Using ruff for linting #03

pyproject.toml

@@ -77,14 +77,14 @@ select = [
     # "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)
+    "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)
+    "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)
+    "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     # "YTT", # flake8-2020 (Detects outdated Python 2/3 compatibility issues)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)

src/lasso/diffcrash/diffcrash_run.py

@@ -14,7 +14,8 @@
 from pathlib import Path
 import psutil
 
-from ..logging import str_error, str_info, str_running, str_success, str_warn
+# from ..logging import str_error, str_info, str_running, str_success, str_warn
+from lasso.logging import str_error, str_info, str_running, str_success, str_warn
 
 # pylint: disable = too-many-lines
 

src/lasso/diffcrash/run.py

@@ -13,7 +13,7 @@
     parse_diffcrash_args,
 )
 
-from ..logging import str_error
+from lasso.logging import str_error
 
 
 def _parse_stages(start_stage: str, end_stage: str):

src/lasso/dimred/dimred_run.py

@@ -18,11 +18,15 @@
 from rich.table import Table
 from rich.text import Text
 
-from ..utils.rich_progress_bars import PlaceHolderBar, WorkingDots
-from .svd.clustering_betas import create_cluster_arg_dict, create_detector_arg_dict, group_betas
-from .svd.plot_beta_clusters import plot_clusters_js
-from .svd.pod_functions import calculate_v_and_betas
-from .svd.subsampling_methods import create_reference_subsample, remap_random_subsample
+from lasso.utils.rich_progress_bars import PlaceHolderBar, WorkingDots
+from lasso.dimred.svd.clustering_betas import (
+    create_cluster_arg_dict,
+    create_detector_arg_dict,
+    group_betas,
+)
+from lasso.dimred.svd.plot_beta_clusters import plot_clusters_js
+from lasso.dimred.svd.pod_functions import calculate_v_and_betas
+from lasso.dimred.svd.subsampling_methods import create_reference_subsample, remap_random_subsample
 
 # pylint: disable = too-many-lines
 

src/lasso/dimred/hashing.py

@@ -9,8 +9,7 @@
 from scipy import integrate
 from sklearn.neighbors import KDTree
 
-
-from ..math.stochastic import jensen_shannon_entropy
+from lasso.math.stochastic import jensen_shannon_entropy
 
 
 def _match_modes(

src/lasso/dimred/svd/subsampling_methods.py

@@ -7,7 +7,7 @@
 import numpy as np
 from sklearn.neighbors import NearestNeighbors
 
-from ...dyna import ArrayType, D3plot
+from lasso.dyna import ArrayType, D3plot
 
 
 def _mark_dead_eles(node_indexes: np.ndarray, alive_shells: np.ndarray) -> np.ndarray:

src/lasso/dyna/d3plot.py

@@ -15,15 +15,15 @@
 
 import numpy as np
 
-from ..femzip.femzip_api import FemzipAPI, FemzipBufferInfo, FemzipVariableCategory
-from ..io.binary_buffer import BinaryBuffer
-from ..io.files import open_file_or_filepath
-from ..logging import get_logger
-from ..plotting import plot_shell_mesh
-from .array_type import ArrayType
-from .d3plot_header import D3plotFiletype, D3plotHeader
-from .femzip_mapper import FemzipMapper, filter_femzip_variables
-from .filter_type import FilterType
+from lasso.femzip.femzip_api import FemzipAPI, FemzipBufferInfo, FemzipVariableCategory
+from lasso.io.binary_buffer import BinaryBuffer
+from lasso.io.files import open_file_or_filepath
+from lasso.logging import get_logger
+from lasso.plotting import plot_shell_mesh
+from lasso.dyna.array_type import ArrayType
+from lasso.dyna.d3plot_header import D3plotFiletype, D3plotHeader
+from lasso.dyna.femzip_mapper import FemzipMapper, filter_femzip_variables
+from lasso.dyna.filter_type import FilterType
 
 # pylint: disable = too-many-lines
 

src/lasso/dyna/d3plot_header.py

@@ -4,8 +4,8 @@
 import numpy as np
 import rich
 
-from ..io.binary_buffer import BinaryBuffer
-from ..logging import get_logger
+from lasso.io.binary_buffer import BinaryBuffer
+from lasso.logging import get_logger
 
 # We have a lot of docstrings here but even if not so, we want to contain the
 # code here.