struphy 2.5.0__tar.gz → 3.0.0__tar.gz

struphy-3.0.0/PKG-INFO

@@ -0,0 +1,208 @@
+Metadata-Version: 2.4
+Name: struphy
+Version: 3.0.0
+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) 2019-2025, 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<=2.2.6
+Requires-Dist: cunumpy<=0.1
+Requires-Dist: pyccel<=2.0.1,>=2.0
+Requires-Dist: scipy<=1.15.3
+Requires-Dist: h5py<=3.14.0
+Requires-Dist: matplotlib<=3.10.5
+Requires-Dist: pyyaml<=6.0.3
+Requires-Dist: vtk<=9.5.2
+Requires-Dist: tqdm<=4.67.1
+Requires-Dist: argcomplete<=3.6.3
+Requires-Dist: pytest<=9.0.1
+Requires-Dist: pytest-mpi<=0.6
+Requires-Dist: line_profiler<=5.0.0
+Provides-Extra: phys
+Requires-Dist: gvec<=1.2.0,>=1.1.0; extra == "phys"
+Requires-Dist: desc-opt<=0.15.0; extra == "phys"
+Provides-Extra: dev
+Requires-Dist: struphy[mpi]; extra == "dev"
+Requires-Dist: notebook<=7.4.7; extra == "dev"
+Requires-Dist: autopep8<=2.3.2; extra == "dev"
+Requires-Dist: isort<=7.0.0; 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: 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: 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"
+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<=7.1.0; extra == "doc"
+Requires-Dist: sphinx<=8.1.3; extra == "doc"
+Requires-Dist: sphinx-design<=0.6.1; 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: m2r2<=0.3.4; extra == "doc"
+Requires-Dist: myst-parser<=4.0.1; extra == "doc"
+Requires-Dist: mistune<=0.8.4; extra == "doc"
+Requires-Dist: docutils<=0.21.2; extra == "doc"
+Requires-Dist: ipyparallel<=9.0.2; 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"
+Dynamic: license-file
+
+<h1 align="center">
+<img src="https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/struphy_header_with_subs.png">
+</h1><br>
+
+[![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)
+[![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)](
+https://pypi.org/project/struphy/)
+
+
+
+# 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. 
+
+Particles in a Tokamak <br> (model "Vlasov")             |  Toroidal Alfvén eigenmode <br> (model "LinearMHDDriftKineticCC") 
+:-------------------------:|:-------------------------:
+![](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/gallery_struphy_tracer6D.png)  |  ![](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/gallery_frontpage_bk.png) 
+**Strong Landau damping <br>(model "VlasovAmpereOneSpecies")** | **Anisotropic diffusion <br> (propagator "ImplicitDiffusion")**
+![](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.
+
+<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">
+</h1>
+
+## 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)
+
+
+## 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.
+
+
+## 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-3.0.0/README.md

@@ -0,0 +1,114 @@
+<h1 align="center">
+<img src="https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/struphy_header_with_subs.png">
+</h1><br>
+
+[![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)
+[![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)](
+https://pypi.org/project/struphy/)
+
+
+
+# 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. 
+
+Particles in a Tokamak <br> (model "Vlasov")             |  Toroidal Alfvén eigenmode <br> (model "LinearMHDDriftKineticCC") 
+:-------------------------:|:-------------------------:
+![](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/gallery_struphy_tracer6D.png)  |  ![](https://raw.githubusercontent.com/struphy-hub/.github/refs/heads/main/profile/gallery_frontpage_bk.png) 
+**Strong Landau damping <br>(model "VlasovAmpereOneSpecies")** | **Anisotropic diffusion <br> (propagator "ImplicitDiffusion")**
+![](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.
+
+<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">
+</h1>
+
+## 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)
+
+
+## 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.
+
+
+## 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-2.5.0 → struphy-3.0.0}/pyproject.toml

@@ -6,12 +6,13 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "2.5.0"
+version = "3.0.0"
 readme = "README.md"
 requires-python = ">=3.10"
 authors = [
     { name = "Max Planck Institute for Plasma Physics" },
     { email = "stefan.possanner@ipp.mpg.de" },
+    { email = "max.lindqvist@ipp.mpg.de" },
     { email = "eric.sonnendruecker@ipp.mpg.de" },
 ]
 description = "Multi-model plasma physics package"
@@ -23,6 +24,7 @@ classifiers = [
 ]
 dependencies = [
     "numpy<=2.2.6",
+    "cunumpy<=0.1",
     "pyccel<=2.0.1, >=2.0",
     "scipy<=1.15.3",
     "h5py<=3.14.0",
@@ -30,9 +32,10 @@ dependencies = [
     "pyyaml<=6.0.3",
     "vtk<=9.5.2",
     "tqdm<=4.67.1",
-    "argcomplete<=3.6.2",
-    "pytest<=8.4.2",
+    "argcomplete<=3.6.3",
+    "pytest<=9.0.1",
     "pytest-mpi<=0.6",
+    "line_profiler<=5.0.0",
 ]
 
 [project.license]
@@ -44,19 +47,20 @@ phys = [
     "desc-opt<=0.15.0",
 ]
 dev = [
+    "struphy[mpi]",
     "notebook<=7.4.7",
     "autopep8<=2.3.2",
-    "isort<=6.0.1",
+    "isort<=7.0.0",
     "flake8<=7.3.0",
-    "pylint<=3.3.8",
+    "pylint<=4.0.2",
     "ssort<=0.15.0",
-    "add-trailing-comma<=3.2.0",
-    "ruff<=0.13.2, >=0.9.1",
-    "pre-commit<=4.3.0",
+    "add-trailing-comma<=4.0.0",
+    "ruff<=0.14.4, >=0.9.1",
+    "pre-commit<=4.4.0",
     "nbstripout<=0.8.1",
     "tabulate<=0.9.0",
     "tomli-w<=1.2.0",
-    "kaleido<=1.1.0",
+    "kaleido<=1.2.0",
     "pandas<=2.3.3",
     "plotly<=6.3.0",
 ]
@@ -65,10 +69,14 @@ mpi = [
 ]
 doc = [
     "struphy[phys]",
+    "jupyter<=1.1.1",
+    "nbconvert<=6.5.4",
+    "ipykernel<=7.1.0",
     "sphinx<=8.1.3",
     "sphinx-design<=0.6.1",
     "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",
     "m2r2<=0.3.4",
@@ -89,11 +97,11 @@ all = [
 ]
 
 [project.urls]
-homepage = "https://struphy.pages.mpcdf.de/struphy/"
-documentation = "https://struphy.pages.mpcdf.de/struphy/"
-repository = "https://gitlab.mpcdf.mpg.de/struphy/struphy"
-changelog = "https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/CHANGELOG.md"
-"Bug Tracker" = "https://gitlab.mpcdf.mpg.de/struphy/struphy/-/issues"
+homepage = "https://struphy-hub.github.io/struphy/index.html"
+documentation = "https://struphy-hub.github.io/struphy/index.html"
+repository = "https://github.com/struphy-hub/struphy"
+changelog = "https://github.com/struphy-hub/struphy/blob/devel/CHANGELOG.md"
+"Bug Tracker" = "https://github.com/struphy-hub/struphy/issues"
 
 [project.scripts]
 struphy = "struphy.console.main:struphy"
@@ -124,7 +132,7 @@ kinetic-diagnostics = "struphy.diagnostics.console_diagn:main"
 ]
 struphy = [
     "compile_struphy.mk",
-    "psydac-2.5.0.dev0-py3-none-any.whl",
+    "psydac-3.0.0.dev0-py3-none-any.whl",
 ]
 
 [tool.autopep8]
@@ -136,14 +144,9 @@ 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
-quote-style = "single"
 
 [tool.ruff]
 line-length = 120
@@ -164,4 +167,15 @@ ignore = [
     "F405",
     "D211",
     "D213",
+    "F841",
+]
+
+[tool.pytest.ini_options]
+markers = [
+    "models",
+    "toy",
+    "fluid",
+    "kinetic",
+    "hybrid",
+    "single",
 ]

struphy-3.0.0/src/struphy/__init__.py

@@ -0,0 +1,77 @@
+import importlib
+import importlib.metadata
+import os
+import re
+import subprocess
+import sys
+
+
+def _install_psydac_if_needed():
+    # Current directory is libpathe root of the project
+    libpath = os.path.dirname(__file__)
+
+    # install psydac from wheel if not there
+    source_install = False
+    for req in importlib.metadata.distribution("struphy").requires:
+        if "psydac" in req:
+            source_install = True
+
+    # Get struphy version
+    struphy_ver = importlib.metadata.version("struphy")
+
+    # Check if psydac is installed
+    try:
+        import psydac
+
+        psydac_ver = importlib.metadata.version("psydac")
+        psydac_installed = True
+    except ModuleNotFoundError:
+        psydac_ver = None
+        psydac_installed = False
+
+    if source_install:
+        # If we are installing psydac from Github
+        if psydac_installed:
+            # only install (from .whl) if psydac not up-to-date
+            if psydac_ver < struphy_ver:
+                print(
+                    f"You have psydac version {psydac_ver}, but version {struphy_ver} is available. Please re-install struphy (e.g. pip install .)\n",
+                )
+                sys.exit(1)
+        else:
+            print("Psydac is not installed. To install it, please re-install struphy (e.g. pip install .)\n")
+            sys.exit(1)
+    else:
+        # If we are installing psydac from a wheel
+        install_psydac = False
+        if psydac_installed:
+            # only install (from .whl) if psydac not up-to-date
+            if ".".join(psydac_ver.split(".")[:3]) != ".".join(struphy_ver.split(".")[:3]):
+                print(f"You have psydac version {psydac_ver}, but version {struphy_ver} is required.\n")
+                install_psydac = True
+        else:
+            install_psydac = True
+
+        if install_psydac:
+            psydac_file = None
+            for filename in os.listdir(libpath):
+                if re.match("psydac-", filename):
+                    psydac_file = filename
+            if psydac_file is None:
+                raise FileNotFoundError("No psydac wheel file found.")
+
+            # Uninstall psydac
+            subprocess.run(["pip", "uninstall", "-y", "psydac"], check=True)
+
+            # Install psydac
+            print("\nInstalling Psydac ...")
+            cmd = [
+                "pip",
+                "install",
+                os.path.join(libpath, psydac_file),
+            ]
+            subprocess.run(cmd, check=True)
+
+
+# Run on import
+_install_psydac_if_needed()