Change dynamic documentation for geos-mesh to static documentation to…

… avoid CI errors.

docs/geos-mesh.rst

@@ -15,14 +15,59 @@ Modules
 
 To list all the modules available through ``mesh-doctor``, you can simply use the ``--help`` option, which will list all available modules as well as a quick summary.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py --help
+      usage: mesh_doctor.py [-h] [-v] [-q] -i VTK_MESH_FILE
+                      {collocated_nodes,element_volumes,fix_elements_orderings,generate_cube,generate_fractures,generate_global_ids,non_conformal,self_intersecting_elements,supported_elements}
+                      ...
+
+      Inspects meshes for GEOSX.
+
+      positional arguments:
+      {collocated_nodes,element_volumes,fix_elements_orderings,generate_cube,generate_fractures,generate_global_ids,non_conformal,self_intersecting_elements,supported_elements}
+            Modules
+         collocated_nodes
+            Checks if nodes are collocated.
+         element_volumes
+            Checks if the volumes of the elements are greater than "min".
+         fix_elements_orderings
+            Reorders the support nodes for the given cell types.
+         generate_cube
+            Generate a cube and its fields.
+         generate_fractures
+            Splits the mesh to generate the faults and fractures. [EXPERIMENTAL]
+         generate_global_ids
+            Adds globals ids for points and cells.
+         non_conformal
+            Detects non conformal elements. [EXPERIMENTAL]
+         self_intersecting_elements
+            Checks if the faces of the elements are self intersecting.
+         supported_elements
+            Check that all the elements of the mesh are supported by GEOSX.
+
+      options:
+      -h, --help
+            show this help message and exit
+      -v    Use -v 'INFO', -vv for 'DEBUG'. Defaults to 'WARNING'.
+      -q    Use -q to reduce the verbosity of the output.
+      -i VTK_MESH_FILE, --vtk-input-file VTK_MESH_FILE
+
+      Note that checks are dynamically loaded.
+      An option may be missing because of an unloaded module.
+      Increase verbosity (-v, -vv) to get full information.
 
 Then, if you are interested in a specific module, you can ask for its documentation using the ``mesh-doctor module_name --help`` pattern.
 For example
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py collocated_nodes --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py collocated_nodes --help
+      usage: mesh_doctor.py collocated_nodes [-h] --tolerance TOLERANCE
+
+      options:
+      -h, --help              show this help message and exit
+      --tolerance TOLERANCE   [float]: The absolute distance between two nodes for them to be considered collocated.
 
 ``mesh-doctor`` loads its module dynamically.
 If a module can't be loaded, ``mesh-doctor`` will proceed and try to load other modules.
@@ -44,17 +89,29 @@ Here is a list and brief description of all the modules available.
 Displays the neighboring nodes that are closer to each other than a prescribed threshold.
 It is not uncommon to define multiple nodes for the exact same position, which will typically be an issue for ``geos`` and should be fixed.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py collocated_nodes --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py collocated_nodes --help
+      usage: mesh_doctor.py collocated_nodes [-h] --tolerance TOLERANCE
+
+      options:
+      -h, --help              show this help message and exit
+      --tolerance TOLERANCE   [float]: The absolute distance between two nodes for them to be considered collocated.
 
 ``element_volumes``
 """""""""""""""""""
 
 Computes the volumes of all the cells and displays the ones that are below a prescribed threshold.
 Cells with negative volumes will typically be an issue for ``geos`` and should be fixed.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py element_volumes --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py element_volumes --help
+      usage: mesh_doctor.py element_volumes [-h] --min 0.0
+
+      options:
+      -h, --help              show this help message and exit
+      --min 0.0               [float]: The minimum acceptable volume. Defaults to 0.0.
 
 ``fix_elements_orderings``
 """"""""""""""""""""""""""
@@ -63,8 +120,29 @@ It sometimes happens that an exported mesh does not abide by the ``vtk`` orderin
 The ``fix_elements_orderings`` module can rearrange the nodes of given types of elements.
 This can be convenient if you cannot regenerate the mesh.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py fix_elements_orderings --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py fix_elements_orderings --help
+      usage: mesh_doctor.py fix_elements_orderings [-h] [--Hexahedron 1,6,5,4,7,0,2,3] [--Prism5 8,2,0,7,6,9,5,1,4,3]
+                                                   [--Prism6 11,2,8,10,5,0,9,7,6,1,4,3] [--Pyramid 3,4,0,2,1]
+                                                   [--Tetrahedron 2,0,3,1] [--Voxel 1,6,5,4,7,0,2,3]
+                                                   [--Wedge 3,5,4,0,2,1] --output OUTPUT [--data-mode binary, ascii]
+
+      options:
+      -h, --help              show this help message and exit
+      --Hexahedron 1,6,5,4,7,0,2,3
+                              [list of integers]: node permutation for "Hexahedron".
+      --Prism5 8,2,0,7,6,9,5,1,4,3
+                              [list of integers]: node permutation for "Prism5".
+      --Prism6 11,2,8,10,5,0,9,7,6,1,4,3
+                              [list of integers]: node permutation for "Prism6".
+      --Pyramid 3,4,0,2,1     [list of integers]: node permutation for "Pyramid".
+      --Tetrahedron 2,0,3,1   [list of integers]: node permutation for "Tetrahedron".
+      --Voxel 1,6,5,4,7,0,2,3 [list of integers]: node permutation for "Voxel".
+      --Wedge 3,5,4,0,2,1     [list of integers]: node permutation for "Wedge".
+      --output OUTPUT         [string]: The vtk output file destination.
+      --data-mode binary, ascii
+                              [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.
 
 ``generate_cube``
 """""""""""""""""
@@ -73,26 +151,84 @@ This module conveniently generates cubic meshes in ``vtk``.
 It can also generate fields with simple values.
 This tool can also be useful to generate a trial mesh that will later be refined or customized.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py generate_cube --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py generate_cube --help
+      usage: mesh_doctor.py generate_cube [-h] [--x 0:1.5:3] [--y 0:5:10] [--z 0:1] [--nx 2:2] [--ny 1:1] [--nz 4]
+                                          [--fields name:support:dim [name:support:dim ...]] [--cells] [--no-cells]      
+                                          [--points] [--no-points] --output OUTPUT [--data-mode binary, ascii]
+
+      options:
+      -h, --help              show this help message and exit
+      --x 0:1.5:3             [list of floats]: X coordinates of the points.
+      --y 0:5:10              [list of floats]: Y coordinates of the points.
+      --z 0:1                 [list of floats]: Z coordinates of the points.
+      --nx 2:2                [list of integers]: Number of elements in the X direction.
+      --ny 1:1                [list of integers]: Number of elements in the Y direction.
+      --nz 4                  [list of integers]: Number of elements in the Z direction.
+      --fields name:support:dim 
+                              [name:support:dim ...]: Create fields on CELLS or POINTS, with given dimension (typically 1 or 3).
+      --cells                 [bool]: Generate global ids for cells. Defaults to true.
+      --no-cells              [bool]: Don't generate global ids for cells.
+      --points                [bool]: Generate global ids for points. Defaults to true.
+      --no-points             [bool]: Don't generate global ids for points.
+      --output OUTPUT         [string]: The vtk output file destination.
+      --data-mode binary, ascii
+                              [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.
 
 ``generate_fractures``
 """"""""""""""""""""""
 
 For a conformal fracture to be defined in a mesh, ``geos`` requires the mesh to be split at the faces where the fracture gets across the mesh.
 The ``generate_fractures`` module will split the mesh and generate the multi-block ``vtk`` files.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py generate_fractures --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py generate_fractures --help
+      usage: mesh_doctor.py generate_fractures [-h] --policy field, internal_surfaces [--name NAME] [--values VALUES]
+                                             --output OUTPUT [--data-mode binary, ascii] --fracture-output
+                                             FRACTURE_OUTPUT [--fracture-data-mode binary, ascii]
+
+      options:
+      -h, --help              show this help message and exit
+      --policy field, internal_surfaces
+                              [string]: The criterion to define the surfaces that will be changed into fracture zones.
+                              Possible values are "field, internal_surfaces"
+      --name NAME             [string]: If the "field" policy is selected, defines which field will be considered to
+                              define the fractures. If the "internal_surfaces" policy is selected, defines the name of
+                              the attribute will be considered to identify the fractures.
+      --values VALUES         [list of comma separated integers]: If the "field" policy is selected, which changes of    
+                              the field will be considered as a fracture. If the "internal_surfaces" policy is
+                              selected, list of the fracture attributes.
+      --output OUTPUT         [string]: The vtk output file destination.
+      --data-mode binary, ascii
+                              [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.
+      --fracture-output FRACTURE_OUTPUT
+                              [string]: The vtk output file destination.
+      --fracture-data-mode binary, ascii
+                              [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.
 
 ``generate_global_ids``
 """""""""""""""""""""""
 
 When running ``geos`` in parallel, `global ids` can be used to refer to data across multiple ranks.
 The ``generate_global_ids`` can generate `global ids` for the imported ``vtk`` mesh.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py generate_global_ids --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py generate_global_ids --help
+      usage: mesh_doctor.py generate_global_ids [-h] [--cells] [--no-cells] [--points] [--no-points] --output OUTPUT
+                                                [--data-mode binary, ascii]
+
+      options:
+      -h, --help              show this help message and exit
+      --cells                 [bool]: Generate global ids for cells. Defaults to true.
+      --no-cells              [bool]: Don't generate global ids for cells.
+      --points                [bool]: Generate global ids for points. Defaults to true.
+      --no-points             [bool]: Don't generate global ids for points.
+      --output OUTPUT         [string]: The vtk output file destination.
+      --data-mode binary, ascii
+                              [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.
 
 ``non_conformal``
 """""""""""""""""
@@ -102,17 +238,35 @@ This module will detect elements which are close enough (there's a user defined
 The angle between two faces can also be precribed.
 This module can be a bit time consuming.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py non_conformal --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py non_conformal --help
+      usage: mesh_doctor.py non_conformal [-h] [--angle_tolerance 10.0] [--point_tolerance POINT_TOLERANCE]
+                                          [--face_tolerance FACE_TOLERANCE]
+
+      options:
+      -h, --help              show this help message and exit
+      --angle_tolerance 10.0  [float]: angle tolerance in degrees. Defaults to 10.0
+      --point_tolerance POINT_TOLERANCE
+                              [float]: tolerance for two points to be considered collocated.
+      --face_tolerance FACE_TOLERANCE
+                              [float]: tolerance for two faces to be considered "touching".
 
 ``self_intersecting_elements``
 """"""""""""""""""""""""""""""
 
 Some meshes can have cells that auto-intersect.
 This module will display the elements that have faces intersecting.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py self_intersecting_elements --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py self_intersecting_elements --help
+      usage: mesh_doctor.py self_intersecting_elements [-h] [--min 2.220446049250313e-16]
+
+      options:
+      -h, --help              show this help message and exit
+      --min 2.220446049250313e-16
+                              [float]: The tolerance in the computation. Defaults to your machine precision 2.220446049250313e-16.
 
 ``supported_elements``
 """"""""""""""""""""""
@@ -125,8 +279,15 @@ But also prismes up to 11 faces.
 The ``supported_elements`` check will validate that no unsupported element is included in the input mesh.
 It will also verify that the ``VTK_POLYHEDRON`` cells can effectively get converted into a supported type of element.
 
-.. command-output:: python src/geos/mesh/doctor/mesh_doctor.py supported_elements --help
-   :cwd: ../geos-mesh
+.. code-block::
+
+      $ python src/geos/mesh/doctor/mesh_doctor.py supported_elements --help
+      usage: mesh_doctor.py supported_elements [-h] [--chunck_size 1] [--nproc 8]
+
+      options:
+      -h, --help              show this help message and exit
+      --chunck_size 1         [int]: Defaults chunk size for parallel processing to 1
+      --nproc 8               [int]: Number of threads used for parallel processing. Defaults to your CPU count 8.