Ruff tardis/io (#2827)

* ruff io auto safe fixes

* ruff io auto unsafe fixes

* black tardis/io/util.py

* black tardis/io/model/readers/arepo.py

tardis/io/atom_data/__init__.py

@@ -1,6 +1,6 @@
 """
-Getting and handling the atomic data. 
+Getting and handling the atomic data.
 """
 
-from tardis.io.atom_data.base import AtomData
 from tardis.io.atom_data.atom_web_download import download_atom_data
+from tardis.io.atom_data.base import AtomData

tardis/io/atom_data/base.py

@@ -1,9 +1,9 @@
 import logging
+from dataclasses import dataclass
 
 import numpy as np
 import pandas as pd
 from astropy.units import Quantity
-from dataclasses import dataclass
 
 from tardis import constants as const
 from tardis.io.atom_data.collision_data import (
@@ -264,7 +264,7 @@ def from_hdf(cls, fname=None):
             )
             if nonavailable:
                 logger.info(
-                    "Non provided Atomic Data: {0}".format(
+                    "Non provided Atomic Data: {}".format(
                         ", ".join(nonavailable)
                     )
                 )

tardis/io/atom_data/util.py

@@ -1,12 +1,11 @@
-import os
 import logging
+import os
 from pathlib import Path
 
-from tardis.io.configuration.config_internal import get_data_dir
 from tardis.io.atom_data.atom_web_download import (
     get_atomic_repo_config,
-    download_atom_data,
 )
+from tardis.io.configuration.config_internal import get_data_dir
 
 logger = logging.getLogger(__name__)
 
@@ -25,7 +24,6 @@ def resolve_atom_data_fname(fname):
         : Path
         resolved fpath
     """
-
     fname = Path(fname)
     if os.path.exists(fname):
         return fname
@@ -41,13 +39,13 @@ def resolve_atom_data_fname(fname):
     atom_data_name = fname.stem
     atom_repo_config = get_atomic_repo_config()
     if atom_data_name in atom_repo_config:
-        raise IOError(
+        raise OSError(
             f"Atom Data {fname} not found in path or in TARDIS data repo - it is available as download:\n"
             f"from tardis.io.atom_data.util import download_atom_data\n"
             f"download_atom_data('{atom_data_name}')"
         )
 
-    raise IOError(
+    raise OSError(
         f"Atom Data {fname} is not found in current path or in TARDIS data repo. {atom_data_name} "
         "is also not a standard known TARDIS atom dataset."
     )

tardis/io/configuration/config_internal.py

@@ -1,11 +1,13 @@
-import logging, shutil
-import yaml
+import logging
 import os
+import shutil
 from pathlib import Path
 
-from tardis import __path__ as TARDIS_PATH
+import yaml
 from astropy.config import get_config_dir
 
+from tardis import __path__ as TARDIS_PATH
+
 TARDIS_PATH = Path(TARDIS_PATH[0])
 DEFAULT_CONFIG_PATH = (
     TARDIS_PATH / "data" / "default_tardis_internal_config.yml"
@@ -46,6 +48,6 @@ def get_data_dir():
         data_dir = DEFAULT_DATA_DIR
 
     if not os.path.exists(data_dir):
-        raise IOError(f"Data directory specified in {data_dir} does not exist")
+        raise OSError(f"Data directory specified in {data_dir} does not exist")
 
     return Path(data_dir)

tardis/io/configuration/config_reader.py

@@ -85,7 +85,7 @@ def __init__(self, value=None):
                 "Cannot specify both model and csvy_model in main config file."
             )
         if hasattr(self, "csvy_model"):
-            model = dict()
+            model = {}
             csvy_model_path = os.path.join(self.config_dirname, self.csvy_model)
             csvy_yml = load_yaml_from_csvy(csvy_model_path)
             if "v_inner_boundary" in csvy_yml:
@@ -109,13 +109,13 @@ def __setitem__(self, key, value):
         dict.__setitem__(self, key, value)
 
     def __getitem__(self, key):
-        return super(ConfigurationNameSpace, self).__getitem__(key)
+        return super().__getitem__(key)
 
     def __getattr__(self, item):
         if item in self:
             return self[item]
         else:
-            super(ConfigurationNameSpace, self).__getattribute__(item)
+            super().__getattribute__(item)
 
     __setattr__ = __setitem__
 
@@ -447,7 +447,7 @@ def parse_convergence_section(convergence_section_dict):
         return convergence_section_dict
 
     def __init__(self, config_dict):
-        super(Configuration, self).__init__(config_dict)
+        super().__init__(config_dict)
 
 
 def quantity_representer(dumper, data):

tardis/io/configuration/config_validator.py

@@ -40,13 +40,12 @@ def set_defaults(validator, properties, instance, schema):
                 if "default" in subschema:
                     instance.setdefault(property, subschema["default"])
 
-        for error in validate_properties(
+        yield from validate_properties(
             validator,
             properties,
             instance,
             schema,
-        ):
-            yield error
+        )
 
     return validators.extend(
         validator_class,

tardis/io/configuration/tests/test_config_reader.py

@@ -1,16 +1,14 @@
 # tests for the config reader module
-import os
-from attr import validate
-import pytest
 import pandas as pd
-from numpy.testing import assert_almost_equal
+import pytest
+from astropy.units import Quantity
 from jsonschema.exceptions import ValidationError
+from numpy.testing import assert_almost_equal
 
 from tardis.io.configuration import config_reader
-from astropy.units import Quantity
 from tardis.io.configuration.config_reader import Configuration
-from tardis.plasma.exceptions import PlasmaConfigError
 from tardis.plasma.assembly.legacy_assembly import assemble_plasma
+from tardis.plasma.exceptions import PlasmaConfigError
 
 
 def test_convergence_section_parser():

tardis/io/configuration/tests/test_configuration_namespace.py

@@ -1,10 +1,11 @@
-from tardis.io.configuration.config_reader import ConfigurationNameSpace
-import pytest
-from astropy import units as u
 import os
 
+import pytest
+from astropy import units as u
 from numpy.testing import assert_almost_equal
 
+from tardis.io.configuration.config_reader import ConfigurationNameSpace
+
 simple_config_dict = {
     "a": {"b": {"param1": 1, "param2": [0, 1, 2 * u.km], "param3": 4.0 * u.km}}
 }

tardis/io/logger/__init__.py

@@ -1,3 +1,3 @@
 """
-Managing the logging output. 
+Managing the logging output.
 """

tardis/io/logger/colored_logger.py

@@ -80,4 +80,3 @@ def __init__(self, name):
         console.setFormatter(color_formatter)
 
         self.addHandler(console)
-        return

tardis/io/logger/logger.py

@@ -1,7 +1,7 @@
 import logging
 import sys
 
-from tardis.io.logger.colored_logger import ColoredFormatter, formatter_message
+from tardis.io.logger.colored_logger import ColoredFormatter
 
 logging.captureWarnings(True)
 logger = logging.getLogger("tardis")
@@ -25,7 +25,7 @@
 DEFAULT_SPECIFIC_STATE = False
 
 
-class FilterLog(object):
+class FilterLog:
     """
     Filter Log Class for Filtering Logging Output
     to a particular level
@@ -77,7 +77,6 @@ def logging_state(log_level, tardis_config, specific_log_level):
     specific_log_level: boolean
         Allows to set specific logging levels. Logs of the `log_level` level would be output.
     """
-
     if "debug" in tardis_config:
         specific_log_level = (
             tardis_config["debug"]["specific_log_level"]
@@ -115,7 +114,7 @@ def logging_state(log_level, tardis_config, specific_log_level):
             specific_log_level = tardis_config["debug"]["specific_log_level"]
 
     logging_level = logging_level.upper()
-    if not logging_level in LOGGING_LEVELS:
+    if logging_level not in LOGGING_LEVELS:
         raise ValueError(
             f"Passed Value for log_level = {logging_level} is Invalid. Must be one of the following {list(LOGGING_LEVELS.keys())}"
         )

tardis/io/logger/montecarlo_tracking.py

@@ -1,5 +1,4 @@
 import logging
-from functools import wraps
 
 DEBUG_MODE = False
 LOG_FILE = False

tardis/io/logger/tests/test_logging.py

@@ -1,11 +1,11 @@
-import pytest
 import logging
 
+import pytest
+
+from tardis import run_tardis
 from tardis.io.configuration.config_reader import Configuration
-from tardis.simulation import Simulation
 from tardis.io.logger.logger import LOGGING_LEVELS
-from tardis import run_tardis
-import pytest
+from tardis.simulation import Simulation
 
 pytestmark = pytest.mark.skip(
     reason="logging testing slow and disabled for now"
@@ -67,7 +67,7 @@ def test_logging_config(
             specific_log_level=specific_log_level,
         )
         for record in caplog.records:
-            if specific_log_level == True:
+            if specific_log_level is True:
                 assert record.levelno == LOGGING_LEVELS[log_level.upper()]
             else:
                 assert record.levelno >= LOGGING_LEVELS[log_level.upper()]
@@ -85,7 +85,7 @@ def test_logging_config_yaml(
         caplog.clear()
         run_tardis(config=config)
         for record in caplog.records:
-            if specific_log_level == True:
+            if specific_log_level is True:
                 assert record.levelno == LOGGING_LEVELS[log_level.upper()]
             else:
                 assert record.levelno >= LOGGING_LEVELS[log_level.upper()]
@@ -107,7 +107,7 @@ def test_logging_both_specified(
             specific_log_level=specific_log_level,
         )
         for record in caplog.records:
-            if specific_log_level == True:
+            if specific_log_level is True:
                 assert record.levelno == LOGGING_LEVELS[log_level.upper()]
             else:
                 assert record.levelno >= LOGGING_LEVELS[log_level.upper()]

tardis/io/model/__init__.py

@@ -1,4 +1,3 @@
-from tardis.io.model.readers.stella import read_stella_model
-
 # from tardis.io.model.stella import read_stella_model
 from tardis.io.model.readers.cmfgen import read_cmfgen_model
+from tardis.io.model.readers.stella import read_stella_model