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Merged
merged 2 commits into from
Apr 22, 2025
Merged

Using ruff for linting #01 #77

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ff78369
* remove black for linting
laraibg786 Apr 22, 2025
df3dc79
format the codebase using ruff
laraibg786 Apr 22, 2025
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2 changes: 1 addition & 1 deletion Taskfile.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ tasks:
lint:
desc: Lints the code and reports on issues.
cmds:
- uv run black --check .
- uv run ruff check .
# - uv run ruff format . --check

build:
desc: Builds the python package
Expand Down
56 changes: 47 additions & 9 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,6 @@ dependencies = [
"scipy==1.*",
"numpy==1.*",
"plotly==5.*",
# "attrs==23.*"
"psutil==5.*",
"rich==13.*",
"pandas==2.*",
Expand All @@ -43,8 +42,7 @@ dimred = "lasso.dimred.run:main"
dev = [
"pytest==8.*",
"pytest-cov==5.*",
"black==24.*",
"ruff==0.3.*",
"ruff==0.11.*",
"mkdocs==1.*",
"mkdocs-material==9.*",
"mkdocstrings[python]==0.*",
Expand All @@ -58,10 +56,50 @@ dev = [
requires = ["setuptools>=78", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

[tool.black]
# We allow longer lines since 80 is quite short
line-length=100
[tool.ruff]
required-version = "==0.11.*"
line-length = 100
indent-width = 4
preview = true

[tool.flake8]
exclude = [".git", "*migrations*"]
max-line-length = 100
# Output serialization format for violations. The default serialization
# format is "full" [env: RUFF_OUTPUT_FORMAT=] [possible values:
# concise, full, json, json-lines, junit, grouped, github, gitlab,
# pylint, rdjson, azure, sarif]
output-format = "grouped"

[tool.ruff.lint]
isort.lines-after-imports = 2
select = [
"C", # Complexity checks (e.g., McCabe complexity, comprehensions)
# "ANN001", "ANN201", "ANN401", # flake8-annotations (required strict type annotations for public functions)
# "S", # flake8-bandit (checks basic security issues in code)
# "BLE", # flake8-blind-except (checks the except blocks that do not specify exception)
# "FBT", # flake8-boolean-trap (ensure that boolean args can be used with kw only)
# "E", # pycodestyle errors (PEP 8 style guide violations)
# "W", # pycodestyle warnings (e.g., extra spaces, indentation issues)
# "DOC", # pydoclint issues (e.g., extra or missing return, yield, warnings)
# "A", # flake8-buitins (check variable and function names to not shadow builtins)
# "N", # Naming convention checks (e.g., PEP 8 variable and function names)
# "F", # Pyflakes errors (e.g., unused imports, undefined variables)
# "I", # isort (Ensures imports are sorted properly)
# "B", # flake8-bugbear (Detects likely bugs and bad practices)
# "TID", # flake8-tidy-imports (Checks for banned or misplaced imports)
# "UP", # pyupgrade (Automatically updates old Python syntax)
# "YTT", # flake8-2020 (Detects outdated Python 2/3 compatibility issues)
# "FLY", # flynt (Converts old-style string formatting to f-strings)
# "PIE", # flake8-pie
# "PL", # pylint
# "RUF", # Ruff-specific rules (Additional optimizations and best practices)
]

ignore = [
"PLR2004", # [magic-value-comparision](https://docs.astral.sh/ruff/rules/magic-value-comparison)
"C90", # [mccabe](https://docs.astral.sh/ruff/rules/#mccabe-c90)
]

[tool.ruff.lint.per-file-ignores]

[tool.ruff.format]
docstring-code-format = true
skip-magic-trailing-comma = true
34 changes: 4 additions & 30 deletions src/lasso/diffcrash/diffcrash_run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -287,7 +287,6 @@ def __init__(
self.n_processes = self._parse_n_processes(n_processes)

def _setup_logger(self) -> logging.Logger:

# better safe than sorry
os.makedirs(self.logfile_dir, exist_ok=True)

Expand All @@ -310,7 +309,6 @@ def _setup_logger(self) -> logging.Logger:
return logger

def _parse_diffcrash_home(self, diffcrash_home) -> str:

diffcrash_home_ok = len(diffcrash_home) != 0

msg = self._msg_option.format("diffcrash-home", diffcrash_home)
Expand All @@ -328,7 +326,6 @@ def _parse_diffcrash_home(self, diffcrash_home) -> str:
return diffcrash_home

def _parse_crash_code(self, crash_code) -> str:

# these guys are allowed
valid_crash_codes = ["dyna", "radioss", "pam"]

Expand All @@ -340,16 +337,14 @@ def _parse_crash_code(self, crash_code) -> str:

if not crash_code_ok:
err_msg = (
f"Invalid crash code '{crash_code}'. "
f"Please use one of: {str(valid_crash_codes)}"
f"Invalid crash code '{crash_code}'. Please use one of: {str(valid_crash_codes)}"
)
self.logger.error(err_msg)
raise RuntimeError(str_error(err_msg))

return crash_code

def _parse_reference_run(self, reference_run) -> str:

reference_run_ok = Path(reference_run).is_file()

msg = self._msg_option.format("reference-run", reference_run)
Expand All @@ -364,7 +359,6 @@ def _parse_reference_run(self, reference_run) -> str:
return reference_run

def _parse_use_id_mapping(self, use_id_mapping) -> bool:

msg = self._msg_option.format("use-id-mapping", use_id_mapping)
print(str_info(msg))
self.logger.info(msg)
Expand All @@ -386,7 +380,6 @@ def _parse_simulation_runs(
reference_run: str,
exclude_runs: typing.Sequence[str],
):

# search all denoted runs
simulation_runs = []
for pattern in simulation_run_patterns:
Expand Down Expand Up @@ -442,19 +435,16 @@ def natural_keys(text):
return simulation_runs

def _parse_config_file(self, config_file) -> Union[str, None]:

_msg_config_file = ""
if len(config_file) > 0 and not Path(config_file).is_file():
config_file = None
_msg_config_file = f"Can not find config file '{config_file}'"

# missing config file
else:

config_file = None
_msg_config_file = (
"Config file missing. "
"Consider specifying the path with the option '--config-file'."
"Config file missing. Consider specifying the path with the option '--config-file'."
)

msg = self._msg_option.format("config-file", config_file)
Expand All @@ -468,7 +458,6 @@ def _parse_config_file(self, config_file) -> Union[str, None]:
return config_file

def _parse_parameter_file(self, parameter_file) -> Union[None, str]:

_msg_parameter_file = ""
if len(parameter_file) > 0 and not Path(parameter_file).is_file():
parameter_file = None
Expand All @@ -492,7 +481,6 @@ def _parse_parameter_file(self, parameter_file) -> Union[None, str]:
return parameter_file

def _parse_n_processes(self, n_processes) -> int:

print(str_info(self._msg_option.format("n-processes", n_processes)))

if n_processes <= 0:
Expand Down Expand Up @@ -640,7 +628,6 @@ def run_import(self, pool: futures.ThreadPoolExecutor):
# entry 0 is the reference run, thus we start at 1
# pylint: disable = consider-using-enumerate
for i_filepath in range(len(self.simulation_runs)):

# parameter file missing
if self.parameter_file is None:
if self.use_id_mapping:
Expand Down Expand Up @@ -691,7 +678,6 @@ def run_import(self, pool: futures.ThreadPoolExecutor):
return_code_future.done() for return_code_future in return_code_futures
)
while n_imports_finished != len(return_code_futures):

# check again
n_new_imports_finished = sum(
return_code_future.done() for return_code_future in return_code_futures
Expand All @@ -717,7 +703,6 @@ def run_import(self, pool: futures.ThreadPoolExecutor):

# print failure
if any(return_code != 0 for return_code in return_codes):

n_failed_runs = 0
for i_run, return_code in enumerate(return_codes):
if return_code != 0:
Expand All @@ -739,7 +724,6 @@ def run_import(self, pool: futures.ThreadPoolExecutor):
# check log files
messages = self.check_if_logfiles_show_success("DFC_Import_*.log")
if messages:

# print failure
msg = f"Running Imports ... done in {time.time() - start_time:.2f}s "
print(str_error(msg))
Expand Down Expand Up @@ -774,14 +758,12 @@ def run_math(self, pool: futures.ThreadPoolExecutor):

start_time = time.time()
return_code_future = pool.submit(
run_subprocess,
[self.diffcrash_home / f"DFC_Math_{self.crash_code}", self.project_dir],
run_subprocess, [self.diffcrash_home / f"DFC_Math_{self.crash_code}", self.project_dir]
)
return_code = return_code_future.result()

# check return code
if return_code != 0:

msg = f"Running Math ... done in {time.time() - start_time:.2f}s "
print(str_error(msg))
self.logger.error(msg)
Expand All @@ -793,7 +775,6 @@ def run_math(self, pool: futures.ThreadPoolExecutor):
# check logs
messages = self.check_if_logfiles_show_success("DFC_MATH*.log")
if messages:

# print failure
msg = f"Running Math ... done in {time.time() - start_time:.2f}s "
print(str_error(msg))
Expand Down Expand Up @@ -889,7 +870,6 @@ def run_export(self, pool: futures.ThreadPoolExecutor):
# check logs
messages = self.check_if_logfiles_show_success("DFC_Export_*")
if messages:

# print failure
msg = f"Running Export ... done in {time.time() - start_time:.2f}s "
print(str_error(msg))
Expand All @@ -900,10 +880,7 @@ def run_export(self, pool: futures.ThreadPoolExecutor):
print(str_error(msg))
self.logger.error(msg)

msg = (
"At least one export failed. "
f"Please check the log files in '{self.logfile_dir}'."
)
msg = f"At least one export failed. Please check the log files in '{self.logfile_dir}'."
self.logger.error(msg)
raise RuntimeError(str_error(msg))

Expand Down Expand Up @@ -945,7 +922,6 @@ def run_matrix(self, pool: futures.ThreadPoolExecutor):

# check return code
if return_code != 0:

# print failure
msg = f"Running Matrix ... done in {time.time() - start_time:.2f}s "
print(str_error(msg))
Expand All @@ -958,7 +934,6 @@ def run_matrix(self, pool: futures.ThreadPoolExecutor):
# check log file
messages = self.check_if_logfiles_show_success("DFC_Matrix_*")
if messages:

# print failure
msg = f"Running Matrix ... done in {time.time() - start_time:.2f}s "
print(str_error(msg))
Expand Down Expand Up @@ -1021,7 +996,6 @@ def run_eigen(self, pool: futures.ThreadPoolExecutor):
# check log file
messages = self.check_if_logfiles_show_success("DFC_Matrix_*")
if messages:

# print failure
msg = f"Running Eigen ... done in {time.time() - start_time:.2f}s "
print(str_error(msg))
Expand Down
2 changes: 0 additions & 2 deletions src/lasso/diffcrash/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@


def _parse_stages(start_stage: str, end_stage: str):

# check validity
if start_stage not in DC_STAGES or end_stage not in DC_STAGES:
raise ValueError(
Expand Down Expand Up @@ -76,7 +75,6 @@ def main():

# initiate threading pool for handling jobs
with futures.ThreadPoolExecutor(max_workers=diffcrash_run.n_processes) as pool:

# setup
if start_stage_index <= DC_STAGES.index(DC_STAGE_SETUP) <= end_stage_index:
diffcrash_run.run_setup(pool)
Expand Down
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