Merge branch 'main' into RomainBaville/feature/VTK_filter_and_PVCreateConstantAttributePerRegion

Update to main.

Author: RomainBaville

.ruff.toml

@@ -1,5 +1,6 @@
 # Exclude a variety of commonly ignored directories.
-extend-exclude = ["tests/data"]
+extend-exclude = ["tests/data", "geos-mesh/src/geos/mesh/model/_bar_label.py"]
+
 
 line-length = 120
 indent-width = 4
@@ -21,12 +22,12 @@ select = [
     "W",    # pycodestyle warnings
     "F",    # pyflakes
 #    "UP",   # pyupgrade deactivate since python39
-    "B",    # flake8-bugbear        
-    "SIM",  # flake8-simplify        
-    "ANN",  # flake8-annotations        
-    "C4",   # flake8-comprehensions    
+    "B",    # flake8-bugbear
+    "SIM",  # flake8-simplify
+    "ANN",  # flake8-annotations
+    "C4",   # flake8-comprehensions
 #    "I",    # isort - manage by yapf
-    "D",    # pydocstyle    
+    "D",    # pydocstyle
 ]
 
 ignore = [

README.md

@@ -17,7 +17,7 @@ Package summary
 * `geos-ats` package includes tools for managing integrated tests for GEOS.
 * `pygeos-tools` package adds a variety of tools for working with *pygeosx* objects.
 
-The next packages are dedicated to pre- and post-process GEOS inputs/outputs. 
+The next packages are dedicated to pre- and post-process GEOS inputs/outputs.
 
 The following packages contain basic utilities used by the other ones:
 
@@ -110,7 +110,7 @@ Installation
 
 * *Manual installation:*
 
-  GEOS Python packages can be manually installed with pip using `python` >= 3.10. 
+  GEOS Python packages can be manually installed with pip using `python` >= 3.10.
 
     To install any package, run the following commands from the geosPythonPackage directory:
 
@@ -131,21 +131,28 @@ Installation
   [!WARNING]
    Due to local package conflicts with `pip install`, it is recommended to use the `--upgrade` option when building packages, or to use the script `install_packages.sh` located at the root of the repository.
   [!NOTE]
-  geos-pv package cannot be build alone, but together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). It is recommended to use Paraview v5.12+, which is based on python 3.10+. Alternatively, plugins from geos-pv/PVplugins can be manually loaded into Paraview ([see documentation](https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html#python-algorithm)).
+  geos-pv package cannot be build alone, but together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). It is recommended to use Paraview v5.12+, which is based on python 3.10+. Alternatively, plugins from `geos-pv/src/geos/pv/plugins` can be manually loaded into Paraview ([see documentation](https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html#python-algorithm)).
 
 
 Contributions
 -------------
 
 GEOS Python packages repository gathers python scripts from any GEOS developpers and users. Feel free to share any scripts that may benefit to the GEOS community.
 
-If you would like to report a bug, please submit an [issue](https://github.com/GEOS-DEV/geosPythonPackages/issues/new). 
+If you would like to report a bug, please submit an [issue](https://github.com/GEOS-DEV/geosPythonPackages/issues/new).
 
 If you would like to contribute to GEOS Python packages, please respect the following guidelines:
 
 1. Create a new branch named from this template: `[CONTRIBUTOR]/[TYPE]/[TITLE]` where CONTRIBUTOR is the name of the contributor, TYPE is the type of contribution among 'feature', 'refactor', 'doc', 'ci', TITLE is a short title for the branch.
 2. Add your code trying to integrate into the current code architecture.
-3. Push the branch, open a new PR respecting naming [semantics](https://gist.github.com/joshbuchea/6f47e86d2510bce28f8e7f42ae84c716), and add reviewers
+3. Run mypy, ruff and yapf in this order
+  ```
+  python -m pip install --upgrade mypy ruff yapf
+  python -m mypy --config-file ./.mypy.ini --check-untyped-defs ./<PACKAGE_NAME>
+  python -m ruff check --fix --config .ruff.toml ./<PACKAGE_NAME>
+  python -m yapf -r -i --style .style.yapf ./<PACKAGE_NAME>
+  ```
+4. Push the branch, open a new PR respecting naming [semantics](https://gist.github.com/joshbuchea/6f47e86d2510bce28f8e7f42ae84c716), and add reviewers
 
 If you do not have the rights to push the code and open new PRs, consider opening a new issue to explain what you want to do and ask for the dev rights.
 

docs/geos-pv.rst

@@ -7,6 +7,10 @@ GEOS Paraview plugins
 
    ./geos_pv_docs/home.rst
 
-   ./geos_pv_docs/modules.rst
+   ./geos_pv_docs/utilities.rst
 
-   ./geos_pv_docs/readers.rst
+   ./geos_pv_docs/readers.rst
+
+   ./geos_pv_docs/meshQuality.rst
+
+   ./geos_pv_docs/processing.rst

docs/geos_mesh_docs/model.rst

@@ -4,10 +4,18 @@ Model
 The `model` module of `geos-mesh` package contains data model.
 
 
-geos.mesh.model.CellTypeCounts filter
+geos.mesh.model.CellTypeCounts module
 --------------------------------------
 
 .. automodule:: geos.mesh.model.CellTypeCounts
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+geos.mesh.model.QualityMetricSummary module
+--------------------------------------------
+
+.. automodule:: geos.mesh.model.QualityMetricSummary
     :members:
     :undoc-members:
     :show-inheritance:

docs/geos_mesh_docs/processing.rst

@@ -11,6 +11,14 @@ geos.mesh.processing.CreateConstantAttributePerRegion filter
     :undoc-members:
     :show-inheritance:
 
+geos.mesh.processing.meshQualityMetricHelpers module
+-----------------------------------------------------
+
+.. automodule:: geos.mesh.processing.meshQualityMetricHelpers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 geos.mesh.processing.SplitMesh filter
 --------------------------------------
 

docs/geos_mesh_docs/stats.rst

@@ -4,10 +4,18 @@ Mesh stats tools
 The `stats` module of `geos-mesh` package contains filter to compute statistics on meshes.
 
 
-geos.mesh.stats.CellTypeCounter filter
---------------------------------------
+geos.mesh.stats.CellTypeCounterEnhanced filter
+-----------------------------------------------
 
-.. automodule:: geos.mesh.stats.CellTypeCounter
+.. automodule:: geos.mesh.stats.CellTypeCounterEnhanced
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+geos.mesh.stats.MeshQualityEnhanced filter
+-------------------------------------------
+
+.. automodule:: geos.mesh.stats.MeshQualityEnhanced
     :members:
     :undoc-members:
     :show-inheritance:

docs/geos_pv_docs/geosLogReaderUtils.rst

@@ -4,42 +4,42 @@ GeosLogReaderUtils functions
 This package define functions dedicated to the GeosLogReader.
 
 
-geos.pv.geosLogReaderUtils.GeosLogReaderAquifers module
+GeosLogReaderAquifers module
 -------------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderAquifers
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.pv.geosLogReaderUtils.geosLogReaderConvergence module
+geosLogReaderConvergence module
 ---------------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderConvergence
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.pv.geosLogReaderUtils.GeosLogReaderFlow module
+GeosLogReaderFlow module
 ---------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderFlow
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.pv.geosLogReaderUtils.GeosLogReaderFunctions module
+GeosLogReaderFunctions module
 --------------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.geosLogReaderFunctions
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.pv.geosLogReaderUtils.GeosLogReaderWells module
+GeosLogReaderWells module
 --------------------------------------------------------------------
 
 .. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderWells
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

docs/geos_pv_docs/home.rst

@@ -1,18 +1,21 @@
 Home
 ====
 
-**geos-pv** is a Python package that gathers `Paraview <https://www.paraview.org/>`_ plugins of GEOS python tools. 
+**geos-pv** is a Python package that gathers `Paraview <https://www.paraview.org/>`_ plugins of GEOS python tools.
 
 It includes:
 
 * Paraview readers allowing to load data;
-* generic tools to processes meshes;
+* generic tools to process meshes;
 * GEOS pre-processing tools to clean and check GEOS input mesh;
 * GEOS post-processing tools to clean GEOS output mesh, compute additional properties, or create specific plots such as Mohr's circle plot.
 
-The packages can be loaded into Paraview using the Plugin Manager from `Tools > Plugin Manager`. On success, you will 
-see the selected plugin in the `Filters`` menu (see `Paraview documentation <https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html>`.
+The packages can be loaded into Paraview using the Plugin Manager from `Tools > Plugin Manager`. On success, you will
+see the selected plugin in the `Filters`` menu (see `Paraview documentation <https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html>`_).
 
-Alternatively, geos-pv package can be build together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). 
+Alternatively, geos-pv package can be build together with Paraview (see `Paraview compilation guide <https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md>`_).
 It is recommended to use Paraview v5.12+, which is based on python 3.10+. If you need to build geos-pv package with the paraview dependency, use the command:
-`pip install Path/To/geosPythonPackages/geos-pv[paraview]`
+
+.. code-block:: bash
+
+    pip install path/to/geosPythonPackages/geos-pv[paraview]

docs/geos_pv_docs/meshQuality.rst

@@ -0,0 +1,13 @@
+Mesh Quality
+================
+
+
+PVCellTypeCounterEnhanced
+----------------------------------
+
+.. automodule:: geos.pv.plugins.PVCellTypeCounterEnhanced
+
+PVMeshQualityEnhanced
+---------------------------
+
+.. automodule:: geos.pv.plugins.PVMeshQualityEnhanced

docs/geos_pv_docs/processing.rst

@@ -0,0 +1,7 @@
+Post-/Pre-processing
+=========================
+
+PVSplitMesh
+----------------------------------
+
+.. automodule:: geos.pv.plugins.PVSplitMesh