struphy 3.0.3__tar.gz → 3.1.0__tar.gz

struphy-3.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: struphy
+Version: 3.1.0
+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) 2019-2026, 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, 
+        including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, 
+        and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, 
+        subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all copies or substantial 
+        portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT 
+        NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
+        IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+        WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+        SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+Project-URL: homepage, https://struphy-hub.github.io/struphy/index.html
+Project-URL: documentation, https://struphy-hub.github.io/struphy/index.html
+Project-URL: repository, https://github.com/struphy-hub/struphy
+Project-URL: changelog, https://github.com/struphy-hub/struphy/blob/devel/CHANGELOG.md
+Project-URL: Bug Tracker, https://github.com/struphy-hub/struphy/issues
+Keywords: plasma physics, fusion, numerical modeling, partial differential equations, energetic particles
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<=2.4.3
+Requires-Dist: cunumpy<=0.1.1
+Requires-Dist: pyccel<=2.2.3,>=2.1
+Requires-Dist: feectools<=0.1.3
+Requires-Dist: scipy<=1.17.1
+Requires-Dist: h5py<=3.16.0
+Requires-Dist: matplotlib<=3.10.8
+Requires-Dist: pyyaml<=6.0.3
+Requires-Dist: vtk<=9.6.1
+Requires-Dist: tqdm<=4.67.3
+Requires-Dist: argcomplete<=3.6.3
+Requires-Dist: ipywidgets<=8.1.8
+Requires-Dist: plotly<=6.6.0
+Requires-Dist: pyvista<=0.47.3
+Requires-Dist: trame<=3.12.0
+Requires-Dist: trame-vtk<=2.11.8
+Requires-Dist: trame-vuetify<=3.2.1
+Requires-Dist: nest_asyncio2<=1.7.2
+Requires-Dist: vtk<=9.6.1
+Requires-Dist: pytest<=9.0.3
+Requires-Dist: pytest-mpi<=0.6
+Requires-Dist: pytest-testmon<=2.2.0
+Requires-Dist: ruff<=0.15.11,>=0.15.0
+Requires-Dist: line_profiler<=5.0.2
+Requires-Dist: scope-profiler<=0.1.9,>=0.1.7
+Requires-Dist: jax-finufft<=1.2.0
+Provides-Extra: phys
+Requires-Dist: gvec<=1.4.1,>=1.1.0; extra == "phys"
+Requires-Dist: desc-opt<=0.17.1; extra == "phys"
+Provides-Extra: dev
+Requires-Dist: struphy[mpi]; extra == "dev"
+Requires-Dist: notebook<=7.5.5; extra == "dev"
+Requires-Dist: autopep8<=2.3.2; extra == "dev"
+Requires-Dist: isort<=8.0.1; extra == "dev"
+Requires-Dist: flake8<=7.3.0; extra == "dev"
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+Requires-Dist: pre-commit<=4.6.0; extra == "dev"
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+Requires-Dist: kaleido<=1.2.0; extra == "dev"
+Requires-Dist: pandas<=3.0.2; extra == "dev"
+Provides-Extra: mpi
+Requires-Dist: mpi4py<=4.1.1; extra == "mpi"
+Provides-Extra: doc
+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<=7.2.0; extra == "doc"
+Requires-Dist: sphinx<=9.1.0; extra == "doc"
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+Requires-Dist: pydata-sphinx-theme<=0.17.1; extra == "doc"
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+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<=9.1.0; extra == "doc"
+Provides-Extra: likwid
+Requires-Dist: struphy[dev]; extra == "likwid"
+Requires-Dist: pylikwid; extra == "likwid"
+Provides-Extra: all
+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
+
+
+
+![STRUPHY Header](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/struphy_header_with_subs.png)
+
+<p>
+
+<a href="https://github.com/struphy-hub/struphy/releases"><img src="https://img.shields.io/github/v/release/struphy-hub/struphy?label=Release" alt="Release"></a> <a href="https://github.com/struphy-hub/struphy/blob/devel/LICENSE"><img src="https://img.shields.io/badge/License-MIT-violet" alt="License"></a> <a href="https://mybinder.org/v2/gh/struphy-hub/struphy-tutorials/main"><img src="https://img.shields.io/badge/launch-tutorials-579ACA.svg?logo=data:image/png;base64,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" alt="badge"></a> <a href="https://github.com/struphy-hub/struphy/actions/workflows/scheduled-ubuntu.yml"><img src="https://github.com/struphy-hub/struphy/actions/workflows/scheduled-ubuntu.yml/badge.svg" alt="Ubuntu latest"></a> <a href="https://github.com/struphy-hub/struphy/actions/workflows/scheduled-macos.yml"><img src="https://github.com/struphy-hub/struphy/actions/workflows/scheduled-macos.yml/badge.svg" alt="MacOS latest"></a> <a href="https://github.com/struphy-hub/struphy/actions/workflows/static_analysis.yml"><img src="https://github.com/struphy-hub/struphy/actions/workflows/static_analysis.yml/badge.svg" alt="isort and ruff"></a> <a href="https://pypi.org/project/struphy/"><img src="https://img.shields.io/pypi/v/struphy?label=PyPI" alt="PyPI"></a> <a href="https://pypi.org/project/struphy/"><img src="https://img.shields.io/pypi/dm/struphy.svg?label=PyPI%20downloads" alt="PyPI Downloads"></a>
+</p>
+
+# Welcome!
+
+**This is a Python package for solving partial differential equations (PDEs) mainly - but not exclusively - for plasma physics.**
+
+**STRUPHY** stands for **STRU**cture-**P**reserving **HY**brid code (or **STRU**cture-preserving **PHY**sics code). The package provides off-the-shelf models for plasma physics problems, such as
+
+- Maxwell’s equations
+- Magneto-hydrodynamics (MHD)
+- Vlasov-Poisson and Vlasov-Maxwell kinetic models
+- Drift-kinetic models for strongly magnetized plasma
+- MHD-kinetic hybrid models
+
+All models can be run on multiple cores through MPI (distributed memory) and OpenMP (shared memory). The compute-intensive parts of the code are translated and compiled (“transpiled”) using [pyccel](https://github.com/pyccel/pyccel), giving you the speed of Fortran or C while working within the familiar Python environment.
+
+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.
+
+![Max Planck Institute Logo](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/MPI_PP_Logo_Vertical_E_green_rgb_centered.png)
+
+## Tutorials
+
+Get familiar with Struphy right away on [mybinder](https://mybinder.org/v2/gh/struphy-hub/struphy-tutorials/main) - no installation needed.
+
+## Quick install
+
+Quick install on your computer (using a virtual environment):
+
+    python -m venv struphy_env
+    source struphy_env/bin/activate
+    pip install -U pip
+    pip install -U struphy
+    struphy compile
+
+In case you face troubles with install/compile:
+
+1.  check the [prerequisites](https://struphy-hub.github.io/struphy/sections/install.html#requirements)
+2.  visit [trouble shooting](https://struphy-hub.github.io/struphy/sections/install.html#trouble-shooting)
+
+## Python API
+
+Try out the Python API in a Jupyter notebook or any Python environment. For example, you can create a simulation object and show the domain and equilibrium magnetic field of the linear MHD model via
+
+``` python
+from struphy import (
+    Simulation,
+    domains,
+    equils,
+)
+from struphy.models import LinearMHD
+
+model = LinearMHD()
+
+domain = domains.DESCunit()
+equil = equils.DESCequilibrium(use_nfp=False)
+
+sim = Simulation(
+    model=model,
+    domain=domain,
+    equil=equil,
+)
+
+sim.show_domain(scalars="absB0", window_size = (850, 250), zoom_factor=2.0)
+```
+
+![](README_files/figure-commonmark/cell-2-output-1.png)
+
+This will show the domain and equilibrium magnetic field of the linear MHD model. You can find more examples in the [documentation](https://struphy-hub.github.io/struphy/index.html).
+
+## 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 params Maxwell
+
+Hit yes when prompted - this will create the file `params_Maxwell.py` in your current working directory (cwd). You can open the file and - if you feel like it already - change some parameters, then run
+
+    python params_Maxwell.py
+
+The default output is in `sim_1/` in your cwd. You can change the output path via the class `EnvironmentOptions` in the parameter file.
+
+Parallel simulations are run for example with
+
+    pip install -U mpi4py
+    mpirun -n 4 python params_Maxwell.py
+
+You can also put the run command in a batch script.
+
+## 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
+
+## Documentation
+
+The doc is on [Github pages](https://struphy-hub.github.io/struphy/index.html), we recommend in particular to visit:
+
+- [Install](https://struphy-hub.github.io/struphy/sections/install.html)
+- [Userguide](https://struphy-hub.github.io/struphy/sections/userguide.html)
+- [Available models](https://struphy-hub.github.io/struphy/sections/models.html)
+- [Numerical methods](https://struphy-hub.github.io/struphy/sections/numerics.html)
+
+## Get in touch
+
+- [Issues](https://github.com/struphy-hub/struphy/issues)
+- [Discussions](https://github.com/struphy-hub/struphy/discussions)
+- [@spossann](https://github.com/spossann) [stefan.possanner@ipp.mpg.de](mailto:spossann@ipp.mpg.de) (Maintainer)
+- [@max-models](https://github.com/max-models) [max.lindqvist@ipp.mpg.de](mailto:Max.Lindqvist@ipp.mpg.de) (Maintainer)
+- [LinkedIn profile](https://www.linkedin.com/company/struphy/)
+
+## Citing Struphy
+
+- S. Possanner, F. Holderied, Y. Li, B.-K. Na, D. Bell, S. Hadjout and Y. Güçlü, [**High-Order Structure-Preserving Algorithms for Plasma Hybrid Models**](https://link.springer.com/chapter/10.1007/978-3-031-38299-4_28), International Conference on Geometric Science of Information 2023, 263-271, Springer Nature Switzerland.

struphy-3.1.0/README.md

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+
+
+![STRUPHY Header](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/struphy_header_with_subs.png)
+
+<p>
+
+<a href="https://github.com/struphy-hub/struphy/releases"><img src="https://img.shields.io/github/v/release/struphy-hub/struphy?label=Release" alt="Release"></a> <a href="https://github.com/struphy-hub/struphy/blob/devel/LICENSE"><img src="https://img.shields.io/badge/License-MIT-violet" alt="License"></a> <a href="https://mybinder.org/v2/gh/struphy-hub/struphy-tutorials/main"><img src="https://img.shields.io/badge/launch-tutorials-579ACA.svg?logo=data:image/png;base64,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" alt="badge"></a> <a href="https://github.com/struphy-hub/struphy/actions/workflows/scheduled-ubuntu.yml"><img src="https://github.com/struphy-hub/struphy/actions/workflows/scheduled-ubuntu.yml/badge.svg" alt="Ubuntu latest"></a> <a href="https://github.com/struphy-hub/struphy/actions/workflows/scheduled-macos.yml"><img src="https://github.com/struphy-hub/struphy/actions/workflows/scheduled-macos.yml/badge.svg" alt="MacOS latest"></a> <a href="https://github.com/struphy-hub/struphy/actions/workflows/static_analysis.yml"><img src="https://github.com/struphy-hub/struphy/actions/workflows/static_analysis.yml/badge.svg" alt="isort and ruff"></a> <a href="https://pypi.org/project/struphy/"><img src="https://img.shields.io/pypi/v/struphy?label=PyPI" alt="PyPI"></a> <a href="https://pypi.org/project/struphy/"><img src="https://img.shields.io/pypi/dm/struphy.svg?label=PyPI%20downloads" alt="PyPI Downloads"></a>
+</p>
+
+# Welcome!
+
+**This is a Python package for solving partial differential equations (PDEs) mainly - but not exclusively - for plasma physics.**
+
+**STRUPHY** stands for **STRU**cture-**P**reserving **HY**brid code (or **STRU**cture-preserving **PHY**sics code). The package provides off-the-shelf models for plasma physics problems, such as
+
+- Maxwell’s equations
+- Magneto-hydrodynamics (MHD)
+- Vlasov-Poisson and Vlasov-Maxwell kinetic models
+- Drift-kinetic models for strongly magnetized plasma
+- MHD-kinetic hybrid models
+
+All models can be run on multiple cores through MPI (distributed memory) and OpenMP (shared memory). The compute-intensive parts of the code are translated and compiled (“transpiled”) using [pyccel](https://github.com/pyccel/pyccel), giving you the speed of Fortran or C while working within the familiar Python environment.
+
+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.
+
+![Max Planck Institute Logo](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/MPI_PP_Logo_Vertical_E_green_rgb_centered.png)
+
+## Tutorials
+
+Get familiar with Struphy right away on [mybinder](https://mybinder.org/v2/gh/struphy-hub/struphy-tutorials/main) - no installation needed.
+
+## Quick install
+
+Quick install on your computer (using a virtual environment):
+
+    python -m venv struphy_env
+    source struphy_env/bin/activate
+    pip install -U pip
+    pip install -U struphy
+    struphy compile
+
+In case you face troubles with install/compile:
+
+1.  check the [prerequisites](https://struphy-hub.github.io/struphy/sections/install.html#requirements)
+2.  visit [trouble shooting](https://struphy-hub.github.io/struphy/sections/install.html#trouble-shooting)
+
+## Python API
+
+Try out the Python API in a Jupyter notebook or any Python environment. For example, you can create a simulation object and show the domain and equilibrium magnetic field of the linear MHD model via
+
+``` python
+from struphy import (
+    Simulation,
+    domains,
+    equils,
+)
+from struphy.models import LinearMHD
+
+model = LinearMHD()
+
+domain = domains.DESCunit()
+equil = equils.DESCequilibrium(use_nfp=False)
+
+sim = Simulation(
+    model=model,
+    domain=domain,
+    equil=equil,
+)
+
+sim.show_domain(scalars="absB0", window_size = (850, 250), zoom_factor=2.0)
+```
+
+![](README_files/figure-commonmark/cell-2-output-1.png)
+
+This will show the domain and equilibrium magnetic field of the linear MHD model. You can find more examples in the [documentation](https://struphy-hub.github.io/struphy/index.html).
+
+## 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 params Maxwell
+
+Hit yes when prompted - this will create the file `params_Maxwell.py` in your current working directory (cwd). You can open the file and - if you feel like it already - change some parameters, then run
+
+    python params_Maxwell.py
+
+The default output is in `sim_1/` in your cwd. You can change the output path via the class `EnvironmentOptions` in the parameter file.
+
+Parallel simulations are run for example with
+
+    pip install -U mpi4py
+    mpirun -n 4 python params_Maxwell.py
+
+You can also put the run command in a batch script.
+
+## 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
+
+## Documentation
+
+The doc is on [Github pages](https://struphy-hub.github.io/struphy/index.html), we recommend in particular to visit:
+
+- [Install](https://struphy-hub.github.io/struphy/sections/install.html)
+- [Userguide](https://struphy-hub.github.io/struphy/sections/userguide.html)
+- [Available models](https://struphy-hub.github.io/struphy/sections/models.html)
+- [Numerical methods](https://struphy-hub.github.io/struphy/sections/numerics.html)
+
+## Get in touch
+
+- [Issues](https://github.com/struphy-hub/struphy/issues)
+- [Discussions](https://github.com/struphy-hub/struphy/discussions)
+- [@spossann](https://github.com/spossann) [stefan.possanner@ipp.mpg.de](mailto:spossann@ipp.mpg.de) (Maintainer)
+- [@max-models](https://github.com/max-models) [max.lindqvist@ipp.mpg.de](mailto:Max.Lindqvist@ipp.mpg.de) (Maintainer)
+- [LinkedIn profile](https://www.linkedin.com/company/struphy/)
+
+## Citing Struphy
+
+- S. Possanner, F. Holderied, Y. Li, B.-K. Na, D. Bell, S. Hadjout and Y. Güçlü, [**High-Order Structure-Preserving Algorithms for Plasma Hybrid Models**](https://link.springer.com/chapter/10.1007/978-3-031-38299-4_28), International Conference on Geometric Science of Information 2023, 263-271, Springer Nature Switzerland.

{struphy-3.0.3 → struphy-3.1.0}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "3.0.3"
+version = "3.1.0"
 readme = "README.md"
 requires-python = ">=3.10"
 authors = [
@@ -23,23 +23,32 @@ classifiers = [
     "Programming Language :: Python :: 3",
 ]
 dependencies = [
-    "numpy<=2.2.6",
-    "cunumpy<=0.1",
-    "pyccel<=2.1.0, >=2.1",
+    "numpy<=2.4.3",
+    "cunumpy<=0.1.1",
+    "pyccel<=2.2.3, >=2.1",
     "feectools<=0.1.3",
-    "scipy<=1.15.3",
-    "h5py<=3.15.1",
-    "matplotlib<=3.10.7",
+    "scipy<=1.17.1",
+    "h5py<=3.16.0",
+    "matplotlib<=3.10.8",
     "pyyaml<=6.0.3",
-    "vtk<=9.6.0",
+    "vtk<=9.6.1",
     "tqdm<=4.67.3",
     "argcomplete<=3.6.3",
-    "plotly<=6.4.0",
-    "pytest<=9.0.2",
+    "ipywidgets<=8.1.8",
+    "plotly<=6.6.0",
+    "pyvista<=0.47.3",
+    "trame<=3.12.0",
+    "trame-vtk<=2.11.8",
+    "trame-vuetify<=3.2.1",
+    "nest_asyncio2<=1.7.2",
+    "vtk<=9.6.1",
+    "pytest<=9.0.3",
     "pytest-mpi<=0.6",
     "pytest-testmon<=2.2.0",
-    "line_profiler<=5.0.1",
-    "scope-profiler<=0.1.7, >=0.1.7",
+    "ruff<=0.15.11, >=0.15.0",
+    "line_profiler<=5.0.2",
+    "scope-profiler<=0.1.9, >=0.1.7",
+    "jax-finufft<=1.2.0",
 ]
 
 [project.license]
@@ -47,25 +56,24 @@ file = "LICENSE"
 
 [project.optional-dependencies]
 phys = [
-    "gvec<=1.3.1, >=1.1.0",
-    "desc-opt<=0.16.0",
+    "gvec<=1.4.1, >=1.1.0",
+    "desc-opt<=0.17.1",
 ]
 dev = [
     "struphy[mpi]",
-    "notebook<=7.5.3",
+    "notebook<=7.5.5",
     "autopep8<=2.3.2",
-    "isort<=8.0.0",
+    "isort<=8.0.1",
     "flake8<=7.3.0",
     "pylint<=4.0.5",
     "ssort<=0.16.0",
     "add-trailing-comma<=4.0.0",
-    "ruff<=0.15.2, >=0.15.0",
-    "pre-commit<=4.5.1",
+    "pre-commit<=4.6.0",
     "nbstripout<=0.9.1",
-    "tabulate<=0.9.0",
+    "tabulate<=0.10.0",
     "tomli-w<=1.2.0",
     "kaleido<=1.2.0",
-    "pandas<=3.0.1",
+    "pandas<=3.0.2",
 ]
 mpi = [
     "mpi4py<=4.1.1",
@@ -74,19 +82,20 @@ doc = [
     "struphy[phys]",
     "jupyter<=1.1.1",
     "nbconvert<=6.5.4",
-    "ipykernel<=7.1.0",
+    "ipykernel<=7.2.0",
     "sphinx<=9.1.0",
     "sphinx-design<=0.7.0",
-    "lxml_html_clean<=0.4.3",
+    "lxml_html_clean<=0.4.4",
     "sphinxcontrib-napoleon<=0.7",
     "sphinx-copybutton<=0.5.2",
-    "pydata-sphinx-theme<=0.16.1",
+    "sphinx-collections<=0.3.1",
+    "pydata-sphinx-theme<=0.17.1",
     "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",
+    "ipyparallel<=9.1.0",
 ]
 likwid = [
     "struphy[dev]",

struphy-3.1.0/src/struphy/__init__.py

@@ -0,0 +1,152 @@
+# Logging parameters and filters
+import atexit
+import logging
+import logging.config
+
+from feectools.ddm.mpi import mpi as MPI
+
+
+class RankZeroFilter(logging.Filter):
+    def __init__(self, rank: int):
+        super().__init__()
+        self.rank = rank
+
+    def filter(self, record):
+        return self.rank == 0
+
+
+# logger configuration
+config = {
+    "version": 1,
+    "disable_existing_loggers": False,
+    "formatters": {
+        "simple": {"format": "%(message)s"},
+        "detailed": {
+            "format": "[%(levelname)s|%(module)s|L%(lineno)d] %(asctime)s: %(message)s",
+            "datefmt": "%Y-%m-%dT%H:%M:%S%z",
+        },
+    },
+    "handlers": {
+        "stderr": {
+            "class": "logging.StreamHandler",
+            "level": "WARNING",
+            "formatter": "simple",
+            "stream": "ext://sys.stderr",
+        },
+        "file": {
+            "class": "logging.handlers.RotatingFileHandler",
+            "level": "WARNING",
+            "formatter": "detailed",
+            "filename": "/tmp/struphy.log",
+            "maxBytes": 10000,
+            "backupCount": 3,
+        },
+    },
+    "loggers": {"struphy": {"level": "WARNING", "handlers": ["stderr", "file"]}},
+}
+
+
+def set_logging_level(level: int = logging.WARNING):
+    """Set logging level for struphy logger and its handlers.
+    
+    Useful levels are:
+    * logging.DEBUG: for detailed debugging information.
+    * logging.INFO: for general informational messages about the simulation setup and progress, plus key events.
+    * logging.WARNING: for warnings about potential issues that do not stop the simulation.
+    * logging.ERROR: for errors that occur during the simulation, which may affect results but do not necessarily stop the simulation.
+    * logging.CRITICAL: for critical errors that likely cause the simulation to stop or produce invalid results.
+    """
+    logger = logging.getLogger("struphy")
+    logger.setLevel(level)
+    for handler in logger.handlers:
+        handler.setLevel(level)
+
+    logger.debug(
+        f"\nNew logger level: {logger.level}, effective: {logger.getEffectiveLevel()}, propagate: {logger.propagate}"
+    )
+    for h in logger.handlers:
+        logger.debug(f"{type(h).__name__}: handler level: {h.level}")
+
+
+def setup_logging(logging_level: int = logging.WARNING):
+    """Setup logging configuration for struphy."""
+    logger = logging.getLogger("struphy")
+
+    logging.config.dictConfig(config)
+
+    set_logging_level(logging_level)
+
+    # Add RankZeroFilter to all handlers
+    rank = MPI.COMM_WORLD.Get_rank()
+    rank_filter = RankZeroFilter(rank)
+
+    # Apply filter to struphy logger handlers
+    for handler in logger.handlers:
+        handler.addFilter(rank_filter)
+
+    # Apply filter to root logger handlers
+    root_logger = logging.getLogger()
+    for handler in root_logger.handlers:
+        handler.addFilter(rank_filter)
+
+    # Start queue handler listener if present
+    queue_handler = None
+    for handler in logger.handlers:
+        if hasattr(handler, "listener"):
+            queue_handler = handler
+            break
+    if queue_handler is not None:
+        queue_handler.listener.start()
+        atexit.register(queue_handler.listener.stop)
+
+
+# Default logging setup
+logger = logging.getLogger("struphy")
+setup_logging(logging_level=logging.WARNING)
+logger.info("Logging setup complete.")
+
+# Import API components
+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 → struphy-3.1.0}/src/struphy/api/simulation/__init__.py

@@ -1,3 +1,5 @@
 from struphy.simulation.sim import Simulation
 
-all = ["Simulation",]
+all = [
+    "Simulation",
+]