def test_GenomeGroup_add_folder_with_exclusions(tmp_path):
"""Ensure excluded files are not used in the GenomeGroup add folder method."""
f = tmp_path / "folder"
f.mkdir()
test_files = [
tmp_path / "first.py",
tmp_path / "second.py",
tmp_path / "test_first.py",
tmp_path / "test_second.py",
tmp_path / "third_test.py",
f / "third.py",
f / "test_third.py",
]
exclude = [(tmp_path / "second.py").resolve(), (f / "third.py").resolve()]
expected = "first.py"
# need at least on valid location operation to return a value for trees/targets
for tf in test_files:
with open(tf, "w") as temp_py:
temp_py.write("x: int = 1 + 2")
ggrp = GenomeGroup()
ggrp.add_folder(tmp_path, exclude_files=exclude)
assert len(ggrp) == 1
assert list(ggrp.keys())[0].name == expected
def get_genome_group(src_loc: Path, config: Config) -> GenomeGroup:
"""Get the ``GenomeGroup`` based on ``src_loc`` and ``config``.
``Config`` is used to set global filter codes and exclude files on group creation.
Args:
src_loc: Path, can be directory or file
config: the running config object
Returns:
``GenomeGroup`` based on ``src_loc`` and config.
"""
ggrp = GenomeGroup()
# check if src_loc is a single file, otherwise assume it's a directory
if src_loc.is_file():
ggrp.add_file(source_file=src_loc)
else:
ggrp.add_folder(source_folder=src_loc,
exclude_files=config.exclude_files,
ignore_test_files=True)
if config.filter_codes:
LOGGER.info("Category restriction, chosen categories: %s",
sorted(config.filter_codes))
ggrp.set_filter(filter_codes=config.filter_codes)
for k, genome in ggrp.items():
LOGGER.info(
"%s",
colorize_output(
f"{len(genome.targets)} mutation targets found in {genome.source_file} AST.",
"green" if len(genome.targets) > 0 else "yellow",
),
)
for e in config.exclude_files:
LOGGER.info("%s", colorize_output(f"{e.resolve()} excluded.",
"yellow"))
return ggrp
def test_GenomeGroup_folder_exception():
"""Invalid folders raise a type error."""
with pytest.raises(TypeError):
ggrp = GenomeGroup()
ggrp.add_folder("somethingrandom")
