struphy 3.0.2__tar.gz → 3.0.4__tar.gz

{struphy-3.0.2/src/struphy.egg-info → struphy-3.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: struphy
-Version: 3.0.2
+Version: 3.0.4
 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
@@ -30,61 +30,61 @@ Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
-Requires-Dist: cunumpy
-Requires-Dist: pyccel>=2.1
-Requires-Dist: feectools
-Requires-Dist: scipy
-Requires-Dist: h5py
-Requires-Dist: matplotlib
-Requires-Dist: pyyaml
-Requires-Dist: vtk
-Requires-Dist: tqdm
-Requires-Dist: argcomplete
-Requires-Dist: pytest
-Requires-Dist: pytest-mpi
-Requires-Dist: pytest-testmon
-Requires-Dist: line_profiler
-Requires-Dist: scope-profiler>=0.1.7
+Requires-Dist: numpy<=2.2.6
+Requires-Dist: cunumpy<=0.1
+Requires-Dist: pyccel<=2.2.0,>=2.2.0
+Requires-Dist: feectools<=0.1.3
+Requires-Dist: scipy<=1.15.3
+Requires-Dist: h5py<=3.15.1
+Requires-Dist: matplotlib<=3.10.7
+Requires-Dist: pyyaml<=6.0.3
+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<=5.0.2
+Requires-Dist: scope-profiler<=0.1.7,>=0.1.7
 Provides-Extra: phys
-Requires-Dist: gvec>=1.1.0; extra == "phys"
-Requires-Dist: desc-opt; 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; extra == "dev"
-Requires-Dist: autopep8; extra == "dev"
-Requires-Dist: isort; extra == "dev"
-Requires-Dist: flake8; extra == "dev"
-Requires-Dist: pylint; extra == "dev"
-Requires-Dist: ssort; extra == "dev"
-Requires-Dist: add-trailing-comma; extra == "dev"
-Requires-Dist: ruff>=0.15.0; extra == "dev"
-Requires-Dist: pre-commit; extra == "dev"
-Requires-Dist: nbstripout; extra == "dev"
-Requires-Dist: tabulate; extra == "dev"
-Requires-Dist: tomli-w; extra == "dev"
-Requires-Dist: kaleido; extra == "dev"
-Requires-Dist: pandas; extra == "dev"
-Requires-Dist: plotly; extra == "dev"
+Requires-Dist: notebook<=7.5.4; extra == "dev"
+Requires-Dist: autopep8<=2.3.2; extra == "dev"
+Requires-Dist: isort<=8.0.0; extra == "dev"
+Requires-Dist: flake8<=7.3.0; 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<=0.15.4,>=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<=3.0.1; extra == "dev"
 Provides-Extra: mpi
-Requires-Dist: mpi4py; extra == "mpi"
+Requires-Dist: mpi4py<=4.1.1; extra == "mpi"
 Provides-Extra: doc
 Requires-Dist: struphy[phys]; extra == "doc"
-Requires-Dist: jupyter; extra == "doc"
-Requires-Dist: nbconvert; extra == "doc"
-Requires-Dist: ipykernel; extra == "doc"
-Requires-Dist: sphinx; extra == "doc"
-Requires-Dist: sphinx-design; extra == "doc"
-Requires-Dist: lxml_html_clean; extra == "doc"
-Requires-Dist: sphinxcontrib-napoleon; extra == "doc"
-Requires-Dist: sphinx-copybutton; extra == "doc"
-Requires-Dist: pydata-sphinx-theme; extra == "doc"
-Requires-Dist: nbsphinx; extra == "doc"
-Requires-Dist: m2r2; extra == "doc"
-Requires-Dist: myst-parser; extra == "doc"
-Requires-Dist: mistune; extra == "doc"
-Requires-Dist: docutils; extra == "doc"
-Requires-Dist: ipyparallel; extra == "doc"
+Requires-Dist: jupyter<=1.1.1; extra == "doc"
+Requires-Dist: nbconvert<=6.5.4; extra == "doc"
+Requires-Dist: ipykernel<=7.2.0; extra == "doc"
+Requires-Dist: sphinx<=9.1.0; extra == "doc"
+Requires-Dist: sphinx-design<=0.7.0; extra == "doc"
+Requires-Dist: lxml_html_clean<=0.4.4; 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<=0.9.8; extra == "doc"
+Requires-Dist: m2r2<=0.3.4; extra == "doc"
+Requires-Dist: myst-parser<=5.0.0; extra == "doc"
+Requires-Dist: mistune<=0.8.4; 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"
 Requires-Dist: pylikwid; extra == "likwid"
@@ -133,7 +133,7 @@ Particles in a Tokamak <br> (model "Vlasov")             |  Toroidal Alfvén eig
 ![](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/gallery_step_1496.png) | ![](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/gallery_struphy_heat.png)
 
 
-The code is freely available under an [MIT license](https://github.com/struphy-hub/struphy/blob/devel/LICENSE) - Copyright (c) 2019-2025, Struphy developers, Max Planck Institute for Plasma Physics.
+The code is freely available under an [MIT license](https://github.com/struphy-hub/struphy/blob/devel/LICENSE) - Copyright (c) 2019-2026, Struphy developers, Max Planck Institute for Plasma Physics.
 
 <h1 align="center">
 <img src="https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/MPI_PP_Logo_Vertical_E_green_rgb.png" width="200">
@@ -162,6 +162,29 @@ In case you face troubles with install/compile:
 2. visit [trouble shooting](https://struphy-hub.github.io/struphy/sections/install.html#trouble-shooting)
 
 
+## Docker
+
+If you want to get started right away without installing anything, you can use the [Docker image](https://hub.docker.com/r/spossann/struphy) - just pull and run:
+
+```
+docker pull spossann/struphy:main
+docker run -it --rm spossann/struphy:main
+ls struphy_*
+```
+This will show three available Struphy environments, which you can activate for example via
+
+```
+source struphy_fortran_/env_fortran_/bin/activate
+```
+
+There is also a [Docker image with just the prerequisites](https://hub.docker.com/r/spossann/ubuntu-for-struphy) (on Ubuntu), so you can install and compile Struphy on top of it yourself:
+
+```
+docker pull spossann/ubuntu-for-struphy:main
+docker run -it --rm spossann/ubuntu-for-struphy:main
+```
+
+
 ## Quick run
 
 As an example, let's say we want to solve Maxwell's equations. We can use the CLI and generate a default launch file via

{struphy-3.0.2 → struphy-3.0.4}/README.md

@@ -35,7 +35,7 @@ Particles in a Tokamak <br> (model "Vlasov")             |  Toroidal Alfvén eig
 ![](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/gallery_step_1496.png) | ![](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/gallery_struphy_heat.png)
 
 
-The code is freely available under an [MIT license](https://github.com/struphy-hub/struphy/blob/devel/LICENSE) - Copyright (c) 2019-2025, Struphy developers, Max Planck Institute for Plasma Physics.
+The code is freely available under an [MIT license](https://github.com/struphy-hub/struphy/blob/devel/LICENSE) - Copyright (c) 2019-2026, Struphy developers, Max Planck Institute for Plasma Physics.
 
 <h1 align="center">
 <img src="https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/MPI_PP_Logo_Vertical_E_green_rgb.png" width="200">
@@ -64,6 +64,29 @@ In case you face troubles with install/compile:
 2. visit [trouble shooting](https://struphy-hub.github.io/struphy/sections/install.html#trouble-shooting)
 
 
+## Docker
+
+If you want to get started right away without installing anything, you can use the [Docker image](https://hub.docker.com/r/spossann/struphy) - just pull and run:
+
+```
+docker pull spossann/struphy:main
+docker run -it --rm spossann/struphy:main
+ls struphy_*
+```
+This will show three available Struphy environments, which you can activate for example via
+
+```
+source struphy_fortran_/env_fortran_/bin/activate
+```
+
+There is also a [Docker image with just the prerequisites](https://hub.docker.com/r/spossann/ubuntu-for-struphy) (on Ubuntu), so you can install and compile Struphy on top of it yourself:
+
+```
+docker pull spossann/ubuntu-for-struphy:main
+docker run -it --rm spossann/ubuntu-for-struphy:main
+```
+
+
 ## Quick run
 
 As an example, let's say we want to solve Maxwell's equations. We can use the CLI and generate a default launch file via

{struphy-3.0.2 → struphy-3.0.4}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "3.0.2"
+version = "3.0.4"
 readme = "README.md"
 requires-python = ">=3.10"
 authors = [
@@ -21,24 +21,25 @@ keywords = [
 ]
 classifiers = [
     "Programming Language :: Python :: 3",
-    ]
+]
 dependencies = [
-    'numpy',
-    'cunumpy',
-    'pyccel>=2.1',
-    'feectools',
-    'scipy',
-    'h5py',
-    'matplotlib',
-    'pyyaml',
-    'vtk',
-    'tqdm',
-    'argcomplete',
-    'pytest',
-    'pytest-mpi',
-    'pytest-testmon',
-    'line_profiler',
-    'scope-profiler>=0.1.7',
+    "numpy<=2.2.6",
+    "cunumpy<=0.1",
+    "pyccel<=2.2.0, >=2.2.0",
+    "feectools<=0.1.3",
+    "scipy<=1.15.3",
+    "h5py<=3.15.1",
+    "matplotlib<=3.10.7",
+    "pyyaml<=6.0.3",
+    "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<=5.0.2",
+    "scope-profiler<=0.1.7, >=0.1.7",
 ]
 
 [project.license]
@@ -46,47 +47,46 @@ file = "LICENSE"
 
 [project.optional-dependencies]
 phys = [
-    'gvec>=1.1.0',
-    'desc-opt',
+    "gvec<=1.3.1, >=1.1.0",
+    "desc-opt<=0.16.0",
 ]
 dev = [
     "struphy[mpi]",
-    "notebook",
-    "autopep8",
-    "isort",
-    "flake8",
-    "pylint",
-    "ssort",
-    "add-trailing-comma",
-    "ruff>=0.15.0",
-    "pre-commit",
-    "nbstripout",
-    "tabulate",
-    "tomli-w",
-    "kaleido",
-    "pandas",
-    "plotly",
+    "notebook<=7.5.4",
+    "autopep8<=2.3.2",
+    "isort<=8.0.0",
+    "flake8<=7.3.0",
+    "pylint<=4.0.5",
+    "ssort<=0.16.0",
+    "add-trailing-comma<=4.0.0",
+    "ruff<=0.15.4, >=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<=3.0.1",
 ]
 mpi = [
-    'mpi4py',
+    "mpi4py<=4.1.1",
 ]
 doc = [
     "struphy[phys]",
-    "jupyter",
-    "nbconvert",
-    "ipykernel",
-    "sphinx",
-    "sphinx-design",
-    "lxml_html_clean",
-    "sphinxcontrib-napoleon",
-    "sphinx-copybutton",
-    "pydata-sphinx-theme",
-    "nbsphinx",
-    "m2r2",
-    "myst-parser",
-    "mistune",
-    "docutils",
-    "ipyparallel",
+    "jupyter<=1.1.1",
+    "nbconvert<=6.5.4",
+    "ipykernel<=7.2.0",
+    "sphinx<=9.1.0",
+    "sphinx-design<=0.7.0",
+    "lxml_html_clean<=0.4.4",
+    "sphinxcontrib-napoleon<=0.7",
+    "sphinx-copybutton<=0.5.2",
+    "pydata-sphinx-theme<=0.16.1",
+    "nbsphinx<=0.9.8",
+    "m2r2<=0.3.4",
+    "myst-parser<=5.0.0",
+    "mistune<=0.8.4",
+    "docutils<=0.22.4",
+    "ipyparallel<=9.0.2",
 ]
 likwid = [
     "struphy[dev]",
@@ -137,17 +137,12 @@ ignore = [
 [tool.isort]
 profile = "black"
 line_length = 120
-# multi_line_output = 3
-# include_trailing_comma = true
-# force_grid_wrap = 0
-# combine_as_imports = true
 
 [tool.pylint]
 max-line-length = 120
 
 [tool.ruff]
 line-length = 120
-# exclude = ["__pyccel__"]
 
 [tool.ruff.lint]
 ignore = [
@@ -165,7 +160,7 @@ ignore = [
     "F405",
     "D211",
     "D213",
-    "F841", # Ignore unused variables
+    "F841",
 ]
 
 [tool.pytest.ini_options]

{struphy-3.0.2 → struphy-3.0.4}/src/struphy/__init__.py

@@ -18,6 +18,8 @@ from struphy.api.particles import (
     WeightsParameters,
 )
 from struphy.api.perturbations import perturbations
+from struphy.api.post_processing import PlottingData, PostProcessor
+from struphy.api.simulation import Simulation
 
 __all__ = [
     "domains",
@@ -36,4 +38,7 @@ __all__ = [
     "DerhamOptions",
     "FieldsBackground",
     "ButcherTableau",
+    "PostProcessor",
+    "PlottingData",
+    "Simulation",
 ]

{struphy-3.0.2 → struphy-3.0.4}/src/struphy/api/models/__init__.py

@@ -6,7 +6,6 @@ from struphy.models.deterministic_particle_diffusion import (
 from struphy.models.drift_kinetic_electrostatic_adiabatic import (
     DriftKineticElectrostaticAdiabatic,
 )
-from struphy.models.euler_sph import EulerSPH
 from struphy.models.guiding_center import GuidingCenter
 from struphy.models.hasegawa_wakatani import HasegawaWakatani
 from struphy.models.linear_extended_mh_duniform import LinearExtendedMHDuniform
@@ -49,7 +48,6 @@ __all__ = [
     "ColdPlasmaVlasov",
     "DeterministicParticleDiffusion",
     "DriftKineticElectrostaticAdiabatic",
-    "EulerSPH",
     "GuidingCenter",
     "HasegawaWakatani",
     "LinearExtendedMHDuniform",

struphy-3.0.4/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-3.0.4/src/struphy/api/simulation/__init__.py

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

{struphy-3.0.2 → struphy-3.0.4}/src/struphy/feec/psydac_derham.py

@@ -890,7 +890,7 @@ class Derham:
         perturbations: Perturbation | list = None,
         domain: Domain = None,
         equil: FluidEquilibrium = None,
-        verbose: bool = True,
+        verbose: bool = False,
     ):
         """Creat a callable spline function.
 
@@ -1442,7 +1442,7 @@ class SplineFunction:
         perturbations: Perturbation | list = None,
         domain: Domain = None,
         equil: FluidEquilibrium = None,
-        verbose: bool = True,
+        verbose: bool = False,
     ):
         self._name = name
         self._space_id = space_id
@@ -1494,7 +1494,7 @@ class SplineFunction:
             print(f"\nAllocated SplineFuntion '{self.name}' in space '{self.space_id}'.")
 
         if self.backgrounds is not None or self.perturbations is not None:
-            self.initialize_coeffs(domain=self.domain, equil=self.equil)
+            self.initialize_coeffs(domain=self.domain, equil=self.equil, verbose=verbose)
 
     @property
     def name(self):
@@ -1675,6 +1675,7 @@ class SplineFunction:
         perturbations: Perturbation | list = None,
         domain: Domain = None,
         equil: FluidEquilibrium = None,
+        verbose: bool = False,
     ):
         """
         Set the initial conditions for self.vector.
@@ -1707,14 +1708,14 @@ class SplineFunction:
         # start from zero coeffs
         self._vector *= 0.0
 
-        if MPI.COMM_WORLD.Get_rank() == 0:
+        if verbose and MPI.COMM_WORLD.Get_rank() == 0:
             print(f"Initializing {self.name} ...")
 
         # add backgrounds to initial vector
         if self.backgrounds is not None:
             for fb in self.backgrounds:
                 assert isinstance(fb, FieldsBackground)
-                if MPI.COMM_WORLD.Get_rank() == 0:
+                if verbose and MPI.COMM_WORLD.Get_rank() == 0:
                     print(f"Adding background {fb} ...")
 
                 # special case of const
@@ -1769,7 +1770,7 @@ class SplineFunction:
         # add perturbations to coefficient vector
         if self.perturbations is not None:
             for ptb in self.perturbations:
-                if MPI.COMM_WORLD.Get_rank() == 0:
+                if verbose and MPI.COMM_WORLD.Get_rank() == 0:
                     print(f"Adding perturbation {ptb} ...")
 
                 # special case of white noise in logical space for different components