Ruff root files (#2849)

* ruff on top level files

* ruff unsafe on cmfgen2tardis

tardis/__init__.py

@@ -22,7 +22,7 @@
         " after TARDIS."
     )
 else:
-    from astropy import physical_constants, astronomical_constants
+    from astropy import astronomical_constants, physical_constants
 
     physical_constants.set("codata2014")
     astronomical_constants.set("iau2012")

tardis/_astropy_init.py

@@ -10,4 +10,5 @@
 
 # Create the test function for self test
 from astropy.tests.runner import TestRunner
+
 test = TestRunner.make_test_runner_in(os.path.dirname(__file__))

tardis/base.py

@@ -4,7 +4,6 @@
 
 import logging
 
-
 logger = logging.getLogger(__name__)
 
 
@@ -70,9 +69,9 @@ def run_tardis(
     -----
     Please see the `logging tutorial <https://tardis-sn.github.io/tardis/io/optional/logging_configuration.html>`_ to know more about `log_level` and `specific` options.
     """
-    from tardis.io.logger.logger import logging_state
-    from tardis.io.configuration.config_reader import Configuration
     from tardis.io.atom_data.base import AtomData
+    from tardis.io.configuration.config_reader import Configuration
+    from tardis.io.logger.logger import logging_state
     from tardis.simulation import Simulation
 
     if isinstance(config, Configuration):

tardis/scripts/cmfgen2tardis.py

@@ -1,11 +1,9 @@
-import os
-import sys
 import argparse
+import os
+
 import numpy as np
 import pandas as pd
 
-from tardis.io.atom_data import AtomData
-
 # The from_hdf() method requires an argument, so the line below doesn't work
 # atomic_dataset = AtomData.from_hdf()
 
@@ -40,7 +38,7 @@ def extract_file_block(f):
 def convert_format(file_path):
     quantities_row = []
     prop_list = ["Velocity", "Density", "Electron density", "Temperature"]
-    with open(file_path, "r") as f:
+    with open(file_path) as f:
         for line in f:
             items = line.replace("(", "").replace(")", "").split()
             n = len(items)
@@ -102,7 +100,7 @@ def parse_file(args):
     )
 
     filename = os.path.splitext(os.path.basename(args.input_path))[0]
-    save_fname = ".".join((filename, "csv"))
+    save_fname = f"{filename}.csv"
     resultant_df = pd.concat([density_df, abundances_df], axis=1)
     resultant_df.columns = pd.MultiIndex.from_tuples(
         zip(resultant_df.columns, quantities_row)

tardis/tests/fixtures/atom_data.py

@@ -1,5 +1,5 @@
 from copy import deepcopy
-from pathlib import Path
+
 import pytest
 
 from tardis.io.atom_data.base import AtomData

tardis/tests/integration_tests/conftest.py

@@ -1,8 +1,9 @@
 import glob
 import os
-import yaml
+
 import pandas as pd
 import pytest
+import yaml
 
 # NOTE: the __githash__ variable is not available anymore
 # on `version.py`. Find another way to fix it!
@@ -87,8 +88,8 @@ def reference(request, data_path):
     else:
         try:
             reference = pd.HDFStore(data_path["reference_path"], "r")
-        except IOError:
-            raise IOError(
+        except OSError:
+            raise OSError(
                 f'Reference file {data_path["reference_path"]} does not exist and is needed'
                 f" for the tests"
             )

tardis/tests/integration_tests/test_integration.py

@@ -1,16 +1,16 @@
 import os
 
-import yaml
-import pytest
 import matplotlib
+import pytest
+import yaml
 
 matplotlib.use("Agg")
 import matplotlib.pyplot as plt
 from numpy.testing import assert_allclose
 
 from tardis.io.atom_data.base import AtomData
-from tardis.simulation import Simulation
 from tardis.io.configuration.config_reader import Configuration
+from tardis.simulation import Simulation
 
 pytestmarker = [pytest.mark.no_cover, pytest.mark.integration]
 
@@ -71,7 +71,7 @@ def model_quantities(request):
     reason="integration tests are not included in this run",
 )
 @pytest.mark.integration
-class TestIntegration(object):
+class TestIntegration:
     """Slow integration test for various setups present in subdirectories of
     ``tardis/tests/integration_tests``.
     """

tardis/tests/test_util.py

@@ -1,27 +1,25 @@
-import pytest
-import numpy as np
-import numpy.testing as npt
+from io import StringIO
 
+import numpy as np
+import pytest
 from astropy import units as u
-from io import StringIO
 
 from tardis.util.base import (
-    MalformedSpeciesError,
     MalformedElementSymbolError,
     MalformedQuantityError,
-    int_to_roman,
-    roman_to_int,
+    MalformedSpeciesError,
+    atomic_number2element_symbol,
     calculate_luminosity,
-    create_synpp_yaml,
+    convert_abundances_format,
+    element_symbol2atomic_number,
+    int_to_roman,
     intensity_black_body,
-    species_tuple_to_string,
-    species_string_to_tuple,
     parse_quantity,
-    element_symbol2atomic_number,
-    atomic_number2element_symbol,
-    reformat_element_symbol,
     quantity_linspace,
-    convert_abundances_format,
+    reformat_element_symbol,
+    roman_to_int,
+    species_string_to_tuple,
+    species_tuple_to_string,
 )