Using ruff for linting #1 (#77)

* * remove black for linting
* bump ruff version
* add config for ruff rules (C only)
* fix linting issues

* format the codebase using ruff

Author: laraibg786

Taskfile.yml

@@ -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

pyproject.toml

@@ -25,7 +25,6 @@ dependencies = [
     "scipy==1.*",
     "numpy==1.*",
     "plotly==5.*",
-    # "attrs==23.*"
     "psutil==5.*",
     "rich==13.*",
     "pandas==2.*",
@@ -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.*",
@@ -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

src/lasso/diffcrash/diffcrash_run.py

@@ -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)
 
@@ -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)
@@ -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"]
 
@@ -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)
@@ -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)
@@ -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:
@@ -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)
@@ -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
@@ -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:
@@ -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:
@@ -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
@@ -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:
@@ -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))
@@ -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)
@@ -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))
@@ -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))
@@ -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))
 
@@ -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))
@@ -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))
@@ -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))

src/lasso/diffcrash/run.py

@@ -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(
@@ -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)