PyHOPE 0.1.1__tar.gz → 0.9.0__tar.gz

{pyhope-0.1.1 → pyhope-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyHOPE
-Version: 0.1.1
+Version: 0.9.0
 Summary: Python High-Order Preprocessing Environment
 License: GPL-3.0-only
 License-File: AUTHORS.md
@@ -17,11 +17,14 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Provides-Extra: numba
 Requires-Dist: alive-progress
 Requires-Dist: gmsh
 Requires-Dist: h5py
 Requires-Dist: hilbertcurve
 Requires-Dist: meshio
+Requires-Dist: numba ; extra == "numba"
 Requires-Dist: numpy (>=2.0.0)
 Requires-Dist: packaging
 Requires-Dist: plotext
@@ -36,9 +39,7 @@ PyHOPE (Python High-Order Preprocessing Environment) is an open-source Python fr
 
 PyHOPE has been developed by the Numerics Research Group (NRG) lead by Prof. Andrea Beck at the Institute of Aerodynamics and Gas Dynamics at the University of Stuttgart, Germany.
 
-PyHOPE is heavily inspired by [HOPR (High Order Preprocessor)](https://github.com/hopr-framework/hopr) and shares the same input/output format. For more information and tutorials, please visit the [HOPR documentation](https://hopr.readthedocs.io). Furthermore, PyHOPE utilizes [Gmsh](https://gmsh.info) for the initial mesh generation and conversion before converting it to its internal representation.
-
-This is a scientific project. If you use PyHOPE for publications or presentations in science, please support the project by citing our publications given at [numericsresearchgroup.org](https://numericsresearchgroup.org/publications.html).
+PyHOPE is heavily inspired by [HOPR (High Order Preprocessor)](https://github.com/hopr-framework/hopr) and shares the same input/output format. Furthermore, PyHOPE utilizes [Gmsh](https://gmsh.info) for the initial mesh generation and conversion before converting it to its internal representation. The internal representation is loosely based on [meshio](https://github.com/nschloe/meshio) but augmented with additional information required for high-order meshes.
 
 # Installation
 PyHOPE is built using standard Python packages. You can install PyHOPE by following these steps. 
@@ -60,6 +61,12 @@ PyHOPE is built using standard Python packages. You can install PyHOPE by follow
     python -m pip install pyhope
     ```
 
+> [!NOTE]  
+> PyHOPE can optionally use [Numba](https://numba.pydata.org) to accelerate some compute-heavy routines. If Numba is not available in your environment, PyHOPE will fall back to pure NumPy implementations.
+> ```bash
+> python -m pip install pyhope[numba]
+> ```
+
 # Testing
 PyHOPE features internal health checks to verify that everything works as expected. The checks can be invoked directly from the terminal.
 ```bash
@@ -71,14 +78,17 @@ pyhope --verify-install [tutorials]  # Run PyHOPE mesh generation checks
 > [!NOTE]  
 >  By default, PyHOPE looks for the `tutorials` directory relative to the current working directory or the git root. If neither exists, PyHOPE downloads the tests from GitHub while using available authentication methods.
 
+> [!IMPORTANT]  
+> Be aware that the PyHOPE repository uses [Git Large File Storage (LFS)](https://git-lfs.com) for some of its larger mesh files.
+
 # Getting Help
-PyHOPE help output is formatted to serve as self-hosting INI format. A list of all options and the default values can be accessed by running the following command.
+PyHOPE help output is formatted to serve as self-hosting [INI format](https://hopr-framework.github.io/PyHOPE/user-guide/parameter-file). A list of all options and the default values can be accessed by running the following command.
 ```bash
 pyhope --help
 ```
 
 # Documentation
-PyHOPE is heavily inspired by [HOPR (High Order Preprocessor)](https://github.com/hopr-framework/hopr) and shares the same input/output format. For more information and tutorials, please visit the [HOPR documentation](https://hopr.readthedocs.io).
+Refer to the [PyHOPE documentation](https://hopr-framework.github.io/PyHOPE) for the getting started guide, examples, and usage instructions. PyHOPE is heavily inspired by [HOPR (High Order Preprocessor)](https://github.com/hopr-framework/hopr) and shares the same input/output format. For technical details and the reference mesh format specification, see the [HOPR documentation](https://hopr.readthedocs.io).
 
 # Usage
 PyHOPE can either be invoked directly from the command line or used as a Python library.
@@ -96,11 +106,12 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 ┃ PyHOPE version x.x.x
 ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 │ INIT PROGRAM...
-│                        nThreads │ 10                              │ DEFAULT │
+│                        nThreads │ nProcs-2                        │ DEFAULT │
 ├─────────────────────────────────────────────
 │ INIT OUTPUT...
 │                     ProjectName │ 1-01-cartbox                    │ *CUSTOM │
 │                    OutputFormat │ 0 [HDF5]                        │ *CUSTOM │
+│                       DebugMesh │ T                               │ *CUSTOM │
 │                       DebugVisu │ F                               │ *CUSTOM │
 ├─────────────────────────────────────────────
 │ INIT MESH...
@@ -111,7 +122,7 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 ├────
 │                          nZones │ 1                               │ *CUSTOM │
 ├── Generating zone 1
-│                          Corner │ (/0.,0.,0. ,,1.,0.,0. ,,1.,1... │ *CUSTOM │
+│                          Corner │ (/0.,0.,0.,,1.,0.,0.,,1.,1.,... │ *CUSTOM │
 │                          nElems │ (/8,8,8/)                       │ *CUSTOM │
 │                        ElemType │ 108 [hexahedron]                │ *CUSTOM │
 │                     StretchType │ (/0,0,0/)                       │ DEFAULT │
@@ -132,9 +143,9 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 │                    BoundaryName │ BC_zplus                        │ *CUSTOM │
 │                    BoundaryType │ (/9,0,0,0/)                     │ *CUSTOM │
 ├────
-│                              vv │ (/1., 0., 0./)                  │ *CUSTOM │
-│                              vv │ (/0., 1., 0./)                  │ *CUSTOM │
-│                              vv │ (/0., 0., 1./)                  │ *CUSTOM │
+│                              vv │ (/1.,0.,0./)                    │ *CUSTOM │
+│                              vv │ (/0.,1.,0./)                    │ *CUSTOM │
+│                              vv │ (/0.,0.,1./)                    │ *CUSTOM │
 ├────
 ├── Generated mesh with 512 cells
 ├─────────────────────────────────────────────
@@ -150,7 +161,7 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 ├─────────────────────────────────────────────
 │ SORT MESH...
 ├────
-│                       doSortIJK │ False                           │ DEFAULT │
+│                     MeshSorting │ 1 [SFC]                         │ DEFAULT │
 ├────
 ├── Sorting elements along space-filling curve
 ├─────────────────────────────────────────────
@@ -201,13 +212,14 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 │         Curved Hexahedra  :          512
 ├────
 ├── Writing HDF5 mesh to "1-01-cartbox_mesh.h5"
+├── Writing XDMF mesh to "1-01-cartbox_DebugMesh.xdmf"
 ┢━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 ┃ PyHOPE completed in [0.25 sec]
 ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 ```
 
 ## Python Library Usage
-PyHOPE can be included in other Python libraries. PyHOPE exposes its functionally via runtime contexts defined by [Context Managers](https://docs.python.org/3/library/stdtypes.html#typecontextmanager). The following Python code loads a HOPR HDF5 mesh and derived quantities. For a complete list of currently implemented functions, see the [source code](pyhope/__init__.py).
+PyHOPE can be included in other Python libraries. PyHOPE exposes its functionally via runtime contexts defined by [Context Managers](https://docs.python.org/3/library/stdtypes.html#typecontextmanager). The following Python code loads a HOPR HDF5 mesh and derived quantities. For a complete list of currently implemented functions, see the [source code](https://github.com/hopr-framework/PyHOPE/blob/main/pyhope/__init__.py).
 ```python
 from pyhope import Basis, Mesh
 with Mesh('1-01-cartbox_mesh.h5') as m:
@@ -215,6 +227,29 @@ with Mesh('1-01-cartbox_mesh.h5') as m:
     lobatto_nodes = Basis.legendre_gauss_lobatto_nodes(order=m.nGeo)
 ```
 
-# Licence
-PyHOPE is licensed under the GPL-3.0 license (see [LICENSE.md](LICENSE.md)).
+# Cite
+This is a scientific project. If you use PyHOPE for publications or presentations in science, please support the project by citing the following article.
+```bibtex
+@article{kopper2025pyhope:joss,
+  title        = {{PyHOPE}: A Python Toolkit for Three-Dimensional Unstructured High-Order Meshes},
+  author       = {Kopper, Patrick and Blind, Marcel P. and Schwarz, Anna and Kurz, Marius and Rodach, Felix and Copplestone, Stephen M. and Beck, Andrea D.},
+  journal      = {Journal of Open Source Software},
+  year         = {2025},
+  volume       = {10}, 
+  number       = {115}, 
+  pages        = {8769},
+  publisher    = {The Open Journal},
+  doi          = {10.21105/joss.08769}
+}
+```
+In addition, you can also directly refer to this repository as
+```bibtex
+@misc{kopper2025pyhope:repo,
+  title        = {{PyHOPE}: A Python Toolkit for Three-Dimensional Unstructured High-Order Meshes},
+  author       = {Kopper, Patrick and Blind, Marcel P. and Schwarz, Anna and Kurz, Marius and Rodach, Felix and Copplestone, Stephen M. and Beck, Andrea D.},
+  year         = {2025},
+  howpublished = {\url{https://github.com/hopr-framework/PyHOPE}},
+  doi          = {10.5281/zenodo.17414843}
+}
+```
 

{pyhope-0.1.1 → pyhope-0.9.0}/README.md

@@ -2,9 +2,7 @@ PyHOPE (Python High-Order Preprocessing Environment) is an open-source Python fr
 
 PyHOPE has been developed by the Numerics Research Group (NRG) lead by Prof. Andrea Beck at the Institute of Aerodynamics and Gas Dynamics at the University of Stuttgart, Germany.
 
-PyHOPE is heavily inspired by [HOPR (High Order Preprocessor)](https://github.com/hopr-framework/hopr) and shares the same input/output format. For more information and tutorials, please visit the [HOPR documentation](https://hopr.readthedocs.io). Furthermore, PyHOPE utilizes [Gmsh](https://gmsh.info) for the initial mesh generation and conversion before converting it to its internal representation.
-
-This is a scientific project. If you use PyHOPE for publications or presentations in science, please support the project by citing our publications given at [numericsresearchgroup.org](https://numericsresearchgroup.org/publications.html).
+PyHOPE is heavily inspired by [HOPR (High Order Preprocessor)](https://github.com/hopr-framework/hopr) and shares the same input/output format. Furthermore, PyHOPE utilizes [Gmsh](https://gmsh.info) for the initial mesh generation and conversion before converting it to its internal representation. The internal representation is loosely based on [meshio](https://github.com/nschloe/meshio) but augmented with additional information required for high-order meshes.
 
 # Installation
 PyHOPE is built using standard Python packages. You can install PyHOPE by following these steps. 
@@ -26,6 +24,12 @@ PyHOPE is built using standard Python packages. You can install PyHOPE by follow
     python -m pip install pyhope
     ```
 
+> [!NOTE]  
+> PyHOPE can optionally use [Numba](https://numba.pydata.org) to accelerate some compute-heavy routines. If Numba is not available in your environment, PyHOPE will fall back to pure NumPy implementations.
+> ```bash
+> python -m pip install pyhope[numba]
+> ```
+
 # Testing
 PyHOPE features internal health checks to verify that everything works as expected. The checks can be invoked directly from the terminal.
 ```bash
@@ -37,14 +41,17 @@ pyhope --verify-install [tutorials]  # Run PyHOPE mesh generation checks
 > [!NOTE]  
 >  By default, PyHOPE looks for the `tutorials` directory relative to the current working directory or the git root. If neither exists, PyHOPE downloads the tests from GitHub while using available authentication methods.
 
+> [!IMPORTANT]  
+> Be aware that the PyHOPE repository uses [Git Large File Storage (LFS)](https://git-lfs.com) for some of its larger mesh files.
+
 # Getting Help
-PyHOPE help output is formatted to serve as self-hosting INI format. A list of all options and the default values can be accessed by running the following command.
+PyHOPE help output is formatted to serve as self-hosting [INI format](https://hopr-framework.github.io/PyHOPE/user-guide/parameter-file). A list of all options and the default values can be accessed by running the following command.
 ```bash
 pyhope --help
 ```
 
 # Documentation
-PyHOPE is heavily inspired by [HOPR (High Order Preprocessor)](https://github.com/hopr-framework/hopr) and shares the same input/output format. For more information and tutorials, please visit the [HOPR documentation](https://hopr.readthedocs.io).
+Refer to the [PyHOPE documentation](https://hopr-framework.github.io/PyHOPE) for the getting started guide, examples, and usage instructions. PyHOPE is heavily inspired by [HOPR (High Order Preprocessor)](https://github.com/hopr-framework/hopr) and shares the same input/output format. For technical details and the reference mesh format specification, see the [HOPR documentation](https://hopr.readthedocs.io).
 
 # Usage
 PyHOPE can either be invoked directly from the command line or used as a Python library.
@@ -62,11 +69,12 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 ┃ PyHOPE version x.x.x
 ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 │ INIT PROGRAM...
-│                        nThreads │ 10                              │ DEFAULT │
+│                        nThreads │ nProcs-2                        │ DEFAULT │
 ├─────────────────────────────────────────────
 │ INIT OUTPUT...
 │                     ProjectName │ 1-01-cartbox                    │ *CUSTOM │
 │                    OutputFormat │ 0 [HDF5]                        │ *CUSTOM │
+│                       DebugMesh │ T                               │ *CUSTOM │
 │                       DebugVisu │ F                               │ *CUSTOM │
 ├─────────────────────────────────────────────
 │ INIT MESH...
@@ -77,7 +85,7 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 ├────
 │                          nZones │ 1                               │ *CUSTOM │
 ├── Generating zone 1
-│                          Corner │ (/0.,0.,0. ,,1.,0.,0. ,,1.,1... │ *CUSTOM │
+│                          Corner │ (/0.,0.,0.,,1.,0.,0.,,1.,1.,... │ *CUSTOM │
 │                          nElems │ (/8,8,8/)                       │ *CUSTOM │
 │                        ElemType │ 108 [hexahedron]                │ *CUSTOM │
 │                     StretchType │ (/0,0,0/)                       │ DEFAULT │
@@ -98,9 +106,9 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 │                    BoundaryName │ BC_zplus                        │ *CUSTOM │
 │                    BoundaryType │ (/9,0,0,0/)                     │ *CUSTOM │
 ├────
-│                              vv │ (/1., 0., 0./)                  │ *CUSTOM │
-│                              vv │ (/0., 1., 0./)                  │ *CUSTOM │
-│                              vv │ (/0., 0., 1./)                  │ *CUSTOM │
+│                              vv │ (/1.,0.,0./)                    │ *CUSTOM │
+│                              vv │ (/0.,1.,0./)                    │ *CUSTOM │
+│                              vv │ (/0.,0.,1./)                    │ *CUSTOM │
 ├────
 ├── Generated mesh with 512 cells
 ├─────────────────────────────────────────────
@@ -116,7 +124,7 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 ├─────────────────────────────────────────────
 │ SORT MESH...
 ├────
-│                       doSortIJK │ False                           │ DEFAULT │
+│                     MeshSorting │ 1 [SFC]                         │ DEFAULT │
 ├────
 ├── Sorting elements along space-filling curve
 ├─────────────────────────────────────────────
@@ -167,13 +175,14 @@ $ pyhope tutorials/1-01-cartbox/parameter.ini
 │         Curved Hexahedra  :          512
 ├────
 ├── Writing HDF5 mesh to "1-01-cartbox_mesh.h5"
+├── Writing XDMF mesh to "1-01-cartbox_DebugMesh.xdmf"
 ┢━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 ┃ PyHOPE completed in [0.25 sec]
 ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 ```
 
 ## Python Library Usage
-PyHOPE can be included in other Python libraries. PyHOPE exposes its functionally via runtime contexts defined by [Context Managers](https://docs.python.org/3/library/stdtypes.html#typecontextmanager). The following Python code loads a HOPR HDF5 mesh and derived quantities. For a complete list of currently implemented functions, see the [source code](pyhope/__init__.py).
+PyHOPE can be included in other Python libraries. PyHOPE exposes its functionally via runtime contexts defined by [Context Managers](https://docs.python.org/3/library/stdtypes.html#typecontextmanager). The following Python code loads a HOPR HDF5 mesh and derived quantities. For a complete list of currently implemented functions, see the [source code](https://github.com/hopr-framework/PyHOPE/blob/main/pyhope/__init__.py).
 ```python
 from pyhope import Basis, Mesh
 with Mesh('1-01-cartbox_mesh.h5') as m:
@@ -181,5 +190,28 @@ with Mesh('1-01-cartbox_mesh.h5') as m:
     lobatto_nodes = Basis.legendre_gauss_lobatto_nodes(order=m.nGeo)
 ```
 
-# Licence
-PyHOPE is licensed under the GPL-3.0 license (see [LICENSE.md](LICENSE.md)).
+# Cite
+This is a scientific project. If you use PyHOPE for publications or presentations in science, please support the project by citing the following article.
+```bibtex
+@article{kopper2025pyhope:joss,
+  title        = {{PyHOPE}: A Python Toolkit for Three-Dimensional Unstructured High-Order Meshes},
+  author       = {Kopper, Patrick and Blind, Marcel P. and Schwarz, Anna and Kurz, Marius and Rodach, Felix and Copplestone, Stephen M. and Beck, Andrea D.},
+  journal      = {Journal of Open Source Software},
+  year         = {2025},
+  volume       = {10}, 
+  number       = {115}, 
+  pages        = {8769},
+  publisher    = {The Open Journal},
+  doi          = {10.21105/joss.08769}
+}
+```
+In addition, you can also directly refer to this repository as
+```bibtex
+@misc{kopper2025pyhope:repo,
+  title        = {{PyHOPE}: A Python Toolkit for Three-Dimensional Unstructured High-Order Meshes},
+  author       = {Kopper, Patrick and Blind, Marcel P. and Schwarz, Anna and Kurz, Marius and Rodach, Felix and Copplestone, Stephen M. and Beck, Andrea D.},
+  year         = {2025},
+  howpublished = {\url{https://github.com/hopr-framework/PyHOPE}},
+  doi          = {10.5281/zenodo.17414843}
+}
+```

{pyhope-0.1.1 → pyhope-0.9.0}/pyhope/__init__.py

@@ -67,7 +67,7 @@ MeshContainer = namedtuple('Mesh',
 
 
 @contextmanager  # pragma: no cover
-def Mesh(*args, stdout=False, stderr=True):
+def Mesh(*args: str, stdout: bool = False, stderr: bool = True):
     """ Mesh context manager to generate a mesh from a given file
 
         Args:
@@ -156,8 +156,8 @@ def Mesh(*args, stdout=False, stderr=True):
 
     finally:
         # Cleanup resources after exiting the context
-        mesh_vars.mesh  = None
-        mesh_vars.nGeo  = None
-        mesh_vars.bcs   = None
-        mesh_vars.elems = None
-        mesh_vars.sides = None
+        del mesh_vars.mesh
+        del mesh_vars.nGeo
+        del mesh_vars.bcs
+        del mesh_vars.elems
+        del mesh_vars.sides