refactor: create geos-pv package (#71)

* Create geos-pv package with geosLogReader

* Move PV tools and delete PVPythonViewConfigurator

* set local dependency path management

* update doc

* fix doc

* update project config

* Manage PV plugins dependency

* typing and linting fix

* add .vscode to .gitignore

* linting and formatting

* bug fix and settup geos-pv tests

* fix doc issues

* fix ci geos-geomecanics and linting

* update geos-pv doc

* Add contribution explanations for geos-pv

* Fix doc ci

* Update pyproject and requirements

* Revert "Update pyproject and requirements"

This reverts commit 2c39455.

* Harmonize dependency versions

* Update installation instructions

---------

Co-authored-by: Martin LEMAY <[email protected]>
Co-authored-by: alexbenedicto <[email protected]>

Author: 3 people

.gitignore

@@ -162,4 +162,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+#.idea/
+
+# VSCode
+.vscode

README.md

@@ -128,7 +128,11 @@ Installation
     python -m pytest ./<PACKAGE_NAME>
     ```
 
-**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)).**
+  [!WARNING]
+  Due to local package conflicts with `pip install`, it is recommended either to build the packages one by one, or to inlude only top-level packages (see dependency tree hereabove) in the build list.
+
+  [!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)).
 
 
 Contributions
@@ -141,8 +145,8 @@ If you would like to report a bug, please submit an [issue](https://github.com/G
 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.
-1. Add your code trying to integrate into the current code architecture.
-1. Push the branch, open a new PR, and add reviewers
+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
 
 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.
 
@@ -170,6 +174,9 @@ dependencies = [
 ]
 ```
 
+[!IMPORTANT]
+geos-pv dependencies are managed using a requirements.txt (together with the setup.py) file where all internal (and external if needed) dependencies are present. It ensures that internal dependency paths are correctly set when plugins are manually loaded into Paraview.
+
 Release
 -------
 

docs/conf.py

@@ -17,7 +17,8 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'geos-xml-viewer', 'hdf5-wrapper', 'pygeos-tools' )
+python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-posp', 'geos-pv', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'geos-xml-viewer', 'hdf5-wrapper', 'pygeos-tools' )
+
 
 for m in python_modules:
     sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m, 'src' ) ) )
@@ -48,7 +49,7 @@
 ]
 
 autoclass_content = 'both'
-autodoc_mock_imports = [ "ats", "colorcet", "h5py", "lxml", "meshio", "mpi4py", "scipy", "paraview", "pygeosx", "pylvarray", "vtk", "xmlschema", "xsdata" ]
+autodoc_mock_imports = [ "ats", "colorcet", "h5py", "lxml", "matplotlib", "meshio", "mpi4py", "scipy", "pandas", "paraview", "pygeosx", "pylvarray", "vtk", "xmlschema", "xsdata", ]
 autodoc_typehints = 'none'
 autodoc_typehints_format = 'short'
 suppress_warnings = [ "autodoc.mocked_object" ]

docs/geos-pv.rst

@@ -0,0 +1,12 @@
+GEOS Paraview plugins
+=====================
+
+.. toctree::
+   :maxdepth: 5
+   :caption: Contents:
+
+   ./geos_pv_docs/home.rst
+
+   ./geos_pv_docs/modules.rst
+
+   ./geos_pv_docs/readers.rst

docs/geos_posp_docs/PVplugins.rst

@@ -75,14 +75,7 @@ PVGeomechanicsWorkflowVolumeWell plugin
 
 .. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeWell
 
-
-PVGeosLogReader plugin
---------------------------------
-
-.. automodule:: PVplugins.PVGeosLogReader
-
-
-PVMergeBlocksEnhanced plugin
+PVplugins.PVMergeBlocksEnhanced module
 --------------------------------------
 
 .. automodule:: PVplugins.PVMergeBlocksEnhanced
@@ -93,14 +86,7 @@ PVMohrCirclePlot plugin
 
 .. automodule:: PVplugins.PVMohrCirclePlot
 
-
-PVPythonViewConfigurator plugin
------------------------------------------
-
-.. automodule:: PVplugins.PVPythonViewConfigurator
-
-
-PVSurfaceGeomechanics plugin
+PVplugins.PVSurfaceGeomechanics module
 --------------------------------------
 
 .. automodule:: PVplugins.PVSurfaceGeomechanics

docs/geos_posp_docs/modules.rst

@@ -6,8 +6,6 @@ Processing
 
    filters
 
-   readers
-
    processing
 
    pyvistaTools

docs/geos_posp_docs/processing.rst

@@ -3,14 +3,6 @@ Processing functions
 
 This package define functions to process data.
 
-geos_posp.processing.geosLogReaderFunctions module
-------------------------------------------------------
-
-.. automodule:: geos_posp.processing.geosLogReaderFunctions
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 geos_posp.processing.multiblockInpectorTreeFunctions module
 ---------------------------------------------------------------
 

docs/geos_posp_docs/readers.rst

@@ -9,6 +9,4 @@ This package includes visualization tools dedicated to Paraview software.
 
    visu.PVUtils
 
-   visu.mohrCircles
-
-   visu.pythonViewUtils
+   visu.mohrCircles