ci: Modify doc CI to return error if warnings and update doc (#79)

* Modify doc ci to return error if warnings are present
Update docs to pass the new ci
Add geos-xml-viewer to the doc

* Add vtk to mock imports

* Add vtk install to remove libGL error

* Try add install libgl1

* Try add install libgl1 with sudo

* change libGL package name

* add doc ci config

* Modify vtk import for doc ci and linting

* Simplify ci config

* Update doc geos-xml-viewer

Author: mlemayTTE

.github/workflows/doc-test.yml

@@ -2,6 +2,11 @@ name: "Pull Request Docs Check"
 on: 
 - pull_request
 
+# Cancels in-progress workflows for a PR when updated
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   docs:
     runs-on: ubuntu-latest
@@ -10,4 +15,4 @@ jobs:
     - uses: ammaraskar/sphinx-action@dev
       with:
         docs-folder: "docs/"
-        build-command: "sphinx-build -b html . _build"
+        build-command: "sphinx-build -b html . _build -W"

docs/conf.py

@@ -17,7 +17,7 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ( 'geos-ats', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'hdf5-wrapper', 'pygeos-tools', 'geos-geomechanics' )
+python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-posp', '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' ) ) )
@@ -43,15 +43,15 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput', 'sphinx.ext.autodoc',
-    'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.todo', 'sphinx.ext.viewcode'
+    'sphinx.ext.napoleon', 'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput', 
+    'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.todo', 'sphinx.ext.viewcode'
 ]
 
 autoclass_content = 'both'
-autodoc_mock_imports = [ "ats", "h5py", "lxml", "paraview", "pygeosx", "pylvarray", "meshio", "mpi4py", "scipy" ]
+autodoc_mock_imports = [ "ats", "colorcet", "h5py", "lxml", "meshio", "mpi4py", "scipy", "paraview", "pygeosx", "pylvarray", "vtk", "xmlschema", "xsdata" ]
 autodoc_typehints = 'none'
 autodoc_typehints_format = 'short'
-suppress_warnings = [ "" ]
+suppress_warnings = [ "autodoc.mocked_object" ]
 typehints_defaults = 'braces'
 
 # The suffix(es) of source filenames.

docs/geos-geomechanics.rst

@@ -1,4 +1,4 @@
-GEOS Post-Processing tools
+GEOS Geomechanics tools
 =============================
 
 .. toctree::

docs/geos-xml-viewer.rst

@@ -0,0 +1,107 @@
+GEOS XML VIEWER
+===============
+
+The `geos-xml-viewer` python package defines tools to read, process, and visualize objects from GEOS input xml file.
+See `Advanced XML Features <https://geosx-geosx.readthedocs-hosted.com/en/latest/coreComponents/fileIO/doc/InputXMLFiles.html#advanced-xml-features>`_ for a detailed description of the input format.
+
+This package defines multiple console scripts and a vtk ilter associated with a Paraview reader.
+
+Consol scripts
+--------------
+
+geos-exporter
+^^^^^^^^^^^^^
+
+Reads the xml file and writes a PartionedDataSetCollection file containing all the mesh objects (mesh, wells, boxes) defind in the xml.
+
+.. argparse::
+   :module: geos_xml_viewer.bin.exporter
+   :func: parsing
+   :prog: geos-exporter
+
+geos-modifier
+^^^^^^^^^^^^^
+
+Rewrite wells into VTK file and modify the xml file accordingly.
+
+.. argparse::
+   :module: geos_xml_viewer.bin.modifier
+   :func: parsing
+   :prog: geos-modifier
+
+geos-splitter
+^^^^^^^^^^^^^
+
+Extract Internal wells into VTK files.
+
+.. argparse::
+   :module: geos_xml_viewer.bin.splitter
+   :func: parsing
+   :prog: geos-splitter
+
+geos-viewer
+^^^^^^^^^^^^^
+
+Viewer dedicated to xml mesh objects (mesh, wells, boxes).
+
+.. argparse::
+   :module: geos_xml_viewer.bin.viewer
+   :func: parsing
+   :prog: geos-viewer
+
+
+WIP consol scripts
+------------------
+
+geos-validate
+^^^^^^^^^^^^^
+
+Validate xml file according to GEOS scheme.
+
+.. argparse::
+   :module: geos_xml_viewer.bin.validate
+   :func: parsing
+   :prog: geos-validate
+
+
+vtk filter
+----------
+
+Geos deck reader
+^^^^^^^^^^^^^^^^
+
+Vtk reader of GEOS xml file to load or build vtk objects (mesh, wells, boxes).
+
+.. automodule:: geos_xml_viewer.filters.geosDeckReader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Paraview plugin
+----------------
+
+Geos Deck Reader
+^^^^^^^^^^^^^^^^
+
+Paraview plugin of Geos Deck Reader.
+
+.. automodule:: PVPlugins.deckReader
+   :no-members:
+   :no-undoc-members:
+
+Utilities
+---------
+
+geos_xml_viewer.algorithms.deck
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: geos_xml_viewer.algorithms.deck
+   :members:
+   :undoc-members:
+
+geos_xml_viewer.algorithms.write_wells
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. automodule:: geos_xml_viewer.algorithms.write_wells
+   :members:
+   :undoc-members:

docs/geos_geomechanics_docs/home.rst

@@ -1,4 +1,4 @@
 GEOS Geomechanics Tools
-=========================
+-----------------------
 
 This package contains geomechanics functions and data models.

docs/geos_geomechanics_docs/model.rst

@@ -1,6 +1,7 @@
 Geomechanics models
 ======================
-This 
+
+This module defines data structures for geomechanics calculations.
 
 geos.geomechanics.model.MohrCircle module
 ------------------------------------------

docs/geos_geomechanics_docs/processing.rst

@@ -1,6 +1,7 @@
 Processing
 ============
-The processing part of `geos-geomechanics` package contains functions tools to compute geomechanical properties.
+
+The processing part of `geos-geomechanics` package contains the basis functions to compute geomechanical properties.
 
 geos.geomechanics.processing.geomechanicsCalculatorFunctions module
 ---------------------------------------------------------------------

docs/geos_posp_docs/PVplugins.rst

@@ -10,122 +10,105 @@ The plugins include:
 * Processing plugins to compute additional geomechanical properties;
 * Visualization plugins to plot Mohr's circles and cross plots using Paraview Python View.
 
-PVplugins.PVAttributeMapping module
+PVAttributeMapping plugin
 -----------------------------------
 
 .. automodule:: PVplugins.PVAttributeMapping
-   :members:
-   :undoc-members:
 
-PVplugins.PVCreateConstantAttributePerRegion module
+
+PVCreateConstantAttributePerRegion plugin
 ---------------------------------------------------
 
 .. automodule:: PVplugins.PVCreateConstantAttributePerRegion
-   :members:
-   :undoc-members:
 
-PVplugins.PVExtractMergeBlocksVolume module
+
+PVExtractMergeBlocksVolume plugin
 -------------------------------------------
 
 .. automodule:: PVplugins.PVExtractMergeBlocksVolume
-   :members:
-   :undoc-members:
 
-PVplugins.PVExtractMergeBlocksVolumeSurface module
+
+PVExtractMergeBlocksVolumeSurface plugin
 --------------------------------------------------
 
 .. automodule:: PVplugins.PVExtractMergeBlocksVolumeSurface
-   :members:
-   :undoc-members:
 
-PVplugins.PVExtractMergeBlocksVolumeSurfaceWell module
+
+PVExtractMergeBlocksVolumeSurfaceWell plugin
 ------------------------------------------------------
 
 .. automodule:: PVplugins.PVExtractMergeBlocksVolumeSurfaceWell
-   :members:
-   :undoc-members:
 
-PVplugins.PVExtractMergeBlocksVolumeWell module
+
+PVExtractMergeBlocksVolumeWell plugin
 -----------------------------------------------
 
 .. automodule:: PVplugins.PVExtractMergeBlocksVolumeWell
-   :members:
-   :undoc-members:
 
-PVplugins.PVGeomechanicsAnalysis module
+
+PVGeomechanicsAnalysis plugin
 ---------------------------------------
 
 .. automodule:: PVplugins.PVGeomechanicsAnalysis
-   :members:
-   :undoc-members:
 
-PVplugins.PVGeomechanicsWorkflowVolume module
+
+PVGeomechanicsWorkflowVolume plugin
 ---------------------------------------------
 
 .. automodule:: PVplugins.PVGeomechanicsWorkflowVolume
-   :members:
-   :undoc-members:
 
-PVplugins.PVGeomechanicsWorkflowVolumeSurface module
+
+PVGeomechanicsWorkflowVolumeSurface plugin
 ----------------------------------------------------
 
 .. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeSurface
-   :members:
-   :undoc-members:
 
-PVplugins.PVGeomechanicsWorkflowVolumeSurfaceWell module
+
+PVGeomechanicsWorkflowVolumeSurfaceWell plugin
 --------------------------------------------------------
 
 .. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeSurfaceWell
-   :members:
-   :undoc-members:
 
-PVplugins.PVGeomechanicsWorkflowVolumeWell module
+
+PVGeomechanicsWorkflowVolumeWell plugin
 -------------------------------------------------
 
 .. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeWell
-   :members:
-   :undoc-members:
 
-PVplugins.PVGeosLogReader module
+
+PVGeosLogReader plugin
 --------------------------------
 
 .. automodule:: PVplugins.PVGeosLogReader
-   :members:
-   :undoc-members:
 
-PVplugins.PVMergeBlocksEnhanced module
+
+PVMergeBlocksEnhanced plugin
 --------------------------------------
 
 .. automodule:: PVplugins.PVMergeBlocksEnhanced
-   :members:
-   :undoc-members:
 
-PVplugins.PVMohrCirclePlot module
+
+PVMohrCirclePlot plugin
 ---------------------------------
 
 .. automodule:: PVplugins.PVMohrCirclePlot
-   :members:
-   :undoc-members:
 
-PVplugins.PVPythonViewConfigurator module
+
+PVPythonViewConfigurator plugin
 -----------------------------------------
 
 .. automodule:: PVplugins.PVPythonViewConfigurator
-   :members:
-   :undoc-members:
 
-PVplugins.PVSurfaceGeomechanics module
+
+PVSurfaceGeomechanics plugin
 --------------------------------------
 
 .. automodule:: PVplugins.PVSurfaceGeomechanics
-   :members:
-   :undoc-members:
 
-PVplugins.PVTransferAttributesVolumeSurface module
+
+PVTransferAttributesVolumeSurface plugin
 --------------------------------------------------
 
 .. automodule:: PVplugins.PVTransferAttributesVolumeSurface
-   :members:
-   :undoc-members:
+
 

docs/geos_posp_docs/home.rst

@@ -1,5 +1,5 @@
 Home
-====
+-----
 
 **Geos-posp** is a Python library to read, process and visualize GEOS simulation software outputs.
 

docs/geos_posp_docs/processing.rst

@@ -3,15 +3,6 @@ Processing functions
 
 This package define functions to process data.
 
-
-geos_posp.processing.geomechanicsCalculatorFunctions module
----------------------------------------------------------------
-
-.. automodule:: geos_posp.processing.geomechanicsCalculatorFunctions
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 geos_posp.processing.geosLogReaderFunctions module
 ------------------------------------------------------
 
@@ -20,22 +11,6 @@ geos_posp.processing.geosLogReaderFunctions module
    :undoc-members:
    :show-inheritance:
 
-geos_posp.processing.MohrCircle module
-------------------------------------------
-
-.. automodule:: geos_posp.processing.MohrCircle
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-geos_posp.processing.MohrCoulomb module
--------------------------------------------
-
-.. automodule:: geos_posp.processing.MohrCoulomb
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 geos_posp.processing.multiblockInpectorTreeFunctions module
 ---------------------------------------------------------------