struphy 3.1.0__tar.gz → 3.2.0__tar.gz

{struphy-3.1.0/src/struphy.egg-info → struphy-3.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: struphy
-Version: 3.1.0
+Version: 3.2.0
 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
@@ -32,68 +32,66 @@ 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: pyccel<=2.2.3,>=2.2.0
 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: tqdm<=4.68.1
 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: plotly<=6.8.0
+Requires-Dist: pyvista<=0.48.0
+Requires-Dist: trame<=3.13.0
 Requires-Dist: trame-vtk<=2.11.8
-Requires-Dist: trame-vuetify<=3.2.1
+Requires-Dist: trame-vuetify<=3.2.2
 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: ruff<=0.15.12,>=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: mpi
+Requires-Dist: mpi4py<=4.1.1; extra == "mpi"
 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"
-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: pre-commit<=4.6.0; extra == "dev"
-Requires-Dist: nbstripout<=0.9.1; extra == "dev"
-Requires-Dist: tabulate<=0.10.0; extra == "dev"
-Requires-Dist: tomli-w<=1.2.0; extra == "dev"
-Requires-Dist: kaleido<=1.2.0; extra == "dev"
-Requires-Dist: pandas<=3.0.2; extra == "dev"
-Provides-Extra: mpi
-Requires-Dist: mpi4py<=4.1.1; extra == "mpi"
+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: 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"
 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"
-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: sphinx-collections<=0.3.1; extra == "doc"
-Requires-Dist: pydata-sphinx-theme<=0.17.1; 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<=9.1.0; 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: sphinx-collections; 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: docutils; extra == "doc"
+Requires-Dist: ipyparallel; extra == "doc"
 Provides-Extra: likwid
 Requires-Dist: struphy[dev]; extra == "likwid"
 Requires-Dist: pylikwid; extra == "likwid"
@@ -122,6 +120,7 @@ Dynamic: license-file
 
 - Maxwell’s equations
 - Magneto-hydrodynamics (MHD)
+- Multi-fluid models
 - Vlasov-Poisson and Vlasov-Maxwell kinetic models
 - Drift-kinetic models for strongly magnetized plasma
 - MHD-kinetic hybrid models
@@ -132,17 +131,10 @@ The code is freely available under an [MIT license](https://github.com/struphy-h
 
 ![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):
+Struphy is available on [PyPI](https://pypi.org/project/struphy/), so you can install it with pip:
 
-    python -m venv struphy_env
-    source struphy_env/bin/activate
-    pip install -U pip
     pip install -U struphy
     struphy compile
 
@@ -151,6 +143,38 @@ 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)
 
+## Example: solve Maxwell’s equations
+
+Use the command line to generate a default launch file:
+
+    struphy params Maxwell
+
+This will create `params_Maxwell.py` in your current working directory (cwd). You can open the file and - if you feel like it already - change some parameters. Start the simulation with
+
+    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.
+
+## Available models
+
+Check the list of currently available models in the [documentation](https://struphy-hub.github.io/struphy/sections/models.html). If you want to see a particular model implemented, please let us know via [issues](https://github.com/struphy-hub/struphy/issues).
+
+## 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)
+
 ## 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
@@ -181,24 +205,9 @@ sim.show_domain(scalars="absB0", window_size = (850, 250), zoom_factor=2.0)
 
 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
+## Tutorials on Binder
 
-You can also put the run command in a batch script.
+Get familiar with Struphy right away on [mybinder](https://mybinder.org/v2/gh/struphy-hub/struphy-tutorials/main) - no installation needed.
 
 ## Docker
 
@@ -217,15 +226,6 @@ There is also a [Docker image with just the prerequisites](https://hub.docker.co
     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)
@@ -234,6 +234,21 @@ The doc is on [Github pages](https://struphy-hub.github.io/struphy/index.html),
 - [@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
+## Publications
+
+- D. Bell, M.C. Pinto, S. Possanner, E. Sonnendrücker,
+[**The linearized Vlasov–Maxwell system as a Hamiltonian system**](https://doi.org/10.1016/j.jcp.2026.114765),
+Journal of Computational Physics, Volume 555, 114765 (2026).
+
+- V. Carlier, M.C. Pinto, [**Variational discretizations of ideal magnetohydrodynamics in smooth regime using structure-preserving finite elements**](https://doi.org/10.1016/j.jcp.2024.113647),
+Journal of Computational Physics, Volume 523, 113647 (2025).
+
+- Y. Li, M.C. Pinto, F. Holderied, S. Possanner, E. Sonnendrücker, [**Geometric Particle-In-Cell discretizations of a plasma hybrid model with kinetic ions and mass-less fluid electrons**](https://doi.org/10.1016/j.jcp.2023.112671), Journal of Computational Physics 498, 112671 (2023).
+
+- 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, 263-271, Springer Nature Switzerland (2023).
+
+- F. Holderied, S. Possanner, [**Magneto-hydrodynamic eigenvalue solver for axisymmetric equilibria based on smooth polar splines**](https://doi.org/10.1016/j.jcp.2022.111329), Journal of Computational Physics 464, 111329 (2022).
+
+- F. Holderied, S. Possanner, X. Wang, [**MHD-kinetic hybrid code based on structure-preserving finite elements with particles-in-cell**](https://doi.org/10.1016/j.jcp.2021.110143), Journal of Computational Physics 433, 110143 (2021).
 
-- 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.
+- F. Holderied, S. Possanner, A. Ratnani, X. Wang, [**Structure-preserving vs. standard particle-in-cell methods: The case of an electron hybrid model**](https://doi.org/10.1016/j.jcp.2019.109108), Journal of Computational Physics 402, 109108 (2020).

{struphy-3.1.0 → struphy-3.2.0}/README.md

@@ -15,6 +15,7 @@
 
 - Maxwell’s equations
 - Magneto-hydrodynamics (MHD)
+- Multi-fluid models
 - Vlasov-Poisson and Vlasov-Maxwell kinetic models
 - Drift-kinetic models for strongly magnetized plasma
 - MHD-kinetic hybrid models
@@ -25,17 +26,10 @@ The code is freely available under an [MIT license](https://github.com/struphy-h
 
 ![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):
+Struphy is available on [PyPI](https://pypi.org/project/struphy/), so you can install it with pip:
 
-    python -m venv struphy_env
-    source struphy_env/bin/activate
-    pip install -U pip
     pip install -U struphy
     struphy compile
 
@@ -44,6 +38,38 @@ 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)
 
+## Example: solve Maxwell’s equations
+
+Use the command line to generate a default launch file:
+
+    struphy params Maxwell
+
+This will create `params_Maxwell.py` in your current working directory (cwd). You can open the file and - if you feel like it already - change some parameters. Start the simulation with
+
+    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.
+
+## Available models
+
+Check the list of currently available models in the [documentation](https://struphy-hub.github.io/struphy/sections/models.html). If you want to see a particular model implemented, please let us know via [issues](https://github.com/struphy-hub/struphy/issues).
+
+## 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)
+
 ## 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
@@ -74,24 +100,9 @@ sim.show_domain(scalars="absB0", window_size = (850, 250), zoom_factor=2.0)
 
 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
+## Tutorials on Binder
 
-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.
+Get familiar with Struphy right away on [mybinder](https://mybinder.org/v2/gh/struphy-hub/struphy-tutorials/main) - no installation needed.
 
 ## Docker
 
@@ -110,15 +121,6 @@ There is also a [Docker image with just the prerequisites](https://hub.docker.co
     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)
@@ -127,6 +129,21 @@ The doc is on [Github pages](https://struphy-hub.github.io/struphy/index.html),
 - [@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
+## Publications
+
+- D. Bell, M.C. Pinto, S. Possanner, E. Sonnendrücker,
+[**The linearized Vlasov–Maxwell system as a Hamiltonian system**](https://doi.org/10.1016/j.jcp.2026.114765),
+Journal of Computational Physics, Volume 555, 114765 (2026).
+
+- V. Carlier, M.C. Pinto, [**Variational discretizations of ideal magnetohydrodynamics in smooth regime using structure-preserving finite elements**](https://doi.org/10.1016/j.jcp.2024.113647),
+Journal of Computational Physics, Volume 523, 113647 (2025).
+
+- Y. Li, M.C. Pinto, F. Holderied, S. Possanner, E. Sonnendrücker, [**Geometric Particle-In-Cell discretizations of a plasma hybrid model with kinetic ions and mass-less fluid electrons**](https://doi.org/10.1016/j.jcp.2023.112671), Journal of Computational Physics 498, 112671 (2023).
+
+- 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, 263-271, Springer Nature Switzerland (2023).
+
+- F. Holderied, S. Possanner, [**Magneto-hydrodynamic eigenvalue solver for axisymmetric equilibria based on smooth polar splines**](https://doi.org/10.1016/j.jcp.2022.111329), Journal of Computational Physics 464, 111329 (2022).
+
+- F. Holderied, S. Possanner, X. Wang, [**MHD-kinetic hybrid code based on structure-preserving finite elements with particles-in-cell**](https://doi.org/10.1016/j.jcp.2021.110143), Journal of Computational Physics 433, 110143 (2021).
 
-- 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.
+- F. Holderied, S. Possanner, A. Ratnani, X. Wang, [**Structure-preserving vs. standard particle-in-cell methods: The case of an electron hybrid model**](https://doi.org/10.1016/j.jcp.2019.109108), Journal of Computational Physics 402, 109108 (2020).

{struphy-3.1.0 → struphy-3.2.0}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "3.1.0"
+version = "3.2.0"
 readme = "README.md"
 requires-python = ">=3.10"
 authors = [
@@ -25,77 +25,75 @@ classifiers = [
 dependencies = [
     "numpy<=2.4.3",
     "cunumpy<=0.1.1",
-    "pyccel<=2.2.3, >=2.1",
+    "pyccel>=2.2.0, <=2.2.3",
     "feectools<=0.1.3",
     "scipy<=1.17.1",
     "h5py<=3.16.0",
     "matplotlib<=3.10.8",
     "pyyaml<=6.0.3",
     "vtk<=9.6.1",
-    "tqdm<=4.67.3",
+    "tqdm<=4.68.1",
     "argcomplete<=3.6.3",
     "ipywidgets<=8.1.8",
-    "plotly<=6.6.0",
-    "pyvista<=0.47.3",
-    "trame<=3.12.0",
+    "plotly<=6.8.0",
+    "pyvista<=0.48.0",
+    "trame<=3.13.0",
     "trame-vtk<=2.11.8",
-    "trame-vuetify<=3.2.1",
+    "trame-vuetify<=3.2.2",
     "nest_asyncio2<=1.7.2",
     "vtk<=9.6.1",
     "pytest<=9.0.3",
     "pytest-mpi<=0.6",
     "pytest-testmon<=2.2.0",
-    "ruff<=0.15.11, >=0.15.0",
+    "ruff>=0.15.0, <=0.15.12",
     "line_profiler<=5.0.2",
-    "scope-profiler<=0.1.9, >=0.1.7",
-    "jax-finufft<=1.2.0",
+    "scope-profiler>=0.1.7, <=0.1.9",
 ]
 
 [project.license]
 file = "LICENSE"
 
 [project.optional-dependencies]
+mpi = [
+    "mpi4py<=4.1.1",
+]
 phys = [
-    "gvec<=1.4.1, >=1.1.0",
+    "gvec>=1.1.0, <=1.4.1",
     "desc-opt<=0.17.1",
 ]
 dev = [
     "struphy[mpi]",
-    "notebook<=7.5.5",
-    "autopep8<=2.3.2",
-    "isort<=8.0.1",
-    "flake8<=7.3.0",
-    "pylint<=4.0.5",
-    "ssort<=0.16.0",
-    "add-trailing-comma<=4.0.0",
-    "pre-commit<=4.6.0",
-    "nbstripout<=0.9.1",
-    "tabulate<=0.10.0",
-    "tomli-w<=1.2.0",
-    "kaleido<=1.2.0",
-    "pandas<=3.0.2",
-]
-mpi = [
-    "mpi4py<=4.1.1",
+    "notebook",
+    "autopep8",
+    "isort",
+    "flake8",
+    "pylint",
+    "ssort",
+    "add-trailing-comma",
+    "pre-commit",
+    "nbstripout",
+    "tabulate",
+    "tomli-w",
+    "kaleido",
+    "pandas",
 ]
 doc = [
     "struphy[phys]",
-    "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",
-    "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<=9.1.0",
+    "jupyter",
+    "nbconvert",
+    "ipykernel",
+    "sphinx",
+    "sphinx-design",
+    "lxml_html_clean",
+    "sphinxcontrib-napoleon",
+    "sphinx-copybutton",
+    "sphinx-collections",
+    "pydata-sphinx-theme",
+    "nbsphinx",
+    "m2r2",
+    "myst-parser",
+    "docutils",
+    "ipyparallel",
 ]
 likwid = [
     "struphy[dev]",

{struphy-3.1.0 → struphy-3.2.0}/src/struphy/__init__.py

@@ -48,7 +48,7 @@ config = {
 
 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.
@@ -123,6 +123,8 @@ from struphy.api.particles import (
     BoundaryParameters,
     KernelDensityPlot,
     LoadingParameters,
+    SavingParameters,
+    SortingParameters,
     WeightsParameters,
 )
 from struphy.api.perturbations import perturbations
@@ -141,6 +143,8 @@ __all__ = [
     "LoadingParameters",
     "WeightsParameters",
     "BoundaryParameters",
+    "SortingParameters",
+    "SavingParameters",
     "BinningPlot",
     "KernelDensityPlot",
     "DerhamOptions",

{struphy-3.1.0 → struphy-3.2.0}/src/struphy/api/particles/__init__.py

@@ -3,12 +3,16 @@ from struphy.particles.parameters import (
     BoundaryParameters,
     KernelDensityPlot,
     LoadingParameters,
+    SavingParameters,
+    SortingParameters,
     WeightsParameters,
 )
 
 __all__ = [
     "LoadingParameters",
     "WeightsParameters",
+    "SortingParameters",
+    "SavingParameters",
     "BoundaryParameters",
     "BinningPlot",
     "KernelDensityPlot",