struphy 3.0.1__tar.gz → 3.0.3__tar.gz

{struphy-3.0.1 → struphy-3.0.3}/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2019-2025, Struphy developers, Max Planck Institute for Plasma Physics
+Copyright (c) 2019-2026, Struphy developers, Max Planck Institute for Plasma Physics
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and 
 associated documentation files (the "Software"), to deal in the Software without restriction, 

{struphy-3.0.1/src/struphy.egg-info → struphy-3.0.3}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: struphy
-Version: 3.0.1
+Version: 3.0.3
 Summary: Multi-model plasma physics package
 Author: Max Planck Institute for Plasma Physics
 Author-email: stefan.possanner@ipp.mpg.de, max.lindqvist@ipp.mpg.de, eric.sonnendruecker@ipp.mpg.de
-License: Copyright (c) 2019-2025, Struphy developers, Max Planck Institute for Plasma Physics
+License: Copyright (c) 2019-2026, Struphy developers, Max Planck Institute for Plasma Physics
         
         Permission is hereby granted, free of charge, to any person obtaining a copy of this software and 
         associated documentation files (the "Software"), to deal in the Software without restriction, 
@@ -32,39 +32,40 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy<=2.2.6
 Requires-Dist: cunumpy<=0.1
-Requires-Dist: pyccel<=2.1.0,>=2.0
-Requires-Dist: feectools<=0.1.0
+Requires-Dist: pyccel<=2.1.0,>=2.1
+Requires-Dist: feectools<=0.1.3
 Requires-Dist: scipy<=1.15.3
-Requires-Dist: h5py<=3.14.0
-Requires-Dist: matplotlib<=3.10.5
+Requires-Dist: h5py<=3.15.1
+Requires-Dist: matplotlib<=3.10.7
 Requires-Dist: pyyaml<=6.0.3
-Requires-Dist: vtk<=9.5.2
-Requires-Dist: tqdm<=4.67.1
+Requires-Dist: vtk<=9.6.0
+Requires-Dist: tqdm<=4.67.3
 Requires-Dist: argcomplete<=3.6.3
+Requires-Dist: plotly<=6.4.0
 Requires-Dist: pytest<=9.0.2
 Requires-Dist: pytest-mpi<=0.6
 Requires-Dist: pytest-testmon<=2.2.0
-Requires-Dist: line_profiler<=5.0.0
+Requires-Dist: line_profiler<=5.0.1
+Requires-Dist: scope-profiler<=0.1.7,>=0.1.7
 Provides-Extra: phys
-Requires-Dist: gvec<=1.2.0,>=1.1.0; extra == "phys"
-Requires-Dist: desc-opt<=0.15.0; extra == "phys"
+Requires-Dist: gvec<=1.3.1,>=1.1.0; extra == "phys"
+Requires-Dist: desc-opt<=0.16.0; extra == "phys"
 Provides-Extra: dev
 Requires-Dist: struphy[mpi]; extra == "dev"
-Requires-Dist: notebook<=7.4.7; extra == "dev"
+Requires-Dist: notebook<=7.5.3; extra == "dev"
 Requires-Dist: autopep8<=2.3.2; extra == "dev"
-Requires-Dist: isort<=7.0.0; extra == "dev"
+Requires-Dist: isort<=8.0.0; extra == "dev"
 Requires-Dist: flake8<=7.3.0; extra == "dev"
-Requires-Dist: pylint<=4.0.2; extra == "dev"
-Requires-Dist: ssort<=0.15.0; extra == "dev"
+Requires-Dist: pylint<=4.0.5; extra == "dev"
+Requires-Dist: ssort<=0.16.0; extra == "dev"
 Requires-Dist: add-trailing-comma<=4.0.0; extra == "dev"
-Requires-Dist: ruff<=0.14.4,>=0.9.1; extra == "dev"
-Requires-Dist: pre-commit<=4.4.0; extra == "dev"
-Requires-Dist: nbstripout<=0.8.1; extra == "dev"
+Requires-Dist: ruff<=0.15.2,>=0.15.0; extra == "dev"
+Requires-Dist: pre-commit<=4.5.1; extra == "dev"
+Requires-Dist: nbstripout<=0.9.1; extra == "dev"
 Requires-Dist: tabulate<=0.9.0; extra == "dev"
 Requires-Dist: tomli-w<=1.2.0; extra == "dev"
 Requires-Dist: kaleido<=1.2.0; extra == "dev"
-Requires-Dist: pandas<=2.3.3; extra == "dev"
-Requires-Dist: plotly<=6.3.0; extra == "dev"
+Requires-Dist: pandas<=3.0.1; extra == "dev"
 Provides-Extra: mpi
 Requires-Dist: mpi4py<=4.1.1; extra == "mpi"
 Provides-Extra: doc
@@ -72,17 +73,17 @@ Requires-Dist: struphy[phys]; extra == "doc"
 Requires-Dist: jupyter<=1.1.1; extra == "doc"
 Requires-Dist: nbconvert<=6.5.4; extra == "doc"
 Requires-Dist: ipykernel<=7.1.0; extra == "doc"
-Requires-Dist: sphinx<=8.1.3; extra == "doc"
-Requires-Dist: sphinx-design<=0.6.1; extra == "doc"
+Requires-Dist: sphinx<=9.1.0; extra == "doc"
+Requires-Dist: sphinx-design<=0.7.0; extra == "doc"
 Requires-Dist: lxml_html_clean<=0.4.3; extra == "doc"
 Requires-Dist: sphinxcontrib-napoleon<=0.7; extra == "doc"
 Requires-Dist: sphinx-copybutton<=0.5.2; extra == "doc"
 Requires-Dist: pydata-sphinx-theme<=0.16.1; extra == "doc"
-Requires-Dist: nbsphinx<=0.9.7; extra == "doc"
+Requires-Dist: nbsphinx<=0.9.8; extra == "doc"
 Requires-Dist: m2r2<=0.3.4; extra == "doc"
-Requires-Dist: myst-parser<=4.0.1; extra == "doc"
+Requires-Dist: myst-parser<=5.0.0; extra == "doc"
 Requires-Dist: mistune<=0.8.4; extra == "doc"
-Requires-Dist: docutils<=0.21.2; extra == "doc"
+Requires-Dist: docutils<=0.22.4; extra == "doc"
 Requires-Dist: ipyparallel<=9.0.2; extra == "doc"
 Provides-Extra: likwid
 Requires-Dist: struphy[dev]; extra == "likwid"
@@ -92,6 +93,7 @@ Requires-Dist: struphy[phys]; extra == "all"
 Requires-Dist: struphy[dev]; extra == "all"
 Requires-Dist: struphy[mpi]; extra == "all"
 Requires-Dist: struphy[doc]; extra == "all"
+Requires-Dist: struphy[likwid]; extra == "all"
 Dynamic: license-file
 
 <h1 align="center">
@@ -101,8 +103,8 @@ Dynamic: license-file
 [![Release](https://img.shields.io/github/v/release/struphy-hub/struphy?label=Release)](https://github.com/struphy-hub/struphy/releases)
 [![License](https://img.shields.io/badge/License-MIT-violet)](https://github.com/struphy-hub/struphy/blob/devel/LICENSE)
 [![badge](https://img.shields.io/badge/launch-tutorials-579ACA.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/struphy-hub/struphy-tutorials/main)
-[![Ubuntu latest](https://github.com/struphy-hub/struphy/actions/workflows/ubuntu-latest.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/ubuntu-latest.yml)
-[![MacOS latest](https://github.com/struphy-hub/struphy/actions/workflows/macos-latest.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/macos-latest.yml)
+[![Ubuntu latest](https://github.com/struphy-hub/struphy/actions/workflows/scheduled-ubuntu.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/scheduled-ubuntu.yml)
+[![MacOS latest](https://github.com/struphy-hub/struphy/actions/workflows/scheduled-macos.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/scheduled-macos.yml)
 [![isort and ruff](https://github.com/struphy-hub/struphy/actions/workflows/static_analysis.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/static_analysis.yml)
 [![PyPI](https://img.shields.io/pypi/v/struphy?label=PyPI)](https://pypi.org/project/struphy/)
 [![PyPI Downloads](https://img.shields.io/pypi/dm/struphy.svg?label=PyPI%20downloads)](

{struphy-3.0.1 → struphy-3.0.3}/README.md

@@ -5,8 +5,8 @@
 [![Release](https://img.shields.io/github/v/release/struphy-hub/struphy?label=Release)](https://github.com/struphy-hub/struphy/releases)
 [![License](https://img.shields.io/badge/License-MIT-violet)](https://github.com/struphy-hub/struphy/blob/devel/LICENSE)
 [![badge](https://img.shields.io/badge/launch-tutorials-579ACA.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/struphy-hub/struphy-tutorials/main)
-[![Ubuntu latest](https://github.com/struphy-hub/struphy/actions/workflows/ubuntu-latest.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/ubuntu-latest.yml)
-[![MacOS latest](https://github.com/struphy-hub/struphy/actions/workflows/macos-latest.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/macos-latest.yml)
+[![Ubuntu latest](https://github.com/struphy-hub/struphy/actions/workflows/scheduled-ubuntu.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/scheduled-ubuntu.yml)
+[![MacOS latest](https://github.com/struphy-hub/struphy/actions/workflows/scheduled-macos.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/scheduled-macos.yml)
 [![isort and ruff](https://github.com/struphy-hub/struphy/actions/workflows/static_analysis.yml/badge.svg)](https://github.com/struphy-hub/struphy/actions/workflows/static_analysis.yml)
 [![PyPI](https://img.shields.io/pypi/v/struphy?label=PyPI)](https://pypi.org/project/struphy/)
 [![PyPI Downloads](https://img.shields.io/pypi/dm/struphy.svg?label=PyPI%20downloads)](

{struphy-3.0.1 → struphy-3.0.3}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "3.0.1"
+version = "3.0.3"
 readme = "README.md"
 requires-python = ">=3.10"
 authors = [
@@ -25,19 +25,21 @@ classifiers = [
 dependencies = [
     "numpy<=2.2.6",
     "cunumpy<=0.1",
-    "pyccel<=2.1.0, >=2.0",
-    "feectools<=0.1.0",
+    "pyccel<=2.1.0, >=2.1",
+    "feectools<=0.1.3",
     "scipy<=1.15.3",
-    "h5py<=3.14.0",
-    "matplotlib<=3.10.5",
+    "h5py<=3.15.1",
+    "matplotlib<=3.10.7",
     "pyyaml<=6.0.3",
-    "vtk<=9.5.2",
-    "tqdm<=4.67.1",
+    "vtk<=9.6.0",
+    "tqdm<=4.67.3",
     "argcomplete<=3.6.3",
+    "plotly<=6.4.0",
     "pytest<=9.0.2",
     "pytest-mpi<=0.6",
     "pytest-testmon<=2.2.0",
-    "line_profiler<=5.0.0",
+    "line_profiler<=5.0.1",
+    "scope-profiler<=0.1.7, >=0.1.7",
 ]
 
 [project.license]
@@ -45,26 +47,25 @@ file = "LICENSE"
 
 [project.optional-dependencies]
 phys = [
-    "gvec<=1.2.0, >=1.1.0",
-    "desc-opt<=0.15.0",
+    "gvec<=1.3.1, >=1.1.0",
+    "desc-opt<=0.16.0",
 ]
 dev = [
     "struphy[mpi]",
-    "notebook<=7.4.7",
+    "notebook<=7.5.3",
     "autopep8<=2.3.2",
-    "isort<=7.0.0",
+    "isort<=8.0.0",
     "flake8<=7.3.0",
-    "pylint<=4.0.2",
-    "ssort<=0.15.0",
+    "pylint<=4.0.5",
+    "ssort<=0.16.0",
     "add-trailing-comma<=4.0.0",
-    "ruff<=0.14.4, >=0.9.1",
-    "pre-commit<=4.4.0",
-    "nbstripout<=0.8.1",
+    "ruff<=0.15.2, >=0.15.0",
+    "pre-commit<=4.5.1",
+    "nbstripout<=0.9.1",
     "tabulate<=0.9.0",
     "tomli-w<=1.2.0",
     "kaleido<=1.2.0",
-    "pandas<=2.3.3",
-    "plotly<=6.3.0",
+    "pandas<=3.0.1",
 ]
 mpi = [
     "mpi4py<=4.1.1",
@@ -74,17 +75,17 @@ doc = [
     "jupyter<=1.1.1",
     "nbconvert<=6.5.4",
     "ipykernel<=7.1.0",
-    "sphinx<=8.1.3",
-    "sphinx-design<=0.6.1",
+    "sphinx<=9.1.0",
+    "sphinx-design<=0.7.0",
     "lxml_html_clean<=0.4.3",
     "sphinxcontrib-napoleon<=0.7",
     "sphinx-copybutton<=0.5.2",
     "pydata-sphinx-theme<=0.16.1",
-    "nbsphinx<=0.9.7",
+    "nbsphinx<=0.9.8",
     "m2r2<=0.3.4",
-    "myst-parser<=4.0.1",
+    "myst-parser<=5.0.0",
     "mistune<=0.8.4",
-    "docutils<=0.21.2",
+    "docutils<=0.22.4",
     "ipyparallel<=9.0.2",
 ]
 likwid = [
@@ -96,6 +97,7 @@ all = [
     "struphy[dev]",
     "struphy[mpi]",
     "struphy[doc]",
+    "struphy[likwid]",
 ]
 
 [project.urls]
@@ -164,7 +166,6 @@ ignore = [
 [tool.pytest.ini_options]
 markers = [
     "models",
-    "toy",
     "fluid",
     "kinetic",
     "hybrid",

struphy-3.0.3/src/struphy/__init__.py

@@ -0,0 +1,44 @@
+from struphy.api.domains import domains
+from struphy.api.equils import equils
+from struphy.api.grids import grids
+from struphy.api.maxwellians import maxwellians
+from struphy.api.ode import ButcherTableau
+from struphy.api.options import (
+    BaseUnits,
+    DerhamOptions,
+    EnvironmentOptions,
+    FieldsBackground,
+    Time,
+)
+from struphy.api.particles import (
+    BinningPlot,
+    BoundaryParameters,
+    KernelDensityPlot,
+    LoadingParameters,
+    WeightsParameters,
+)
+from struphy.api.perturbations import perturbations
+from struphy.api.post_processing import PlottingData, PostProcessor
+from struphy.api.simulation import Simulation
+
+__all__ = [
+    "domains",
+    "equils",
+    "grids",
+    "maxwellians",
+    "EnvironmentOptions",
+    "BaseUnits",
+    "Time",
+    "perturbations",
+    "LoadingParameters",
+    "WeightsParameters",
+    "BoundaryParameters",
+    "BinningPlot",
+    "KernelDensityPlot",
+    "DerhamOptions",
+    "FieldsBackground",
+    "ButcherTableau",
+    "PostProcessor",
+    "PlottingData",
+    "Simulation",
+]

struphy-3.0.3/src/struphy/api/domains/__init__.py

@@ -0,0 +1,3 @@
+from struphy.geometry import domains
+
+__all__ = ["domains"]

struphy-3.0.3/src/struphy/api/equils/__init__.py

@@ -0,0 +1,3 @@
+from struphy.fields_background import equils
+
+__all__ = ["equils"]

struphy-3.0.3/src/struphy/api/grids/__init__.py

@@ -0,0 +1,3 @@
+from struphy.topology import grids
+
+__all__ = ["grids"]

struphy-3.0.3/src/struphy/api/maxwellians/__init__.py

@@ -0,0 +1,3 @@
+from struphy.kinetic_background import maxwellians
+
+__all__ = ["maxwellians"]

struphy-3.0.3/src/struphy/api/models/__init__.py

@@ -0,0 +1,81 @@
+from struphy.models.cold_plasma import ColdPlasma
+from struphy.models.cold_plasma_vlasov import ColdPlasmaVlasov
+from struphy.models.deterministic_particle_diffusion import (
+    DeterministicParticleDiffusion,
+)
+from struphy.models.drift_kinetic_electrostatic_adiabatic import (
+    DriftKineticElectrostaticAdiabatic,
+)
+from struphy.models.guiding_center import GuidingCenter
+from struphy.models.hasegawa_wakatani import HasegawaWakatani
+from struphy.models.linear_extended_mh_duniform import LinearExtendedMHDuniform
+from struphy.models.linear_mhd import LinearMHD
+from struphy.models.linear_mhd_driftkinetic_cc import LinearMHDDriftkineticCC
+from struphy.models.linear_mhd_vlasov_cc import LinearMHDVlasovCC
+from struphy.models.linear_mhd_vlasov_pc import LinearMHDVlasovPC
+from struphy.models.linear_vlasov_ampere_one_species import LinearVlasovAmpereOneSpecies
+from struphy.models.linear_vlasov_maxwell_one_species import (
+    LinearVlasovMaxwellOneSpecies,
+)
+from struphy.models.maxwell import Maxwell
+from struphy.models.poisson import Poisson
+from struphy.models.pressure_less_sph import PressureLessSPH
+from struphy.models.random_particle_diffusion import RandomParticleDiffusion
+from struphy.models.shear_alfven import ShearAlfven
+from struphy.models.two_fluid_quasi_neutral_toy import TwoFluidQuasiNeutralToy
+from struphy.models.variational_barotropic_fluid import VariationalBarotropicFluid
+from struphy.models.variational_compressible_fluid import VariationalCompressibleFluid
+from struphy.models.variational_pressureless_fluid import VariationalPressurelessFluid
+from struphy.models.visco_resistive_deltaf_mhd import ViscoResistiveDeltafMHD
+from struphy.models.visco_resistive_deltaf_mhd_with_q import (
+    ViscoResistiveDeltafMHD_with_q,
+)
+from struphy.models.visco_resistive_linear_mhd import ViscoResistiveLinearMHD
+from struphy.models.visco_resistive_linear_mhd_with_q import (
+    ViscoResistiveLinearMHD_with_q,
+)
+from struphy.models.visco_resistive_mhd import ViscoResistiveMHD
+from struphy.models.visco_resistive_mhd_with_p import ViscoResistiveMHD_with_p
+from struphy.models.visco_resistive_mhd_with_q import ViscoResistiveMHD_with_q
+from struphy.models.viscous_euler_sph import ViscousEulerSPH
+from struphy.models.viscous_fluid import ViscousFluid
+from struphy.models.vlasov import Vlasov
+from struphy.models.vlasov_ampere_one_species import VlasovAmpereOneSpecies
+from struphy.models.vlasov_maxwell_one_species import VlasovMaxwellOneSpecies
+
+__all__ = [
+    "ColdPlasma",
+    "ColdPlasmaVlasov",
+    "DeterministicParticleDiffusion",
+    "DriftKineticElectrostaticAdiabatic",
+    "GuidingCenter",
+    "HasegawaWakatani",
+    "LinearExtendedMHDuniform",
+    "LinearMHD",
+    "LinearMHDDriftkineticCC",
+    "LinearMHDVlasovCC",
+    "LinearMHDVlasovPC",
+    "LinearVlasovAmpereOneSpecies",
+    "LinearVlasovMaxwellOneSpecies",
+    "Maxwell",
+    "Poisson",
+    "PressureLessSPH",
+    "RandomParticleDiffusion",
+    "ShearAlfven",
+    "TwoFluidQuasiNeutralToy",
+    "VariationalBarotropicFluid",
+    "VariationalCompressibleFluid",
+    "VariationalPressurelessFluid",
+    "ViscoResistiveDeltafMHD",
+    "ViscoResistiveDeltafMHD_with_q",
+    "ViscoResistiveLinearMHD",
+    "ViscoResistiveLinearMHD_with_q",
+    "ViscoResistiveMHD",
+    "ViscoResistiveMHD_with_p",
+    "ViscoResistiveMHD_with_q",
+    "ViscousEulerSPH",
+    "ViscousFluid",
+    "Vlasov",
+    "VlasovAmpereOneSpecies",
+    "VlasovMaxwellOneSpecies",
+]

struphy-3.0.3/src/struphy/api/ode/__init__.py

@@ -0,0 +1,3 @@
+from struphy.ode.utils import ButcherTableau
+
+all = ["ButcherTableau"]

struphy-3.0.3/src/struphy/api/options/__init__.py

@@ -0,0 +1,16 @@
+from struphy.io.options import (
+    BaseUnits,
+    DerhamOptions,
+    EnvironmentOptions,
+    FieldsBackground,
+    Time,
+)
+
+__all__ = [
+    "EnvironmentOptions",
+    "BaseUnits",
+    "Time",
+    #
+    "DerhamOptions",
+    "FieldsBackground",
+]

struphy-3.0.3/src/struphy/api/particles/__init__.py

@@ -0,0 +1,15 @@
+from struphy.particles.parameters import (
+    BinningPlot,
+    BoundaryParameters,
+    KernelDensityPlot,
+    LoadingParameters,
+    WeightsParameters,
+)
+
+__all__ = [
+    "LoadingParameters",
+    "WeightsParameters",
+    "BoundaryParameters",
+    "BinningPlot",
+    "KernelDensityPlot",
+]

struphy-3.0.3/src/struphy/api/perturbations/__init__.py

@@ -0,0 +1,3 @@
+from struphy.initial import perturbations
+
+__all__ = ["perturbations"]

struphy-3.0.3/src/struphy/api/post_processing/__init__.py

@@ -0,0 +1,3 @@
+from struphy.post_processing.post_processing_tools import PlottingData, PostProcessor
+
+__all__ = ["PostProcessor", "PlottingData"]

struphy-3.0.3/src/struphy/api/simulation/__init__.py

@@ -0,0 +1,3 @@
+from struphy.simulation.sim import Simulation
+
+all = ["Simulation",]

{struphy-3.0.1 → struphy-3.0.3}/src/struphy/compile_struphy.mk

@@ -35,7 +35,7 @@ all: $(OUTPUTS)
 	@for dep in $^ ; do \
 		echo $$dep ; \
     done
-	pyccel $(FLAGS) $(FLAGS_openmp_pic) $(FLAGS_openmp_mhd) $<
+	pyccel compile -v $(FLAGS) $(FLAGS_openmp_pic) $(FLAGS_openmp_mhd) $<
 	@echo ""
 
 #--------------------------------------

{struphy-3.0.1 → struphy-3.0.3}/src/struphy/console/compile.py

@@ -1,6 +1,4 @@
-import sys
-
-from struphy.utils.utils import subp_run
+from struphy.utils.utils import STRUPHY_LIBPATH, subp_run
 
 
 def struphy_compile(
@@ -21,7 +19,7 @@ def struphy_compile(
     Parameters
     ----------
     language : str
-        Either "c" (default) or "fortran".
+        Either "fortran" (default) or "c".
 
     compiler : str
         Either "GNU" (default), "intel", "PGI", "nvidia", or "LLVM"
@@ -67,7 +65,7 @@ def struphy_compile(
     import struphy.dependencies as depmod
     import struphy.utils.utils as utils
 
-    libpath = struphy.__path__[0]
+    libpath = STRUPHY_LIBPATH
 
     so_suffix = sysconfig.get_config_var("EXT_SUFFIX")
 
@@ -107,6 +105,11 @@ def struphy_compile(
     if delete:
         # (change dir not to be in source path)
         print("\nDeleting .f90/.c and .so files ...")
+        # TODO: for using pyccel clean in the future
+        # cmd = [
+        #     "pyccel",
+        #     "clean",
+        # ]
         cmd = [
             "make",
             "clean",
@@ -272,6 +275,15 @@ def struphy_compile(
 
         # compilation
         print("\nCompiling Struphy kernels ...")
+        kernel_file = os.path.join(libpath, "kernels.txt")
+        # TODO: for using pyccel make in the future
+        # cmd = [
+        #     "pyccel",
+        #     "make",
+        #     "-d",
+        #     kernel_file,
+        #     "-v",
+        # ]
         cmd = [
             "make",
             "-f",
@@ -290,11 +302,3 @@ def struphy_compile(
             "--status",
         ]
         subp_run(cmd)
-
-        # collect available models
-        print("")
-        cmd = [
-            "struphy",
-            "--refresh-models",
-        ]
-        subp_run(cmd)

{struphy-3.0.1 → struphy-3.0.3}/src/struphy/console/format.py

@@ -73,6 +73,8 @@ generate_html_table_from_combined_data(combined_data, sort_descending=True)
 
 import ast
 import fileinput
+import importlib
+import inspect
 import json
 import os
 import re
@@ -86,6 +88,7 @@ from collections import defaultdict
 from tabulate import tabulate
 
 import struphy
+from struphy.models.base import StruphyModel
 
 LIBPATH = struphy.__path__[0]
 
@@ -1269,27 +1272,27 @@ def run_linters_on_files(linters, python_files, flags, verbose):
                     print(line, end="")
 
 
-def construct_models_init_file() -> str:
+def construct_models_init_file(models_dir: str = "src/struphy/models") -> str:
     """
-    Constructs the content for the __init__.py file for the models module.
-
-    Returns:
-        str: The content for the __init__.py file as a string.
+    Constructs __init__.py for all generated model files by reading actual class names.
+    Skips base.py and __init__.py.
     """
-    import struphy.models.fluid as fluid
-    import struphy.models.hybrid as hybrid
-    import struphy.models.kinetic as kinetic
-    import struphy.models.toy as toy
-    from struphy.models.base import StruphyModel
-
     models_init = ""
-
     model_names = []
-    for model_type in [toy, fluid, hybrid, kinetic]:
-        for _, cls in model_type.__dict__.items():
-            if isinstance(cls, type) and issubclass(cls, StruphyModel) and cls != StruphyModel:
-                model_names.append(cls.__name__)
-                models_init += f"from {model_type.__name__} import {cls.__name__}\n"
+
+    for file_name in sorted(os.listdir(models_dir)):
+        if file_name.endswith(".py") and file_name not in ["__init__.py", "base.py"]:
+            module_name = file_name[:-3]  # strip .py
+            module = importlib.import_module(f"struphy.models.{module_name}")
+
+            # Loop over all classes in the module
+            for _, cls in inspect.getmembers(module, inspect.isclass):
+                # Only subclasses of StruphyModel defined in this module
+                if issubclass(cls, StruphyModel) and cls.__module__ == module.__name__ and cls != StruphyModel:
+                    class_name = cls.__name__
+                    models_init += f"from struphy.models.{module_name} import {class_name}\n"
+                    model_names.append(class_name)
+
     models_init += "\n\n"
     models_init += f"__all__ = {model_names}\n"
     return models_init
@@ -1352,17 +1355,20 @@ def struphy_format(config, verbose, yes=False):
         input_type = "path"
 
     if input_type == "__init__.py":
-        print(f"Rewriting {PROPAGATORS_INIT_PATH}")
-        propagators_init = construct_propagators_init_file()
-        with open(PROPAGATORS_INIT_PATH, "w") as f:
-            f.write(propagators_init)
+        # print(f"Rewriting {PROPAGATORS_INIT_PATH}")
+        # propagators_init = construct_propagators_init_file()
+        # with open(PROPAGATORS_INIT_PATH, "w") as f:
+        #     f.write(propagators_init)
 
         print(f"Rewriting {MODELS_INIT_PATH}")
         models_init = construct_models_init_file()
         with open(MODELS_INIT_PATH, "w") as f:
             f.write(models_init)
 
-        python_files = [PROPAGATORS_INIT_PATH, MODELS_INIT_PATH]
+        python_files = [
+            # PROPAGATORS_INIT_PATH,
+            MODELS_INIT_PATH,
+        ]
         input_type = "path"
     else:
         python_files = get_python_files(input_type, path)