joinpath(
"Sources").is_file(), "Packages file should exist"
assert local_repo_dir.joinpath(
"Packages").stat().st_size > 0, "Packages file should be non-empty"
assert local_repo_dir.joinpath(
"Sources").stat().st_size > 0, "Sources file should be non-empty"
def test_cluster_npy(self, script_runner: ScriptRunner,
tmp_path: Path) -> None:
"""Test plot subcommand with binary NumPy input file.
GIVEN a data file
WHEN invoking the plot subcommand with cluster option
THEN saves a plotted image to disk
Parameters
----------
script_runner : ScriptRunner
Command-line runner
tmp_path : Path
Temporary directory
"""
outfile = tmp_path.joinpath("pca-cluster.png")
logfile = tmp_path.joinpath("plot.log")
result = script_runner.run(
"qaa",
"plot",
"-i",
CLUSTNPY,
"-c",
CENTNPY,
"--label",
LABELS,
"-o",
outfile.as_posix(),
"-l",
logfile.as_posix(),
"--pca",
"--cluster",
"--verbose",
)
assert result.success
assert logfile.exists()
assert outfile.exists()
assert outfile.stat().st_size > 0
def test_cluster_save(self, script_runner: ScriptRunner,
tmp_path: Path) -> None:
"""Test save option.
GIVEN trajectory, topology and data files
WHEN the '--save' option is provided
THEN PDB files will be saved
Parameters
----------
script_runner : ScriptRunner
Command-line runner
tmp_path : Path
Temporary directory
"""
logfile = tmp_path.joinpath("cluster.log")
result = script_runner.run(
"qaa",
"cluster",
"-s",
TOPWW,
"-f",
TRJWW,
"-i",
PROJ,
"-o",
tmp_path.as_posix(),
"-l",
logfile.as_posix(),
"--pca",
"--save",
"--verbose",
)
assert result.success
assert logfile.exists()
assert len(tuple(tmp_path.glob("*.pdb"))) == 3
def test_align_verbose(self, script_runner: ScriptRunner,
tmp_path: Path) -> None:
"""Test align subcommand with verbose option.
GIVEN a trajectory file
WHEN invoking the align subcommand
THEN an aligned trajectory and average structure file will be written
Parameters
----------
script_runner : ScriptRunner
Command-line runner
tmp_path : Path
Temporary directory
"""
logfile = tmp_path.joinpath("align.log")
result = script_runner.run(
"qaa",
"align",
"-s",
TOPWW,
"-f",
TRJWW,
"-r",
tmp_path.joinpath("average.pdb").as_posix(),
"-o",
tmp_path.joinpath("align.nc").as_posix(),
"-l",
logfile.as_posix(),
"-m",
"ca",
"--verbose",
)
assert result.success
assert logfile.exists()
def test_command_names_in_help(script_runner: ScriptRunner):
ret = script_runner.run('bldr', '--help')
assert ret.success
for command_name in ['build', 'shell', 'reindex', 'selftest']:
assert command_name in ret.stdout
def test_version(script_runner: ScriptRunner):
ret = script_runner.run('bldr', '--version')
assert ret.success, "version print should be succeded"
assert ret.stdout == 'bldr {}\n'.format(get_version())
assert ret.stderr == '', "nothing should be written to stderr"
def test_selftest(script_runner: ScriptRunner):
ret = script_runner.run('bldr', 'selftest')
assert ret.success, "selftest command should be succeded"
assert ret.stderr == '', "nothing should be written to stderr"
def test_no_arguments(self, script_runner: ScriptRunner):
args = ["stac-client"]
result = script_runner.run(*args, print_result=False)
assert result.success