Upgrade pre-commit versions

.pre-commit-config.yaml

@@ -2,14 +2,14 @@
 exclude: ^.*\.DAT$|.*\.dat$|.*\.tex$|.*\.PPF$|.*\.FLD$|.*\.ps$|ref_dicts.json$|.*\.md$
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-merge-conflict
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.3
+    rev: v0.15.10
     hooks:
       - id: ruff
         args: [--fix]
@@ -22,14 +22,14 @@ repos:
         args: [--mapping, '2', --sequence, '4', --offset, '2']
 
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.8
+    rev: v2.4.11
     hooks:
       - id: biome-format
         types: [json]
         args: [--indent-style=space, --indent-width=2, --line-width=89]
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.5.0
+    rev: 0.9.1
     hooks:
       - id: nbstripout
         args: [--extra-keys=metadata.language_info.version]

documentation/scripts/plotting_scripts/2nd_gen_rebco_critical_surface.py

@@ -2,7 +2,7 @@
 import numpy as np
 import plotly.graph_objects as go
 
-import process.models.superconductors as superconductors
+from process.models import superconductors
 
 temp_c0max = 90.0  # Critical temperature (K) at zero field and strain
 b_c20max = (

documentation/scripts/plotting_scripts/bi_2212_critical_surface.py

@@ -2,7 +2,7 @@
 import numpy as np
 import plotly.graph_objects as go
 
-import process.models.superconductors as superconductors
+from process.models import superconductors
 
 # Create a grid of temperature and field values
 temp_conductor = np.linspace(1, 11.0, 50)  # Temperature range (K)

documentation/scripts/plotting_scripts/durham_nbti_critical_surface.py

@@ -2,7 +2,7 @@
 import numpy as np
 import plotly.graph_objects as go
 
-import process.models.superconductors as superconductors
+from process.models import superconductors
 
 # Create a grid of temperature and field values
 temp_conductor = np.linspace(1, 8.0, 50)  # Temperature range (K)

documentation/scripts/plotting_scripts/durham_rebco_critical_surface.py

@@ -2,7 +2,7 @@
 import numpy as np
 import plotly.graph_objects as go
 
-import process.models.superconductors as superconductors
+from process.models import superconductors
 
 # Create a grid of temperature and field values
 temp_conductor = np.linspace(4.2, 30.0, 50)  # Temperature range (K)

documentation/scripts/plotting_scripts/eutf4_nb3sn_critical_surface.py

@@ -2,7 +2,7 @@
 import numpy as np
 import plotly.graph_objects as go
 
-import process.models.superconductors as superconductors
+from process.models import superconductors
 
 temp_c0max = 16.06  # Critical temperature (K) at zero field and strain
 b_c20max = (

documentation/scripts/plotting_scripts/hazelton_zhai_rebco_critical_surface.py

@@ -2,7 +2,7 @@
 import numpy as np
 import plotly.graph_objects as go
 
-import process.models.superconductors as superconductors
+from process.models import superconductors
 
 # Create a grid of temperature and field values
 temp_conductor = np.linspace(4.2, 40.0, 50)  # Temperature range (K)

documentation/scripts/plotting_scripts/old_empirical_nbti_critical_surface.py

@@ -2,7 +2,7 @@
 import numpy as np
 import plotly.graph_objects as go
 
-import process.models.superconductors as superconductors
+from process.models import superconductors
 
 # Create a grid of temperature and field values
 temp_conductor = np.linspace(1, 10.0, 50)  # Temperature range (K)

documentation/scripts/plotting_scripts/western_nb3sn_critical_surface.py

@@ -2,7 +2,7 @@
 import numpy as np
 import plotly.graph_objects as go
 
-import process.models.superconductors as superconductors
+from process.models import superconductors
 
 temp_c0max = 16.34  # Critical temperature (K) at zero field and strain
 b_c20max = (

process/__init__.py

@@ -3,7 +3,7 @@
 
 # setup the package "root" logger, every other logger in PROCESS
 # will inherit from this (implicitly, based on the namespace)
-root_logger = logging.getLogger(__name__)
-root_logger.setLevel(logging.DEBUG)
+root_logger = logging.getLogger(__name__)  # noqa: RUF067
+root_logger.setLevel(logging.DEBUG)  # noqa: RUF067
 
 __version__ = version("process")

process/core/init.py

@@ -108,7 +108,8 @@ def get_git_summary() -> tuple[str, str]:
         directory = Path(process.__file__).parent
 
         git_branch = (
-            subprocess.run(
+            subprocess
+            .run(
                 "git rev-parse --abbrev-ref HEAD",
                 shell=True,
                 capture_output=True,
@@ -120,7 +121,8 @@ def get_git_summary() -> tuple[str, str]:
         )
 
         git_tag = (
-            subprocess.run(
+            subprocess
+            .run(
                 "git describe --tags",
                 shell=True,
                 capture_output=True,
@@ -409,7 +411,7 @@ def check_process(inputs):  # noqa: ARG001
         data_structure.buildings_variables.triv = 0.0
         data_structure.heat_transport_variables.p_tritium_plant_electric_mw = 0.0
 
-    if data_structure.impurity_radiation_module.f_nd_impurity_electrons[1] != 0.1:
+    if data_structure.impurity_radiation_module.f_nd_impurity_electrons[1] != 0.1:  # noqa: RUF069
         raise ProcessValidationError(
             "The thermal alpha/electron density ratio should be controlled using f_nd_alpha_electron (itv 109) and not f_nd_impurity_electrons(2)."
             "f_nd_impurity_electrons(2) should be removed from the input file, or set to the default value 0.1D0."
@@ -741,11 +743,13 @@ def check_process(inputs):  # noqa: ARG001
             )
 
         # Check if a single null divertor is used in double null machine
+        # ruff: disable[RUF069]
         if data_structure.physics_variables.i_single_null == 0 and (
             data_structure.physics_variables.f_p_div_lower == 1.0
             or data_structure.physics_variables.f_p_div_lower == 0.0
         ):
             warn("Operating with a single null in a double null machine", stacklevel=2)
+        # ruff: enable[RUF069]
 
         # Set the TF coil shape to picture frame (if default value)
         if data_structure.tfcoil_variables.i_tf_shape == TFCoilShapeModel.DEFAULT:

process/core/io/cli_tools.py

@@ -70,7 +70,7 @@ def _lazy_load(self, cmd_name):
         cmd_object = getattr(mod, cmd_object_name)
         # check the result to make debugging easier
         if not isinstance(cmd_object, click.Command):
-            raise ValueError(
+            raise ValueError(  # noqa: TRY004
                 f"Lazy loading of {import_path} failed by returning a non-command object"
             )
         return cmd_object

process/core/io/data_structure_dicts.py

@@ -171,8 +171,8 @@ def slice_file(file, re1, re2):
         lines:List of lines from file between re1 and re2 inclusive
     """
 
-    with open(file, encoding="utf-8") as file:
-        filetext = file.readlines()
+    with open(file, encoding="utf-8") as fh:
+        filetext = fh.readlines()
     start = None
     for i in range(len(filetext)):
         # look for first match

process/core/io/in_dat/base.py

@@ -9,8 +9,8 @@
                 generation script imports, and inspects, process.
 """
 
+import sys
 from re import sub
-from sys import stderr
 
 from process.core.exceptions import ProcessValidationError
 from process.core.io.data_structure_dicts import get_dicts
@@ -679,7 +679,7 @@ def add_parameter(data, parameter_name, parameter_value):
                 print(
                     f"Warning: Description for {parameter_name}",
                     "specified in IN.DAT not in dictionary.",
-                    file=stderr,
+                    file=sys.stderr,
                 )
                 comment = ""
 
@@ -938,7 +938,7 @@ def variable_constraint_type_check(item_number, var_type):
         except ValueError:
             print(
                 f"Value {item_number} for {var_type} not valid. Check value!",
-                file=stderr,
+                file=sys.stderr,
             )
 
     # Check if item is in float format
@@ -959,7 +959,7 @@ def variable_constraint_type_check(item_number, var_type):
 
     # Value not recognised
     else:
-        raise ValueError(
+        raise ValueError(  # noqa: TRY004
             f"Value {item_number} for {var_type} not a recognised format. Check value!"
         )
 
@@ -1063,7 +1063,7 @@ def __repr__(self):
 
     @property
     def get_value(self):
-        """ """
+        """Get value of variables"""
         if self.v_type != "Bound":
             return parameter_type(self.name, self.value)
         return self.value
@@ -1132,7 +1132,7 @@ def read_in_dat(self):
                     print(
                         "Warning: Line below is causing a problem. Check "
                         f"that line in IN.DAT is valid. Line skipped!\n{line}",
-                        file=stderr,
+                        file=sys.stderr,
                     )
 
                     # Store the first part of the unrecognised line (probably a
@@ -1246,9 +1246,9 @@ def process_parameter(self, line):
                     no_comment_line,
                     "\n Please note, that our Python Library cannot cope with",
                     " variable definitions on multiple lines.",
-                    file=stderr,
+                    file=sys.stderr,
                 )
-                exit()
+                sys.exit()
         else:
             try:
                 value = no_comment_line[1].strip().replace(",", "")
@@ -1258,9 +1258,9 @@ def process_parameter(self, line):
                     no_comment_line,
                     "\n Please note, that our Python Library cannot cope with",
                     " variable definitions on multiple lines.",
-                    file=stderr,
+                    file=sys.stderr,
                 )
-                exit()
+                sys.exit()
 
         # Find group of variables the parameter belongs to
         parameter_group = find_parameter_group(name)

process/core/io/mfile/base.py

@@ -62,8 +62,7 @@ def set_scan(self, scan_number, scan_value):
             value of parameter for scan
         """
         self[f"scan{scan_number:02}"] = scan_value
-        if scan_number > self.latest_scan:
-            self.latest_scan = scan_number
+        self.latest_scan = max(self.latest_scan, scan_number)
 
     def get_scan(self, scan_number):
         """Returns the value of a specific scan. For scan = -1 or None the last

process/core/io/plot/sankey.py

@@ -276,11 +276,10 @@ def power_balance_sankey(m_file: Path):
         #
         # Neutrons to CP shield, should only show if CP shield is present
         m_file.get("p_cp_shield_nuclear_heat_mw", scan=-1),  # 51
-        #
         m_file.get("p_plasma_separatrix_mw", scan=-1),  # 52
         m_file.get("p_div_secondary_heat_mw", scan=-1),  # 53
         m_file.get("p_shld_secondary_heat_mw", scan=-1),  # 54
-        m_file.get("p_fw_hcd_nuclear_heat_mw", scan=-1),  #
+        m_file.get("p_fw_hcd_nuclear_heat_mw", scan=-1),
         m_file.get("p_fw_hcd_rad_total_mw", scan=-1),  # 56
         m_file.get("p_plant_secondary_heat_mw", scan=-1),  # 57
         m_file.get("p_hcd_secondary_heat_mw", scan=-1),  # 58
@@ -399,7 +398,7 @@ def add(
         rotation: float = 0,
         **kwargs,
     ):
-        __doc__ = super().__doc__  # noqa: F841, A001
+        __doc__ = super().__doc__  # noqa: F841
         # Here we first check if the "add" method has received arguments that
         # the Sankey class can't handle.
         if future is None:

process/core/io/plot/scans.py

@@ -23,6 +23,7 @@
 """
 
 import math
+import sys
 from collections.abc import Iterable, Sequence
 from pathlib import Path
 
@@ -179,7 +180,7 @@ def plot_scan(
             f"ERROR : nsweep = {nsweep_ref} not supported by the utility\n"
             "ERROR : Please update the 'nsweep_dict' dict"
         )
-        exit()
+        sys.exit()
 
     # Check if the scan variable is present in the
     if scan_var_name not in m_file.data:
@@ -188,7 +189,7 @@ def plot_scan(
             "ERROR : The scan variable is probably an upper/lower boundary\n"
             "ERROR : Please modify 'nsweep_dict' dict with the constrained var"
         )
-        exit()
+        sys.exit()
 
     # Check if the second scan variable is present in the
     if is_2D_scan and (scan_2_var_name not in m_file.data):
@@ -197,12 +198,12 @@ def plot_scan(
             "ERROR : The scan variable is probably an upper/lower boundary\n"
             "ERROR : Please modify 'nsweep_dict' dict with the constrained var"
         )
-        exit()
+        sys.exit()
 
     # Only one imput must be used for a 2D scan
     if is_2D_scan and len(input_files) > 1:
         print("ERROR : Only one input file can be used for 2D scans\nERROR : Exiting")
-        exit()
+        sys.exit()
     # ------
 
     # Plot settings
@@ -264,12 +265,12 @@ def _format_lists(inp, output_names):
                     "ERROR : You must use inputs files with the same scan variables\n"
                     "ERROR : Exiting"
                 )
-                exit()
+                sys.exit()
 
             # No D scans
             if "nsweep_2" in m_file.data:
                 print("ERROR : You cannot mix 1D with 2D scans\nERROR : Exiting")
-                exit()
+                sys.exit()
             # ---
 
             # Only selecting the scans that has converged