From a12d3f793137db5dbc81c35acc125b09f16740c6 Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Wed, 25 Sep 2024 22:30:46 +0530
Subject: [PATCH] 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               |  4 +-
 tardis/io/atom_data/base.py                   |  4 +-
 tardis/io/atom_data/util.py                   | 10 ++---
 tardis/io/configuration/config_internal.py    | 10 +++--
 tardis/io/configuration/config_reader.py      |  8 ++--
 tardis/io/configuration/config_validator.py   |  5 +--
 .../configuration/tests/test_config_reader.py | 10 ++---
 .../tests/test_configuration_namespace.py     |  7 +--
 tardis/io/logger/__init__.py                  |  2 +-
 tardis/io/logger/colored_logger.py            |  1 -
 tardis/io/logger/logger.py                    |  7 ++-
 tardis/io/logger/montecarlo_tracking.py       |  1 -
 tardis/io/logger/tests/test_logging.py        | 14 +++---
 tardis/io/model/__init__.py                   |  3 +-
 tardis/io/model/readers/arepo.py              | 43 ++++++-------------
 tardis/io/model/readers/artis.py              |  3 +-
 tardis/io/model/readers/base.py               | 13 +++---
 tardis/io/model/readers/blondin_toymodel.py   |  4 +-
 tardis/io/model/readers/cmfgen.py             |  5 +--
 tardis/io/model/readers/cmfgen_deprecated.py  |  9 ++--
 tardis/io/model/readers/csvy.py               |  7 +--
 tardis/io/model/readers/generic_readers.py    |  1 -
 tardis/io/model/readers/stella.py             |  1 -
 .../model/readers/tests/test_arepo_parser.py  | 22 +++++-----
 .../model/readers/tests/test_ascii_readers.py | 12 ++----
 .../model/readers/tests/test_cmfgen_reader.py |  5 +--
 .../model/readers/tests/test_csvy_reader.py   | 12 +++---
 .../model/readers/tests/test_stella_reader.py |  6 +--
 tardis/io/tests/test_HDFWriter.py             |  4 +-
 tardis/io/tests/test_atomic.py                |  4 +-
 tardis/io/tests/test_decay.py                 |  4 +-
 tardis/io/tests/test_model_reader.py          |  1 -
 tardis/io/util.py                             | 11 ++---
 33 files changed, 104 insertions(+), 149 deletions(-)

diff --git a/tardis/io/atom_data/__init__.py b/tardis/io/atom_data/__init__.py
index 39d2bbdfef1..af7e471a7dd 100644
--- a/tardis/io/atom_data/__init__.py
+++ b/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
diff --git a/tardis/io/atom_data/base.py b/tardis/io/atom_data/base.py
index 3f53408a210..33e8e4bbca2 100644
--- a/tardis/io/atom_data/base.py
+++ b/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)
                     )
                 )
diff --git a/tardis/io/atom_data/util.py b/tardis/io/atom_data/util.py
index ce4b2765bce..3f4f5eb52b7 100644
--- a/tardis/io/atom_data/util.py
+++ b/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."
     )
diff --git a/tardis/io/configuration/config_internal.py b/tardis/io/configuration/config_internal.py
index 5c622be66ae..408eb80f66a 100644
--- a/tardis/io/configuration/config_internal.py
+++ b/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)
diff --git a/tardis/io/configuration/config_reader.py b/tardis/io/configuration/config_reader.py
index bc67fe0324f..c4efb949031 100644
--- a/tardis/io/configuration/config_reader.py
+++ b/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):
diff --git a/tardis/io/configuration/config_validator.py b/tardis/io/configuration/config_validator.py
index 5205ac9d205..dd061b311c1 100644
--- a/tardis/io/configuration/config_validator.py
+++ b/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,
diff --git a/tardis/io/configuration/tests/test_config_reader.py b/tardis/io/configuration/tests/test_config_reader.py
index 784797a2f03..5fb3557c268 100644
--- a/tardis/io/configuration/tests/test_config_reader.py
+++ b/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():
diff --git a/tardis/io/configuration/tests/test_configuration_namespace.py b/tardis/io/configuration/tests/test_configuration_namespace.py
index c9445c8f1ec..3d32f476e56 100644
--- a/tardis/io/configuration/tests/test_configuration_namespace.py
+++ b/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}}
 }
diff --git a/tardis/io/logger/__init__.py b/tardis/io/logger/__init__.py
index 78bc5622358..d8a1c931684 100644
--- a/tardis/io/logger/__init__.py
+++ b/tardis/io/logger/__init__.py
@@ -1,3 +1,3 @@
 """
-Managing the logging output. 
+Managing the logging output.
 """
diff --git a/tardis/io/logger/colored_logger.py b/tardis/io/logger/colored_logger.py
index a03d88a1fac..3f049c93a68 100644
--- a/tardis/io/logger/colored_logger.py
+++ b/tardis/io/logger/colored_logger.py
@@ -80,4 +80,3 @@ def __init__(self, name):
         console.setFormatter(color_formatter)
 
         self.addHandler(console)
-        return
diff --git a/tardis/io/logger/logger.py b/tardis/io/logger/logger.py
index 70fcabcc4e9..44da5fa187f 100644
--- a/tardis/io/logger/logger.py
+++ b/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())}"
         )
diff --git a/tardis/io/logger/montecarlo_tracking.py b/tardis/io/logger/montecarlo_tracking.py
index f3d37fa4876..d4216a0f031 100644
--- a/tardis/io/logger/montecarlo_tracking.py
+++ b/tardis/io/logger/montecarlo_tracking.py
@@ -1,5 +1,4 @@
 import logging
-from functools import wraps
 
 DEBUG_MODE = False
 LOG_FILE = False
diff --git a/tardis/io/logger/tests/test_logging.py b/tardis/io/logger/tests/test_logging.py
index 7ab6d8e638b..ee6df7d5c06 100644
--- a/tardis/io/logger/tests/test_logging.py
+++ b/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()]
diff --git a/tardis/io/model/__init__.py b/tardis/io/model/__init__.py
index 9a877f17b98..7f3011d3ee5 100644
--- a/tardis/io/model/__init__.py
+++ b/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
diff --git a/tardis/io/model/readers/arepo.py b/tardis/io/model/readers/arepo.py
index a60acd983a8..98a1bc63b94 100644
--- a/tardis/io/model/readers/arepo.py
+++ b/tardis/io/model/readers/arepo.py
@@ -1,8 +1,8 @@
-import os
 import argparse
+import os
 
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 from scipy import stats
 
 
@@ -45,7 +45,6 @@ def __init__(
             of-sight to the x-axis. Only usable with snapshots.
             Default: 0.0
         """
-
         try:
             import gadget_snap
         except ModuleNotFoundError:
@@ -145,7 +144,6 @@ def __init__(self, pos, vel, rho, mass, xnuc, time):
             Time of the data
 
         """
-
         self.pos = pos
         self.vel = vel
         self.rho = rho
@@ -190,7 +188,6 @@ def plot_profile(self, save=None, dpi=600, **kwargs):
         -------
         fig : matplotlib figure object
         """
-
         fig, (ax1, ax2) = plt.subplots(2, 1, figsize=[9.8, 9.6])
 
         # Positive direction plots
@@ -253,7 +250,7 @@ def plot_profile(self, save=None, dpi=600, **kwargs):
             labels,
             loc="upper left",
             bbox_to_anchor=(1.05, 1.05),
-            title="Time = {:.2f} s".format(self.time),
+            title=f"Time = {self.time:.2f} s",
         )
         if save is not None:
             plt.savefig(
@@ -280,7 +277,6 @@ def rebin(self, nshells):
         self : Profile object
 
         """
-
         self.vel_prof_p, bins_p = stats.binned_statistic(
             self.pos_prof_p,
             self.vel_prof_p * self.mass_prof_p,
@@ -406,7 +402,6 @@ def export(
         filename : str
             Name of the actual saved file
         """
-
         # Find a free filename
         if str(filename).endswith(".csvy"):
             filename = str(filename).replace(".csvy", "")
@@ -426,12 +421,8 @@ def export(
                     [
                         "---\n",
                         "name: csvy_full\n",
-                        "model_density_time_0: {:g} day\n".format(
-                            self.time / (3600 * 24)
-                        ),  # TODO astropy units
-                        "model_isotope_time_0: {:g} day\n".format(
-                            self.time / (3600 / 24)
-                        ),  # TODO astropy units
+                        f"model_density_time_0: {self.time / (3600 * 24):g} day\n",  # TODO astropy units
+                        f"model_isotope_time_0: {self.time / (3600 / 24):g} day\n",  # TODO astropy units
                         "description: Config file for TARDIS from Arepo snapshot.\n",
                         "tardis_model_config_version: v1.0\n",
                         "datatype:\n",
@@ -450,27 +441,19 @@ def export(
                 f.write(
                     "".join(
                         [
-                            "    -  name: %s\n" % spec.capitalize(),
-                            "       desc: fractional %s abundance.\n"
-                            % spec.capitalize(),
+                            f"    -  name: {spec.capitalize()}\n",
+                            f"       desc: fractional {spec.capitalize()} abundance.\n",
                         ]
                     )
                 )
 
-            f.write(
-                "".join(
-                    [
-                        "\n",
-                        "---\n",
-                    ]
-                )
-            )
+            f.write("\n---\n")
 
             # WRITE DATA
             datastring = ["velocity,", "density,"]
             for spec in self.species[:-1]:
-                datastring.append("%s," % spec.capitalize())
-            datastring.append("%s" % self.species[-1].capitalize())
+                datastring.append(f"{spec.capitalize()},")
+            datastring.append(f"{self.species[-1].capitalize()}")
             f.write("".join(datastring))
 
             # Rebin data to nshells
@@ -498,8 +481,8 @@ def export(
             for i in inds:
                 f.write("\n")
                 for ii in range(len(exp) - 1):
-                    f.write("%g," % exp[ii][i])
-                f.write("%g" % exp[-1][i])
+                    f.write(f"{exp[ii][i]:g},")
+                f.write(f"{exp[-1][i]:g}")
 
         return filename
 
@@ -553,7 +536,6 @@ def create_profile(
         profile : ConeProfile object
 
         """
-
         # Convert Cartesian coordinates into cylindrical coordinates
         # P(x,y,z) -> P(x,r,theta)
         cyl = np.array(
@@ -720,7 +702,6 @@ def create_profile(
         profile : FullProfile object
 
         """
-
         pos_p = np.sqrt(
             (self.pos[0]) ** 2 + (self.pos[1]) ** 2 + (self.pos[2]) ** 2
         ).flatten()
diff --git a/tardis/io/model/readers/artis.py b/tardis/io/model/readers/artis.py
index 21a353d0d94..e2963cdb57a 100644
--- a/tardis/io/model/readers/artis.py
+++ b/tardis/io/model/readers/artis.py
@@ -1,6 +1,6 @@
 import numpy as np
-from astropy import units as u
 import pandas as pd
+from astropy import units as u
 
 
 def read_artis_density(fname):
@@ -24,7 +24,6 @@ def read_artis_density(fname):
     data : pandas.DataFrame
         data frame containing index, velocity (in km/s) and density
     """
-
     with open(fname) as fh:
         for i, line in enumerate(open(fname)):
             if i == 0:
diff --git a/tardis/io/model/readers/base.py b/tardis/io/model/readers/base.py
index ec0ac37dd54..6df9633758c 100644
--- a/tardis/io/model/readers/base.py
+++ b/tardis/io/model/readers/base.py
@@ -1,3 +1,7 @@
+import numpy as np
+import pandas as pd
+
+from tardis.io.model.readers.artis import read_artis_density
 from tardis.io.model.readers.cmfgen_deprecated import (
     read_cmfgen_composition,
     read_cmfgen_density,
@@ -5,17 +9,11 @@
 from tardis.io.model.readers.generic_readers import (
     ConfigurationError,
     read_csv_composition,
-    read_simple_ascii_mass_fractions,
     read_simple_ascii_density,
+    read_simple_ascii_mass_fractions,
 )
 
 
-import numpy as np
-import pandas as pd
-
-from tardis.io.model.readers.artis import read_artis_density
-
-
 def read_mass_fractions_file(
     mass_fractions_filename,
     mass_fractions_filetype,
@@ -36,7 +34,6 @@ def read_mass_fractions_file(
     outer_boundary_index : int
         index of the outer shell, default None
     """
-
     file_parsers = {
         "simple_ascii": read_simple_ascii_mass_fractions,
         "artis": read_simple_ascii_mass_fractions,
diff --git a/tardis/io/model/readers/blondin_toymodel.py b/tardis/io/model/readers/blondin_toymodel.py
index e1fbd22e688..b5b2dd9db15 100644
--- a/tardis/io/model/readers/blondin_toymodel.py
+++ b/tardis/io/model/readers/blondin_toymodel.py
@@ -28,7 +28,7 @@ def read_blondin_toymodel(fname):
     blondin_csv : pandas.DataFrame
         DataFrame containing the csv part of the toymodel
     """
-    with open(fname, "r") as fh:
+    with open(fname) as fh:
         for line in fh:
             if line.startswith("#idx"):
                 break
@@ -91,7 +91,7 @@ def read_blondin_toymodel(fname):
     )
     blondin_csv["velocity"] = new_velocities
 
-    with open(fname, "r") as fh:
+    with open(fname) as fh:
         t0_string = T0_PATTERN.findall(fh.read())[0]
 
     t0 = parse_quantity(t0_string.replace("DAYS", "day"))
diff --git a/tardis/io/model/readers/cmfgen.py b/tardis/io/model/readers/cmfgen.py
index 77865a3a5d4..3ab63589a36 100644
--- a/tardis/io/model/readers/cmfgen.py
+++ b/tardis/io/model/readers/cmfgen.py
@@ -1,8 +1,8 @@
+import dataclasses
 import re
+
 import pandas as pd
 from astropy import units as u
-from pathlib import Path
-import dataclasses
 
 
 @dataclasses.dataclass
@@ -26,7 +26,6 @@ def read_cmfgen_model(fname):
 
     Parameters
     ----------
-
     fname : str
 
     Returns
diff --git a/tardis/io/model/readers/cmfgen_deprecated.py b/tardis/io/model/readers/cmfgen_deprecated.py
index 898f7a5dc2c..fd750acc94c 100644
--- a/tardis/io/model/readers/cmfgen_deprecated.py
+++ b/tardis/io/model/readers/cmfgen_deprecated.py
@@ -1,12 +1,10 @@
-from tardis.io.model.readers.util import read_csv_isotope_mass_fractions
-from tardis.util.base import parse_quantity
-
+import warnings
 
 import pandas as pd
 from astropy import units as u
 
-
-import warnings
+from tardis.io.model.readers.util import read_csv_isotope_mass_fractions
+from tardis.util.base import parse_quantity
 
 
 def read_cmfgen_density(fname: str):
@@ -81,7 +79,6 @@ def read_cmfgen_composition(fname, delimiter=r"\s+"):
     fname : str
         filename of the csv file
     """
-
     warnings.warn(
         "The current CMFGEN model parser is deprecated", DeprecationWarning
     )
diff --git a/tardis/io/model/readers/csvy.py b/tardis/io/model/readers/csvy.py
index 7e6c1f1c73b..62d77473eb5 100644
--- a/tardis/io/model/readers/csvy.py
+++ b/tardis/io/model/readers/csvy.py
@@ -1,9 +1,11 @@
 import logging
+
 import numpy as np
+import pandas as pd
+import yaml
 from radioactivedecay import Nuclide
 from radioactivedecay.utils import Z_DICT, elem_to_Z
-import yaml
-import pandas as pd
+
 from tardis.io.util import YAMLLoader
 from tardis.util.base import is_valid_nuclide_or_elem
 
@@ -110,7 +112,6 @@ def parse_csv_mass_fractions(csvy_data):
     mass_fractions : pandas.DataFrame
     isotope_mass_fraction : pandas.MultiIndex
     """
-
     mass_fraction_col_names = [
         name for name in csvy_data.columns if is_valid_nuclide_or_elem(name)
     ]
diff --git a/tardis/io/model/readers/generic_readers.py b/tardis/io/model/readers/generic_readers.py
index 38acb03fec3..ac24226e253 100644
--- a/tardis/io/model/readers/generic_readers.py
+++ b/tardis/io/model/readers/generic_readers.py
@@ -1,4 +1,3 @@
-from pathlib import Path
 from typing import Any, Tuple
 
 import numpy as np
diff --git a/tardis/io/model/readers/stella.py b/tardis/io/model/readers/stella.py
index 41074c8c725..30f34888115 100644
--- a/tardis/io/model/readers/stella.py
+++ b/tardis/io/model/readers/stella.py
@@ -31,7 +31,6 @@ def read_stella_model(fname):
 
     Parameters
     ----------
-
     fname : str
 
     Returns
diff --git a/tardis/io/model/readers/tests/test_arepo_parser.py b/tardis/io/model/readers/tests/test_arepo_parser.py
index 7d831f3df3f..fd88eaaec8f 100644
--- a/tardis/io/model/readers/tests/test_arepo_parser.py
+++ b/tardis/io/model/readers/tests/test_arepo_parser.py
@@ -1,9 +1,11 @@
+import json
+import os
 from pathlib import Path
-from tardis.io.model.readers import arepo
-import pytest
+
 import numpy as np
-import os
-import json
+import pytest
+
+from tardis.io.model.readers import arepo
 
 
 @pytest.fixture()
@@ -13,7 +15,7 @@ def arepo_snapshot_fname(tardis_regression_path):
 
 @pytest.fixture
 def get_cone_csvy_model(arepo_snapshot_fname, example_model_file_dir):
-    with open(arepo_snapshot_fname, "r") as json_file:
+    with open(arepo_snapshot_fname) as json_file:
         data = json.loads(json.load(json_file))
 
     pos, vel, rho, mass, nucs, time = (
@@ -45,7 +47,7 @@ def get_cone_csvy_model(arepo_snapshot_fname, example_model_file_dir):
         20, example_model_file_dir / "arepo_parser_test.csvy"
     )
 
-    with open(testfile, "r") as file:
+    with open(testfile) as file:
         data = file.readlines()
 
     print(testfile)
@@ -56,7 +58,7 @@ def get_cone_csvy_model(arepo_snapshot_fname, example_model_file_dir):
 
 @pytest.fixture
 def get_full_csvy_model(arepo_snapshot_fname, example_model_file_dir):
-    with open(arepo_snapshot_fname, "r") as json_file:
+    with open(arepo_snapshot_fname) as json_file:
         data = json.loads(json.load(json_file))
 
     pos, vel, rho, mass, nucs, time = (
@@ -86,7 +88,7 @@ def get_full_csvy_model(arepo_snapshot_fname, example_model_file_dir):
         20, example_model_file_dir / "arepo_parser_test.csvy"
     )
 
-    with open(testfile, "r") as file:
+    with open(testfile) as file:
         data = file.readlines()
 
     os.remove(testfile)
@@ -97,7 +99,7 @@ def get_full_csvy_model(arepo_snapshot_fname, example_model_file_dir):
 @pytest.fixture
 def get_cone_reference_data(example_model_file_dir):
     with open(
-        example_model_file_dir / "arepo_cone_reference_model.csvy", "r"
+        example_model_file_dir / "arepo_cone_reference_model.csvy"
     ) as file:
         data = file.readlines()
 
@@ -107,7 +109,7 @@ def get_cone_reference_data(example_model_file_dir):
 @pytest.fixture
 def get_full_reference_data(example_model_file_dir):
     with open(
-        example_model_file_dir / "arepo_full_reference_model.csvy", "r"
+        example_model_file_dir / "arepo_full_reference_model.csvy"
     ) as file:
         data = file.readlines()
 
diff --git a/tardis/io/model/readers/tests/test_ascii_readers.py b/tardis/io/model/readers/tests/test_ascii_readers.py
index 10fb6bf5bca..7e338054cfa 100644
--- a/tardis/io/model/readers/tests/test_ascii_readers.py
+++ b/tardis/io/model/readers/tests/test_ascii_readers.py
@@ -1,20 +1,14 @@
 import os
-from astropy import units as u
-from tardis import io
-from tardis.io.model.readers.generic_readers import ConfigurationError
 
 import numpy.testing as npt
-
 import pytest
+from astropy import units as u
 
-import numpy as np
-
-from pathlib import Path
 from tardis.io.model.readers.base import read_density_file
-
 from tardis.io.model.readers.generic_readers import (
-    read_simple_ascii_mass_fractions,
+    ConfigurationError,
     read_simple_ascii_density,
+    read_simple_ascii_mass_fractions,
 )
 
 test_data_directory = os.path.dirname(__file__)
diff --git a/tardis/io/model/readers/tests/test_cmfgen_reader.py b/tardis/io/model/readers/tests/test_cmfgen_reader.py
index 25ba9fefc87..34832a1289c 100644
--- a/tardis/io/model/readers/tests/test_cmfgen_reader.py
+++ b/tardis/io/model/readers/tests/test_cmfgen_reader.py
@@ -1,9 +1,8 @@
-import numpy as np
-
 from pathlib import Path
 
+import numpy as np
 from pytest import fixture
-from astropy import units as u
+
 from tardis.io.model.readers.cmfgen import read_cmfgen_model
 
 MODEL_DATA_PATH = Path(__file__).parent / "data"
diff --git a/tardis/io/model/readers/tests/test_csvy_reader.py b/tardis/io/model/readers/tests/test_csvy_reader.py
index daf283eca55..c87525da348 100644
--- a/tardis/io/model/readers/tests/test_csvy_reader.py
+++ b/tardis/io/model/readers/tests/test_csvy_reader.py
@@ -1,12 +1,12 @@
+import os
 from pathlib import Path
+
+import numpy.testing as npt
+import pytest
+
 import tardis
-from tardis.io.model.readers import csvy
 from tardis.io.configuration.config_validator import validate_dict
-from jsonschema import exceptions as json_schema_exc
-import pytest
-import os
-from astropy import units as u
-import numpy.testing as npt
+from tardis.io.model.readers import csvy
 
 
 @pytest.fixture
diff --git a/tardis/io/model/readers/tests/test_stella_reader.py b/tardis/io/model/readers/tests/test_stella_reader.py
index ace192118c9..055cae778ff 100644
--- a/tardis/io/model/readers/tests/test_stella_reader.py
+++ b/tardis/io/model/readers/tests/test_stella_reader.py
@@ -1,9 +1,9 @@
-import numpy as np
-
 from pathlib import Path
 
-from pytest import fixture
+import numpy as np
 from astropy import units as u
+from pytest import fixture
+
 from tardis.io.model import read_stella_model
 
 MODEL_DATA_PATH = Path(__file__).parent / "data"
diff --git a/tardis/io/tests/test_HDFWriter.py b/tardis/io/tests/test_HDFWriter.py
index bc7be113880..d890817834e 100644
--- a/tardis/io/tests/test_HDFWriter.py
+++ b/tardis/io/tests/test_HDFWriter.py
@@ -2,12 +2,10 @@
 import pandas as pd
 import pytest
 from astropy import units as u
-
-from numpy.testing import assert_almost_equal, assert_array_almost_equal
+from numpy.testing import assert_array_almost_equal
 
 from tardis.io.util import HDFWriterMixin
 
-
 # Test Cases
 
 # DataFrame
diff --git a/tardis/io/tests/test_atomic.py b/tardis/io/tests/test_atomic.py
index 5fdf4c9ba41..4c810b8a7f2 100644
--- a/tardis/io/tests/test_atomic.py
+++ b/tardis/io/tests/test_atomic.py
@@ -1,7 +1,7 @@
 import pytest
-
-from astropy.tests.helper import assert_quantity_allclose
 from astropy import units as u
+from astropy.tests.helper import assert_quantity_allclose
+
 from tardis import constants as const
 
 
diff --git a/tardis/io/tests/test_decay.py b/tardis/io/tests/test_decay.py
index b8a317fca1c..3dee2f0410e 100644
--- a/tardis/io/tests/test_decay.py
+++ b/tardis/io/tests/test_decay.py
@@ -1,8 +1,8 @@
-import pytest
 import pandas as pd
+import pytest
+from numpy.testing import assert_almost_equal
 
 from tardis.model.matter.decay import IsotopicMassFraction
-from numpy.testing import assert_almost_equal
 
 
 @pytest.fixture
diff --git a/tardis/io/tests/test_model_reader.py b/tardis/io/tests/test_model_reader.py
index d1ed9808a75..6694c5dca77 100644
--- a/tardis/io/tests/test_model_reader.py
+++ b/tardis/io/tests/test_model_reader.py
@@ -1,4 +1,3 @@
-import h5py
 import numpy as np
 import pytest
 from astropy import units as u
diff --git a/tardis/io/util.py b/tardis/io/util.py
index 06937aaec7f..8d1e1e9de12 100644
--- a/tardis/io/util.py
+++ b/tardis/io/util.py
@@ -59,7 +59,7 @@ def quantity_from_str(text):
     return u.Quantity(value, unit_str)
 
 
-class MockRegexPattern(object):
+class MockRegexPattern:
     """
     A mock class to be used in place of a compiled regular expression
     when a type check is needed instead of a regex match.
@@ -188,9 +188,9 @@ def check_equality(item1, item2):
         return True
 
 
-class HDFWriterMixin(object):
+class HDFWriterMixin:
     def __new__(cls, *args, **kwargs):
-        instance = super(HDFWriterMixin, cls).__new__(cls)
+        instance = super().__new__(cls)
         instance.optional_hdf_properties = []
         instance.__init__(*args, **kwargs)
         return instance
@@ -382,9 +382,7 @@ def to_hdf(
             If the HDF file path already exists, whether to overwrite it or not
         """
         self.collection = collection
-        super(PlasmaWriterMixin, self).to_hdf(
-            file_path_or_buf, path, name, overwrite
-        )
+        super().to_hdf(file_path_or_buf, path, name, overwrite)
 
 
 @lru_cache(maxsize=None)
@@ -400,7 +398,6 @@ def download_from_url(url, dst, checksum, src=None, retries=3):
     src : tuple
         List of URLs to use as mirrors
     """
-
     cached_file_path = download_file(url, sources=src, pkgname="tardis")
 
     with open(cached_file_path, "rb") as f: