Drop Python 3.9 support and update packages (#121)

* Update packages

* Run ruff

* Pre-commit

* Repair use of "floating" as type modifier

* Update poetry lock file

* Ignore problematic link

* Bump version to 7.1.0

Author: tbody-cfs

.github/workflows/workflow_actions.yml

@@ -19,7 +19,7 @@ on:
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   radas:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v4
@@ -56,11 +56,11 @@ jobs:
   build:
     needs: radas
     # The type of runner that the job will run on
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']  # should test the versions we allow for in pyproject.toml
+        python-version: ['3.10', '3.11', '3.12']  # should test the versions we allow for in pyproject.toml
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -132,7 +132,7 @@ jobs:
   build_release:
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     needs: build
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
@@ -151,7 +151,7 @@ jobs:
   publish:
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     needs: build_release
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     environment:
       name: pypi-publish
       url: https://pypi.org/project/cfspopcon/

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 # per default we only run over the files in the python package
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
     -   id: check-added-large-files
         # but no large files anywhere ;)

cfspopcon/__init__.py

@@ -19,18 +19,18 @@
 
 # export main classes users should need as well as the option enums
 __all__ = [
+    "Algorithm",
+    "AtomicData",
+    "CompositeAlgorithm",
+    "convert_to_default_units",
+    "convert_units",
+    "file_io",
     "formulas",
-    "named_options",
     "magnitude_in_default_units",
-    "convert_to_default_units",
+    "named_options",
     "process_input_dictionary",
-    "set_default_units",
-    "convert_units",
     "read_case",
     "read_plot_style",
-    "Algorithm",
-    "CompositeAlgorithm",
-    "file_io",
-    "AtomicData",
+    "set_default_units",
     "shaping_and_selection",
 ]

cfspopcon/algorithm_class.py

@@ -5,7 +5,7 @@
 import inspect
 from collections.abc import Callable, Sequence
 from functools import wraps
-from pathlib import Path  # noqa: TCH003
+from pathlib import Path  # noqa: TC003
 from typing import Any, ClassVar, Optional, Union
 from warnings import warn
 
@@ -164,7 +164,7 @@ def wrapped_function(**kwargs: Any) -> dict:
     def register_algorithm(
         cls, return_keys: list[str], name: Optional[str] = None, skip_unit_conversion: bool = False
     ) -> GenericFunctionType:
-        """Decorate a function and turn it into an Algorithm. Usage: @Algorithm.register_algorithm(return_keys=["..."])."""  # noqa: D402
+        """Decorate a function and turn it into an Algorithm. Usage: @Algorithm.register_algorithm(return_keys=["..."])."""
 
         def function_wrapper(func: GenericFunctionType) -> GenericFunctionType:
             Algorithm.from_single_function(

cfspopcon/formulas/__init__.py

@@ -17,17 +17,17 @@
 )
 
 __all__ = [
-    "geometry",
+    "atomic_data",
+    "auxiliary_power",
     "energy_confinement",
     "fusion_power",
+    "geometry",
+    "impurities",
     "metrics",
     "plasma_current",
+    "plasma_pressure",
     "plasma_profiles",
     "radiated_power",
     "scrape_off_layer",
-    "plasma_pressure",
-    "auxiliary_power",
     "separatrix_conditions",
-    "impurities",
-    "atomic_data",
 ]

cfspopcon/formulas/energy_confinement/__init__.py

@@ -9,10 +9,10 @@
 )
 
 __all__ = [
+    "ConfinementScaling",
     "calc_plasma_stored_energy",
     "read_confinement_scalings",
-    "ConfinementScaling",
     "solve_energy_confinement_scaling_for_input_power",
-    "switch_to_linearised_ohmic_confinement_below_threshold",
     "switch_to_L_mode_confinement_below_threshold",
+    "switch_to_linearised_ohmic_confinement_below_threshold",
 ]

cfspopcon/formulas/fusion_power/__init__.py

@@ -15,17 +15,17 @@
 from .fusion_rates import calc_fusion_power, calc_neutron_flux_to_walls
 
 __all__ = [
-    "fusion_data",
-    "calc_average_ion_mass",
-    "FusionReaction",
-    "DTFusionBoschHale",
-    "DTFusionHively",
     "DDFusionBoschHale",
     "DDFusionHively",
     "DHe3Fusion",
-    "pB11Fusion",
+    "DTFusionBoschHale",
+    "DTFusionHively",
+    "FusionReaction",
+    "calc_average_ion_mass",
     "calc_fusion_gain",
-    "calc_triple_product",
     "calc_fusion_power",
     "calc_neutron_flux_to_walls",
+    "calc_triple_product",
+    "fusion_data",
+    "pB11Fusion",
 ]

cfspopcon/formulas/geometry/__init__.py

@@ -15,15 +15,15 @@
 from .volume_integral import integrate_profile_over_volume
 
 __all__ = [
+    "calc_areal_elongation_from_elongation_at_psi95",
+    "calc_elongation_at_psi95_from_areal_elongation",
+    "calc_inverse_aspect_ratio",
+    "calc_minor_radius_from_inverse_aspect_ratio",
+    "calc_plasma_poloidal_circumference",
     "calc_plasma_surface_area",
     "calc_plasma_volume",
-    "integrate_profile_over_volume",
     "calc_separatrix_elongation_from_areal_elongation",
     "calc_separatrix_triangularity_from_triangularity95",
-    "calc_minor_radius_from_inverse_aspect_ratio",
     "calc_vertical_minor_radius_from_elongation_and_minor_radius",
-    "calc_areal_elongation_from_elongation_at_psi95",
-    "calc_inverse_aspect_ratio",
-    "calc_plasma_poloidal_circumference",
-    "calc_elongation_at_psi95_from_areal_elongation",
+    "integrate_profile_over_volume",
 ]

cfspopcon/formulas/impurities/__init__.py

@@ -14,10 +14,10 @@
 __all__ = [
     "calc_P_radiation_from_core_seeded_impurity",
     "calc_core_seeded_impurity_concentration",
-    "calc_min_P_radiation_from_fraction",
-    "calc_min_P_radiation_from_LH_factor",
     "calc_edge_impurity_concentration",
     "calc_impurity_charge_state",
+    "calc_min_P_radiation_from_LH_factor",
+    "calc_min_P_radiation_from_fraction",
     "calc_zeff_and_dilution_due_to_impurities",
     "set_up_impurity_concentration_array",
 ]

cfspopcon/formulas/metrics/__init__.py

@@ -21,15 +21,15 @@
 )
 
 __all__ = [
-    "calc_coulomb_logarithm",
-    "calc_normalised_collisionality",
-    "calc_greenwald_density_limit",
-    "calc_greenwald_fraction",
     "calc_PB_over_R",
     "calc_PBpRnSq",
-    "calc_rho_star",
-    "calc_larmor_radius",
     "calc_alpha_t",
-    "calc_edge_collisionality",
     "calc_average_electron_density_from_greenwald_fraction",
+    "calc_coulomb_logarithm",
+    "calc_edge_collisionality",
+    "calc_greenwald_density_limit",
+    "calc_greenwald_fraction",
+    "calc_larmor_radius",
+    "calc_normalised_collisionality",
+    "calc_rho_star",
 ]